---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T09:01:00Z
date_updated: 2019-08-13T09:01:00Z
file_id: '6811'
file_name: Novak_thesis.pdf
file_size: 3564901
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checksum: 30808d2f7ca920e09f63a95cdc49bffd
content_type: application/pdf
creator: dernst
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date_updated: 2021-02-22T13:42:47Z
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file_date_updated: 2021-02-22T13:42:47Z
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1358'
abstract:
- lang: eng
text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA
interactions. Limited specificity may lead to crosstalk: a regulatory state in
which a gene is either incorrectly activated due to noncognate TF–DNA interactions
or remains erroneously inactive. As each TF can have numerous interactions with
noncognate cis-regulatory elements, crosstalk is inherently a global problem,
yet has previously not been studied as such. We construct a theoretical framework
to analyse the effects of global crosstalk on gene regulation. We find that crosstalk
presents a significant challenge for organisms with low-specificity TFs, such
as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting
at equilibrium, including variants of cooperativity and combinatorial regulation.
Our results suggest that crosstalk imposes a previously unexplored global constraint
on the functioning and evolution of regulatory networks, which is qualitatively
distinct from the known constraints that act at the level of individual gene regulatory
elements.'
article_number: '12307'
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to
gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016).
Intrinsic limits to gene regulation by global crosstalk. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms12307
chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and
Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature
Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic
limits to gene regulation by global crosstalk,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits
to gene regulation by global crosstalk. Nature Communications. 7, 12307.
mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”
Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2023-09-07T12:53:49Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
file:
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checksum: fe3f3a1526d180b29fe691ab11435b78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4919'
file_name: IST-2016-627-v1+1_ncomms12307.pdf
file_size: 861805
relation: main_file
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checksum: 164864a1a675f3ad80e9917c27aba07f
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creator: system
date_created: 2018-12-12T10:12:02Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4920'
file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf
file_size: 1084703
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file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5887'
pubrep_id: '627'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Intrinsic limits to gene regulation by global crosstalk
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2023-09-20T11:56:33Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1382'
abstract:
- lang: eng
text: Background and aims Angiosperms display remarkable diversity in flower colour,
implying that transitions between pigmentation phenotypes must have been common.
Despite progress in understanding transitions between anthocyanin (blue, purple,
pink or red) and unpigmented (white) flowers, little is known about the evolutionary
patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented
flowers. This study investigates the relative rates of evolutionary transitions
between different combinations of yellow- and anthocyanin-pigmentation phenotypes
in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on
anthocyanin and yellow floral pigmentation for 369 species across the tribe. We
then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative
methods to estimate transition rates among pigmentation phenotypes across the
phylogeny. Key Results In contrast to previous studies we found a bias towards
transitions involving a gain in pigmentation, although transitions to phenotypes
with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite
the dominance of yellow and anthocyanin-pigmented taxa, transitions between these
phenotypes are constrained to move through a white intermediate stage, whereas
transitions to double-pigmentation are very rare. The most abundant transitions
are between anthocyanin-pigmented and unpigmented flowers, and similarly the most
abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented
flowers. Conclusions Our findings show that pigment evolution is limited by the
presence of other floral pigments. This interaction between anthocyanin and yellow
pigments constrains the breadth of potential floral diversity observed in nature.
In particular, they suggest that selection has repeatedly acted to promote the
spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore,
the correlation between transition rates and polymorphism suggests that the forces
causing and maintaining variance in the short term reflect evolutionary processes
on longer time scales.
acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous
reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for
her efforts in tracking down the more obscure references.
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in
flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140.
doi:10.1093/aob/mcw043
apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin
pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany.
Oxford University Press. https://doi.org/10.1093/aob/mcw043
chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin
Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany.
Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.
ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae,” Annals of Botany, vol.
117, no. 7. Oxford University Press, pp. 1133–1140, 2016.
ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.
mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation
in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol.
117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.
short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.
date_created: 2018-12-11T11:51:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-02-21T13:49:53Z
day: '1'
department:
- _id: NiBa
doi: 10.1093/aob/mcw043
intvolume: ' 117'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 1133 - 1140
publication: Annals of Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5828'
quality_controlled: '1'
related_material:
record:
- id: '5550'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions
in the Antirrhineae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...
---
_id: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2024-02-21T13:51:39Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: '10.15479/AT:ISTA:TH_526 '
file:
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publication_identifier:
issn:
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publication_status: published
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status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
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checksum: 66cb61a59943e4fb7447c6a86be5ef51
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:53:52Z
date_updated: 2019-08-13T08:53:52Z
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file_name: Tugrul_thesis_w_signature_page.pdf
file_size: 3695257
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content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:45:20Z
date_updated: 2021-02-22T11:45:20Z
file_id: '9182'
file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:45:20Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
record:
- id: '1666'
relation: part_of_dissertation
status: public
- id: '5554'
relation: research_data
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1430'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse their runtime on many illustrative
problems. Here we apply this theory to a simple model of natural evolution. In
the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (1+1)
EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing
fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking
advantage of information on the fitness gradient.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: 1
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1519'
abstract:
- lang: eng
text: Evolutionary biologists have an array of powerful theoretical techniques that
can accurately predict changes in the genetic composition of populations. Changes
in gene frequencies and genetic associations between loci can be tracked as they
respond to a wide variety of evolutionary forces. However, it is often less clear
how to decompose these various forces into components that accurately reflect
the underlying biology. Here, we present several issues that arise in the definition
and interpretation of selection and selection coefficients, focusing on insights
gained through the examination of selection coefficients in multilocus notation.
Using this notation, we discuss how its flexibility-which allows different biological
units to be identified as targets of selection-is reflected in the interpretation
of the coefficients that the notation generates. In many situations, it can be
difficult to agree on whether loci can be considered to be under "direct"
versus "indirect" selection, or to quantify this selection. We present
arguments for what the terms direct and indirect selection might best encompass,
considering a range of issues, from viability and sexual selection to kin selection.
We show how multilocus notation can discriminate between direct and indirect selection,
and describe when it can do so.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: Servedio, Maria
last_name: Servedio
citation:
ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution.
2015;69(5):1101-1112. doi:10.1111/evo.12641
apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients.
Evolution. Wiley. https://doi.org/10.1111/evo.12641
chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection
Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.
ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,”
Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.
ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients.
Evolution. 69(5), 1101–1112.
mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.”
Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.
short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.
date_created: 2018-12-11T11:52:29Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:20Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.12641
ec_funded: 1
file:
- access_level: open_access
checksum: fd8d23f476bc194419929b72ca265c02
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:34Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4822'
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creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
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has_accepted_license: '1'
intvolume: ' 69'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1101 - 1112
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '5656'
pubrep_id: '560'
quality_controlled: '1'
scopus_import: 1
status: public
title: The interpretation of selection coefficients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: 1
status: public
title: Toward a unifying framework for evolutionary processes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2015'
...
---
_id: '1699'
abstract:
- lang: eng
text: By hybridization and backcrossing, alleles can surmount species boundaries
and be incorporated into the genome of a related species. This introgression of
genes is of particular evolutionary relevance if it involves the transfer of adaptations
between populations. However, any beneficial allele will typically be associated
with other alien alleles that are often deleterious and hamper the introgression
process. In order to describe the introgression of an adaptive allele, we set
up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious
alleles. Based on the theory of reducible multitype branching processes, we derive
a recursive expression for the establishment probability of the beneficial allele
after a single hybridization event. We furthermore study the probability that
slightly deleterious alleles hitchhike to fixation. The key to the analysis is
a split of the process into a stochastic phase in which the advantageous alleles
establishes and a deterministic phase in which it sweeps to fixation. We thereafter
apply the theory to a set of biologically relevant scenarios such as introgression
in the presence of many unlinked or few closely linked deleterious alleles. A
comparison to computer simulations shows that the approximations work well over
a large parameter range.
acknowledgement: This work was made possible with financial support by the Vienna
Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG),
Research Unit 1078 Natural selection in structured populations, by the Austrian
Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics,
and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with
the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial
support from the Federal Ministry for Science and Research Austria).
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Derek
full_name: Setter, Derek
last_name: Setter
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y
apa: Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression
after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y
chicago: Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene
Introgression after Secondary Contact.” Journal of Mathematical Biology.
Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.
ieee: H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after
secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer,
pp. 1523–1580, 2015.
ista: Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 70(7), 1523–1580.
mla: Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.”
Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80,
doi:10.1007/s00285-014-0802-y.
short: H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015)
1523–1580.
date_created: 2018-12-11T11:53:32Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:10:36Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1007/s00285-014-0802-y
file:
- access_level: open_access
checksum: 00e3a67bda05d4cc165b3a48b41ef9ad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:27Z
date_updated: 2020-07-14T12:45:12Z
file_id: '5079'
file_name: IST-2016-458-v1+1_s00285-014-0802-y.pdf
file_size: 1321527
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1523 - 1580
project:
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: L'OREAL Fellowship
publication: Journal of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '5442'
pubrep_id: '458'
quality_controlled: '1'
scopus_import: 1
status: public
title: Adaptive gene introgression after secondary contact
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2015'
...
---
_id: '1703'
abstract:
- lang: eng
text: Vegetation clearing and land-use change have depleted many natural plant communities
to the point where restoration is required. A major impediment to the success
of rebuilding complex vegetation communities is having regular access to sufficient
quantities of high-quality seed. Seed-production areas (SPAs) can help generate
this seed, but these must be underpinned by a broad genetic base to maximise the
evolutionary potential of restored populations. However, genetic bottlenecks can
occur at the collection, establishment and production stages in SPAs, requiring
genetic evaluation. This is especially relevant for species that may take many
years before a return on SPA investment is realised. Two recently established
yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated
to determine whether genetic bottlenecks had occurred between seed collection
and SPA establishment. No evidence was found to suggest that a significant loss
of genetic diversity had occurred at this stage, although there was a significant
difference in diversity between the two SPAs. Complex population genetic structure
was also observed in the seed used to source the SPAs, with up to eight groups
identified. Plant survival in the SPAs was influenced by seed collection location
but not by SPA location and was not associated with genetic diversity. There were
also no associations between genetic diversity and plant growth. These data highlighted
the importance of chance events when establishing SPAs and indicated that the
two yellow box SPAs are likely to provide genetically diverse seed sources for
future restoration projects, especially by pooling seed from both SPAs.
author:
- first_name: Linda
full_name: Broadhurst, Linda
last_name: Broadhurst
- first_name: Graham
full_name: Fifield, Graham
last_name: Fifield
- first_name: Bindi
full_name: Vanzella, Bindi
last_name: Vanzella
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic
structure of seed sources and the maintenance of genetic diversity during establishment
of two yellow box (Eucalyptus melliodora) seed-production areas. Australian
Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023
apa: Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation
of the genetic structure of seed sources and the maintenance of genetic diversity
during establishment of two yellow box (Eucalyptus melliodora) seed-production
areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023
chicago: Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup.
“An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of
Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora)
Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023.
ieee: L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas,”
Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.
ista: Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas.
Australian Journal of Botany. 63(5), 455–466.
mla: Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources
and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box
(Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany,
vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.
short: L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of
Botany 63 (2015) 455–466.
date_created: 2018-12-11T11:53:34Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '26'
department:
- _id: NiBa
doi: 10.1071/BT15023
intvolume: ' 63'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 455 - 466
publication: Australian Journal of Botany
publication_status: published
publisher: CSIRO
publist_id: '5434'
quality_controlled: '1'
scopus_import: 1
status: public
title: An evaluation of the genetic structure of seed sources and the maintenance
of genetic diversity during establishment of two yellow box (Eucalyptus melliodora)
seed-production areas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2015'
...
---
_id: '1818'
abstract:
- lang: eng
text: 'Why do species not adapt to ever-wider ranges of conditions, gradually expanding
their ecological niche and geographic range? Gene flow across environments has
two conflicting effects: although it increases genetic variation, which is a prerequisite
for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane
proposed that, when the environment varies across space, "swamping"
by gene flow creates a positive feedback between low population size and maladaptation,
leading to a sharp range margin. However, current deterministic theory shows that,
when variance can evolve, there is no such limit. Using simple analytical tools
and simulations, we show that genetic drift can generate a sharp margin to a species''
range, by reducing genetic variance below the level needed for adaptation to spatially
variable conditions. Aided by separation of ecological and evolutionary timescales,
the identified effective dimensionless parameters reveal a simple threshold that
predicts when adaptation at the range margin fails. Two observable parameters
determine the threshold: (i) the effective environmental gradient, which can be
measured by the loss of fitness due to dispersal to a different environment; and
(ii) the efficacy of selection relative to genetic drift. The theory predicts
sharp range margins even in the absence of abrupt changes in the environment.
Furthermore, it implies that gradual worsening of conditions across a species''
habitat may lead to a sudden range fragmentation, when adaptation to a wide span
of conditions within a single species becomes impossible.'
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Limits to adaptation along environmental gradients.
PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112
apa: Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental
gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112
chicago: Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.
ieee: J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,”
PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.
ista: Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients.
PNAS. 112(20), 6401–6406.
mla: Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015,
pp. 6401–06, doi:10.1073/pnas.1421515112.
short: J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.
date_created: 2018-12-11T11:54:11Z
date_published: 2015-05-19T00:00:00Z
date_updated: 2021-01-12T06:53:24Z
day: '19'
department:
- _id: NiBa
doi: 10.1073/pnas.1421515112
ec_funded: 1
external_id:
pmid:
- '25941385'
intvolume: ' 112'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/
month: '05'
oa: 1
oa_version: Submitted Version
page: 6401 - 6406
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5288'
quality_controlled: '1'
scopus_import: 1
status: public
title: Limits to adaptation along environmental gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1850'
abstract:
- lang: eng
text: 'Entomopathogenic fungi are potent biocontrol agents that are widely used
against insect pests, many of which are social insects. Nevertheless, theoretical
investigations of their particular life history are scarce. We develop a model
that takes into account the main distinguishing features between traditionally
studied diseases and obligate killing pathogens, like the (biocontrol-relevant)
insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic
fungi produce new infectious particles (conidiospores) only after host death and
not yet on the living host. Second, the killing rates of entomopathogenic fungi
depend strongly on the initial exposure dosage, thus we explicitly consider the
pathogen load of individual hosts. Further, we make the model applicable not only
to solitary host species, but also to group living species by incorporating social
interactions between hosts, like the collective disease defences of insect societies.
Our results identify the optimal killing rate for the pathogen that minimises
its invasion threshold. Furthermore, we find that the rate of contact between
hosts has an ambivalent effect: dense interaction networks between individuals
are considered to facilitate disease outbreaks because of increased pathogen transmission.
In social insects, this is compensated by their collective disease defences, i.e.,
social immunity. For the type of pathogens considered here, we show that even
without social immunity, high contact rates between live individuals dilute the
pathogen in the host colony and hence can reduce individual pathogen loads below
disease-causing levels.'
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing
rates and the ambivalent effect of high social interaction rates. Journal of
Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018'
apa: 'Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies:
Optimal killing rates and the ambivalent effect of high social interaction rates.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018'
chicago: 'Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect
Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction
Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.'
ieee: 'S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal
killing rates and the ambivalent effect of high social interaction rates,” Journal
of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.'
ista: 'Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal
killing rates and the ambivalent effect of high social interaction rates. Journal
of Theoretical Biology. 372(5), 54–64.'
mla: 'Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies:
Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.”
Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64,
doi:10.1016/j.jtbi.2015.02.018.'
short: S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.
date_created: 2018-12-11T11:54:21Z
date_published: 2015-05-07T00:00:00Z
date_updated: 2021-01-12T06:53:37Z
day: '07'
ddc:
- '576'
department:
- _id: NiBa
- _id: SyCr
doi: 10.1016/j.jtbi.2015.02.018
ec_funded: 1
file:
- access_level: open_access
checksum: 3c0dcacc900bc45cc65a453dfda4ca43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:07Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5326'
file_name: IST-2015-329-v1+1_manuscript.pdf
file_size: 1546914
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 372'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 54 - 64
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '5251'
pubrep_id: '329'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Fungal disease dynamics in insect societies: Optimal killing rates and the
ambivalent effect of high social interaction rates'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 372
year: '2015'
...
---
_id: '1851'
abstract:
- lang: eng
text: We consider mating strategies for females who search for males sequentially
during a season of limited length. We show that the best strategy rejects a given
male type if encountered before a time-threshold but accepts him after. For frequency-independent
benefits, we obtain the optimal time-thresholds explicitly for both discrete and
continuous distributions of males, and allow for mistakes being made in assessing
the correct male type. When the benefits are indirect (genes for the offspring)
and the population is under frequency-dependent ecological selection, the benefits
depend on the mating strategy of other females as well. This case is particularly
relevant to speciation models that seek to explore the stability of reproductive
isolation by assortative mating under frequency-dependent ecological selection.
We show that the indirect benefits are to be quantified by the reproductive values
of couples, and describe how the evolutionarily stable time-thresholds can be
found. We conclude with an example based on the Levene model, in which we analyze
the evolutionarily stable assortative mating strategies and the strength of reproductive
isolation provided by them.
article_processing_charge: No
article_type: original
author:
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: Eva
full_name: Kisdi, Eva
last_name: Kisdi
- first_name: Mats
full_name: Gyllenberg, Mats
last_name: Gyllenberg
citation:
ama: Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions
for sequentially searching females and the stability of reproductive isolation
by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618
apa: Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable
mating decisions for sequentially searching females and the stability of reproductive
isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618
chicago: Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable
Mating Decisions for Sequentially Searching Females and the Stability of Reproductive
Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.
ieee: T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions
for sequentially searching females and the stability of reproductive isolation
by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026,
2015.
ista: Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions
for sequentially searching females and the stability of reproductive isolation
by assortative mating. Evolution. 69(4), 1015–1026.
mla: Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially
Searching Females and the Stability of Reproductive Isolation by Assortative Mating.”
Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.
short: T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.
date_created: 2018-12-11T11:54:21Z
date_published: 2015-02-09T00:00:00Z
date_updated: 2022-06-07T10:52:37Z
day: '09'
ddc:
- '570'
department:
- _id: NiBa
- _id: KrCh
doi: 10.1111/evo.12618
ec_funded: 1
external_id:
pmid:
- '25662095'
file:
- access_level: open_access
checksum: 1e8be0b1d7598a78cd2623d8ee8e7798
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creator: dernst
date_created: 2020-05-15T09:05:34Z
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has_accepted_license: '1'
intvolume: ' 69'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 1015 - 1026
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
publist_id: '5249'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionarily stable mating decisions for sequentially searching females and
the stability of reproductive isolation by assortative mating
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2015'
...
---
_id: '1883'
abstract:
- lang: eng
text: "We introduce a one-parametric family of tree growth models, in which branching
probabilities decrease with branch age τ as τ-α. Depending on the exponent α,
the scaling of tree depth with tree size n displays a transition between the logarithmic
scaling of random trees and an algebraic growth. At the transition (α=1) tree
depth grows as (logn)2. This anomalous scaling is in good agreement with the trend
observed in evolution of biological species, thus providing a theoretical support
for age-dependent speciation and associating it to the occurrence of a critical
point.\r\n"
article_number: '022803'
article_processing_charge: No
article_type: original
author:
- first_name: Stephanie
full_name: Keller-Schmidt, Stephanie
last_name: Keller-Schmidt
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Víctor
full_name: Eguíluz, Víctor
last_name: Eguíluz
- first_name: Emilio
full_name: Hernandez Garcia, Emilio
last_name: Hernandez Garcia
- first_name: Konstantin
full_name: Klemm, Konstantin
last_name: Klemm
citation:
ama: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous
scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803
apa: Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm,
K. (2015). Anomalous scaling in an age-dependent branching model. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.91.022803
chicago: Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez
Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.
ieee: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm,
“Anomalous scaling in an age-dependent branching model,” Physical Review E
Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute
of Physics, 2015.
ista: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015.
Anomalous scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 91(2), 022803.
mla: Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.
short: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm,
Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:31Z
date_published: 2015-02-02T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '02'
department:
- _id: NiBa
doi: 10.1103/PhysRevE.91.022803
external_id:
arxiv:
- '1012.3298'
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1012.3298
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anomalous scaling in an age-dependent branching model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
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has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
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title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s003
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9712'
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison
& for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness
models for comparison & for interacting TFBSs. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1005639.s001
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other
Fitness Models for Comparison & for Interacting TFBSs.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for
comparison & for interacting TFBSs.” Public Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison
& for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting
TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
date_created: 2021-07-23T12:00:37Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-23T10:09:08Z
day: '06'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1666'
relation: used_in_publication
status: public
status: public
title: Other fitness models for comparison & for interacting TFBSs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9715'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015.
doi:10.1371/journal.pone.0126907.s001
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of
the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference
of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.
ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results,
Public Library of Science, 10.1371/journal.pone.0126907.s001.
mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public
Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-07-23T12:11:30Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s001
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Mathematical inference of the results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-09-07T11:53:49Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
file:
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checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
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month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
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title: Dynamics of transcription factor binding site evolution
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1835'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs
–an important problem of interest in evolutionary biology– more efficiently than
the classical simulation method. We specify the property in linear temporal logics.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
acknowledgement: "SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2
148797.\r\n"
alternative_title:
- LNCS
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47
apa: 'Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &
Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS:
Tools and Algorithms for the Construction and Analysis of Systems, London, United
Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47'
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture
Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model
checking gene regulatory networks. 9035, 469–483.
mla: Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol.
9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035
(2015) 469–483.
conference:
end_date: 2015-04-18
location: London, United Kingdom
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2015-04-11
date_created: 2018-12-11T11:54:16Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-20T11:06:03Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/978-3-662-46681-0_47
ec_funded: 1
intvolume: ' 9035'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.7704
month: '04'
oa: 1
oa_version: Preprint
page: 469 - 483
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5267'
quality_controlled: '1'
related_material:
record:
- id: '1351'
relation: later_version
status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Model checking gene regulatory networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9035
year: '2015'
...
---
_id: '1681'
abstract:
- lang: eng
text: In many social situations, individuals endeavor to find the single best possible
partner, but are constrained to evaluate the candidates in sequence. Examples
include the search for mates, economic partnerships, or any other long-term ties
where the choice to interact involves two parties. Surprisingly, however, previous
theoretical work on mutual choice problems focuses on finding equilibrium solutions,
while ignoring the evolutionary dynamics of decisions. Empirically, this may be
of high importance, as some equilibrium solutions can never be reached unless
the population undergoes radical changes and a sufficient number of individuals
change their decisions simultaneously. To address this question, we apply a mutual
choice sequential search problem in an evolutionary game-theoretical model that
allows one to find solutions that are favored by evolution. As an example, we
study the influence of sequential search on the evolutionary dynamics of cooperation.
For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.
article_processing_charge: No
article_type: original
author:
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Priklopil T, Chatterjee K. Evolution of decisions in population games with
sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413
apa: Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population
games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413
chicago: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in
Population Games with Sequentially Searching Individuals.” Games. MDPI,
2015. https://doi.org/10.3390/g6040413.
ieee: T. Priklopil and K. Chatterjee, “Evolution of decisions in population games
with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp.
413–437, 2015.
ista: Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games
with sequentially searching individuals. Games. 6(4), 413–437.
mla: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population
Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI,
2015, pp. 413–37, doi:10.3390/g6040413.
short: T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.
date_created: 2018-12-11T11:53:26Z
date_published: 2015-09-29T00:00:00Z
date_updated: 2023-10-17T11:42:52Z
day: '29'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.3390/g6040413
ec_funded: 1
file:
- access_level: open_access
checksum: 912e1acbaf201100f447a43e4d5958bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:41Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4959'
file_name: IST-2016-448-v1+1_games-06-00413.pdf
file_size: 518832
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 413 - 437
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Games
publication_identifier:
eissn:
- 2073-4336
publication_status: published
publisher: MDPI
publist_id: '5467'
pubrep_id: '448'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of decisions in population games with sequentially searching individuals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1896'
abstract:
- lang: eng
text: 'Biopolymer length regulation is a complex process that involves a large number
of biological, chemical, and physical subprocesses acting simultaneously across
multiple spatial and temporal scales. An illustrative example important for genomic
stability is the length regulation of telomeres - nucleoprotein structures at
the ends of linear chromosomes consisting of tandemly repeated DNA sequences and
a specialized set of proteins. Maintenance of telomeres is often facilitated by
the enzyme telomerase but, particularly in telomerase-free systems, the maintenance
of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms
mediated by recombination. Various linear and circular DNA structures were identified
to participate in ALT, however, dynamics of the whole process is still poorly
understood. We propose a chemical kinetics model of ALT with kinetic rates systematically
derived from the biophysics of DNA diffusion and looping. The reaction system
is reduced to a coagulation-fragmentation system by quasi-steady-state approximation.
The detailed treatment of kinetic rates yields explicit formulas for expected
size distributions of telomeres that demonstrate the key role played by the J
factor, a quantitative measure of bending of polymers. The results are in agreement
with experimental data and point out interesting phenomena: an appearance of very
long telomeric circles if the total telomere density exceeds a critical value
(excess mass) and a nonlinear response of the telomere size distributions to the
amount of telomeric DNA in the system. The results can be of general importance
for understanding dynamics of telomeres in telomerase-independent systems as this
mode of telomere maintenance is similar to the situation in tumor cells lacking
telomerase activity. Furthermore, due to its universality, the model may also
serve as a prototype of an interaction between linear and circular DNA structures
in various settings.'
acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and
K.B.).
article_number: '032701'
article_processing_charge: No
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Jozef
full_name: Nosek, Jozef
last_name: Nosek
- first_name: Ľubomír
full_name: Tomáška, Ľubomír
last_name: Tomáška
citation:
ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism
of telomere length maintenance. Physical Review E Statistical Nonlinear and
Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701
apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model
of alternative mechanism of telomere length maintenance. Physical Review E
Statistical Nonlinear and Soft Matter Physics. American Institute of Physics.
https://doi.org/10.1103/PhysRevE.89.032701
chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical
Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2014. https://doi.org/10.1103/PhysRevE.89.032701.
ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative
mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.
ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative
mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear
and Soft Matter Physics. 89(3), 032701.
mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere
Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter
Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.
short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical
Nonlinear and Soft Matter Physics 89 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2022-08-01T10:50:10Z
day: '04'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.89.032701
intvolume: ' 89'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0430
month: '03'
oa: 1
oa_version: Submitted Version
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5198'
scopus_import: '1'
status: public
title: Mathematical model of alternative mechanism of telomere length maintenance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '1909'
abstract:
- lang: eng
text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms
to track environmental change. The challenge for organisms is to construct phenotypes
using the most accurate environmental cue. Here, we use a quantitative genetic
model of adaptation by additive genetic variance, within- and transgenerational
plasticity via linear reaction norms and indirect genetic effects respectively.
We show how the relative influence on the eventual phenotype of these components
depends on the predictability of environmental change (fast or slow, sinusoidal
or stochastic) and the developmental lag τ between when the environment is perceived
and when selection acts. We then decompose expected mean fitness into three components
(variance load, adaptation and fluctuation load) to study the fitness costs of
within- and transgenerational plasticity. A strongly negative maternal effect
coefficient m minimizes the variance load, but a strongly positive m minimises
the fluctuation load. The adaptation term is maximized closer to zero, with positive
or negative m preferred under different environmental scenarios. Phenotypic plasticity
is higher when τ is shorter and when the environment changes frequently between
seasonal extremes. Expected mean population fitness is highest away from highest
observed levels of phenotypic plasticity. Within- and transgenerational plasticity
act in concert to deliver well-adapted phenotypes, which emphasizes the need to
study both simultaneously when investigating phenotypic evolution.'
acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number:
EP/H031928/1'
author:
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701.
doi:10.1111/1365-2435.12207
apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation
via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell.
https://doi.org/10.1111/1365-2435.12207
chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of
Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology.
Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.
ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic
plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell,
pp. 693–701, 2014.
ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity
and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell,
2014, pp. 693–701, doi:10.1111/1365-2435.12207.
short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:00Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1111/1365-2435.12207
file:
- access_level: open_access
checksum: 3cbe8623174709a8ceec2103246f8fe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:45Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5167'
file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf
file_size: 536154
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 28'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 693 - 701
publication: Functional Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5186'
pubrep_id: '419'
scopus_import: 1
status: public
title: The fitness costs of adaptation via phenotypic plasticity and maternal effects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2014'
...
---
_id: '1908'
abstract:
- lang: eng
text: In large populations, multiple beneficial mutations may be simultaneously
spreading. In asexual populations, these mutations must either arise on the same
background or compete against each other. In sexual populations, recombination
can bring together beneficial alleles from different backgrounds, but tightly
linked alleles may still greatly interfere with each other. We show for well-mixed
populations that when this interference is strong, the genome can be seen as consisting
of many effectively asexual stretches linked together. The rate at which beneficial
alleles fix is thus roughly proportional to the rate of recombination and depends
only logarithmically on the mutation supply and the strength of selection. Our
scaling arguments also allow us to predict, with reasonable accuracy, the fitness
distribution of fixed mutations when the mutational effect sizes are broad. We
focus on the regime in which crossovers occur more frequently than beneficial
mutations, as is likely to be the case for many natural populations.
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Oskar
full_name: Hallatschek, Oskar
last_name: Hallatschek
citation:
ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705
apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large
sexual populations with linear chromosomes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.160705
chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large
Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.160705.
ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations
with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of
America, pp. 1167–1183, 2014.
ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 196(4), 1167–1183.
mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual
Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics
Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.
short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.
date_created: 2018-12-11T11:54:39Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.160705
ec_funded: 1
intvolume: ' 196'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0737
month: '04'
oa: 1
oa_version: Submitted Version
page: 1167 - 1183
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5187'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of adaptation in large sexual populations with linear chromosomes
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 196
year: '2014'
...
---
_id: '1936'
abstract:
- lang: eng
text: 'The social intelligence hypothesis states that the need to cope with complexities
of social life has driven the evolution of advanced cognitive abilities. It is
usually invoked in the context of challenges arising from complex intragroup structures,
hierarchies, and alliances. However, a fundamental aspect of group living remains
largely unexplored as a driving force in cognitive evolution: the competition
between individuals searching for resources (producers) and conspecifics that
parasitize their findings (scroungers). In populations of social foragers, abilities
that enable scroungers to steal by outsmarting producers, and those allowing producers
to prevent theft by outsmarting scroungers, are likely to be beneficial and may
fuel a cognitive arms race. Using analytical theory and agent-based simulations,
we present a general model for such a race that is driven by the producer-scrounger
game and show that the race''s plausibility is dramatically affected by the nature
of the evolving abilities. If scrounging and scrounging avoidance rely on separate,
strategy-specific cognitive abilities, arms races are short-lived and have a limited
effect on cognition. However, general cognitive abilities that facilitate both
scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus,
ubiquitous foraging interactions may lead to the evolution of general cognitive
abilities in social animals, without the requirement of complex intragroup structures.'
author:
- first_name: Michal
full_name: Arbilly, Michal
last_name: Arbilly
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Uri
full_name: Grodzinski, Uri
last_name: Grodzinski
citation:
ama: Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers
and scroungers can drive the evolution of social cognition. Behavioral Ecology.
2014;25(3):487-495. doi:10.1093/beheco/aru002
apa: Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms
race between producers and scroungers can drive the evolution of social cognition.
Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002
chicago: Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An
Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.”
Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.
ieee: M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between
producers and scroungers can drive the evolution of social cognition,” Behavioral
Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.
ista: Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between
producers and scroungers can drive the evolution of social cognition. Behavioral
Ecology. 25(3), 487–495.
mla: Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can
Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25,
no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.
short: M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25
(2014) 487–495.
date_created: 2018-12-11T11:54:48Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:54:11Z
day: '13'
department:
- _id: NiBa
doi: 10.1093/beheco/aru002
ec_funded: 1
intvolume: ' 25'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/
month: '02'
oa: 1
oa_version: Submitted Version
page: 487 - 495
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Behavioral Ecology
publication_status: published
publisher: Oxford University Press
publist_id: '5157'
quality_controlled: '1'
scopus_import: 1
status: public
title: An arms race between producers and scroungers can drive the evolution of social
cognition
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2014'
...
---
_id: '1932'
abstract:
- lang: eng
text: The existence of complex (multiple-step) genetic adaptations that are "irreducible"
(i.e., all partial combinations are less fit than the original genotype) is one
of the longest standing problems in evolutionary biology. In standard genetics
parlance, these adaptations require the crossing of a wide adaptive valley of
deleterious intermediate stages. Here, we demonstrate, using a simple model, that
evolution can cross wide valleys to produce "irreducibly complex" adaptations
by making use of previously cryptic mutations. When revealed by an evolutionary
capacitor, previously cryptic mutants have higher initial frequencies than do
new mutations, bringing them closer to a valley-crossing saddle in allele frequency
space. Moreover, simple combinatorics implies an enormous number of candidate
combinations exist within available cryptic genetic variation. We model the dynamics
of crossing of a wide adaptive valley after a capacitance event using both numerical
simulations and analytical approximations. Although individual valley crossing
events become less likely as valleys widen, by taking the combinatorics of genotype
space into account, we see that revealing cryptic variation can cause the frequent
evolution of complex adaptations.
acknowledgement: "Funded by National Institutes of Health. Grant Numbers: R01GM076041,
R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n"
author:
- first_name: Meredith
full_name: Trotter, Meredith
last_name: Trotter
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Grant
full_name: Peterson, Grant
last_name: Peterson
- first_name: Kayla
full_name: Peck, Kayla
last_name: Peck
- first_name: Joanna
full_name: Masel, Joanna
last_name: Masel
citation:
ama: Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation
can make "irreducible complexity" a common mode of adaptation
in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517
apa: Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014).
Cryptic genetic variation can make "irreducible complexity"
a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell.
https://doi.org/10.1111/evo.12517
chicago: Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna
Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity"
a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1111/evo.12517.
ieee: M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell,
pp. 3357–3367, 2014.
ista: Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations. Evolution. 68(12), 3357–3367.
mla: Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible
Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution,
vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.
short: M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014)
3357–3367.
date_created: 2018-12-11T11:54:47Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-01-12T06:54:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.12517
ec_funded: 1
intvolume: ' 68'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.6077
month: '12'
oa: 1
oa_version: Submitted Version
page: 3357 - 3367
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5162'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cryptic genetic variation can make "irreducible complexity" a common
mode of adaptation in sexual populations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '2168'
abstract:
- lang: eng
text: Many species have an essentially continuous distribution in space, in which
there are no natural divisions between randomly mating subpopulations. Yet, the
standard approach to modelling these populations is to impose an arbitrary grid
of demes, adjusting deme sizes and migration rates in an attempt to capture the
important features of the population. Such indirect methods are required because
of the failure of the classical models of isolation by distance, which have been
shown to have major technical flaws. A recently introduced model of extinction
and recolonisation in two dimensions solves these technical problems, and provides
a rigorous technical foundation for the study of populations evolving in a spatial
continuum. The coalescent process for this model is simply stated, but direct
simulation is very inefficient for large neighbourhood sizes. We present efficient
and exact algorithms to simulate this coalescent process for arbitrary sample
sizes and numbers of loci, and analyse these algorithms in detail.
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space:
Algorithms for large neighbourhood size. Theoretical Population Biology.
2014;95:13-23. doi:10.1016/j.tpb.2014.05.001'
apa: 'Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation
in continuous space: Algorithms for large neighbourhood size. Theoretical Population
Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001'
chicago: 'Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent
Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical
Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001.'
ieee: 'J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous
space: Algorithms for large neighbourhood size,” Theoretical Population Biology,
vol. 95. Academic Press, pp. 13–23, 2014.'
ista: 'Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous
space: Algorithms for large neighbourhood size. Theoretical Population Biology.
95, 13–23.'
mla: 'Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms
for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95,
Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.'
short: J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95
(2014) 13–23.
date_created: 2018-12-11T11:56:06Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T06:55:44Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2014.05.001
ec_funded: 1
file:
- access_level: open_access
checksum: 979d7a8034e9df198f068f0d251f31bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:49Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4839'
file_name: IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf
file_size: 569005
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 95'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 13 - 23
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '4816'
pubrep_id: '391'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Coalescent simulation in continuous space: Algorithms for large neighbourhood
size'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2014'
...
---
_id: '2169'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer
science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111
apa: Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection
in evolution and computer science. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1410107111
chicago: Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of
Selection in Evolution and Computer Science.” PNAS. National Academy of
Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.
ieee: N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution
and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences,
pp. 10398–10399, 2014.
ista: Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution
and computer science. PNAS. 111(29), 10398–10399.
mla: Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer
Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp.
10398–99, doi:10.1073/pnas.1410107111.
short: N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.
date_created: 2018-12-11T11:56:07Z
date_published: 2014-07-22T00:00:00Z
date_updated: 2021-01-12T06:55:45Z
day: '22'
department:
- _id: NiBa
doi: 10.1073/pnas.1410107111
intvolume: ' 111'
issue: '29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/
month: '07'
oa: 1
oa_version: Submitted Version
page: 10398 - 10399
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4815'
quality_controlled: '1'
scopus_import: 1
status: public
title: Diverse forms of selection in evolution and computer science
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '2174'
abstract:
- lang: eng
text: 'When polygenic traits are under stabilizing selection, many different combinations
of alleles allow close adaptation to the optimum. If alleles have equal effects,
all combinations that result in the same deviation from the optimum are equivalent.
Furthermore, the genetic variance that is maintained by mutation-selection balance
is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing
selection. In reality, alleles vary in their effects, making the fitness landscape
asymmetric and complicating analysis of the equilibria. We show that that the
resulting genetic variance depends on the fraction of alleles near fixation, which
contribute by 2μ/S, and on the total mutational effects of alleles that are at
intermediate frequency. The inpplayfi between stabilizing selection and mutation
leads to a sharp transition: alleles with effects smaller than a threshold value
of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic
load in equilibrium is less than for traits of equal effects, and the fitness
equilibria are more similar. We find p the optimum is displaced, alleles with
effects close to the threshold value sweep first, and their rate of increase is
bounded by Long-term response leads in general to well-adapted traits, unlike
the case of equal effects that often end up at a suboptimal fitness peak. However,
the particular peaks to which the populations converge are extremely sensitive
to the initial states and to the speed of the shift of the optimum trait value.'
author:
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing
selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111
apa: De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic
traits to stabilizing selection and mutation. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.159111
chicago: De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.159111.
ieee: H. De Vladar and N. H. Barton, “Stability and response of polygenic traits
to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics
Society of America, pp. 749–767, 2014.
ista: De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to
stabilizing selection and mutation. Genetics. 197(2), 749–767.
mla: De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no.
2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.
short: H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.
date_created: 2018-12-11T11:56:08Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:55:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.159111
ec_funded: 1
intvolume: ' 197'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.1017
month: '06'
oa: 1
oa_version: Submitted Version
page: 749 - 767
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4809'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stability and response of polygenic traits to stabilizing selection and mutation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2014'
...
---
_id: '2252'
abstract:
- lang: eng
text: The pattern of inheritance and mechanism of sex determination can have important
evolutionary consequences. We studied probabilistic sex determination in the ciliate
Tetrahymena thermophila, which was previously shown to cause evolution of skewed
sex ratios. We find that the genetic background alters the sex determination patterns
of mat alleles in heterozygotes and that allelic interaction can differentially
influence the expression probability of the 7 sexes. We quantify the dominance
relationships between several mat alleles and find that A-type alleles, which
specify sex I, are indeed recessive to B-type alleles, which are unable to specify
that sex. Our results provide additional support for the presence of modifier
loci and raise implications for the dynamics of sex ratios in populations of T.
thermophila.
article_processing_charge: No
author:
- first_name: Sujal
full_name: Phadke, Sujal
last_name: Phadke
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tuan
full_name: Pham, Tuan
last_name: Pham
- first_name: Stephanie
full_name: Pham, Stephanie
last_name: Pham
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance
relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal
of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic
background alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063
chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall.
“Genetic Background Alters Dominance Relationships between Mat Alleles in the
Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University
Press, 2014. https://doi.org/10.1093/jhered/est063.
ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background
alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press,
pp. 130–135, 2014.
ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters
dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila.
Journal of Heredity. 105(1), 130–135.
mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between
Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity,
vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105
(2014) 130–135.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-08-25T14:45:42Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jhered/est063
intvolume: ' 105'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 130 - 135
publication: Journal of Heredity
publication_identifier:
issn:
- '00221503'
publication_status: published
publisher: Oxford University Press
publist_id: '4695'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic background alters dominance relationships between mat alleles in the
ciliate Tetrahymena Thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2014'
...
---
_id: '537'
abstract:
- lang: eng
text: Transgenerational effects are broader than only parental relationships. Despite
mounting evidence that multigenerational effects alter phenotypic and life-history
traits, our understanding of how they combine to determine fitness is not well
developed because of the added complexity necessary to study them. Here, we derive
a quantitative genetic model of adaptation to an extraordinary new environment
by an additive genetic component, phenotypic plasticity, maternal and grandmaternal
effects. We show how, at equilibrium, negative maternal and negative grandmaternal
effects maximize expected population mean fitness. We define negative transgenerational
effects as those that have a negative effect on trait expression in the subsequent
generation, that is, they slow, or potentially reverse, the expected evolutionary
dynamic. When maternal effects are positive, negative grandmaternal effects are
preferred. As expected under Mendelian inheritance, the grandmaternal effects
have a lower impact on fitness than the maternal effects, but this dual inheritance
model predicts a more complex relationship between maternal and grandmaternal
effects to constrain phenotypic variance and so maximize expected population mean
fitness in the offspring.
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150
apa: Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal
and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150
chicago: Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences
of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1002/ece3.1150.
ieee: R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal
effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145,
2014.
ista: Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 4(15), 3139–3145.
mla: Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal
Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014,
pp. 3139–45, doi:10.1002/ece3.1150.
short: R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
date_created: 2018-12-11T11:47:02Z
date_published: 2014-07-19T00:00:00Z
date_updated: 2021-01-12T08:01:30Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1002/ece3.1150
file:
- access_level: open_access
checksum: e32abf75a248e7a11811fd7f60858769
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:31Z
date_updated: 2020-07-14T12:46:38Z
file_id: '4886'
file_name: IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf
file_size: 621582
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '15'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 3139 - 3145
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7280'
pubrep_id: '934'
scopus_import: 1
status: public
title: Fitness consequences of maternal and grandmaternal effects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '2170'
abstract:
- lang: eng
text: ' Short-read sequencing technologies have in principle made it feasible to
draw detailed inferences about the recent history of any organism. In practice,
however, this remains challenging due to the difficulty of genome assembly in
most organisms and the lack of statistical methods powerful enough to discriminate
between recent, nonequilibrium histories. We address both the assembly and inference
challenges. We develop a bioinformatic pipeline for generating outgroup-rooted
alignments of orthologous sequence blocks from de novo low-coverage short-read
data for a small number of genomes, and show how such sequence blocks can be used
to fit explicit models of population divergence and admixture in a likelihood
framework. To illustrate our approach, we reconstruct the Pleistocene history
of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common
with many other taxa, was restricted during Pleistocene ice ages to a longitudinal
series of southern refugia spanning the Western Palaearctic. Our analysis of sequence
blocks sampled from a single genome from each of three major glacial refugia reveals
support for an unexpected history dominated by recent admixture. Despite the fact
that 80% of the genome is affected by admixture during the last glacial cycle,
we are able to infer the deeper divergence history of these populations. These
inferences are robust to variation in block length, mutation model and the sampling
location of individual genomes within refugia. This combination of de novo assembly
and numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.'
acknowledgement: This work was funded by NERC grants to G Stone, J Nicholls, K Lohse
and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
- first_name: James
full_name: Nicholls, James
last_name: Nicholls
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
citation:
ama: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578
apa: Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse,
K. (2014). Likelihood-based inference of population history from low-coverage
de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578
chicago: Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H
Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell,
2014. https://doi.org/10.1111/mec.12578.
ieee: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse,
“Likelihood-based inference of population history from low-coverage de novo genome
assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211,
2014.
ista: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 23(1), 198–211.
mla: Hearn, Jack, et al. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no.
1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.
short: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular
Ecology 23 (2014) 198–211.
date_created: 2018-12-11T11:56:07Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T14:07:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.12578
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publication: Molecular Ecology
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publisher: Wiley-Blackwell
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title: Likelihood-based inference of population history from low-coverage de novo
genome assemblies
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2014'
...
---
_id: '2023'
abstract:
- lang: eng
text: 'Understanding the evolution of dispersal is essential for understanding and
predicting the dynamics of natural populations. Two main factors are known to
influence dispersal evolution: spatio-temporal variation in the environment and
relatedness between individuals. However, the relation between these factors is
still poorly understood, and they are usually treated separately. In this article,
I present a theoretical framework that contains and connects effects of both environmental
variation and relatedness, and reproduces and extends their known features. Spatial
habitat variation selects for balanced dispersal strategies, whereby the population
is kept at an ideal free distribution. Within this class of dispersal strategies,
I explain how increased dispersal is promoted by perturbations to the dispersal
type frequencies. An explicit formula shows the magnitude of the selective advantage
of increased dispersal in terms of the spatial variability in the frequencies
of the different dispersal strategies present. These variances are capable of
capturing various sources of stochasticity and hence establish a common scale
for their effects on the evolution of dispersal. The results furthermore indicate
an alternative approach to identifying effects of relatedness on dispersal evolution.'
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Habitat heterogeneities versus spatial type frequency variances as
driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597.
doi:10.1002/ece3.1289
apa: Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell.
https://doi.org/10.1002/ece3.1289
chicago: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency
Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution.
Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.
ieee: S. Novak, “Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution,” Ecology and Evolution, vol.
4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.
ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.
mla: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances
as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol.
4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.
short: S. Novak, Ecology and Evolution 4 (2014) 4589–4597.
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/ece3.1289
ec_funded: 1
file:
- access_level: open_access
checksum: 9ab43db1b0fede7bfe560ed77e177b76
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:28Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4946'
file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf
file_size: 118813
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
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intvolume: ' 4'
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language:
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month: '11'
oa: 1
oa_version: Published Version
page: 4589 - 4597
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5049'
pubrep_id: '462'
quality_controlled: '1'
related_material:
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scopus_import: 1
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title: Habitat heterogeneities versus spatial type frequency variances as driving
forces of dispersal evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '10899'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed.
Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9'
apa: Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity
(2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9
chicago: Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity,
2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.
ieee: N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd
ed., Elsevier, 2013, pp. 508–515.
ista: 'Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.'
mla: Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity,
2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.
short: N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013,
pp. 508–515.
date_created: 2022-03-21T07:46:22Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2022-06-20T09:18:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/b978-0-12-384719-5.00031-9
edition: '2'
keyword:
- Adaptive landscape
- Cline
- Coalescent process
- Gene flow
- Hybrid zone
- Local adaptation
- Natural selection
- Neutral theory
- Population structure
- Speciation
language:
- iso: eng
month: '01'
oa_version: None
page: 508-515
publication: Encyclopedia of Biodiversity
publication_identifier:
isbn:
- 978-0-12-384720-1
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differentiation
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2287'
abstract:
- lang: eng
text: Negative frequency-dependent selection should result in equal sex ratios in
large populations of dioecious flowering plants, but deviations from equality
are commonly reported. A variety of ecological and genetic factors can explain
biased sex ratios, although the mechanisms involved are not well understood. Most
dioecious species are long-lived and/or clonal complicating efforts to identify
stages during the life cycle when biases develop. We investigated the demographic
correlates of sex-ratio variation in two chromosome races of Rumex hastatulus,
an annual, wind-pollinated colonizer of open habitats from the southern USA. We
examined sex ratios in 46 populations and evaluated the hypothesis that the proximity
of males in the local mating environment, through its influence on gametophytic
selection, is the primary cause of female-biased sex ratios. Female-biased sex
ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62),
with significant female bias in 89% of populations. Large, high-density populations
had the highest proportion of females, whereas smaller, low-density populations
had sex ratios closer to equality. Progeny sex ratios were more female biased
when males were in closer proximity to females, a result consistent with the gametophytic
selection hypothesis. Our results suggest that interactions between demographic
and genetic factors are probably the main cause of female-biased sex ratios in
R. hastatulus. The annual life cycle of this species may limit the scope for selection
against males and may account for the weaker degree of bias in comparison with
perennial Rumex species.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Pickup M, Barrett S. The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution.
2013;3(3):629-639. doi:10.1002/ece3.465
apa: Pickup, M., & Barrett, S. (2013). The influence of demography and local
mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology
and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465
chicago: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and
Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.”
Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.
ieee: M. Pickup and S. Barrett, “The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution,
vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.
ista: Pickup M, Barrett S. 2013. The influence of demography and local mating environment
on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3),
629–639.
mla: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local
Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology
and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465.
short: M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.
date_created: 2018-12-11T11:56:47Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T06:56:32Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/ece3.465
file:
- access_level: open_access
checksum: b5531bab4c0dec396bf5c8497fe178bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:35Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5290'
file_name: IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf
file_size: 626949
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 629 - 639
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4644'
pubrep_id: '416'
quality_controlled: '1'
scopus_import: 1
status: public
title: The influence of demography and local mating environment on sex ratios in a
wind-pollinated dioecious plant
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '2473'
abstract:
- lang: eng
text: 'When a mutation with selective advantage s spreads through a panmictic population,
it may cause two lineages at a linked locus to coalesce; the probability of coalescence
is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid
individuals, and r is the recombination rate. Population structure delays fixation,
and so weakens the effect of a selective sweep. However, favourable alleles spread
through a spatially continuous population behind a narrow wavefront; ancestral
lineages are confined at the tip of this front, and so coalesce rapidly. In extremely
dense populations, coalescence is dominated by rare fluctuations ahead of the
front. However, we show that for moderate densities, a simple quasi-deterministic
approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ),
where ρ is the population density and is the characteristic scale of the wavefront;
g(η) depends only on the strength of random drift, . The net effect of a sweep
on coalescence also depends crucially on whether two lineages are ever both within
the wavefront at the same time: even in the extreme case when coalescence within
the front is instantaneous, the net rate of coalescence may be lower than in a
single panmictic population. Sweeps can also have a substantial impact on the
rate of gene flow. A single lineage will jump to a new location when it is hit
by a sweep, with mean square displacement ; this can be substantial if the species’
range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R,
is small. This effect is half as strong in two dimensions. In contrast, the rate
of coalescence between lineages, at random locations in space and on the genetic
map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average,
one-dimensional structure is likely to reduce coalescence due to sweeps, relative
to panmixis. In two dimensions, genes must move along the front before they can
coalesce; this process is rapid, being dominated by rare fluctuations. This leads
to a dramatically higher rate of coalescence within the wavefront than if lineages
simply diffused along the front. Nevertheless, the net rate of coalescence due
to a sweep through a two-dimensional population is likely to be lower than it
would be with panmixis.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially
extended populations. Theoretical Population Biology. 2013;87(8):75-89.
doi:10.1016/j.tpb.2012.12.001
apa: Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic
hitch-hiking in spatially extended populations. Theoretical Population Biology.
Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001
chicago: Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population
Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001.
ieee: N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking
in spatially extended populations,” Theoretical Population Biology, vol.
87, no. 8. Elsevier, pp. 75–89, 2013.
ista: Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in
spatially extended populations. Theoretical Population Biology. 87(8), 75–89.
mla: Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.”
Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89,
doi:10.1016/j.tpb.2012.12.001.
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 75–89.
date_created: 2018-12-11T11:57:52Z
date_published: 2013-01-03T00:00:00Z
date_updated: 2021-01-12T06:57:42Z
day: '03'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2012.12.001
ec_funded: 1
file:
- access_level: open_access
checksum: 4274ec1f433b838a7d5b941cc9684ca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:54Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5376'
file_name: IST-2013-118-v1+1_bartonetalRevision.pdf
file_size: 1706282
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '8'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 75 - 89
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '4428'
pubrep_id: '118'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic hitch-hiking in spatially extended populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2718'
abstract:
- lang: eng
text: Even though both population and quantitative genetics, and evolutionary computation,
deal with the same questions, they have developed largely independently of each
other. I review key results from each field, emphasising those that apply independently
of the (usually unknown) relation between genotype and phenotype. The infinitesimal
model provides a simple framework for predicting the response of complex traits
to selection, which in biology has proved remarkably successful. This allows one
to choose the schedule of population sizes and selection intensities that will
maximise the response to selection, given that the total number of individuals
realised, C = ∑t Nt, is constrained. This argument shows that for an additive
trait (i.e., determined by the sum of effects of the genes), the optimum population
size and the maximum possible response (i.e., the total change in trait mean)
are both proportional to √C.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: 'Barton NH, Paixao T. Can quantitative and population genetics help us understand
evolutionary computation? In: Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568'
apa: 'Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics
help us understand evolutionary computation? In Proceedings of the 15th annual
conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam,
Netherlands: ACM. https://doi.org/10.1145/2463372.2463568'
chicago: Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population
Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the
15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM,
2013. https://doi.org/10.1145/2463372.2463568.
ieee: N. H. Barton and T. Paixao, “Can quantitative and population genetics help
us understand evolutionary computation?,” in Proceedings of the 15th annual
conference on Genetic and evolutionary computation, Amsterdam, Netherlands,
2013, pp. 1573–1580.
ista: 'Barton NH, Paixao T. 2013. Can quantitative and population genetics help
us understand evolutionary computation? Proceedings of the 15th annual conference
on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation
conference, 1573–1580.'
mla: Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics
Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual
Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80,
doi:10.1145/2463372.2463568.
short: N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
date_created: 2018-12-11T11:59:14Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463568
ec_funded: 1
file:
- access_level: open_access
checksum: 9d9be9090ce5c20766e0eb076ace5b98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5159'
file_name: IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf
file_size: 475844
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 1573 - 1580
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4174'
pubrep_id: '564'
quality_controlled: '1'
scopus_import: 1
status: public
title: Can quantitative and population genetics help us understand evolutionary computation?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2720'
abstract:
- lang: eng
text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding
the process of evolution. Mutations are inherently difficult to study because
they are rare and are frequently eliminated by natural selection. In the ciliate
Tetrahymena thermophila, mutations can accumulate in the germline genome without
being exposed to selection. We have conducted a mutation accumulation (MA) experiment
in this species. Assuming that all mutations are deleterious and have the same
effect, we estimate that the deleterious mutation rate per haploid germline genome
per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that
germline mutations decrease fitness by s = 11% when expressed in a homozygous
state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially
recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal
mutations is <10% of the deleterious mutation rate. Comparisons between the
observed evolutionary responses in the germline and somatic genomes and the results
from individual-based simulations of MA suggest that the two genomes have similar
mutational parameters. These are the first estimates of the deleterious mutation
rate and fitness effects from the eukaryotic supergroup Chromalveolata and are
within the range of those of other eukaryotes.'
article_processing_charge: No
author:
- first_name: Hongan
full_name: Long, Hongan
last_name: Long
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Ricardo
full_name: Azevedo, Ricardo
last_name: Azevedo
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540.
doi:10.1534/genetics.113.153536
apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of
spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.113.153536
chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation
of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics.
Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.
ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous
mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195,
no. 2. Genetics Society of America, pp. 527–540, 2013.
ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate
Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of
America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.
date_created: 2018-12-11T11:59:15Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:59:16Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1534/genetics.113.153536
ec_funded: 1
external_id:
pmid:
- '23934880'
intvolume: ' 195'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/
month: '10'
oa: 1
oa_version: Submitted Version
page: 527-540
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4172'
quality_controlled: '1'
scopus_import: 1
status: public
title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 195
year: '2013'
...
---
_id: '2719'
abstract:
- lang: eng
text: Prediction of the evolutionary process is a long standing problem both in
the theory of evolutionary biology and evolutionary computation (EC). It has long
been realized that heritable variation is crucial to both the response to selection
and the success of genetic algorithms. However, not all variation contributes
in the same way to the response. Quantitative genetics has developed a large body
of work trying to estimate and understand how different components of the variance
in fitness in the population contribute to the response to selection. We illustrate
how to apply some concepts of quantitative genetics to the analysis of genetic
algorithms. In particular, we derive estimates for the short term prediction of
the response to selection and we use variance decomposition to gain insight on
local aspects of the landscape. Finally, we propose a new population based genetic
algorithm that uses these methods to improve its operation.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of
genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic
and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470'
apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach
to the analysis of genetic algorithms. In Proceedings of the 15th annual conference
on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands:
ACM. https://doi.org/10.1145/2463372.2463470'
chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach
to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis
of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic
and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis
of genetic algorithms. Proceedings of the 15th annual conference on Genetic and
evolutionary computation. GECCO: Genetic and evolutionary computation conference,
845–852.'
mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to
the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
date_created: 2018-12-11T11:59:15Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463470
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 845 - 852
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4173'
quality_controlled: '1'
scopus_import: 1
status: public
title: A variance decomposition approach to the analysis of genetic algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2817'
abstract:
- lang: eng
text: The basic idea of evolutionary game theory is that payoff determines reproductive
rate. Successful individuals have a higher payoff and produce more offspring.
But in evolutionary and ecological situations there is not only reproductive rate
but also carrying capacity. Individuals may differ in their exposure to density
limiting effects. Here we explore an alternative approach to evolutionary game
theory by assuming that the payoff from the game determines the carrying capacity
of individual phenotypes. Successful strategies are less affected by density limitation
(crowding) and reach higher equilibrium abundance. We demonstrate similarities
and differences between our framework and the standard replicator equation. Our
equation is defined on the positive orthant, instead of the simplex, but has the
same equilibrium points as the replicator equation. Linear stability analysis
produces the classical conditions for asymptotic stability of pure strategies,
but the stability properties of internal equilibria can differ in the two frameworks.
For example, in a two-strategy game with an internal equilibrium that is always
stable under the replicator equation, the corresponding equilibrium can be unstable
in the new framework resulting in a limit cycle.
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology.
2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029
apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal
of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029
chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.”
Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.
ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical
Biology, vol. 334. Elsevier, pp. 26–34, 2013.
ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical
Biology. 334, 26–34.
mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology,
vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.
short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013)
26–34.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-10-07T00:00:00Z
date_updated: 2021-01-12T06:59:55Z
day: '07'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.1016/j.jtbi.2013.05.029
ec_funded: 1
file:
- access_level: open_access
checksum: 3c29059ab03a4b8f97a07646b817ddbb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:54Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5110'
file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf
file_size: 834604
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 334'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 26 - 34
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '3984'
pubrep_id: '400'
quality_controlled: '1'
scopus_import: 1
status: public
title: Density games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 334
year: '2013'
...
---
_id: '2823'
abstract:
- lang: eng
text: The primary goal of restoration is to create self-sustaining ecological communities
that are resilient to periodic disturbance. Currently, little is known about how
restored communities respond to disturbance events such as fire and how this response
compares to remnant vegetation. Following the 2003 fires in south-eastern Australia
we examined the post-fire response of revegetation plantings and compared this
to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed
for each of three types of vegetation (direct seeding revegetation, revegetation
using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites
were surveyed 6months after fire to quantify the initial survival of mid- and
overstorey plant species in each type of vegetation. Three and 5years after fire
all sites were resurveyed to assess vegetation structure, species diversity and
vigour, as well as indicators of soil function. Overall, revegetation showed high
(>60%) post-fire survival, but this varied among species depending on regeneration
strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey
in both types of plantings showed rapid recovery of vegetation structure and cover
within 3years of fire. This recovery was similar to the burnt remnant woodlands.
Non-native (exotic) ground cover initially increased after fire, but was no different
in burnt and unburnt sites 5years after fire. Fire had no effect on species richness,
but burnt direct seeding sites had reduced species diversity (Simpson's Diversity
Index) while diversity was higher in burnt remnant woodlands. Indices of soil
function in all types of vegetation had recovered to levels found in unburnt sites
5years after fire. These results indicate that even young revegetation (stands
<10years old) showed substantial recovery from disturbance by fire. This suggests
that revegetation can provide an important basis for restoring woodland communities
in the fire-prone Australian environment.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Susie
full_name: Wilson, Susie
last_name: Wilson
- first_name: David
full_name: Freudenberger, David
last_name: Freudenberger
- first_name: Nick
full_name: Nicholls, Nick
last_name: Nicholls
- first_name: Lori
full_name: Gould, Lori
last_name: Gould
- first_name: Sarah
full_name: Hnatiuk, Sarah
last_name: Hnatiuk
- first_name: Jeni
full_name: Delandre, Jeni
last_name: Delandre
citation:
ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated
woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312.
doi:10.1111/j.1442-9993.2012.02404.x
apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk,
S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities
in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x
chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori
Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland
Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell,
2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.
ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities
in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell,
pp. 300–312, 2013.
ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre
J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern
Australia. Austral Ecology. 38(3), 300–312.
mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities
in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell,
2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.
short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk,
J. Delandre, Austral Ecology 38 (2013) 300–312.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1442-9993.2012.02404.x
intvolume: ' 38'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 300 - 312
publication: Austral Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3978'
quality_controlled: '1'
scopus_import: 1
status: public
title: Post-fire recovery of revegetated woodland communities in south-eastern Australia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2842'
abstract:
- lang: eng
text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal
rate, σ2, based on either allele frequencies or on the lengths of sequence blocks
that are shared between genomes. Over intermediate timescales (10-100 generations,
say), populations that live in two dimensions approach a quasi-equilibrium that
is independent of both their local structure and their deeper history. Over such
scales, the standardised covariance of allele frequencies (i.e. pairwise FS T)
falls with the logarithm of distance, and depends only on neighbourhood size,
N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We
show how spatial correlations can be accounted for, assuming a Gaussian distribution
of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively,
inferences can be based on the distribution of the lengths of sequence that are
identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about
intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood
size, the distribution of long blocks is given directly by the classical Wright-Malécot
formula; this relationship can be used to infer both N and σ2. With small neighbourhood
size, there is an appreciable chance that recombinant lineages will coalesce back
before escaping into the distant past. For this case, we show that if genomes
are sampled from some distance apart, then the distribution of lengths of blocks
that are identical in state is geometric, with a mean that depends on N and σ2.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001'
apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference
in two dimensions: Allele frequencies versus lengths of shared sequence blocks.
Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence
Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.'
ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two
dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical
Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.'
ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 87(1), 105–119.'
mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies
versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology,
vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.'
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 105–119.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2013.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 9bf9d9a6fd03dd9df50906891f393bf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:33Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5288'
file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf
file_size: 1554712
relation: main_file
- access_level: open_access
checksum: 2bceddb76edacd0cd5fad73051e2a928
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:34Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5289'
file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf
file_size: 822964
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 105 - 119
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '3953'
pubrep_id: '558'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence
blocks'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2910'
abstract:
- lang: eng
text: "Coalescent simulation has become an indispensable tool in population genetics
and many complex evolutionary scenarios have been incorporated into the basic
algorithm. Despite many years of intense interest in spatial structure, however,
there are no available methods to simulate the ancestry of a sample of genes that
occupy a spatial continuum. This is mainly due to the severe technical problems
encountered by the classical model of isolation\r\nby distance. A recently introduced
model solves these technical problems and provides a solid theoretical basis for
the study of populations evolving in continuous space. We present a detailed algorithm
to simulate the coalescent process in this model, and provide an efficient implementation
of a generalised version of this algorithm as a freely available Python module."
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space.
Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067
apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation
in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067
chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent
Simulation in Continuous Space.” Bioinformatics. Oxford University Press,
2013. https://doi.org/10.1093/bioinformatics/btt067.
ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous
space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956,
2013.
ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous
space. Bioinformatics. 29(7), 955–956.
mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics,
vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.
short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T07:00:38Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/bioinformatics/btt067
ec_funded: 1
file:
- access_level: open_access
checksum: a3b54d7477fac923815ac082403d9bd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:04Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5189'
file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf
file_size: 170197
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 955 - 956
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '3833'
pubrep_id: '556'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coalescent simulation in continuous space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '2909'
abstract:
- lang: eng
text: "We survey a class of models for spatially structured populations\r\nwhich
we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework
for modelling in which the key innovation is that random genetic drift\r\nis driven
by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes
some of the obstructions to modelling populations which evolve in two-\r\n(and
higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved
in data and how it fits with classical models. Finally we outline some\r\ndirections
for future research."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002
apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in
a spatial continuum. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution
in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial
continuum,” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 1. IOP Publishing Ltd., 2013.
ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013(1).
mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing
Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.
short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory
and Experiment 2013 (2013).
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1088/1742-5468/2013/01/P01002
ec_funded: 1
file:
- access_level: open_access
checksum: ce8a4424385b3086138a1e054e16e0e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:52Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5242'
file_name: IST-2016-557-v1+1_BEVrevised.pdf
file_size: 702583
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 2013'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3834'
pubrep_id: '557'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modelling evolution in a spatial continuum
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2908'
abstract:
- lang: eng
text: 'Hybridization is an almost inevitable component of speciation, and its study
can tell us much about that process. However, hybridization itself may have a
negligible influence on the origin of species: on the one hand, universally favoured
alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous
selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional
hybridisation may hardly affect the process of divergence.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015
apa: Barton, N. H. (2013). Does hybridisation influence speciation? . Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015
chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.
ieee: N. H. Barton, “Does hybridisation influence speciation? ,” Journal of
Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.
ista: Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 26(2), 267–269.
mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69,
doi:10.1111/jeb.12015.
short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '17'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/jeb.12015
file:
- access_level: open_access
checksum: 716e88714c3411cd0bd70928b14ea692
content_type: text/rtf
creator: system
date_created: 2018-12-12T10:09:38Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4762'
file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf
file_size: 13339
relation: main_file
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checksum: 957fd07c71c1b1eac2c65ae3311aca78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:39Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4763'
file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf
file_size: 103437
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 267 - 269
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3835'
pubrep_id: '111'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Does hybridisation influence speciation? '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2907'
abstract:
- lang: eng
text: 'Sex and recombination are among the most striking features of the living
world, and they play a crucial role in allowing the evolution of complex adaptation.
The sharing of genomes through the sexual union of different individuals requires
elaborate behavioral and physiological adaptations. At the molecular level, the
alignment of two DNA double helices, followed by their precise cutting and rejoining,
is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary
consequences: distinct sexes, elaborate mating displays, selfish genetic elements,
and so on.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution.
Princeton University Press; 2013:328-333.'
apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution
(pp. 328–333). Princeton University Press.
chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide
to Evolution, 328–33. Princeton University Press, 2013.
ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–333.
ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution.
, 328–333.'
mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–33.
short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University
Press, 2013, pp. 328–333.
date_created: 2018-12-11T12:00:16Z
date_published: 2013-11-04T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '04'
ddc:
- '576'
department:
- _id: NiBa
file:
- access_level: open_access
checksum: 8332ca9cb40f7e66d1006b175ce36b60
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: system
date_created: 2018-12-12T10:16:47Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5237'
file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx
file_size: 79838
relation: main_file
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checksum: 849f418620fb78d6ba23bb4f488ee93f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:48Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5238'
file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf
file_size: 144131
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 328 - 333
publication: The Princeton Guide to Evolution
publication_identifier:
isbn:
- '9780691149776'
publication_status: published
publisher: Princeton University Press
publist_id: '3839'
pubrep_id: '119'
quality_controlled: '1'
status: public
title: Recombination and sex
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '450'
abstract:
- lang: eng
text: Understanding the relative importance of heterosis and outbreeding depression
over multiple generations is a key question in evolutionary biology and is essential
for identifying appropriate genetic sources for population and ecosystem restoration.
Here we use 2455 experimental crosses between 12 population pairs of the rare
perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational
(F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no
evidence of outbreeding depression, with inter-population hybrids and backcrosses
showing either similar fitness or significant heterosis for fitness components
across the three generations. Variation in heterosis among population pairs was
best explained by characteristics of the foreign source or home population, and
was greatest when the source population was large, with high genetic diversity
and low inbreeding, and the home population was small and inbred. Our results
indicate that the primary consideration for maximizing progeny fitness following
population augmentation or restoration is the use of seed from large, genetically
diverse populations.
article_number: '2058'
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect
heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1750).
doi:10.1098/rspb.2012.2058
apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population
characteristics affect heterosis following genetic rescue of fragmented plant
populations. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058
chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population
Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant
Populations.” Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058.
ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1750. Royal Society, The, 2013.
ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.
mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis
Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1750,
2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058.
short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
date_created: 2018-12-11T11:46:32Z
date_published: 2013-01-07T00:00:00Z
date_updated: 2021-01-12T07:57:25Z
day: '07'
department:
- _id: NiBa
doi: 10.1098/rspb.2012.2058
external_id:
pmid:
- '23173202'
intvolume: ' 280'
issue: '1750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '7372'
quality_controlled: '1'
status: public
title: Source population characteristics affect heterosis following genetic rescue
of fragmented plant populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 280
year: '2013'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2023-02-23T14:07:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-23T10:31:17Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '2917'
abstract:
- lang: eng
text: 'The search for extra-terrestrial intelligence (SETI) has been performed principally
as a one-way survey, listening of radio frequencies across the Milky Way and other
galaxies. However, scientists have engaged in an active messaging only rarely.
This suggests the simple rationale that if other civilizations exist and take
a similar approach to ours, namely listening but not broadcasting, the result
is a silent universe. A simple game theoretical model, the prisoner''s dilemma,
explains this situation: each player (civilization) can passively search (defect),
or actively search and broadcast (cooperate). In order to maximize the payoff
(or, equivalently, minimize the risks) the best strategy is not to broadcast.
In fact, the active search has been opposed on the basis that it might be dangerous
to expose ourselves. However, most of these ideas have not been based on objective
arguments, and ignore accounting of the possible gains and losses. Thus, the question
stands: should we perform an active search? I develop a game-theoretical framework
where civilizations can be of different types, and explicitly apply it to a situation
where societies are either interested in establishing a two-way communication
or belligerent and in urge to exploit ours. The framework gives a quantitative
solution (a mixed-strategy), which is how frequent we should perform the active
SETI. This frequency is roughly proportional to the inverse of the risk, and can
be extremely small. However, given the immense amount of stars being scanned,
it supports active SETI. The model is compared with simulations, and the possible
actions are evaluated through the San Marino scale, measuring the risks of messaging.'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. The game of active search for extra terrestrial intelligence Breaking
the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62.
doi:10.1017/S1473550412000407
apa: de Vladar, H. (2012). The game of active search for extra terrestrial intelligence
Breaking the Great Silence . International Journal of Astrobiology. Cambridge
University Press. https://doi.org/10.1017/S1473550412000407
chicago: Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence
Breaking the Great Silence .” International Journal of Astrobiology. Cambridge
University Press, 2012. https://doi.org/10.1017/S1473550412000407.
ieee: H. de Vladar, “The game of active search for extra terrestrial intelligence
Breaking the Great Silence ,” International Journal of Astrobiology, vol.
12, no. 1. Cambridge University Press, pp. 53–62, 2012.
ista: de Vladar H. 2012. The game of active search for extra terrestrial intelligence
Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62.
mla: de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence
Breaking the Great Silence .” International Journal of Astrobiology, vol.
12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407.
short: H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.
date_created: 2018-12-11T12:00:19Z
date_published: 2012-11-06T00:00:00Z
date_updated: 2021-01-12T07:00:41Z
day: '06'
department:
- _id: NiBa
doi: 10.1017/S1473550412000407
intvolume: ' 12'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 53 - 62
publication: International Journal of Astrobiology
publication_status: published
publisher: Cambridge University Press
publist_id: '3821'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The game of active search for extra terrestrial intelligence Breaking the
Great Silence '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2012'
...
---
_id: '2962'
abstract:
- lang: eng
text: The choice of summary statistics is a crucial step in approximate Bayesian
computation (ABC). Since statistics are often not sufficient, this choice involves
a trade-off between loss of information and reduction of dimensionality. The latter
may increase the efficiency of ABC. Here, we propose an approach for choosing
summary statistics based on boosting, a technique from the machine learning literature.
We consider different types of boosting and compare them to partial least squares
regression as an alternative. To mitigate the lack of sufficiency, we also propose
an approach for choosing summary statistics locally, in the putative neighborhood
of the true parameter value. We study a demographic model motivated by the re-introduction
of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are
the mean and standard deviation across microsatellites of the scaled ancestral
mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to
matings per breeding season (ω). By simulation, we assess the properties of the
posterior distribution obtained with the various methods. According to our criteria,
ABC with summary statistics chosen locally via boosting with the L2-loss performs
best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find
that most of the variation across loci of the ancestral mutation rate u is between
7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access
to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent
estimates.
acknowledged_ssus:
- _id: ScienComp
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
citation:
ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary
statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047.
doi:10.1534/genetics.112.143164
apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach
for choosing summary statistics in approximate Bayesian computation. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.112.143164
chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach
for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics.
Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.
ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing
summary statistics in approximate Bayesian computation,” Genetics, vol.
192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.
ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing
summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.
mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics
in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics
Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.
short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
pmid:
- '22960215'
intvolume: ' 192'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1027 - 1047
pmid: 1
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3763'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel approach for choosing summary statistics in approximate Bayesian computation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 192
year: '2012'
...
---
_id: '3122'
abstract:
- lang: eng
text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin
1877), understanding the mechanisms maintaining the diverse sexual strategies
of plants has remained an important challenge for evolutionary biologists. In
some species, populations are sexually polymorphic and contain two or more mating
morphs (sex phenotypes). Differences in morphology or phenology among the morphs
influence patterns of non-random mating. In these populations, negative frequency-dependent
selection arising from disassortative (intermorph) mating is usually required
for the evolutionary maintenance of sexual polymorphism, but few studies have
demonstrated the required patterns of non-random mating. In the current issue
of Molecular Ecology, Shang (2012) make an important contribution to our understanding
of how disassortative mating influences sex phenotype ratios in Acer pictum subsp.
mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They
monitored sex expression in 97 adults and used paternity analysis of open-pollinated
seed to examine disassortative mating among three sex phenotypes. Using a deterministic
''pollen transfer'' model, Shang et al. present convincing evidence that differences
in the degree of disassortative mating in progeny arrays of the sex phenotypes
can explain their uneven frequencies in the adult population. This study provides
a useful example of how the deployment of genetic markers, demographic monitoring
and modelling can be integrated to investigate the maintenance of sexual diversity
in plants. '
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism
in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x
apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance
of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell.
https://doi.org/10.1111/j.1365-294X.2012.05643.x
chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell,
2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.
ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual
polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell,
pp. 3640–3643, 2012.
ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual
polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.
mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no.
15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.
short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.
date_created: 2018-12-11T12:01:31Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:13Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05643.x
intvolume: ' 21'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3640 - 3643
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3577'
quality_controlled: '1'
scopus_import: 1
status: public
title: Disassortative mating and the maintenance of sexual polymorphism in painted
maple
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '3131'
abstract:
- lang: eng
text: 'In large populations, many beneficial mutations may be simultaneously available
and may compete with one another, slowing adaptation. By finding the probability
of fixation of a favorable allele in a simple model of a haploid sexual population,
we find limits to the rate of adaptive substitution, Λ, that depend on simple
parameter combinations. When variance in fitness is low and linkage is loose,
the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the
rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage.
Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under
polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans,
interference is yet stronger. We use a scaling argument to show that the density
of adaptive substitutions depends on s, N, U, and R only through the baseline
density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different
sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference
prevents the rate of adaptive substitution from exceeding one per centimorgan
per 200 generations. Simulations and numerical calculations confirm the scaling
argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R,
the rate of adaptation grows above R/2, but only very slowly. We also consider
the effect of sweeps on neutral diversity and show that, while even occasional
sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become
more common-diversity can be maintained even in populations experiencing very
strong interference. Our results indicate that for some organisms the rate of
adaptive substitution may be primarily recombination-limited, depending only weakly
on the mutation supply and the strength of selection.'
acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth,
O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers
for their helpful suggestions."
article_number: e1002740
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual
populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740
apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution
in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740
chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive
Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science,
2012. https://doi.org/10.1371/journal.pgen.1002740.
ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution
in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of
Science, 2012.
ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in
sexual populations. PLoS Genetics. 8(6), e1002740.
mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution
in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002740.
short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-07T00:00:00Z
date_updated: 2021-01-12T07:41:17Z
day: '07'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1002740
ec_funded: 1
file:
- access_level: open_access
checksum: 729a4becda7d786c4c3db8f9a1f77953
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:00Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4659'
file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf
file_size: 1284801
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3566'
pubrep_id: '114'
quality_controlled: '1'
scopus_import: 1
status: public
title: Limits to the rate of adaptive substitution in sexual populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3166'
abstract:
- lang: eng
text: 'There is evidence that the genetic code was established prior to the existence
of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms
had to rely on simple anaerobic bioenergetic processes. In this work I propose
that amino acid fermentation powered metabolism in the RNA world, and that this
was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were
used as carbon sources rather than as catalytic or structural elements. In modern
bacteria, amino acid fermentation is known as the Stickland reaction. This pathway
involves two amino acids: the first undergoes oxidative deamination, and the second
acts as an electron acceptor through reductive deamination. This redox reaction
results in two keto acids that are employed to synthesise ATP via substrate-level
phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some
bacteria of the genus Clostridium. Two other facts support Stickland fermentation
in the RNA world. First, several Stickland amino acid pairs are synthesised in
abiotic amino acid synthesis. This suggests that amino acids that could be used
as an energy substrate were freely available. Second, anticodons that have complementary
sequences often correspond to amino acids that form Stickland pairs. The main
hypothesis of this paper is that pairs of complementary proto-adapters were assigned
to Stickland amino acids pairs. There are signatures of this hypothesis in the
genetic code. Furthermore, it is argued that the proto-adapters formed double
strands that brought amino acid pairs into proximity to facilitate their mutual
redox reaction, structurally constraining the anticodon pairs that are assigned
to these amino acid pairs. Significance tests which randomise the code are performed
to study the extent of the variability of the energetic (ATP) yield. Random assignments
can lead to a substantial yield of ATP and maintain enough variability, thus selection
can act and refine the assignments into a proto-code that optimises the energetic
yield. Monte Carlo simulations are performed to evaluate the establishment of
these simple proto-codes, based on amino acid substitutions and codon swapping.
In all cases, donor amino acids are assigned to anticodons composed of U+G, and
have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to
the the remaining codons. These bioenergetic and structural constraints allow
for a metabolic role for amino acids before their co-option as catalyst cofactors.
Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary
(nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)'
acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152
SELECTIONINFORMATION. '
article_number: '6'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology
Direct. 2012;7. doi:10.1186/1745-6150-7-6
apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic
code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6
chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic
Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.
ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,”
Biology Direct, vol. 7. BioMed Central, 2012.
ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code.
Biology Direct. 7, 6.
mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.”
Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.
short: H. de Vladar, Biology Direct 7 (2012).
date_created: 2018-12-11T12:01:46Z
date_published: 2012-02-10T00:00:00Z
date_updated: 2021-01-12T07:41:31Z
day: '10'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1186/1745-6150-7-6
ec_funded: 1
file:
- access_level: open_access
checksum: e511e401e239ef608a7fd79b21a06d78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:44Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5166'
file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf
file_size: 4099536
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '3518'
pubrep_id: '99'
quality_controlled: '1'
status: public
title: Amino acid fermentation at the origin of the genetic code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3277'
abstract:
- lang: eng
text: The problem of the origin of metazoa is becoming more urgent in the context
of astrobiology. By now it is clear that clues to the understanding of this crucial
transition in the evolution of life can arise in a fourth pathway besides the
three possibilities in the quest for simplicity outlined by Bonner in his classical
book. In other words, solar system exploration seems to be one way in the long-term
to elucidate the simplicity of evolutionary development. We place these ideas
in the context of different inheritance systems, namely the genotypic and phenotypic
replicators with limited or unlimited heredity, and ask which of these can support
multicellular development, and to which degree of complexity. However, the quest
for evidence on the evolution of biotas from planets around other stars does not
seem to be feasible with present technology with direct visualization of living
organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter
where there is a possibility of detecting reliable biomarkers in the next decade
with the Europa Jupiter System Mission, in view of recent progress by landing
micropenetrators on planetary, or satellite surfaces. Mars is a second possibility
in the inner Solar System, in spite of the multiple difficulties faced by the
fleet of past, present and future missions. We discuss a series of preliminary
ideas for elucidating the origin of metazoan analogues with available instrumentation
in potential payloads of feasible space missions to the Galilean moons.
alternative_title:
- Cellular Origin, Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Julian
full_name: Chela Flores, Julian
last_name: Chela Flores
citation:
ama: 'de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated
in the exploration of the solar system? In: Life on Earth and Other Planetary
Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22'
apa: de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity
be anticipated in the exploration of the solar system? In Life on Earth and
other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22
chicago: Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” In Life on Earth and
Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22.
ieee: H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be
anticipated in the exploration of the solar system?,” in Life on Earth and
other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.
ista: 'de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be
anticipated in the exploration of the solar system? In: Life on Earth and other
planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology,
vol. 24, 387–405.'
mla: de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other
Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.
short: H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies,
Springer, 2012, pp. 387–405.
date_created: 2018-12-11T12:02:25Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/978-94-007-4966-5_22
intvolume: ' 24'
language:
- iso: eng
month: '01'
oa_version: None
page: 387 - 405
publication: Life on Earth and other planetary bodies
publication_status: published
publisher: Springer
publist_id: '3369'
quality_controlled: '1'
status: public
title: Can the evolution of multicellularity be anticipated in the exploration of
the solar system?
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '498'
abstract:
- lang: eng
text: Understanding patterns and correlates of local adaptation in heterogeneous
landscapes can provide important information in the selection of appropriate seed
sources for restoration. We assessed the extent of local adaptation of fitness
components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides
(Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance,
quantitative (QST) and neutral (FST) genetic differentiation, and size of the
local and foreign populations could predict patterns of adaptive differentiation.
Local adaptation varied among populations and fitness components. Including all
population pairs, local adaptation was observed for seedling survival, but not
for biomass, while foreign genotype advantage was observed for reproduction (number
of inflorescences). Among population pairs, local adaptation increased with QST
and local population size for biomass. QST was associated with environmental distance,
suggesting ecological selection for phenotypic divergence. However, low FST and
variation in population structure in small populations demonstrates the interaction
of gene flow and drift in constraining local adaptation in R. leptorrhynchoides.
Our study indicates that for species in heterogeneous landscapes, collecting seed
from large populations from similar environments to candidate sites is likely
to provide the most appropriate seed sources for restoration.
acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and
Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment
and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability
and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer
C. H. Barrett for comments that improved the quality of the manuscript.\r\n"
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented
plant populations: Implications for restoration genetics. Evolutionary Applications.
2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x'
apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local
adaptation in fragmented plant populations: Implications for restoration genetics.
Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x'
chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting
Local Adaptation in Fragmented Plant Populations: Implications for Restoration
Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.'
ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation
in fragmented plant populations: Implications for restoration genetics,” Evolutionary
Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.'
ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in
fragmented plant populations: Implications for restoration genetics. Evolutionary
Applications. 5(8), 913–924.'
mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations:
Implications for Restoration Genetics.” Evolutionary Applications, vol.
5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.'
short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012)
913–924.
date_created: 2018-12-11T11:46:48Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/j.1752-4571.2012.00284.x
file:
- access_level: open_access
checksum: 233007138606aca5a2f75f7ae1742f43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:33Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4821'
file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf
file_size: 396136
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 913 - 924
publication: Evolutionary Applications
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7322'
pubrep_id: '942'
quality_controlled: '1'
status: public
title: 'Predicting local adaptation in fragmented plant populations: Implications
for restoration genetics'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2012'
...
---
_id: '9758'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. 2012. doi:10.5061/dryad.274b1'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate
Bayesian computation for modular inference problems with many parameters: the
example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates.” Dryad, 2012.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates, Dryad, 10.5061/dryad.274b1.'
mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation
for Modular Inference Problems with Many Parameters: The Example of Migration
Rates. Dryad, 2012, doi:10.5061/dryad.274b1.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012).
date_created: 2021-07-30T12:36:39Z
date_published: 2012-11-14T00:00:00Z
date_updated: 2023-02-23T11:05:19Z
day: '14'
department:
- _id: NiBa
doi: 10.5061/dryad.274b1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.274b1
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2944'
relation: used_in_publication
status: public
status: public
title: 'Data from: Approximate Bayesian computation for modular inference problems
with many parameters: the example of migration rates'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '2968'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya
stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop
a likelihood method to numerically estimate models of divergence between three
populations from multilocus data. We investigate the power of this framework on
simulated data, and-using triplet alignments of intronic loci-quantify the support
for all possible divergence relationships between refugial populations in the
four parasitoids. Although an East to West order of population divergence has
highest support in all but one species, we cannot rule out alternative population
tree topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times. © 2012 Blackwell Publishing Ltd.
acknowledgement: "This work was supported by funding from the UK Natural Environment
Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1,
NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe
thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing
specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on
earlier versions of the manuscript. "
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: George
full_name: Melika, George
last_name: Melika
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
citation:
ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population
histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617.
doi:10.1111/j.1365-294X.2012.05700.x
apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood
based comparison of population histories in a parasitoid guild. Molecular Ecology.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x
chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood
Based Comparison of Population Histories in a Parasitoid Guild.” Molecular
Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.
ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison
of population histories in a parasitoid guild,” Molecular Ecology, vol.
21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.
ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison
of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617.
mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories
in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell,
2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.
short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.
date_created: 2018-12-11T12:00:36Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2023-05-30T13:07:47Z
day: '01'
ddc:
- '570'
- '579'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05700.x
ec_funded: 1
file:
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checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb
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creator: system
date_created: 2018-12-12T10:17:47Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5304'
file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf
file_size: 235820
relation: main_file
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creator: system
date_created: 2018-12-12T10:17:48Z
date_updated: 2020-07-14T12:45:57Z
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has_accepted_license: '1'
intvolume: ' 21'
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 4605 - 4617
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3746'
pubrep_id: '296'
quality_controlled: '1'
related_material:
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- id: '13075'
relation: research_data
status: public
scopus_import: 1
status: public
title: A likelihood based comparison of population histories in a parasitoid guild
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '13075'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota
and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood
method to numerically estimate models of divergence between three populations
from multilocus data. We investigate the power of this framework on simulated
data, and - using triplet alignments of intronic loci - quantify the support for
all possible divergence relationships between refugial populations in the four
parasitoids. Although an East to West order of population divergence has highest
support in all but one species, we cannot rule out alternative population tree
topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times.
article_processing_charge: No
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: George
full_name: Melika, George
last_name: Melika
citation:
ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison
of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS'
apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A
likelihood-based comparison of population histories in a parasitoid guild. Dryad.
https://doi.org/10.5061/DRYAD.0G0FS'
chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data
from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.”
Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.'
ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based
comparison of population histories in a parasitoid guild.” Dryad, 2012.'
ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based
comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.'
mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population
Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.'
short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).
date_created: 2023-05-23T17:01:02Z
date_published: 2012-06-08T00:00:00Z
date_updated: 2023-05-30T13:07:48Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.0G0FS
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.0g0fs
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
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- id: '2968'
relation: used_in_publication
status: public
status: public
title: 'Data from: A likelihood-based comparison of population histories in a parasitoid
guild'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '3372'
abstract:
- lang: eng
text: Nowak et al.1 argue that inclusive fitness theory has been of little value
in explaining the natural world, and that it has led to negligible progress in
explaining the evolution of eusociality. However, we believe that their arguments
are based upon a misunderstanding of evolutionary theory and a misrepresentation
of the empirical literature. We will focus our comments on three general issues.
author:
- first_name: Patrick
full_name: Abbot, Patrick
last_name: Abbot
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: John
full_name: Alcock, John
last_name: Alcock
- first_name: Samuel
full_name: Alizon, Samuel
last_name: Alizon
- first_name: Joao
full_name: Alpedrinha, Joao
last_name: Alpedrinha
- first_name: Malte
full_name: Andersson, Malte
last_name: Andersson
- first_name: Jean
full_name: Andre, Jean
last_name: Andre
- first_name: Minus
full_name: Van Baalen, Minus
last_name: Van Baalen
- first_name: Francois
full_name: Balloux, Francois
last_name: Balloux
- first_name: Sigal
full_name: Balshine, Sigal
last_name: Balshine
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Leo
full_name: Beukeboom, Leo
last_name: Beukeboom
- first_name: Jay
full_name: Biernaskie, Jay
last_name: Biernaskie
- first_name: Trine
full_name: Bilde, Trine
last_name: Bilde
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Breed, Michael
last_name: Breed
- first_name: Sam
full_name: Brown, Sam
last_name: Brown
- first_name: Redouan
full_name: Bshary, Redouan
last_name: Bshary
- first_name: Angus
full_name: Buckling, Angus
last_name: Buckling
- first_name: Nancy
full_name: Burley, Nancy
last_name: Burley
- first_name: Max
full_name: Burton Chellew, Max
last_name: Burton Chellew
- first_name: Michael
full_name: Cant, Michael
last_name: Cant
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Eric
full_name: Charnov, Eric
last_name: Charnov
- first_name: Tim
full_name: Clutton Brock, Tim
last_name: Clutton Brock
- first_name: Andrew
full_name: Cockburn, Andrew
last_name: Cockburn
- first_name: Blaine
full_name: Cole, Blaine
last_name: Cole
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Leda
full_name: Cosmides, Leda
last_name: Cosmides
- first_name: Iain
full_name: Couzin, Iain
last_name: Couzin
- first_name: Jerry
full_name: Coyne, Jerry
last_name: Coyne
- first_name: Scott
full_name: Creel, Scott
last_name: Creel
- first_name: Bernard
full_name: Crespi, Bernard
last_name: Crespi
- first_name: Robert
full_name: Curry, Robert
last_name: Curry
- first_name: Sasha
full_name: Dall, Sasha
last_name: Dall
- first_name: Troy
full_name: Day, Troy
last_name: Day
- first_name: Janis
full_name: Dickinson, Janis
last_name: Dickinson
- first_name: Lee
full_name: Dugatkin, Lee
last_name: Dugatkin
- first_name: Claire
full_name: El Mouden, Claire
last_name: El Mouden
- first_name: Stephen
full_name: Emlen, Stephen
last_name: Emlen
- first_name: Jay
full_name: Evans, Jay
last_name: Evans
- first_name: Regis
full_name: Ferriere, Regis
last_name: Ferriere
- first_name: Jeremy
full_name: Field, Jeremy
last_name: Field
- first_name: Susanne
full_name: Foitzik, Susanne
last_name: Foitzik
- first_name: Kevin
full_name: Foster, Kevin
last_name: Foster
- first_name: William
full_name: Foster, William
last_name: Foster
- first_name: Charles
full_name: Fox, Charles
last_name: Fox
- first_name: Juergen
full_name: Gadau, Juergen
last_name: Gadau
- first_name: Sylvain
full_name: Gandon, Sylvain
last_name: Gandon
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Michael
full_name: Gardner, Michael
last_name: Gardner
- first_name: Thomas
full_name: Getty, Thomas
last_name: Getty
- first_name: Michael
full_name: Goodisman, Michael
last_name: Goodisman
- first_name: Alan
full_name: Grafen, Alan
last_name: Grafen
- first_name: Rick
full_name: Grosberg, Rick
last_name: Grosberg
- first_name: Christina
full_name: Grozinger, Christina
last_name: Grozinger
- first_name: Pierre
full_name: Gouyon, Pierre
last_name: Gouyon
- first_name: Darryl
full_name: Gwynne, Darryl
last_name: Gwynne
- first_name: Paul
full_name: Harvey, Paul
last_name: Harvey
- first_name: Ben
full_name: Hatchwell, Ben
last_name: Hatchwell
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Heikki
full_name: Helantera, Heikki
last_name: Helantera
- first_name: Ken
full_name: Helms, Ken
last_name: Helms
- first_name: Kim
full_name: Hill, Kim
last_name: Hill
- first_name: Natalie
full_name: Jiricny, Natalie
last_name: Jiricny
- first_name: Rufus
full_name: Johnstone, Rufus
last_name: Johnstone
- first_name: Alex
full_name: Kacelnik, Alex
last_name: Kacelnik
- first_name: E Toby
full_name: Kiers, E Toby
last_name: Kiers
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Jan
full_name: Komdeur, Jan
last_name: Komdeur
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
- first_name: Laurent
full_name: Lehmann, Laurent
last_name: Lehmann
- first_name: Timothy
full_name: Linksvayer, Timothy
last_name: Linksvayer
- first_name: Sébastien
full_name: Lion, Sébastien
last_name: Lion
- first_name: Bruce
full_name: Lyon, Bruce
last_name: Lyon
- first_name: James
full_name: Marshall, James
last_name: Marshall
- first_name: Richard
full_name: Mcelreath, Richard
last_name: Mcelreath
- first_name: Yannis
full_name: Michalakis, Yannis
last_name: Michalakis
- first_name: Richard
full_name: Michod, Richard
last_name: Michod
- first_name: Douglas
full_name: Mock, Douglas
last_name: Mock
- first_name: Thibaud
full_name: Monnin, Thibaud
last_name: Monnin
- first_name: Robert
full_name: Montgomerie, Robert
last_name: Montgomerie
- first_name: Allen
full_name: Moore, Allen
last_name: Moore
- first_name: Ulrich
full_name: Mueller, Ulrich
last_name: Mueller
- first_name: Ronald
full_name: Noë, Ronald
last_name: Noë
- first_name: Samir
full_name: Okasha, Samir
last_name: Okasha
- first_name: Pekka
full_name: Pamilo, Pekka
last_name: Pamilo
- first_name: Geoff
full_name: Parker, Geoff
last_name: Parker
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Ido
full_name: Pen, Ido
last_name: Pen
- first_name: David
full_name: Pfennig, David
last_name: Pfennig
- first_name: David
full_name: Queller, David
last_name: Queller
- first_name: Daniel
full_name: Rankin, Daniel
last_name: Rankin
- first_name: Sarah
full_name: Reece, Sarah
last_name: Reece
- first_name: Hudson
full_name: Reeve, Hudson
last_name: Reeve
- first_name: Max
full_name: Reuter, Max
last_name: Reuter
- first_name: Gilbert
full_name: Roberts, Gilbert
last_name: Roberts
- first_name: Simon
full_name: Robson, Simon
last_name: Robson
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Francois
full_name: Rousset, Francois
last_name: Rousset
- first_name: Olav
full_name: Rueppell, Olav
last_name: Rueppell
- first_name: Joel
full_name: Sachs, Joel
last_name: Sachs
- first_name: Lorenzo
full_name: Santorelli, Lorenzo
last_name: Santorelli
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Tom
full_name: Scott Phillips, Tom
last_name: Scott Phillips
- first_name: Janet
full_name: Shellmann Sherman, Janet
last_name: Shellmann Sherman
- first_name: Paul
full_name: Sherman, Paul
last_name: Sherman
- first_name: David
full_name: Shuker, David
last_name: Shuker
- first_name: Jeff
full_name: Smith, Jeff
last_name: Smith
- first_name: Joseph
full_name: Spagna, Joseph
last_name: Spagna
- first_name: Beverly
full_name: Strassmann, Beverly
last_name: Strassmann
- first_name: Andrew
full_name: Suarez, Andrew
last_name: Suarez
- first_name: Liselotte
full_name: Sundström, Liselotte
last_name: Sundström
- first_name: Michael
full_name: Taborsky, Michael
last_name: Taborsky
- first_name: Peter
full_name: Taylor, Peter
last_name: Taylor
- first_name: Graham
full_name: Thompson, Graham
last_name: Thompson
- first_name: John
full_name: Tooby, John
last_name: Tooby
- first_name: Neil
full_name: Tsutsui, Neil
last_name: Tsutsui
- first_name: Kazuki
full_name: Tsuji, Kazuki
last_name: Tsuji
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Francisco
full_name: Úbeda, Francisco
last_name: Úbeda
- first_name: Edward
full_name: Vargo, Edward
last_name: Vargo
- first_name: Bernard
full_name: Voelkl, Bernard
last_name: Voelkl
- first_name: Tom
full_name: Wenseleers, Tom
last_name: Wenseleers
- first_name: Stuart
full_name: West, Stuart
last_name: West
- first_name: Mary
full_name: West Eberhard, Mary
last_name: West Eberhard
- first_name: David
full_name: Westneat, David
last_name: Westneat
- first_name: Diane
full_name: Wiernasz, Diane
last_name: Wiernasz
- first_name: Geoff
full_name: Wild, Geoff
last_name: Wild
- first_name: Richard
full_name: Wrangham, Richard
last_name: Wrangham
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
- first_name: David
full_name: Zeh, David
last_name: Zeh
- first_name: Jeanne
full_name: Zeh, Jeanne
last_name: Zeh
- first_name: Andrew
full_name: Zink, Andrew
last_name: Zink
citation:
ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality.
Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831
apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M.,
… Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature09831
chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte
Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature.
Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831.
ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature,
vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.
ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339),
E1–E4.
mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature,
vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831.
short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre,
M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie,
T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M.
Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn,
B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi,
R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen,
J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J.
Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R.
Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze,
H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers,
H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer,
S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock,
T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo,
G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H.
Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J.
Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann
Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez,
L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji,
S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West
Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J.
Zeh, A. Zink, Nature 471 (2011) E1–E4.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-23T00:00:00Z
date_updated: 2021-01-12T07:43:02Z
day: '23'
department:
- _id: NiBa
doi: 10.1038/nature09831
external_id:
pmid:
- '21430721'
intvolume: ' 471'
issue: '7339'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/
month: '03'
oa: 1
oa_version: Submitted Version
page: E1 - E4
pmid: 1
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3237'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inclusive fitness theory and eusociality
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 471
year: '2011'
...
---
_id: '3394'
abstract:
- lang: eng
text: 'Random genetic drift shifts clines in space, alters their width, and distorts
their shape. Such random fluctuations complicate inferences from cline width and
position. Notably, the effect of genetic drift on the expected shape of the cline
is opposite to the naive (but quite common) misinterpretation of classic results
on the expected cline. While random drift on average broadens the overall cline
in expected allele frequency, it narrows the width of any particular cline. The
opposing effects arise because locally, drift drives alleles to fixation—but fluctuations
in position widen the expected cline. The effect of genetic drift can be predicted
from standardized variance in allele frequencies, averaged across the habitat:
〈F〉. A cline maintained by spatially varying selection (step change) is expected
to be narrower by a factor of relative to the cline in the absence of drift.
The expected cline is broader by the inverse of this factor. In a tension zone
maintained by underdominance, the expected cline width is narrower by about 1
– 〈F〉relative to the width in the absence of drift. Individual clines can differ
substantially from the expectation, and we give quantitative predictions for the
variance in cline position and width. The predictions apply to clines in almost
one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or
along a coast line and give a guide to what patterns to expect in two dimensions.'
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows
the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817
apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected
cline but narrows the expected cline width. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.111.129817
chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society
of America, 2011. https://doi.org/10.1534/genetics.111.129817.
ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but
narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics
Society of America, pp. 227–235, 2011.
ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but
narrows the expected cline width. Genetics. 189(1), 227–235.
mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1,
Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817.
short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129817
ec_funded: 1
intvolume: ' 189'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/
month: '09'
oa: 1
oa_version: Submitted Version
page: 227 - 235
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic drift widens the expected cline but narrows the expected cline width
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3390'
abstract:
- lang: eng
text: 'What determines the genetic contribution that an individual makes to future
generations? With biparental reproduction, each individual leaves a ''pedigree''
of descendants, determined by the biparental relationships in the population.
The pedigree of an individual constrains the lines of descent of each of its genes.
An individual''s reproductive value is the expected number of copies of each of
its genes that is passed on to distant generations conditional on its pedigree.
For the simplest model of biparental reproduction analogous to the Wright-Fisher
model, an individual''s reproductive value is determined within ~10 generations,
independent of population size. Partial selfing and subdivision do not greatly
slow this convergence. Our central result is that the probability that a gene
will survive is proportional to the reproductive value of the individual that
carries it, and that conditional on survival, after a few tens of generations,
the distribution of the number of surviving copies is the same for all individuals,
whatever their reproductive value. These results can be generalized to the joint
distribution of surviving blocks of ancestral genome. Selection on unlinked loci
in the genetic background may greatly increase the variance in reproductive value,
but the above results nevertheless still hold. The almost linear relationship
between survival probability and reproductive value also holds for weakly favored
alleles. Thus, the influence of the complex pedigree of descendants on an individual''s
genetic contribution to the population can be summarized through a single number:
its reproductive value.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The relation between reproductive value and genetic
contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555
apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive
value and genetic contribution. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.111.127555
chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics. Genetics Society of America,
2011. https://doi.org/10.1534/genetics.111.127555.
ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and
genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America,
pp. 953–973, 2011.
ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and
genetic contribution. Genetics. 188(4), 953–973.
mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society
of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555.
short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:09Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.127555
ec_funded: 1
intvolume: ' 188'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/
month: '08'
oa: 1
oa_version: Submitted Version
page: 953 - 973
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3217'
quality_controlled: '1'
scopus_import: 1
status: public
title: The relation between reproductive value and genetic contribution
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2011'
...
---
_id: '3391'
abstract:
- lang: eng
text: 'Evolutionary biology shares many concepts with statistical physics: both
deal with populations, whether of molecules or organisms, and both seek to simplify
evolution in very many dimensions. Often, methodologies have undergone parallel
and independent development, as with stochastic methods in population genetics.
Here, we discuss aspects of population genetics that have embraced methods from
physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo
methods, among others, have been used to study polygenic evolution, rates of adaptation
and range expansions. These applications indicate that evolutionary biology can
further benefit from interactions with other areas of statistical physics; for
example, by following the distribution of paths taken by a population through
time'
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002
apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical
physics to evolutionary biology. Trends in Ecology and Evolution. Cell
Press. https://doi.org/10.1016/j.tree.2011.04.002
chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell
Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002.
ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to
evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8.
Cell Press, pp. 424–432, 2011.
ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 26(8), 424–432.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol.
26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002.
short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/j.tree.2011.04.002
ec_funded: 1
intvolume: ' 26'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.2854
month: '08'
oa: 1
oa_version: Submitted Version
page: 424 - 432
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '3216'
quality_controlled: '1'
scopus_import: 1
status: public
title: The contribution of statistical physics to evolutionary biology
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2011'
...
---
_id: '3784'
abstract:
- lang: eng
text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal
trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005.
Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage
phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology
is described and illustrated. This constitutes the second complete description
of a Scyllaridae phyllosoma with its specific identity being validated by molecular
techniques (the first was S. pygmaeus). These results also solved a long lasting
taxonomic anomaly of several species assigned to the ancient genus Phyllosoma
Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of
S. arctus shows closer affinities with the American scyllarid Scyllarus depressus
or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its
sympatric species S. pygmaeus.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda:
Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological
description. Journal of the Marine Biological Association of the United Kingdom.
2011;91(2):485-492. doi:10.1017/S0025315410000287'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus
(Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis,
with morphological description. Journal of the Marine Biological Association
of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus
Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by
DNA Analysis, with Morphological Description.” Journal of the Marine Biological
Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description,” Journal of the Marine Biological Association of
the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492,
2011.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description. Journal of the Marine Biological Association of the
United Kingdom. 91(2), 485–492.'
mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae)
Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.”
Journal of the Marine Biological Association of the United Kingdom, vol.
91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological
Association of the United Kingdom 91 (2011) 485–492.
date_created: 2018-12-11T12:05:09Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1017/S0025315410000287
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf
month: '03'
oa: 1
oa_version: Published Version
page: 485 - 492
publication: Journal of the Marine Biological Association of the United Kingdom
publication_status: published
publisher: Cambridge University Press
publist_id: '2443'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma
identified by DNA analysis, with morphological description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2011'
...
---
_id: '3290'
abstract:
- lang: eng
text: 'Analysis of genomic data requires an efficient way to calculate likelihoods
across very large numbers of loci. We describe a general method for finding the
distribution of genealogies: we allow migration between demes, splitting of demes
[as in the isolation-with-migration (IM) model], and recombination between linked
loci. These processes are described by a set of linear recursions for the generating
function of branch lengths. Under the infinite-sites model, the probability of
any configuration of mutations can be found by differentiating this generating
function. Such calculations are feasible for small numbers of sampled genomes:
as an example, we show how the generating function can be derived explicitly for
three genes under the two-deme IM model. This derivation is done automatically,
using Mathematica. Given data from a large number of unlinked and nonrecombining
blocks of sequence, these results can be used to find maximum-likelihood estimates
of model parameters by tabulating the probabilities of all relevant mutational
configurations and then multiplying across loci. The feasibility of the method
is demonstrated by applying it to simulated data and to a data set previously
analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila
simulans and D. melanogaster. Our results suggest that such likelihood calculations
are scalable to genomic data as long as the numbers of sampled individuals and
mutations per sequence block are small.'
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Richard
full_name: Harrison, Richard
last_name: Harrison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods
under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569
apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating
likelihoods under the coalescent process. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.111.129569
chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method
for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics
Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.
ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating
likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics
Society of America, pp. 977–987, 2011.
ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods
under the coalescent process. Genetics. 189(3), 977–987.
mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the
Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America,
2011, pp. 977–87, doi:10.1534/genetics.111.129569.
short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.
date_created: 2018-12-11T12:02:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
intvolume: ' 189'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/
month: '11'
oa: 1
oa_version: Submitted Version
page: 977 - 987
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3355'
quality_controlled: '1'
scopus_import: 1
status: public
title: A general method for calculating likelihoods under the coalescent process
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3380'
abstract:
- lang: eng
text: Linkage between markers and genes that affect a phenotype of interest may
be determined by examining differences in marker allele frequency in the extreme
progeny of a cross between two inbred lines. This strategy is usually employed
when pooling is used to reduce genotyping costs. When the cross progeny are asexual,
the extreme progeny may be selected by multiple generations of asexual reproduction
and selection. We analyse this method of measuring phenotype in asexual progeny
and examine the changes in marker allele frequency due to selection over many
generations. Stochasticity in marker frequency in the selected population arises
due to the finite initial population size. We derive the distribution of marker
frequency as a result of selection at a single major locus, and show that in order
to avoid spurious changes in marker allele frequency in the selected population,
the initial population size should be in the low to mid hundreds.
article_processing_charge: No
article_type: original
author:
- first_name: Sayanthan
full_name: Logeswaran, Sayanthan
last_name: Logeswaran
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using
changes in marker allele frequency. Genetical Research. 2011;93(3):221-232.
doi:10.1017/S0016672311000115
apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual
progeny using changes in marker allele frequency. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672311000115
chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits
in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research.
Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.
ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency,” Genetical Research, vol. 93,
no. 3. Cambridge University Press, pp. 221–232, 2011.
ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency. Genetical Research. 93(3), 221–232.
mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in
Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research,
vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.
short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-05-18T00:00:00Z
date_updated: 2021-01-12T07:43:05Z
day: '18'
department:
- _id: NiBa
doi: 10.1017/S0016672311000115
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf
month: '05'
oa: 1
oa_version: Published Version
page: 221 - 232
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '3227'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping Mendelian traits in asexual progeny using changes in marker allele
frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2011'
...
---
_id: '3778'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206.
doi:10.1038/hdy.2010.67
apa: Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature
Publishing Group. https://doi.org/10.1038/hdy.2010.67
chicago: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity.
Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67.
ieee: N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106,
no. 2. Nature Publishing Group, pp. 205–206, 2011.
ista: Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.
mla: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol.
106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67.
short: N.H. Barton, Heredity 106 (2011) 205–206.
date_created: 2018-12-11T12:05:07Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T07:52:08Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2010.67
external_id:
pmid:
- '20502479'
intvolume: ' 106'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/
month: '02'
oa: 1
oa_version: Submitted Version
page: 205 - 206
pmid: 1
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2449'
scopus_import: 1
status: public
title: Estimating linkage disequilibria
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2011'
...
---
_id: '3395'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies aiming to evaluate the genetic health of the exploited populations. The
present study is based on a set of ten nuclear markers amplified in 331 individuals
from ten different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and instead showed a large and stable
historical effective size. This result could be accounted for by specific life-history
traits (reproduction and longevity) and the limitations of molecular markers in
covering recent timescales for nontemporal samples. The findings of the present
study emphasize the need to integrate information on effective population sizes
and life-history parameters when evaluating population connectivity levels from
genetic data.
acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the
Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded
by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors
are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the
Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418.
doi:10.1111/j.1095-8312.2011.01728.x
apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas. Biological Journal of the
Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x
chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic
Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal
of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.
ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas,” Biological Journal of the
Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.
ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2),
407–418.
mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on
the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.”
Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell,
2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological
Journal of the Linnean Society 104 (2011) 407–418.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2023-02-23T14:07:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
intvolume: ' 104'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 407 - 418
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3212'
quality_controlled: '1'
related_material:
record:
- id: '9762'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of oceanographic barriers and overfishing on the population genetic
structure of the European spiny lobster Palinurus elephas
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 104
year: '2011'
...
---
_id: '9762'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies to evaluate the genetic health of the exploited populations. The present
work is based on a set of 10 nuclear markers amplified in 331 individuals from
10 different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and showed a large and stable historical
effective size instead. This result could be accounted for by specific life history
traits (reproduction and longevity) and the limitations of molecular markers in
covering very recent timescales for non temporal samples. Our study emphasizes
the necessity of integrating information on effective population sizes and life
history parameters when evaluating population connectivity levels from genetic
data.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8'
apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas). IST Austria.
https://doi.org/10.5061/dryad.299h8'
chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population
Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria,
2011. https://doi.org/10.5061/dryad.299h8.'
ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.'
ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.'
mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and
Overfishing on the Population Genetic Structure of the European Spiny Lobster
(Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.'
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).
date_created: 2021-08-02T07:11:19Z
date_published: 2011-05-12T00:00:00Z
date_updated: 2023-02-23T11:25:25Z
day: '12'
department:
- _id: NiBa
doi: 10.5061/dryad.299h8
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.299h8
month: '05'
oa: 1
oa_version: Published Version
publisher: IST Austria
related_material:
record:
- id: '3395'
relation: used_in_publication
status: public
status: public
title: 'Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas)'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2011'
...
---
_id: '3375'
abstract:
- lang: eng
text: 'By exploiting an analogy between population genetics and statistical mechanics,
we study the evolution of a polygenic trait under stabilizing selection, mutation
and genetic drift. This requires us to track only four macroscopic variables,
instead of the distribution of all the allele frequencies that influence the trait.
These macroscopic variables are the expectations of: the trait mean and its square,
the genetic variance, and of a measure of heterozygosity, and are derived from
a generating function that is in turn derived by maximizing an entropy measure.
These four macroscopics are enough to accurately describe the dynamics of the
trait mean and of its genetic variance (and in principle of any other quantity).
Unlike previous approaches that were based on an infinite series of moments or
cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined
approximation procedure. We apply the framework to abrupt and gradual changes
in the optimum, as well as to changes in the strength of stabilizing selection.
Our approximations are surprisingly accurate, even for systems with as few as
five loci. We find that when the effects of drift are included, the expected genetic
variance is hardly altered by directional selection, even though it fluctuates
in any particular instance. We also find hysteresis, showing that even after averaging
over the microscopic variables, the macroscopic trajectories retain a memory of
the underlying genetic states.'
article_processing_charge: No
article_type: original
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: de Vladar H, Barton NH. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society
Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438
apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic
character under stabilizing selection mutation and drift. Journal of the Royal
Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438
chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of
a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438.
ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift,” Journal of the Royal Society
Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.
ista: de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society Interface.
8(58), 720–739.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a
Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp.
720–39, doi:10.1098/rsif.2010.0438.
short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011)
720–739.
date_created: 2018-12-11T12:02:58Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2023-10-18T06:39:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1098/rsif.2010.0438
ec_funded: 1
external_id:
pmid:
- '21084341'
intvolume: ' 8'
issue: '58'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/
month: '05'
oa: 1
oa_version: Submitted Version
page: 720 - 739
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of the Royal Society Interface
publication_status: published
publisher: The Royal Society
publist_id: '3232'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The statistical mechanics of a polygenic character under stabilizing selection
mutation and drift
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2011'
...
---
_id: '3393'
abstract:
- lang: eng
text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread
throughout a species range once introduced anywhere, “bistable” variants, such
as chromosome translocations, have two alternative stable frequencies, absence
and (near) fixation. Analogous to populations with Allee effects, bistable variants
tend to increase locally only once they become sufficiently common, and their
spread depends on their rate of increase averaged over all frequencies. Several
proposed manipulations of insect populations, such as using Wolbachia or “engineered
underdominance” to suppress vector-borne diseases, produce bistable rather than
Fisherian dynamics. We synthesize and extend theoretical analyses concerning three
features of their spatial behavior: rate of spread, conditions to initiate spread
from a localized introduction, and wave stopping caused by variation in population
densities or dispersal rates. Unlike Fisherian variants, bistable variants tend
to spread spatially only for particular parameter combinations and initial conditions.
Wave initiation requires introduction over an extended region, while subsequent
spatial spread is slower than for Fisherian waves and can easily be halted by
local spatial inhomogeneities. We present several new results, including robust
sufficient conditions to initiate (and stop) spread, using a one-parameter cubic
approximation applicable to several models. The results have both basic and applied
implications.'
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic
and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75.
doi:10.1086/661246'
apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable
dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist.
The University of Chicago Press. https://doi.org/10.1086/661246'
chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with
Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American
Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.'
ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects,” American Naturalist,
vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.'
ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3),
E48–E75.'
mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable
Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist,
vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.'
short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2023-10-18T08:01:43Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/661246
file:
- access_level: open_access
checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:31Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4692'
file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf
file_size: 629130
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 178'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: E48 - E75
publication: American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: The University of Chicago Press
publist_id: '3214'
pubrep_id: '554'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues
of Allee effects'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2011'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
intvolume: ' 186'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3337'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2010'
...
---
_id: '3604'
abstract:
- lang: eng
text: We investigated temporal changes in hybridization and introgression between
native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on
the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples
of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that
either the proportion of recent hybrids, or the levels of introgression had changed
over the study period. Nevertheless, in one population where the two species have
been in contact since ∼1970, 44% of individuals sampled during the study were
hybrids. This suggests that hybridization between these species can proceed fairly
rapidly. By analysing the number of alleles that have introgressed from polymorphic
red deer into the genetically homogenous sika population, we reconstructed the
haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization
events could account for all the recently hybridized sika-like individuals found
across a large section of the Peninsula. Although we demonstrate that low rates
of F1 hybridization can lead to substantial introgression, the progress of hybridization
and introgression appears to be unpredictable over the short timescales.
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal
changes in hybridisation and introgression between invasive sika (Cervus nippon)
and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular
Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x
apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010).
Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x
chicago: Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine
Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010.
https://doi.org/10.1111/j.1365-294X.2009.04497.x.
ieee: H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,”
Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.
ista: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland.
Molecular Ecology. 19(5), 910–924.
mla: Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell,
2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.
short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology
19 (2010) 910–924.
date_created: 2018-12-11T12:04:12Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T07:44:36Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2009.04497.x
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 910 - 924
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2779'
quality_controlled: '1'
scopus_import: 1
status: public
title: Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2010'
...
---
_id: '3783'
abstract:
- lang: eng
text: MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that
facilitates several tasks when scoring microsatellites. It implements new subroutines
in R and PERL and takes advantage of features provided by previously developed
freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification
through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite
markers according to their multiplex group, fluorochrome type, and size range.
After peak selection, binning of alleles can be carried out 1) automatically through
AlleloBin or 2) by manual bin definition through Binator. In both cases, several
features for quality checking and further binning improvement are provided. The
genotype table can then be converted into input files for several population genetics
programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence
intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT
is the only freely available public-domain software that facilitates full multiplex
microsatellite scoring, from electropherogram files to user-defined text files
to be used with population genetics software. MICROSATELIGHT has been created
for the Windows XP operating system and has been successfully tested under Windows
7. It is available at http://sourceforge.net/projects/microsatelight/.
acknowledgement: "Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635).
M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya.
F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel
Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us
pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat
de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous
referees for their valuable comments. These comments certainly helped to improve
the manuscript."
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Fernando
full_name: González Candelas, Fernando
last_name: González Candelas
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite
microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111
apa: Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight
– Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford
University Press. https://doi.org/10.1093/jhered/esq111
chicago: Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight
– Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford
University Press, 2010. https://doi.org/10.1093/jhered/esq111.
ieee: F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline
to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no.
2. Oxford University Press, pp. 247–249, 2010.
ista: Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline
to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.
mla: Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite
Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press,
2010, pp. 247–49, doi:10.1093/jhered/esq111.
short: F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010)
247–249.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-12-02T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '02'
department:
- _id: NiBa
doi: 10.1093/jhered/esq111
intvolume: ' 102'
issue: '2'
language:
- iso: eng
month: '12'
oa_version: None
page: 247 - 249
publication: Journal of Heredity
publication_status: published
publisher: Oxford University Press
publist_id: '2444'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microsatelight – Pipeline to expedite microsatellite analysis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2010'
...
---
_id: '4134'
abstract:
- lang: eng
text: 'All species are restricted in their distribution. Currently, ecological models
can only explain such limits if patches vary in quality, leading to asymmetrical
dispersal, or if genetic variation is too low at the margins for adaptation. However,
population genetic models suggest that the increase in genetic variance resulting
from dispersal should allow adaptation to almost any ecological gradient. Clearly
therefore, these models miss something that prevents evolution in natural populations.
We developed an individual-based simulation to explore stochastic effects in these
models. At high carrying capacities, our simulations largely agree with deterministic
predictions. However, when carrying capacity is low, the population fails to establish
for a wide range of parameter values where adaptation was expected from previous
models. Stochastic or transient effects appear critical around the boundaries
in parameter space between simulation behaviours. Dispersal, gradient steepness,
and population density emerge as key factors determining adaptation on an ecological
gradient. '
acknowledgement: We are very grateful to Nick Barton.
author:
- first_name: Jon
full_name: Bridle, Jon
last_name: Bridle
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Masakado
full_name: Kawata, Masakado
last_name: Kawata
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological
margins? New insights from individual-based simulations. Ecology Letters.
2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x
apa: Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation
prevented at ecological margins? New insights from individual-based simulations.
Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x
chicago: Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is
Adaptation Prevented at Ecological Margins? New Insights from Individual-Based
Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x.
ieee: J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented
at ecological margins? New insights from individual-based simulations,” Ecology
Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010.
ista: Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented
at ecological margins? New insights from individual-based simulations. Ecology
Letters. 13(4), 485–494.
mla: Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New
Insights from Individual-Based Simulations.” Ecology Letters, vol. 13,
no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x.
short: J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010)
485–494.
date_created: 2018-12-11T12:07:08Z
date_published: 2010-03-15T00:00:00Z
date_updated: 2021-01-12T07:54:45Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/j.1461-0248.2010.01442.x
ec_funded: 1
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 485 - 494
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1987'
quality_controlled: '1'
scopus_import: 1
status: public
title: Why is adaptation prevented at ecological margins? New insights from individual-based
simulations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2010'
...
---
_id: '4243'
abstract:
- lang: eng
text: We investigate a new model for populations evolving in a spatial continuum.
This model can be thought of as a spatial version of the Lambda-Fleming-Viot process.
It explicitly incorporates both small scale reproduction events and large scale
extinction-recolonisation events. The lineages ancestral to a sample from a population
evolving according to this model can be described in terms of a spatial version
of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence
and uniqueness in law for the model. We then investigate the asymptotic behaviour
of the genealogy of a finite number of individuals sampled uniformly at random
(or more generally `far enough apart') from a two-dimensional torus of sidelength
L as L tends to infinity. Under appropriate conditions (and on a suitable timescale)
we can obtain as limiting genealogical processes a Kingman coalescent, a more
general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local
coalescence mechanism).
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum.
Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741
apa: Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution
in a spatial continuum. Electronic Journal of Probability. Institute of
Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model
for Evolution in a Spatial Continuum.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a
spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7.
Institute of Mathematical Statistics, pp. 162–216, 2010.
ista: Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial
continuum. Electronic Journal of Probability. 15(7), 162–216.
mla: Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.”
Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical
Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741.
short: N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15
(2010) 162–216.
date_created: 2018-12-11T12:07:48Z
date_published: 2010-02-03T00:00:00Z
date_updated: 2021-01-12T07:55:34Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1214/EJP.v15-741
file:
- access_level: open_access
checksum: bab577546dd4e8f882e9a9dd645cd01e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:21Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5140'
file_name: IST-2015-369-v1+1_741-2535-1-PB.pdf
file_size: 450171
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 162 - 216
publication: Electronic Journal of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '1863'
pubrep_id: '369'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new model for evolution in a spatial continuum
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2010'
...
---
_id: '3776'
abstract:
- lang: eng
text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling
questions in biology. The most compelling general explanation is that recombination
facilitates selection by breaking down the negative associations generated by
random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of
HRI owing to: deleterious mutation, balancing selection and selective sweeps on:
neutral diversity, rates of adaptation and the mutation load. These effects are
mediated primarily by the density of deleterious mutations and of selective sweeps.
Sequence polymorphism and divergence suggest that these rates may be high enough
to cause significant interference even in genomic regions of high recombination.
However, neither seems able to generate enough variance in fitness to select strongly
for high rates of recombination. It is plausible that spatial and temporal fluctuations
in selection generate much more fitness variance, and hence selection for recombination,
than can be explained by uniformly deleterious mutations or species-wide selective
sweeps.'
acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would
like to thank Brian Charlesworth and Sally Otto for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569.
doi:10.1098/rstb.2010.0106
apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2010.0106
chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.
ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1552. Royal Society, pp. 2559–2569, 2010.
ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.
mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 2559–2569.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
file:
- access_level: open_access
checksum: 4d8aade10db030124ab158b622e337e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:40Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5093'
file_name: IST-2016-555-v1+1_RS2009_revised.pdf
file_size: 250255
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 365'
issue: '1552'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 2559 - 2569
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2450'
pubrep_id: '555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic linkage and natural selection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3773'
abstract:
- lang: eng
text: If distinct biological species are to coexist in sympatry, they must be reproductively
isolated and must exploit different limiting resources. A two-niche Levene model
is analysed, in which habitat preference and survival depend on underlying additive
traits. The population genetics of preference and viability are equivalent. However,
there is a linear trade-off between the chances of settling in either niche, whereas
viabilities may be constrained arbitrarily. With a convex trade-off, a sexual
population evolves a single generalist genotype, whereas with a concave trade-off,
disruptive selection favours maximal variance. A pure habitat preference evolves
to global linkage equilibrium if mating occurs in a single pool, but remarkably,
evolves to pairwise linkage equilibrium within niches if mating is within those
niches--independent of the genetics. With a concave trade-off, the population
shifts sharply between a unimodal distribution with high gene flow and a bimodal
distribution with strong isolation, as the underlying genetic variance increases.
However, these alternative states are only simultaneously stable for a narrow
parameter range. A sharp threshold is only seen if survival in the 'wrong' niche
is low; otherwise, strong isolation is impossible. Gene flow from divergent demes
makes speciation much easier in parapatry than in sympatry.
acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish
Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He
also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n"
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001
apa: Barton, N. H. (2010). What role does natural selection play in speciation?
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001
chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.
ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.
ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547),
1825–1840.
mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1825–1840.
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
pmid:
- '20439284'
intvolume: ' 365'
issue: '1547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20439284
month: '06'
oa: 1
oa_version: Submitted Version
page: 1825 - 1840
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2455'
quality_controlled: '1'
scopus_import: 1
status: public
title: What role does natural selection play in speciation?
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3777'
abstract:
- lang: eng
text: 'Under the classical view, selection depends more or less directly on mutation:
standing genetic variance is maintained by a balance between selection and mutation,
and adaptation is fuelled by new favourable mutations. Recombination is favoured
if it breaks negative associations among selected alleles, which interfere with
adaptation. Such associations may be generated by negative epistasis, or by random
drift (leading to the Hill-Robertson effect). Both deterministic and stochastic
explanations depend primarily on the genomic mutation rate, U. This may be large
enough to explain high recombination rates in some organisms, but seems unlikely
to be so in general. Random drift is a more general source of negative linkage
disequilibria, and can cause selection for recombination even in large populations,
through the chance loss of new favourable mutations. The rate of species-wide
substitutions is much too low to drive this mechanism, but local fluctuations
in selection, combined with gene flow, may suffice. These arguments are illustrated
by comparing the interaction between good and bad mutations at unlinked loci under
the infinitesimal model.'
acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this
special issue, and the Royal Society and Wolfson Foundation for their support. Also,
A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Mutation and the evolution of recombination. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294.
doi:10.1098/rstb.2009.0320
apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2009.0320
chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.
ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.
ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544),
1281–1294.
mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1281–1294.
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
pmid:
- '20308104'
intvolume: ' 365'
issue: '1544'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20308104
month: '04'
oa: 1
oa_version: Submitted Version
page: 1281 - 1294
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2451'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutation and the evolution of recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3774'
abstract:
- lang: eng
text: 1. Hybridisation with an invasive species has the potential to alter the phenotype
and hence the ecology of a native counterpart. 2. Here data from populations of
native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland
is used to assess the extent to which hybridisation between them is causing phenotypic
change. This is done by regression of phenotypic traits against genetic hybrid
scores. 3. Hybridisation is causing increases in the body weight of sika-like
deer and decreases in the body weight of red-like females. Hybridisation is causing
increases in jaw length and increases in incisor arcade breadth in sika-like females.
Hybridisation is also causing decreases in incisor arcade breadth in red-like
females. 4. There is currently no evidence that hybridisation is causing changes
in the kidney fat weight or pregnancy rates of either population. 5. Increased
phenotypic similarity between the two species is likely to lead to further hybridisation.
The ecological consequences of this are difficult to predict.
acknowledgement: "This project was funded through a NERC studentship to HVS which
was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission
Scotland rangers for all their help with providing the larder data for and samples
from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice
and Steve Albon for helpful comments on the manuscript."
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal
Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x
apa: Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010).
Phenotypic correlates of hybridisation between red and sika deer (genus Cervus).
Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x
chicago: Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine
Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus
Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.
ieee: H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic
correlates of hybridisation between red and sika deer (genus Cervus),” Journal
of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.
ista: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology.
79(2), 414–425.
mla: Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and
Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell,
2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.
short: H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal
Ecology 79 (2010) 414–425.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-2656.2009.01633.x
external_id:
pmid:
- '20002231'
intvolume: ' 79'
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
page: 414 - 425
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2453'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2010'
...
---
_id: '3772'
article_number: e1000987
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics.
2010;6(6). doi:10.1371/journal.pgen.1000987
apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987
chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.
ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics,
vol. 6, no. 6. Public Library of Science, 2010.
ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics.
6(6), e1000987.
mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.
short: N.H. Barton, PLoS Genetics 6 (2010).
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
file:
- access_level: open_access
checksum: 5c14de2680ab483cb835096c99ee734d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:24Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5075'
file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF
file_size: 349965
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '2454'
pubrep_id: '524'
quality_controlled: '1'
scopus_import: 1
status: public
title: Understanding adaptation in large populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '3787'
abstract:
- lang: eng
text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean
tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown
that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors
impede PCR success when dealing with formalin-fixed material. Instead, amplification
success from formalin-fixed tissue appears to depend on the presence of unmodified
DNA in the extracted sample. A staining method that facilitates the targeting
of samples with a high content of unmodified DNA is provided.
acknowledgement: "The authors would like to thank two anonymous reviewers for their
remarks, which helped to improve the manuscript. This project was supported by the
Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract
no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology
Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal
Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government
of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS
Project http://www.synthesys. info/ which is financed by European Community Research
Infrastructure Action under the FP6 “Structuring the European Research Area” Programme.
Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical
point drying, P.Crabb for helping with the UV-light photography setting and our
colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology
NHM \r\n\r\n"
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Sally
full_name: Hall, Sally
last_name: Hall
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: Jackie
full_name: Mackenzie Dodds, Jackie
last_name: Mackenzie Dodds
- first_name: Sven
full_name: Thatje, Sven
last_name: Thatje
citation:
ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction
from formalin-fixed tissue: new light from the deep sea. Scientia Marina.
2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465'
apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &
Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the
deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas.
https://doi.org/10.3989/scimar.2010.74n3465'
chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie
Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones
Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.'
ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje,
“DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia
Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp.
465–470, 2010.'
ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010.
DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia
Marina. 74(3), 465–470.'
mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de
Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.'
short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje,
Scientia Marina 74 (2010) 465–470.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:11Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
intvolume: ' 74'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.soton.ac.uk/68731/
month: '09'
oa: 1
oa_version: Submitted Version
page: 465 - 470
publication: Scientia Marina
publication_status: published
publisher: Consejo Superior de Investigaciones Científicas
publist_id: '2440'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2010'
...
---
_id: '3786'
abstract:
- lang: eng
text: Four rare palinurid phyllosoma larvae, one mid-stage and three final stage,
were found among the unclassified collections in the Crustacea Section, Natural
History Museum, London. Detailed morphological analysis of the larvae indicated
that they belong to several Palinustus species given the presence of incipient
blunt-horns, length of antennula, length ratio of segments of antennular peduncle,
distribution of pereiopod spines, and shape of uropods and telson. Moreover, the
size of the final-stage larvae agrees with that expected given the size of the
recently described puerulus stage of Palinustus mossambicus. This constitutes
the first description of a complete phyllosoma assigned to Palinustus species.
The phyllosoma described in the present study include the largest Palinuridae
larva ever found.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma
of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage
Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata:
Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press,
2010. https://doi.org/10.11646/zootaxa.2403.1.4.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of
Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press,
pp. 42–58, 2010.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2403(1), 42–58.'
mla: 'Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards,
1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.”
Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2022-03-21T08:22:58Z
day: '19'
department:
- _id: NiBa
doi: 10.11646/zootaxa.2403.1.4
intvolume: ' 2403'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 42 - 58
publication: Zootaxa
publication_status: published
publisher: Magnolia Press
publist_id: '2441'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda:
Achelata: Palinuridae)-The first complete description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2403
year: '2010'
...
---
_id: '474'
abstract:
- lang: eng
text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale
patterns; they predict much more genetic diversity than is observed; and they
assume that loosely linked genetic loci evolve independently. We propose a new
model that deals with these problems. Extinction events kill some fraction of
individuals in a region. These are replaced by offspring from a small number of
parents, drawn from the preexisting population. This model of evolution forwards
in time corresponds to a backwards model, in which ancestral lineages jump to
a new location if they are hit by an event, and may coalesce with other lineages
that are hit by the same event. We derive an expression for the identity in allelic
state, and show that, over scales much larger than the largest event, this converges
to the classical value derived by Wright and Malécot. However, rare events that
cover large areas cause low genetic diversity, large-scale patterns, and correlations
in ancestry between unlinked loci.'
acknowledgement: This work has made use of the resources provided by the Edinburgh
Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative.
NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant
EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization
in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715.
doi:10.1111/j.1558-5646.2010.01019.x'
apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x'
chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model
for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.”
Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.'
ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography,” Evolution,
vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.'
ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and
recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9),
2701–2715.'
mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization
in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no.
9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.'
short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.
date_created: 2018-12-11T11:46:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T08:00:52Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2010.01019.x
intvolume: ' 64'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2701 - 2715
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A new model for extinction and recolonization in two dimensions: Quantifying
phylogeography'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2010'
...
---
_id: '3779'
abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T14:07:34Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
file:
- access_level: open_access
checksum: ee1ce2fb283a6b4127544ae532d0b4a1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5060'
file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf
file_size: 1089530
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2448'
pubrep_id: '366'
quality_controlled: '1'
related_material:
record:
- id: '9764'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cryptic variation between species and the basis of hybrid performance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '9764'
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the
drift load. 2010. doi:10.1371/journal.pbio.1000429.s003
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010.
https://doi.org/10.1371/journal.pbio.1000429.s003.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis
and the drift load.” Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis
and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.
mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.s003.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).
date_created: 2021-08-02T09:45:39Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T11:42:17Z
day: '20'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '3779'
relation: used_in_publication
status: public
status: public
title: Heterosis and the drift load
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2010'
...
---
_id: '3785'
abstract:
- lang: eng
text: Most fisheries involving spiny lobsters of the genus Palinurus have been over
exploited during the last decades, so there is a raising concern about management
decisions for these valuable resources. A total of 13 microsatellite DNA loci
recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave
amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus
barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth
distribution was taken into account, shallower waters pecies consistently showed
larger historical effective population sizes than their deeper-water counterparts. This
could explain why deeper-water species are more sensitive to overfishing, and
would indicate that overexploitation may have a larger impact on their long-term
genetic diversity.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: E.
full_name: Macpherson, E.
last_name: Macpherson
- first_name: C.
full_name: Matthee, C.
last_name: Matthee
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1'
apa: 'Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010).
Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus
(Decapoda: Achelata). Journal of Crustacean Biology. Oxford University
Press. https://doi.org/10.1651/09-3192.1'
chicago: 'Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual.
“Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus
(Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University
Press, 2010. https://doi.org/10.1651/09-3192.1.'
ieee: 'F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic
diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda:
Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University
Press, pp. 658–663, 2010.'
ista: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 30(4), 658–663.'
mla: 'Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny
Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean
Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.'
short: F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean
Biology 30 (2010) 658–663.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-10-16T09:51:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1651/09-3192.1
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 658 - 663
publication: Journal of Crustacean Biology
publication_identifier:
eissn:
- 1937-240X
issn:
- 0278-0372
publication_status: published
publisher: Oxford University Press
publist_id: '2442'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genetic diversity levels in fishery-exploited spiny lobsters of the Genus
Palinurus (Decapoda: Achelata)'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2010'
...
---
_id: '3780'
abstract:
- lang: eng
text: Why are sinistral snails so rare? Two main hypotheses are that selection acts
against the establishment of new coiling morphs, because dextral and sinistral
snails have trouble mating, or else a developmental constraint prevents the establishment
of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in
which sinistrals are rare, and populations of Partula suturalis, in which sinistrals
are common, as well as a mathematical model, to understand the circumstances by
which new morphs evolve. The main finding is that the sinistral genotype is associated
with reduced egg viability in L. stagnalis, but in P. suturalis individuals of
sinistral and dextral genotype appear equally fecund, implying a lack of a constraint.
As positive frequency-dependent selection against the rare chiral morph in P.
suturalis also operates over a narrow range (< 3%), the results suggest a model
for chiral evolution in snails in which weak positive frequency-dependent selection
may be overcome by a negative frequency-dependent selection, such as reproductive
character displacement. In snails, there is not always a developmental constraint.
As the direction of cleavage, and thus the directional asymmetry of the entire
body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans,
sipunculids and nemerteans), it remains an open question as to whether this is
because of a constraint and/or because most taxa do not have a conspicuous external
asymmetry (like a shell) upon which selection can act.
acknowledgement: We owe a great debt to Jim Murray for his many contributions to the
study of Partula, in the field, in the laboratory, in the interpretation of data,
and in generating new ideas about evolution. With pleasure and respect we dedicate
this paper to him. Jim Murray played a leading role in making the collections used
here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with
collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift
of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund
Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis.
Comments from an anonymous referee, A. Richard Palmer and the editorial board improved
the manuscript. Work in the field was supported by the Royal Society, The Carnegie
Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research
Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society
and the University of Nottingham supported work in the laboratory.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Bryan
full_name: Clarke, Bryan
last_name: Clarke
citation:
ama: 'Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype
on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications
for the evolution of sinistral snails. Journal of Evolutionary Biology.
2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x'
apa: 'Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality
phenotype and genotype on the fecundity and viability of Partula suturalis and
Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal
of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x'
chicago: 'Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality
Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and
Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal
of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.'
ieee: 'A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype
and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails,” Journal of Evolutionary
Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.'
ista: 'Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and
genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails. Journal of Evolutionary Biology.
22(8), 1624–1635.'
mla: 'Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on
the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications
for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology,
vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.'
short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009)
1624–1635.
date_created: 2018-12-11T12:05:08Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1420-9101.2009.01770.x
file:
- access_level: open_access
checksum: f70c15c6ab9306121d4153a3be0d2346
content_type: application/pdf
creator: dernst
date_created: 2019-02-22T09:21:44Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6044'
file_name: Davison_JEB_v31_2009.pdf
file_size: 2583812
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 1624 - 1635
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley
publist_id: '2447'
pubrep_id: '553'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The effect of chirality phenotype and genotype on the fecundity and viability
of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral
snails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2009'
...
---
_id: '4136'
abstract:
- lang: eng
text: 'Populations living in a spatially and temporally changing environment can
adapt to the changing optimum and/or migrate toward favorable habitats. Here we
extend previous analyses with a static optimum to allow the environment to vary
in time as well as in space. The model follows both population dynamics and the
trait mean under stabilizing selection, and the outcomes can be understood by
comparing the loads due to genetic variance, dispersal, and temporal change. With
fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform
along the environmental gradient and that responds to the moving optimum as expected
for panmictic populations and when the spatial gradient is sufficiently steep,
and (2) a population with limited range that adapts more slowly than the environmental
optimum changes in both time and space; the population therefore becomes locally
extinct and migrates toward suitable habitat. We also use a population‐genetic
model with many loci to allow genetic variance to evolve, and we show that the
only solution now has uniform adaptation.'
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Glenn
full_name: Marion, Glenn
last_name: Marion
citation:
ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and
time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958'
apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation
in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958'
chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range:
Adaptation in Space and Time.” American Naturalist. University of Chicago
Press, 2009. https://doi.org/10.1086/605958.'
ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in
space and time,” American Naturalist, vol. 174, no. 5. University of Chicago
Press, pp. E186–E204, 2009.'
ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space
and time. American Naturalist. 174(5), E186–E204.'
mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American
Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204,
doi:10.1086/605958.'
short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.
date_created: 2018-12-11T12:07:09Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/605958
external_id:
pmid:
- ' 19788353'
intvolume: ' 174'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1086/605958
month: '11'
oa: 1
oa_version: Published Version
page: E186 - E204
pmid: 1
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1986'
pubrep_id: '552'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/659642
scopus_import: 1
status: public
title: 'Species'' range: Adaptation in space and time'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2009'
...
---
_id: '4242'
abstract:
- lang: eng
text: 'Felsenstein distinguished two ways by which selection can directly strengthen
isolation. First, a modifier that strengthens prezygotic isolation can be favored
everywhere. This fits with the traditional view of reinforcement as an adaptation
to reduce deleterious hybridization by strengthening assortative mating. Second,
selection can favor association between different incompatibilities, despite recombination.
We generalize this “two allele” model to follow associations among any number
of incompatibilities, which may include both assortment and hybrid inviability.
Our key argument is that this process, of coupling between incompatibilities,
may be quite different from the usual view of reinforcement: strong isolation
can evolve through the coupling of any kind of incompatibility, whether prezygotic
or postzygotic. Single locus incompatibilities become coupled because associations
between them increase the variance in compatibility, which in turn increases mean
fitness if there is positive epistasis. Multiple incompatibilities, each maintained
by epistasis, can become coupled in the same way. In contrast, a single-locus
incompatibility can become coupled with loci that reduce the viability of haploid
hybrids because this reduces harmful recombination. We obtain simple approximations
for the limits of tight linkage, and strong assortment, and show how assortment
alleles can invade through associations with other components of reproductive
isolation.'
acknowledgement: "This work was supported by a Royal Society/Wolfson Research Merit
award, and by a grant from the Natural Environment Research Council.\r\nWe are very
grateful for insightful comments from S. P. Otto, and for helpful suggestions from
the referees and the Associate Editor, Maria Servedio."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: De Cara, Maria
last_name: De Cara
citation:
ama: Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution;
International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x
apa: Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive
isolation. Evolution; International Journal of Organic Evolution. Wiley.
https://doi.org/10.1111/j.1558-5646.2009.00622.x
chicago: Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution. Wiley,
2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x.
ieee: N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,”
Evolution; International Journal of Organic Evolution, vol. 63, no. 5.
Wiley, pp. 1171–1190, 2009.
ista: Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation.
Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.
mla: Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution, vol.
63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x.
short: N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution
63 (2009) 1171–1190.
date_created: 2018-12-11T12:07:48Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:55:33Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2009.00622.x
file:
- access_level: open_access
checksum: 1920d2e25ef335833764256c1a47bbfb
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creator: system
date_created: 2018-12-12T10:11:46Z
date_updated: 2020-07-14T12:46:25Z
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file_size: 720913
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date_created: 2018-12-12T10:11:47Z
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has_accepted_license: '1'
intvolume: ' 63'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 1171 - 1190
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley
publist_id: '1866'
pubrep_id: '551'
quality_controlled: '1'
scopus_import: 1
status: public
title: The evolution of strong reproductive isolation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2009'
...
---
_id: '3675'
abstract:
- lang: eng
text: "Sex and recombination have long been seen as adaptations that facilitate
natural selection by generating favorable variations. If recombination is to aid
selection, there must be negative linkage disequilibria—favorable alleles must
be found together less often than expected by chance. These negative linkage disequilibria
can be generated directly by selection, but this must involve negative epistasis
of just the right strength, which is not expected, from either experiment or theory.
Random drift provides a more general source of negative associations: Favorable
mutations almost always arise on different genomes, and negative associations
tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
can understand how recombination aids adaptation by determining the maximum possible
rate of adaptation. With unlinked loci, this rate increases only logarithmically
with the influx of favorable mutations. With a linear genome, a scaling argument
shows that in a large population, the rate of adaptive substitution depends only
on the expected rate in the absence of interference, divided by the total rate
of recombination. A two-locus approximation predicts an upper bound on the rate
of substitution, proportional to recombination rate.\r\n\r\nIf associations between
linked loci do impede adaptation, there can be substantial selection for modifiers
that increase recombination. Whether this can account for the maintenance of high
rates of sex and recombination depends on the extent of selection. It is clear
that the rate of species-wide substitutions is typically far too low to generate
appreciable selection for recombination. However, local sweeps within a subdivided
population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
(GR/ T11753/01)
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
doi:10.1101/sqb.2009.74.030'
apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor
Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030
chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor
Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory
Press, 2009. https://doi.org/10.1101/sqb.2009.74.030.
ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–195.
ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. vol. 74, 187–195.'
mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–95, doi:10.1101/sqb.2009.74.030.
short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
Spring Harbor Laboratory Press, 2009, pp. 187–195.
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
intvolume: ' 74'
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Why sex and recombination? '
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2009'
...
---
_id: '3775'
abstract:
- lang: eng
text: There is a close analogy between statistical thermodynamics and the evolution
of allele frequencies under mutation, selection and random drift. Wright's formula
for the stationary distribution of allele frequencies is analogous to the Boltzmann
distribution in statistical physics. Population size, 2N, plays the role of the
inverse temperature, 1/kT, and determines the magnitude of random fluctuations.
Log mean fitness, View the MathML source, tends to increase under selection, and
is analogous to a (negative) energy; a potential function, U, increases under
mutation in a similar way. An entropy, SH, can be defined which measures the deviation
from the distribution of allele frequencies expected under random drift alone;
the sum View the MathML source gives a free fitness that increases as the population
evolves towards its stationary distribution. Usually, we observe the distribution
of a few quantitative traits that depend on the frequencies of very many alleles.
The mean and variance of such traits are analogous to observable quantities in
statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures
the volume of allele frequency space that is consistent with the observed trait
distribution. The stationary distribution of the traits is View the MathML source;
this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are
distinct, but converge when there are so many alleles that traits fluctuate close
to their expectations. Populations tend to evolve towards states that can be realised
in many ways (i.e., large SΩ), which may lead to a substantial drop below the
adaptive peak; we illustrate this point with a simple model of genetic redundancy.
This analogy with statistical thermodynamics brings together previous ideas in
a general framework, and justifies a maximum entropy approximation to the dynamics
of quantitative traits.
acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by
grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates,
H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jason
full_name: Coe, Jason
last_name: Coe
citation:
ama: Barton NH, Coe J. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019
apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics
to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019
chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009.
https://doi.org/10.1016/j.jtbi.2009.03.019.
ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary
biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp.
317–324, 2009.
ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 259(2), 317–324.
mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no.
2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.
short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
date_created: 2018-12-11T12:05:06Z
date_published: 2009-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '21'
department:
- _id: NiBa
doi: 10.1016/j.jtbi.2009.03.019
intvolume: ' 259'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00554594/document
month: '07'
oa: 1
oa_version: Submitted Version
page: 317 - 324
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2452'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the application of statistical physics to evolutionary biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2009'
...
---
_id: '4231'
abstract:
- lang: eng
text: The evolution of quantitative characters depends on the frequencies of the
alleles involved, yet these frequencies cannot usually be measured. Previous groups
have proposed an approximation to the dynamics of quantitative traits, based on
an analogy with statistical mechanics. We present a modified version of that approach,
which makes the analogy more precise and applies quite generally to describe the
evolution of allele frequencies. We calculate explicitly how the macroscopic quantities
(i.e., quantities that depend on the quantitative trait) depend on evolutionary
forces, in a way that is independent of the microscopic details. We first show
that the stationary distribution of allele frequencies under drift, selection,
and mutation maximizes a certain measure of entropy, subject to constraints on
the expectation of observable quantities. We then approximate the dynamical changes
in these expectations, assuming that the distribution of allele frequencies always
maximizes entropy, conditional on the expected values. When applied to directional
selection on an additive trait, this gives a very good approximation to the evolution
of the trait mean and the genetic variance, when the number of mutations per generation
is sufficiently high (4Nμ > 1). We show how the method can be modified for
small mutation rates (4Nμ → 0). We outline how this method describes epistatic
interactions as, for example, with stabilizing selection.
acknowledgement: "N.B. was supported by the Engineering and Physical Sciences Research
Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to
Ellen Baake for helping to initiate this project and for her comments on this manuscript.
We also thank Michael Turelli for his comments on the manuscript and I. Pen for
discussions and support in this project. This project was a result of a collaboration
supported by the European Science Foundation grant “Integrating population genetics
and conservation biology.” "
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
citation:
ama: Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309
apa: Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution
of polygenic quantitative traits. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.108.099309
chicago: Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the
Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society
of America, 2009. https://doi.org/10.1534/genetics.108.099309.
ieee: N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of
polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society
of America, pp. 997–1011, 2009.
ista: Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 181(3), 997–1011.
mla: Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution
of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics
Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309.
short: N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.
date_created: 2018-12-11T12:07:44Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T07:55:29Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.108.099309
intvolume: ' 181'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 997 - 1011
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1882'
quality_controlled: '1'
scopus_import: 1
status: public
title: Statistical mechanics and the evolution of polygenic quantitative traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2009'
...
---
_id: '517'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: ' 89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...