---
_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
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file_name: Novak_thesis.pdf
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content_type: application/pdf
creator: dernst
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success: 1
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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
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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
content_type: application/pdf
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
license: https://creativecommons.org/licenses/by/4.0/
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: '5550'
abstract:
- lang: eng
text: "We collected flower colour information on species in the tribe Antirrhineae
from taxonomic literature. We also retreived molecular data from GenBank for as
many of these species as possible to estimate phylogenetic relationships among
these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary
transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor
full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in
yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”,
Annals of Botany (in press)"
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
- 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. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34
apa: Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS)
files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34
chicago: Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS)
Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.
ieee: T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:34.
mla: Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS)
Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34.
short: T. Ellis, D. Field, (2016).
datarep_id: '34'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:49:54Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:34
file:
- access_level: open_access
checksum: 950f85b80427d357bfeff09608ba02e9
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:27Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5594'
file_name: IST-2016-34-v1+1_tellis_flower_colour_data.zip
file_size: 4468543
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '5828'
related_material:
record:
- id: '1382'
relation: research_paper
status: public
status: public
title: Flower colour data and phylogeny (NEXUS) files
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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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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
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creator: dernst
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file_size: 3880811
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
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publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
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relation: part_of_dissertation
status: public
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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: '5553'
abstract:
- lang: eng
text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
1127 open-pollinated progeny from a natural hybrid zone, collected as part of
Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
removed from this dataset.\r\n\r\nOther data were retreived from an online database
of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37
apa: Field, D., & Ellis, T. (2016). Inference of mating patterns among wild
snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:37
chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.
ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
2016.
ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
10.15479/AT:ISTA:37.
mla: Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology
Austria, 2016, doi:10.15479/AT:ISTA:37.
short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:14Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
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checksum: 4ae751b1fa4897fa216241f975a57313
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:02Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5620'
file_name: IST-2016-37-v1+1_paternity_archive.zip
file_size: 132808
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
in 2012
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5551'
abstract:
- lang: eng
text: "Data from array experiments investigating pollinator behaviour on snapdragons
in controlled conditions, and their effect on plant mating. Data were collected
as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a
total of 36 plants in a grid inside a closed organza tent, with a single hive
of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered
Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus,
at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn
how to deal with snapdragons, I observed pollinators foraging on plants, and recorded
the transitions between plants. Thereafter seeds on plants were allowed to develops.
A sample of these were grown to maturity when their flower colour could be determined,
and they were scored as yellow, magenta, or hybrid."
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. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35
apa: Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35
chicago: Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.
ieee: T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:35.
mla: Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '35'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:27Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:35
file:
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checksum: aa3eb85d52b110cd192aa23147c4d4f3
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creator: system
date_created: 2018-12-12T13:05:12Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5640'
file_name: IST-2016-35-v1+1_array_data.zip
file_size: 32775
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title: Data on pollinator observations and offpsring phenotypes
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...
---
_id: '5552'
abstract:
- lang: eng
text: "Data on pollinator visitation to wild snapdragons in a natural hybrid zone,
collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon
flowers have a mouth-like structure which pollinators must open to access nectar.
We placed 5mm cellophane tags in these mouths, which are held in place by the
pressure of the flower until a pollinator visits. When she opens the flower, the
tag drops out, and one can infer a visit. We surveyed plants over multiple days
in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic
variables which may be explanatory variables for pollinator visitation."
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. Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36
apa: Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:36
chicago: Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data.” Institute of Science and Technology Austria,
2016. https://doi.org/10.15479/AT:ISTA:36.
ieee: T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data., Institute of Science and Technology Austria,
10.15479/AT:ISTA:36.
mla: Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data. Institute of Science and Technology Austria,
2016, doi:10.15479/AT:ISTA:36.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '36'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:40Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:36
file:
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checksum: cbc61b523d4d475a04a737d50dc470ef
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:07Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5625'
file_name: IST-2016-36-v1+1_tag_assay_archive.zip
file_size: 44905
relation: main_file
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month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic
and frequency data.
type: research_data
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year: '2016'
...
---
_id: '5554'
abstract:
- lang: eng
text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which
is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena
Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments
and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student
in Jon Bollback's group at IST Austria) performed the experiments and created
the data on lac promoter evolution."
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. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.
2016. doi:10.15479/AT:ISTA:43
apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43
chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.
ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA
Polymerase.” Institute of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.
mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.
short: M. Tugrul, (2016).
contributor:
- contributor_type: researcher
first_name: Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
- contributor_type: researcher
first_name: Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
datarep_id: '43'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-05-12T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.15479/AT:ISTA:43
file:
- access_level: open_access
checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:08Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5626'
file_name: IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip
file_size: 1123495
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has_accepted_license: '1'
keyword:
- RNAP binding
- de novo promoter evolution
- lac promoter
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1131'
relation: used_in_publication
status: public
status: public
title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf
file_size: 188872
relation: main_file
- access_level: open_access
checksum: b774911e70044641d556e258efcb52ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf
file_size: 577415
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T09:05:34Z
date_updated: 2020-07-14T12:45:19Z
file_id: '7855'
file_name: 2015_Evolution_Priklopil.pdf
file_size: 967214
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
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:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
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'
quality_controlled: '1'
related_material:
record:
- id: '9715'
relation: research_data
status: public
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relation: research_data
status: public
scopus_import: 1
status: public
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
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
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'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Dynamics of transcription factor binding site 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: 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
file:
- access_level: open_access
checksum: 4de1ab255976a8ae77eb0e55ad62ecc9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:52Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4651'
file_name: IST-2016-559-v1+1_Hearn_et_al.pdf
file_size: 807444
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checksum: 01a8073e071c088500425f910b0f1f71
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:53Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4652'
file_name: IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf
file_size: 1518088
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 198 - 211
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4814'
pubrep_id: '559'
quality_controlled: '1'
related_material:
record:
- id: '9754'
relation: research_data
status: public
scopus_import: 1
status: public
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
has_accepted_license: '1'
intvolume: ' 4'
issue: '24'
language:
- iso: eng
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:
record:
- id: '1125'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
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'
...