---
_id: '2719'
abstract:
- lang: eng
text: Prediction of the evolutionary process is a long standing problem both in
the theory of evolutionary biology and evolutionary computation (EC). It has long
been realized that heritable variation is crucial to both the response to selection
and the success of genetic algorithms. However, not all variation contributes
in the same way to the response. Quantitative genetics has developed a large body
of work trying to estimate and understand how different components of the variance
in fitness in the population contribute to the response to selection. We illustrate
how to apply some concepts of quantitative genetics to the analysis of genetic
algorithms. In particular, we derive estimates for the short term prediction of
the response to selection and we use variance decomposition to gain insight on
local aspects of the landscape. Finally, we propose a new population based genetic
algorithm that uses these methods to improve its operation.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of
genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic
and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470'
apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach
to the analysis of genetic algorithms. In Proceedings of the 15th annual conference
on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands:
ACM. https://doi.org/10.1145/2463372.2463470'
chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach
to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis
of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic
and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis
of genetic algorithms. Proceedings of the 15th annual conference on Genetic and
evolutionary computation. GECCO: Genetic and evolutionary computation conference,
845–852.'
mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to
the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
date_created: 2018-12-11T11:59:15Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:59:15Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463470
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 845 - 852
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4173'
quality_controlled: '1'
scopus_import: 1
status: public
title: A variance decomposition approach to the analysis of genetic algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2817'
abstract:
- lang: eng
text: The basic idea of evolutionary game theory is that payoff determines reproductive
rate. Successful individuals have a higher payoff and produce more offspring.
But in evolutionary and ecological situations there is not only reproductive rate
but also carrying capacity. Individuals may differ in their exposure to density
limiting effects. Here we explore an alternative approach to evolutionary game
theory by assuming that the payoff from the game determines the carrying capacity
of individual phenotypes. Successful strategies are less affected by density limitation
(crowding) and reach higher equilibrium abundance. We demonstrate similarities
and differences between our framework and the standard replicator equation. Our
equation is defined on the positive orthant, instead of the simplex, but has the
same equilibrium points as the replicator equation. Linear stability analysis
produces the classical conditions for asymptotic stability of pure strategies,
but the stability properties of internal equilibria can differ in the two frameworks.
For example, in a two-strategy game with an internal equilibrium that is always
stable under the replicator equation, the corresponding equilibrium can be unstable
in the new framework resulting in a limit cycle.
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology.
2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029
apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal
of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029
chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.”
Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.
ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical
Biology, vol. 334. Elsevier, pp. 26–34, 2013.
ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical
Biology. 334, 26–34.
mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology,
vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.
short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013)
26–34.
date_created: 2018-12-11T11:59:45Z
date_published: 2013-10-07T00:00:00Z
date_updated: 2021-01-12T06:59:55Z
day: '07'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.1016/j.jtbi.2013.05.029
ec_funded: 1
file:
- access_level: open_access
checksum: 3c29059ab03a4b8f97a07646b817ddbb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:54Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5110'
file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf
file_size: 834604
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 334'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 26 - 34
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '3984'
pubrep_id: '400'
quality_controlled: '1'
scopus_import: 1
status: public
title: Density games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 334
year: '2013'
...
---
_id: '2823'
abstract:
- lang: eng
text: The primary goal of restoration is to create self-sustaining ecological communities
that are resilient to periodic disturbance. Currently, little is known about how
restored communities respond to disturbance events such as fire and how this response
compares to remnant vegetation. Following the 2003 fires in south-eastern Australia
we examined the post-fire response of revegetation plantings and compared this
to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed
for each of three types of vegetation (direct seeding revegetation, revegetation
using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites
were surveyed 6months after fire to quantify the initial survival of mid- and
overstorey plant species in each type of vegetation. Three and 5years after fire
all sites were resurveyed to assess vegetation structure, species diversity and
vigour, as well as indicators of soil function. Overall, revegetation showed high
(>60%) post-fire survival, but this varied among species depending on regeneration
strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey
in both types of plantings showed rapid recovery of vegetation structure and cover
within 3years of fire. This recovery was similar to the burnt remnant woodlands.
Non-native (exotic) ground cover initially increased after fire, but was no different
in burnt and unburnt sites 5years after fire. Fire had no effect on species richness,
but burnt direct seeding sites had reduced species diversity (Simpson's Diversity
Index) while diversity was higher in burnt remnant woodlands. Indices of soil
function in all types of vegetation had recovered to levels found in unburnt sites
5years after fire. These results indicate that even young revegetation (stands
<10years old) showed substantial recovery from disturbance by fire. This suggests
that revegetation can provide an important basis for restoring woodland communities
in the fire-prone Australian environment.
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Susie
full_name: Wilson, Susie
last_name: Wilson
- first_name: David
full_name: Freudenberger, David
last_name: Freudenberger
- first_name: Nick
full_name: Nicholls, Nick
last_name: Nicholls
- first_name: Lori
full_name: Gould, Lori
last_name: Gould
- first_name: Sarah
full_name: Hnatiuk, Sarah
last_name: Hnatiuk
- first_name: Jeni
full_name: Delandre, Jeni
last_name: Delandre
citation:
ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated
woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312.
doi:10.1111/j.1442-9993.2012.02404.x
apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk,
S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities
in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x
chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori
Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland
Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell,
2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.
ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities
in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell,
pp. 300–312, 2013.
ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre
J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern
Australia. Austral Ecology. 38(3), 300–312.
mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities
in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell,
2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.
short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk,
J. Delandre, Austral Ecology 38 (2013) 300–312.
date_created: 2018-12-11T11:59:47Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:59:58Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1442-9993.2012.02404.x
intvolume: ' 38'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 300 - 312
publication: Austral Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3978'
quality_controlled: '1'
scopus_import: 1
status: public
title: Post-fire recovery of revegetated woodland communities in south-eastern Australia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2013'
...
---
_id: '2842'
abstract:
- lang: eng
text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal
rate, σ2, based on either allele frequencies or on the lengths of sequence blocks
that are shared between genomes. Over intermediate timescales (10-100 generations,
say), populations that live in two dimensions approach a quasi-equilibrium that
is independent of both their local structure and their deeper history. Over such
scales, the standardised covariance of allele frequencies (i.e. pairwise FS T)
falls with the logarithm of distance, and depends only on neighbourhood size,
N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We
show how spatial correlations can be accounted for, assuming a Gaussian distribution
of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively,
inferences can be based on the distribution of the lengths of sequence that are
identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about
intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood
size, the distribution of long blocks is given directly by the classical Wright-Malécot
formula; this relationship can be used to infer both N and σ2. With small neighbourhood
size, there is an appreciable chance that recombinant lineages will coalesce back
before escaping into the distant past. For this case, we show that if genomes
are sampled from some distance apart, then the distribution of lengths of blocks
that are identical in state is geometric, with a mean that depends on N and σ2.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001'
apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference
in two dimensions: Allele frequencies versus lengths of shared sequence blocks.
Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence
Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.'
ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two
dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical
Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.'
ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions:
Allele frequencies versus lengths of shared sequence blocks. Theoretical Population
Biology. 87(1), 105–119.'
mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies
versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology,
vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.'
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 105–119.
date_created: 2018-12-11T11:59:53Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T07:00:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2013.03.001
ec_funded: 1
file:
- access_level: open_access
checksum: 9bf9d9a6fd03dd9df50906891f393bf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:33Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5288'
file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf
file_size: 1554712
relation: main_file
- access_level: open_access
checksum: 2bceddb76edacd0cd5fad73051e2a928
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:34Z
date_updated: 2020-07-14T12:45:50Z
file_id: '5289'
file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf
file_size: 822964
relation: main_file
file_date_updated: 2020-07-14T12:45:50Z
has_accepted_license: '1'
intvolume: ' 87'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 105 - 119
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '3953'
pubrep_id: '558'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence
blocks'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2013'
...
---
_id: '2910'
abstract:
- lang: eng
text: "Coalescent simulation has become an indispensable tool in population genetics
and many complex evolutionary scenarios have been incorporated into the basic
algorithm. Despite many years of intense interest in spatial structure, however,
there are no available methods to simulate the ancestry of a sample of genes that
occupy a spatial continuum. This is mainly due to the severe technical problems
encountered by the classical model of isolation\r\nby distance. A recently introduced
model solves these technical problems and provides a solid theoretical basis for
the study of populations evolving in continuous space. We present a detailed algorithm
to simulate the coalescent process in this model, and provide an efficient implementation
of a generalised version of this algorithm as a freely available Python module."
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space.
Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067
apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation
in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067
chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent
Simulation in Continuous Space.” Bioinformatics. Oxford University Press,
2013. https://doi.org/10.1093/bioinformatics/btt067.
ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous
space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956,
2013.
ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous
space. Bioinformatics. 29(7), 955–956.
mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics,
vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.
short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-02-07T00:00:00Z
date_updated: 2021-01-12T07:00:38Z
day: '07'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/bioinformatics/btt067
ec_funded: 1
file:
- access_level: open_access
checksum: a3b54d7477fac923815ac082403d9bd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:04Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5189'
file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf
file_size: 170197
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 955 - 956
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '3833'
pubrep_id: '556'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coalescent simulation in continuous space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2013'
...
---
_id: '2909'
abstract:
- lang: eng
text: "We survey a class of models for spatially structured populations\r\nwhich
we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework
for modelling in which the key innovation is that random genetic drift\r\nis driven
by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes
some of the obstructions to modelling populations which evolve in two-\r\n(and
higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved
in data and how it fits with classical models. Finally we outline some\r\ndirections
for future research."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002
apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in
a spatial continuum. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution
in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial
continuum,” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 1. IOP Publishing Ltd., 2013.
ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013(1).
mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing
Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.
short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory
and Experiment 2013 (2013).
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1088/1742-5468/2013/01/P01002
ec_funded: 1
file:
- access_level: open_access
checksum: ce8a4424385b3086138a1e054e16e0e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:52Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5242'
file_name: IST-2016-557-v1+1_BEVrevised.pdf
file_size: 702583
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 2013'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '3834'
pubrep_id: '557'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modelling evolution in a spatial continuum
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2013
year: '2013'
...
---
_id: '2908'
abstract:
- lang: eng
text: 'Hybridization is an almost inevitable component of speciation, and its study
can tell us much about that process. However, hybridization itself may have a
negligible influence on the origin of species: on the one hand, universally favoured
alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous
selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional
hybridisation may hardly affect the process of divergence.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015
apa: Barton, N. H. (2013). Does hybridisation influence speciation? . Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015
chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.
ieee: N. H. Barton, “Does hybridisation influence speciation? ,” Journal of
Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.
ista: Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 26(2), 267–269.
mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69,
doi:10.1111/jeb.12015.
short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '17'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/jeb.12015
file:
- access_level: open_access
checksum: 716e88714c3411cd0bd70928b14ea692
content_type: text/rtf
creator: system
date_created: 2018-12-12T10:09:38Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4762'
file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf
file_size: 13339
relation: main_file
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checksum: 957fd07c71c1b1eac2c65ae3311aca78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:39Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4763'
file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf
file_size: 103437
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 267 - 269
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3835'
pubrep_id: '111'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Does hybridisation influence speciation? '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2013'
...
---
_id: '2907'
abstract:
- lang: eng
text: 'Sex and recombination are among the most striking features of the living
world, and they play a crucial role in allowing the evolution of complex adaptation.
The sharing of genomes through the sexual union of different individuals requires
elaborate behavioral and physiological adaptations. At the molecular level, the
alignment of two DNA double helices, followed by their precise cutting and rejoining,
is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary
consequences: distinct sexes, elaborate mating displays, selfish genetic elements,
and so on.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution.
Princeton University Press; 2013:328-333.'
apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution
(pp. 328–333). Princeton University Press.
chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide
to Evolution, 328–33. Princeton University Press, 2013.
ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–333.
ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution.
, 328–333.'
mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–33.
short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University
Press, 2013, pp. 328–333.
date_created: 2018-12-11T12:00:16Z
date_published: 2013-11-04T00:00:00Z
date_updated: 2021-01-12T07:00:37Z
day: '04'
ddc:
- '576'
department:
- _id: NiBa
file:
- access_level: open_access
checksum: 8332ca9cb40f7e66d1006b175ce36b60
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: system
date_created: 2018-12-12T10:16:47Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5237'
file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx
file_size: 79838
relation: main_file
- access_level: open_access
checksum: 849f418620fb78d6ba23bb4f488ee93f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:48Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5238'
file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf
file_size: 144131
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 328 - 333
publication: The Princeton Guide to Evolution
publication_identifier:
isbn:
- '9780691149776'
publication_status: published
publisher: Princeton University Press
publist_id: '3839'
pubrep_id: '119'
quality_controlled: '1'
status: public
title: Recombination and sex
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '450'
abstract:
- lang: eng
text: Understanding the relative importance of heterosis and outbreeding depression
over multiple generations is a key question in evolutionary biology and is essential
for identifying appropriate genetic sources for population and ecosystem restoration.
Here we use 2455 experimental crosses between 12 population pairs of the rare
perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational
(F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no
evidence of outbreeding depression, with inter-population hybrids and backcrosses
showing either similar fitness or significant heterosis for fitness components
across the three generations. Variation in heterosis among population pairs was
best explained by characteristics of the foreign source or home population, and
was greatest when the source population was large, with high genetic diversity
and low inbreeding, and the home population was small and inbred. Our results
indicate that the primary consideration for maximizing progeny fitness following
population augmentation or restoration is the use of seed from large, genetically
diverse populations.
article_number: '2058'
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect
heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1750).
doi:10.1098/rspb.2012.2058
apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population
characteristics affect heterosis following genetic rescue of fragmented plant
populations. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058
chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population
Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant
Populations.” Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058.
ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1750. Royal Society, The, 2013.
ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.
mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis
Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1750,
2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058.
short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
date_created: 2018-12-11T11:46:32Z
date_published: 2013-01-07T00:00:00Z
date_updated: 2021-01-12T07:57:25Z
day: '07'
department:
- _id: NiBa
doi: 10.1098/rspb.2012.2058
external_id:
pmid:
- '23173202'
intvolume: ' 280'
issue: '1750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '7372'
quality_controlled: '1'
status: public
title: Source population characteristics affect heterosis following genetic rescue
of fragmented plant populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 280
year: '2013'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2023-02-23T14:07:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-23T10:31:17Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '2917'
abstract:
- lang: eng
text: 'The search for extra-terrestrial intelligence (SETI) has been performed principally
as a one-way survey, listening of radio frequencies across the Milky Way and other
galaxies. However, scientists have engaged in an active messaging only rarely.
This suggests the simple rationale that if other civilizations exist and take
a similar approach to ours, namely listening but not broadcasting, the result
is a silent universe. A simple game theoretical model, the prisoner''s dilemma,
explains this situation: each player (civilization) can passively search (defect),
or actively search and broadcast (cooperate). In order to maximize the payoff
(or, equivalently, minimize the risks) the best strategy is not to broadcast.
In fact, the active search has been opposed on the basis that it might be dangerous
to expose ourselves. However, most of these ideas have not been based on objective
arguments, and ignore accounting of the possible gains and losses. Thus, the question
stands: should we perform an active search? I develop a game-theoretical framework
where civilizations can be of different types, and explicitly apply it to a situation
where societies are either interested in establishing a two-way communication
or belligerent and in urge to exploit ours. The framework gives a quantitative
solution (a mixed-strategy), which is how frequent we should perform the active
SETI. This frequency is roughly proportional to the inverse of the risk, and can
be extremely small. However, given the immense amount of stars being scanned,
it supports active SETI. The model is compared with simulations, and the possible
actions are evaluated through the San Marino scale, measuring the risks of messaging.'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. The game of active search for extra terrestrial intelligence Breaking
the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62.
doi:10.1017/S1473550412000407
apa: de Vladar, H. (2012). The game of active search for extra terrestrial intelligence
Breaking the Great Silence . International Journal of Astrobiology. Cambridge
University Press. https://doi.org/10.1017/S1473550412000407
chicago: Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence
Breaking the Great Silence .” International Journal of Astrobiology. Cambridge
University Press, 2012. https://doi.org/10.1017/S1473550412000407.
ieee: H. de Vladar, “The game of active search for extra terrestrial intelligence
Breaking the Great Silence ,” International Journal of Astrobiology, vol.
12, no. 1. Cambridge University Press, pp. 53–62, 2012.
ista: de Vladar H. 2012. The game of active search for extra terrestrial intelligence
Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62.
mla: de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence
Breaking the Great Silence .” International Journal of Astrobiology, vol.
12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407.
short: H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.
date_created: 2018-12-11T12:00:19Z
date_published: 2012-11-06T00:00:00Z
date_updated: 2021-01-12T07:00:41Z
day: '06'
department:
- _id: NiBa
doi: 10.1017/S1473550412000407
intvolume: ' 12'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 53 - 62
publication: International Journal of Astrobiology
publication_status: published
publisher: Cambridge University Press
publist_id: '3821'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The game of active search for extra terrestrial intelligence Breaking the
Great Silence '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2012'
...
---
_id: '2962'
abstract:
- lang: eng
text: The choice of summary statistics is a crucial step in approximate Bayesian
computation (ABC). Since statistics are often not sufficient, this choice involves
a trade-off between loss of information and reduction of dimensionality. The latter
may increase the efficiency of ABC. Here, we propose an approach for choosing
summary statistics based on boosting, a technique from the machine learning literature.
We consider different types of boosting and compare them to partial least squares
regression as an alternative. To mitigate the lack of sufficiency, we also propose
an approach for choosing summary statistics locally, in the putative neighborhood
of the true parameter value. We study a demographic model motivated by the re-introduction
of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are
the mean and standard deviation across microsatellites of the scaled ancestral
mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to
matings per breeding season (ω). By simulation, we assess the properties of the
posterior distribution obtained with the various methods. According to our criteria,
ABC with summary statistics chosen locally via boosting with the L2-loss performs
best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find
that most of the variation across loci of the ancestral mutation rate u is between
7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access
to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent
estimates.
acknowledged_ssus:
- _id: ScienComp
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
citation:
ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary
statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047.
doi:10.1534/genetics.112.143164
apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach
for choosing summary statistics in approximate Bayesian computation. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.112.143164
chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach
for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics.
Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.
ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing
summary statistics in approximate Bayesian computation,” Genetics, vol.
192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.
ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing
summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.
mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics
in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics
Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.
short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
pmid:
- '22960215'
intvolume: ' 192'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1027 - 1047
pmid: 1
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3763'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel approach for choosing summary statistics in approximate Bayesian computation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 192
year: '2012'
...
---
_id: '3122'
abstract:
- lang: eng
text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin
1877), understanding the mechanisms maintaining the diverse sexual strategies
of plants has remained an important challenge for evolutionary biologists. In
some species, populations are sexually polymorphic and contain two or more mating
morphs (sex phenotypes). Differences in morphology or phenology among the morphs
influence patterns of non-random mating. In these populations, negative frequency-dependent
selection arising from disassortative (intermorph) mating is usually required
for the evolutionary maintenance of sexual polymorphism, but few studies have
demonstrated the required patterns of non-random mating. In the current issue
of Molecular Ecology, Shang (2012) make an important contribution to our understanding
of how disassortative mating influences sex phenotype ratios in Acer pictum subsp.
mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They
monitored sex expression in 97 adults and used paternity analysis of open-pollinated
seed to examine disassortative mating among three sex phenotypes. Using a deterministic
''pollen transfer'' model, Shang et al. present convincing evidence that differences
in the degree of disassortative mating in progeny arrays of the sex phenotypes
can explain their uneven frequencies in the adult population. This study provides
a useful example of how the deployment of genetic markers, demographic monitoring
and modelling can be integrated to investigate the maintenance of sexual diversity
in plants. '
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism
in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x
apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance
of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell.
https://doi.org/10.1111/j.1365-294X.2012.05643.x
chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell,
2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.
ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual
polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell,
pp. 3640–3643, 2012.
ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual
polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.
mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance
of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no.
15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.
short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.
date_created: 2018-12-11T12:01:31Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:13Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05643.x
intvolume: ' 21'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3640 - 3643
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3577'
quality_controlled: '1'
scopus_import: 1
status: public
title: Disassortative mating and the maintenance of sexual polymorphism in painted
maple
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '3131'
abstract:
- lang: eng
text: 'In large populations, many beneficial mutations may be simultaneously available
and may compete with one another, slowing adaptation. By finding the probability
of fixation of a favorable allele in a simple model of a haploid sexual population,
we find limits to the rate of adaptive substitution, Λ, that depend on simple
parameter combinations. When variance in fitness is low and linkage is loose,
the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the
rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage.
Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under
polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans,
interference is yet stronger. We use a scaling argument to show that the density
of adaptive substitutions depends on s, N, U, and R only through the baseline
density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different
sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference
prevents the rate of adaptive substitution from exceeding one per centimorgan
per 200 generations. Simulations and numerical calculations confirm the scaling
argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R,
the rate of adaptation grows above R/2, but only very slowly. We also consider
the effect of sweeps on neutral diversity and show that, while even occasional
sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become
more common-diversity can be maintained even in populations experiencing very
strong interference. Our results indicate that for some organisms the rate of
adaptive substitution may be primarily recombination-limited, depending only weakly
on the mutation supply and the strength of selection.'
acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth,
O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers
for their helpful suggestions."
article_number: e1002740
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual
populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740
apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution
in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740
chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive
Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science,
2012. https://doi.org/10.1371/journal.pgen.1002740.
ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution
in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of
Science, 2012.
ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in
sexual populations. PLoS Genetics. 8(6), e1002740.
mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution
in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002740.
short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-07T00:00:00Z
date_updated: 2021-01-12T07:41:17Z
day: '07'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1002740
ec_funded: 1
file:
- access_level: open_access
checksum: 729a4becda7d786c4c3db8f9a1f77953
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:00Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4659'
file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf
file_size: 1284801
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3566'
pubrep_id: '114'
quality_controlled: '1'
scopus_import: 1
status: public
title: Limits to the rate of adaptive substitution in sexual populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3166'
abstract:
- lang: eng
text: 'There is evidence that the genetic code was established prior to the existence
of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms
had to rely on simple anaerobic bioenergetic processes. In this work I propose
that amino acid fermentation powered metabolism in the RNA world, and that this
was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were
used as carbon sources rather than as catalytic or structural elements. In modern
bacteria, amino acid fermentation is known as the Stickland reaction. This pathway
involves two amino acids: the first undergoes oxidative deamination, and the second
acts as an electron acceptor through reductive deamination. This redox reaction
results in two keto acids that are employed to synthesise ATP via substrate-level
phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some
bacteria of the genus Clostridium. Two other facts support Stickland fermentation
in the RNA world. First, several Stickland amino acid pairs are synthesised in
abiotic amino acid synthesis. This suggests that amino acids that could be used
as an energy substrate were freely available. Second, anticodons that have complementary
sequences often correspond to amino acids that form Stickland pairs. The main
hypothesis of this paper is that pairs of complementary proto-adapters were assigned
to Stickland amino acids pairs. There are signatures of this hypothesis in the
genetic code. Furthermore, it is argued that the proto-adapters formed double
strands that brought amino acid pairs into proximity to facilitate their mutual
redox reaction, structurally constraining the anticodon pairs that are assigned
to these amino acid pairs. Significance tests which randomise the code are performed
to study the extent of the variability of the energetic (ATP) yield. Random assignments
can lead to a substantial yield of ATP and maintain enough variability, thus selection
can act and refine the assignments into a proto-code that optimises the energetic
yield. Monte Carlo simulations are performed to evaluate the establishment of
these simple proto-codes, based on amino acid substitutions and codon swapping.
In all cases, donor amino acids are assigned to anticodons composed of U+G, and
have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to
the the remaining codons. These bioenergetic and structural constraints allow
for a metabolic role for amino acids before their co-option as catalyst cofactors.
Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary
(nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)'
acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152
SELECTIONINFORMATION. '
article_number: '6'
author:
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology
Direct. 2012;7. doi:10.1186/1745-6150-7-6
apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic
code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6
chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic
Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.
ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,”
Biology Direct, vol. 7. BioMed Central, 2012.
ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code.
Biology Direct. 7, 6.
mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.”
Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.
short: H. de Vladar, Biology Direct 7 (2012).
date_created: 2018-12-11T12:01:46Z
date_published: 2012-02-10T00:00:00Z
date_updated: 2021-01-12T07:41:31Z
day: '10'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1186/1745-6150-7-6
ec_funded: 1
file:
- access_level: open_access
checksum: e511e401e239ef608a7fd79b21a06d78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:44Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5166'
file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf
file_size: 4099536
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '3518'
pubrep_id: '99'
quality_controlled: '1'
status: public
title: Amino acid fermentation at the origin of the genetic code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2012'
...
---
_id: '3277'
abstract:
- lang: eng
text: The problem of the origin of metazoa is becoming more urgent in the context
of astrobiology. By now it is clear that clues to the understanding of this crucial
transition in the evolution of life can arise in a fourth pathway besides the
three possibilities in the quest for simplicity outlined by Bonner in his classical
book. In other words, solar system exploration seems to be one way in the long-term
to elucidate the simplicity of evolutionary development. We place these ideas
in the context of different inheritance systems, namely the genotypic and phenotypic
replicators with limited or unlimited heredity, and ask which of these can support
multicellular development, and to which degree of complexity. However, the quest
for evidence on the evolution of biotas from planets around other stars does not
seem to be feasible with present technology with direct visualization of living
organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter
where there is a possibility of detecting reliable biomarkers in the next decade
with the Europa Jupiter System Mission, in view of recent progress by landing
micropenetrators on planetary, or satellite surfaces. Mars is a second possibility
in the inner Solar System, in spite of the multiple difficulties faced by the
fleet of past, present and future missions. We discuss a series of preliminary
ideas for elucidating the origin of metazoan analogues with available instrumentation
in potential payloads of feasible space missions to the Galilean moons.
alternative_title:
- Cellular Origin, Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Julian
full_name: Chela Flores, Julian
last_name: Chela Flores
citation:
ama: 'de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated
in the exploration of the solar system? In: Life on Earth and Other Planetary
Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22'
apa: de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity
be anticipated in the exploration of the solar system? In Life on Earth and
other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22
chicago: Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” In Life on Earth and
Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22.
ieee: H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be
anticipated in the exploration of the solar system?,” in Life on Earth and
other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.
ista: 'de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be
anticipated in the exploration of the solar system? In: Life on Earth and other
planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology,
vol. 24, 387–405.'
mla: de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity
Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other
Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.
short: H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies,
Springer, 2012, pp. 387–405.
date_created: 2018-12-11T12:02:25Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:20Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/978-94-007-4966-5_22
intvolume: ' 24'
language:
- iso: eng
month: '01'
oa_version: None
page: 387 - 405
publication: Life on Earth and other planetary bodies
publication_status: published
publisher: Springer
publist_id: '3369'
quality_controlled: '1'
status: public
title: Can the evolution of multicellularity be anticipated in the exploration of
the solar system?
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2012'
...
---
_id: '498'
abstract:
- lang: eng
text: Understanding patterns and correlates of local adaptation in heterogeneous
landscapes can provide important information in the selection of appropriate seed
sources for restoration. We assessed the extent of local adaptation of fitness
components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides
(Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance,
quantitative (QST) and neutral (FST) genetic differentiation, and size of the
local and foreign populations could predict patterns of adaptive differentiation.
Local adaptation varied among populations and fitness components. Including all
population pairs, local adaptation was observed for seedling survival, but not
for biomass, while foreign genotype advantage was observed for reproduction (number
of inflorescences). Among population pairs, local adaptation increased with QST
and local population size for biomass. QST was associated with environmental distance,
suggesting ecological selection for phenotypic divergence. However, low FST and
variation in population structure in small populations demonstrates the interaction
of gene flow and drift in constraining local adaptation in R. leptorrhynchoides.
Our study indicates that for species in heterogeneous landscapes, collecting seed
from large populations from similar environments to candidate sites is likely
to provide the most appropriate seed sources for restoration.
acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and
Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment
and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability
and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer
C. H. Barrett for comments that improved the quality of the manuscript.\r\n"
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented
plant populations: Implications for restoration genetics. Evolutionary Applications.
2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x'
apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local
adaptation in fragmented plant populations: Implications for restoration genetics.
Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x'
chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting
Local Adaptation in Fragmented Plant Populations: Implications for Restoration
Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.'
ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation
in fragmented plant populations: Implications for restoration genetics,” Evolutionary
Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.'
ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in
fragmented plant populations: Implications for restoration genetics. Evolutionary
Applications. 5(8), 913–924.'
mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations:
Implications for Restoration Genetics.” Evolutionary Applications, vol.
5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.'
short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012)
913–924.
date_created: 2018-12-11T11:46:48Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/j.1752-4571.2012.00284.x
file:
- access_level: open_access
checksum: 233007138606aca5a2f75f7ae1742f43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:33Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4821'
file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf
file_size: 396136
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 913 - 924
publication: Evolutionary Applications
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7322'
pubrep_id: '942'
quality_controlled: '1'
status: public
title: 'Predicting local adaptation in fragmented plant populations: Implications
for restoration genetics'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2012'
...
---
_id: '9758'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. 2012. doi:10.5061/dryad.274b1'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate
Bayesian computation for modular inference problems with many parameters: the
example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates.” Dryad, 2012.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates, Dryad, 10.5061/dryad.274b1.'
mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation
for Modular Inference Problems with Many Parameters: The Example of Migration
Rates. Dryad, 2012, doi:10.5061/dryad.274b1.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012).
date_created: 2021-07-30T12:36:39Z
date_published: 2012-11-14T00:00:00Z
date_updated: 2023-02-23T11:05:19Z
day: '14'
department:
- _id: NiBa
doi: 10.5061/dryad.274b1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.274b1
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
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relation: used_in_publication
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status: public
title: 'Data from: Approximate Bayesian computation for modular inference problems
with many parameters: the example of migration rates'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '2968'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya
stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop
a likelihood method to numerically estimate models of divergence between three
populations from multilocus data. We investigate the power of this framework on
simulated data, and-using triplet alignments of intronic loci-quantify the support
for all possible divergence relationships between refugial populations in the
four parasitoids. Although an East to West order of population divergence has
highest support in all but one species, we cannot rule out alternative population
tree topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times. © 2012 Blackwell Publishing Ltd.
acknowledgement: "This work was supported by funding from the UK Natural Environment
Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1,
NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe
thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing
specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on
earlier versions of the manuscript. "
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: George
full_name: Melika, George
last_name: Melika
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
citation:
ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population
histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617.
doi:10.1111/j.1365-294X.2012.05700.x
apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood
based comparison of population histories in a parasitoid guild. Molecular Ecology.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x
chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood
Based Comparison of Population Histories in a Parasitoid Guild.” Molecular
Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.
ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison
of population histories in a parasitoid guild,” Molecular Ecology, vol.
21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.
ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison
of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617.
mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories
in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell,
2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.
short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.
date_created: 2018-12-11T12:00:36Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2023-05-30T13:07:47Z
day: '01'
ddc:
- '570'
- '579'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05700.x
ec_funded: 1
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date_updated: 2020-07-14T12:45:57Z
file_id: '5304'
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file_size: 235820
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intvolume: ' 21'
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month: '09'
oa: 1
oa_version: Submitted Version
page: 4605 - 4617
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3746'
pubrep_id: '296'
quality_controlled: '1'
related_material:
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- id: '13075'
relation: research_data
status: public
scopus_import: 1
status: public
title: A likelihood based comparison of population histories in a parasitoid guild
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '13075'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota
and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood
method to numerically estimate models of divergence between three populations
from multilocus data. We investigate the power of this framework on simulated
data, and - using triplet alignments of intronic loci - quantify the support for
all possible divergence relationships between refugial populations in the four
parasitoids. Although an East to West order of population divergence has highest
support in all but one species, we cannot rule out alternative population tree
topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times.
article_processing_charge: No
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: George
full_name: Melika, George
last_name: Melika
citation:
ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison
of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS'
apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A
likelihood-based comparison of population histories in a parasitoid guild. Dryad.
https://doi.org/10.5061/DRYAD.0G0FS'
chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data
from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.”
Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.'
ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based
comparison of population histories in a parasitoid guild.” Dryad, 2012.'
ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based
comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.'
mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population
Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.'
short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).
date_created: 2023-05-23T17:01:02Z
date_published: 2012-06-08T00:00:00Z
date_updated: 2023-05-30T13:07:48Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.0G0FS
main_file_link:
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url: https://doi.org/10.5061/dryad.0g0fs
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
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status: public
title: 'Data from: A likelihood-based comparison of population histories in a parasitoid
guild'
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image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
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year: '2012'
...
---
_id: '3372'
abstract:
- lang: eng
text: Nowak et al.1 argue that inclusive fitness theory has been of little value
in explaining the natural world, and that it has led to negligible progress in
explaining the evolution of eusociality. However, we believe that their arguments
are based upon a misunderstanding of evolutionary theory and a misrepresentation
of the empirical literature. We will focus our comments on three general issues.
author:
- first_name: Patrick
full_name: Abbot, Patrick
last_name: Abbot
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: John
full_name: Alcock, John
last_name: Alcock
- first_name: Samuel
full_name: Alizon, Samuel
last_name: Alizon
- first_name: Joao
full_name: Alpedrinha, Joao
last_name: Alpedrinha
- first_name: Malte
full_name: Andersson, Malte
last_name: Andersson
- first_name: Jean
full_name: Andre, Jean
last_name: Andre
- first_name: Minus
full_name: Van Baalen, Minus
last_name: Van Baalen
- first_name: Francois
full_name: Balloux, Francois
last_name: Balloux
- first_name: Sigal
full_name: Balshine, Sigal
last_name: Balshine
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Leo
full_name: Beukeboom, Leo
last_name: Beukeboom
- first_name: Jay
full_name: Biernaskie, Jay
last_name: Biernaskie
- first_name: Trine
full_name: Bilde, Trine
last_name: Bilde
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Breed, Michael
last_name: Breed
- first_name: Sam
full_name: Brown, Sam
last_name: Brown
- first_name: Redouan
full_name: Bshary, Redouan
last_name: Bshary
- first_name: Angus
full_name: Buckling, Angus
last_name: Buckling
- first_name: Nancy
full_name: Burley, Nancy
last_name: Burley
- first_name: Max
full_name: Burton Chellew, Max
last_name: Burton Chellew
- first_name: Michael
full_name: Cant, Michael
last_name: Cant
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Eric
full_name: Charnov, Eric
last_name: Charnov
- first_name: Tim
full_name: Clutton Brock, Tim
last_name: Clutton Brock
- first_name: Andrew
full_name: Cockburn, Andrew
last_name: Cockburn
- first_name: Blaine
full_name: Cole, Blaine
last_name: Cole
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Leda
full_name: Cosmides, Leda
last_name: Cosmides
- first_name: Iain
full_name: Couzin, Iain
last_name: Couzin
- first_name: Jerry
full_name: Coyne, Jerry
last_name: Coyne
- first_name: Scott
full_name: Creel, Scott
last_name: Creel
- first_name: Bernard
full_name: Crespi, Bernard
last_name: Crespi
- first_name: Robert
full_name: Curry, Robert
last_name: Curry
- first_name: Sasha
full_name: Dall, Sasha
last_name: Dall
- first_name: Troy
full_name: Day, Troy
last_name: Day
- first_name: Janis
full_name: Dickinson, Janis
last_name: Dickinson
- first_name: Lee
full_name: Dugatkin, Lee
last_name: Dugatkin
- first_name: Claire
full_name: El Mouden, Claire
last_name: El Mouden
- first_name: Stephen
full_name: Emlen, Stephen
last_name: Emlen
- first_name: Jay
full_name: Evans, Jay
last_name: Evans
- first_name: Regis
full_name: Ferriere, Regis
last_name: Ferriere
- first_name: Jeremy
full_name: Field, Jeremy
last_name: Field
- first_name: Susanne
full_name: Foitzik, Susanne
last_name: Foitzik
- first_name: Kevin
full_name: Foster, Kevin
last_name: Foster
- first_name: William
full_name: Foster, William
last_name: Foster
- first_name: Charles
full_name: Fox, Charles
last_name: Fox
- first_name: Juergen
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last_name: Gadau
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full_name: Gandon, Sylvain
last_name: Gandon
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Michael
full_name: Gardner, Michael
last_name: Gardner
- first_name: Thomas
full_name: Getty, Thomas
last_name: Getty
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full_name: Goodisman, Michael
last_name: Goodisman
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full_name: Grafen, Alan
last_name: Grafen
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full_name: Grosberg, Rick
last_name: Grosberg
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last_name: Grozinger
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full_name: Gouyon, Pierre
last_name: Gouyon
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last_name: Gwynne
- first_name: Paul
full_name: Harvey, Paul
last_name: Harvey
- first_name: Ben
full_name: Hatchwell, Ben
last_name: Hatchwell
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Heikki
full_name: Helantera, Heikki
last_name: Helantera
- first_name: Ken
full_name: Helms, Ken
last_name: Helms
- first_name: Kim
full_name: Hill, Kim
last_name: Hill
- first_name: Natalie
full_name: Jiricny, Natalie
last_name: Jiricny
- first_name: Rufus
full_name: Johnstone, Rufus
last_name: Johnstone
- first_name: Alex
full_name: Kacelnik, Alex
last_name: Kacelnik
- first_name: E Toby
full_name: Kiers, E Toby
last_name: Kiers
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Jan
full_name: Komdeur, Jan
last_name: Komdeur
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
- first_name: Laurent
full_name: Lehmann, Laurent
last_name: Lehmann
- first_name: Timothy
full_name: Linksvayer, Timothy
last_name: Linksvayer
- first_name: Sébastien
full_name: Lion, Sébastien
last_name: Lion
- first_name: Bruce
full_name: Lyon, Bruce
last_name: Lyon
- first_name: James
full_name: Marshall, James
last_name: Marshall
- first_name: Richard
full_name: Mcelreath, Richard
last_name: Mcelreath
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last_name: Michalakis
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last_name: Mock
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last_name: Montgomerie
- first_name: Allen
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last_name: Moore
- first_name: Ulrich
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last_name: Mueller
- first_name: Ronald
full_name: Noë, Ronald
last_name: Noë
- first_name: Samir
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last_name: Okasha
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last_name: Pamilo
- first_name: Geoff
full_name: Parker, Geoff
last_name: Parker
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
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full_name: Pen, Ido
last_name: Pen
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last_name: Pfennig
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last_name: Queller
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last_name: Rankin
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last_name: Reece
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last_name: Reeve
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last_name: Reuter
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last_name: Roberts
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last_name: Robson
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last_name: Roze
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full_name: Rousset, Francois
last_name: Rousset
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- first_name: Joel
full_name: Sachs, Joel
last_name: Sachs
- first_name: Lorenzo
full_name: Santorelli, Lorenzo
last_name: Santorelli
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Tom
full_name: Scott Phillips, Tom
last_name: Scott Phillips
- first_name: Janet
full_name: Shellmann Sherman, Janet
last_name: Shellmann Sherman
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full_name: Sherman, Paul
last_name: Sherman
- first_name: David
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last_name: Shuker
- first_name: Jeff
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last_name: Smith
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last_name: Spagna
- first_name: Beverly
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last_name: Strassmann
- first_name: Andrew
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last_name: Suarez
- first_name: Liselotte
full_name: Sundström, Liselotte
last_name: Sundström
- first_name: Michael
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last_name: Taborsky
- first_name: Peter
full_name: Taylor, Peter
last_name: Taylor
- first_name: Graham
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last_name: Thompson
- first_name: John
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last_name: Tooby
- first_name: Neil
full_name: Tsutsui, Neil
last_name: Tsutsui
- first_name: Kazuki
full_name: Tsuji, Kazuki
last_name: Tsuji
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Francisco
full_name: Úbeda, Francisco
last_name: Úbeda
- first_name: Edward
full_name: Vargo, Edward
last_name: Vargo
- first_name: Bernard
full_name: Voelkl, Bernard
last_name: Voelkl
- first_name: Tom
full_name: Wenseleers, Tom
last_name: Wenseleers
- first_name: Stuart
full_name: West, Stuart
last_name: West
- first_name: Mary
full_name: West Eberhard, Mary
last_name: West Eberhard
- first_name: David
full_name: Westneat, David
last_name: Westneat
- first_name: Diane
full_name: Wiernasz, Diane
last_name: Wiernasz
- first_name: Geoff
full_name: Wild, Geoff
last_name: Wild
- first_name: Richard
full_name: Wrangham, Richard
last_name: Wrangham
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
- first_name: David
full_name: Zeh, David
last_name: Zeh
- first_name: Jeanne
full_name: Zeh, Jeanne
last_name: Zeh
- first_name: Andrew
full_name: Zink, Andrew
last_name: Zink
citation:
ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality.
Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831
apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M.,
… Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature09831
chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte
Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature.
Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831.
ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature,
vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.
ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339),
E1–E4.
mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature,
vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831.
short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre,
M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie,
T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M.
Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn,
B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi,
R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen,
J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J.
Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R.
Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze,
H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers,
H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer,
S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock,
T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo,
G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H.
Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J.
Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann
Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez,
L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji,
S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West
Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J.
Zeh, A. Zink, Nature 471 (2011) E1–E4.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-23T00:00:00Z
date_updated: 2021-01-12T07:43:02Z
day: '23'
department:
- _id: NiBa
doi: 10.1038/nature09831
external_id:
pmid:
- '21430721'
intvolume: ' 471'
issue: '7339'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/
month: '03'
oa: 1
oa_version: Submitted Version
page: E1 - E4
pmid: 1
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3237'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inclusive fitness theory and eusociality
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 471
year: '2011'
...
---
_id: '3394'
abstract:
- lang: eng
text: 'Random genetic drift shifts clines in space, alters their width, and distorts
their shape. Such random fluctuations complicate inferences from cline width and
position. Notably, the effect of genetic drift on the expected shape of the cline
is opposite to the naive (but quite common) misinterpretation of classic results
on the expected cline. While random drift on average broadens the overall cline
in expected allele frequency, it narrows the width of any particular cline. The
opposing effects arise because locally, drift drives alleles to fixation—but fluctuations
in position widen the expected cline. The effect of genetic drift can be predicted
from standardized variance in allele frequencies, averaged across the habitat:
〈F〉. A cline maintained by spatially varying selection (step change) is expected
to be narrower by a factor of relative to the cline in the absence of drift.
The expected cline is broader by the inverse of this factor. In a tension zone
maintained by underdominance, the expected cline width is narrower by about 1
– 〈F〉relative to the width in the absence of drift. Individual clines can differ
substantially from the expectation, and we give quantitative predictions for the
variance in cline position and width. The predictions apply to clines in almost
one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or
along a coast line and give a guide to what patterns to expect in two dimensions.'
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Genetic drift widens the expected cline but narrows
the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817
apa: Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected
cline but narrows the expected cline width. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.111.129817
chicago: Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society
of America, 2011. https://doi.org/10.1534/genetics.111.129817.
ieee: J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but
narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics
Society of America, pp. 227–235, 2011.
ista: Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but
narrows the expected cline width. Genetics. 189(1), 227–235.
mla: Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected
Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1,
Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817.
short: J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129817
ec_funded: 1
intvolume: ' 189'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/
month: '09'
oa: 1
oa_version: Submitted Version
page: 227 - 235
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic drift widens the expected cline but narrows the expected cline width
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3390'
abstract:
- lang: eng
text: 'What determines the genetic contribution that an individual makes to future
generations? With biparental reproduction, each individual leaves a ''pedigree''
of descendants, determined by the biparental relationships in the population.
The pedigree of an individual constrains the lines of descent of each of its genes.
An individual''s reproductive value is the expected number of copies of each of
its genes that is passed on to distant generations conditional on its pedigree.
For the simplest model of biparental reproduction analogous to the Wright-Fisher
model, an individual''s reproductive value is determined within ~10 generations,
independent of population size. Partial selfing and subdivision do not greatly
slow this convergence. Our central result is that the probability that a gene
will survive is proportional to the reproductive value of the individual that
carries it, and that conditional on survival, after a few tens of generations,
the distribution of the number of surviving copies is the same for all individuals,
whatever their reproductive value. These results can be generalized to the joint
distribution of surviving blocks of ancestral genome. Selection on unlinked loci
in the genetic background may greatly increase the variance in reproductive value,
but the above results nevertheless still hold. The almost linear relationship
between survival probability and reproductive value also holds for weakly favored
alleles. Thus, the influence of the complex pedigree of descendants on an individual''s
genetic contribution to the population can be summarized through a single number:
its reproductive value.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The relation between reproductive value and genetic
contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555
apa: Barton, N. H., & Etheridge, A. (2011). The relation between reproductive
value and genetic contribution. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.111.127555
chicago: Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics. Genetics Society of America,
2011. https://doi.org/10.1534/genetics.111.127555.
ieee: N. H. Barton and A. Etheridge, “The relation between reproductive value and
genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America,
pp. 953–973, 2011.
ista: Barton NH, Etheridge A. 2011. The relation between reproductive value and
genetic contribution. Genetics. 188(4), 953–973.
mla: Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive
Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society
of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555.
short: N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:09Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.127555
ec_funded: 1
intvolume: ' 188'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/
month: '08'
oa: 1
oa_version: Submitted Version
page: 953 - 973
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3217'
quality_controlled: '1'
scopus_import: 1
status: public
title: The relation between reproductive value and genetic contribution
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2011'
...
---
_id: '3391'
abstract:
- lang: eng
text: 'Evolutionary biology shares many concepts with statistical physics: both
deal with populations, whether of molecules or organisms, and both seek to simplify
evolution in very many dimensions. Often, methodologies have undergone parallel
and independent development, as with stochastic methods in population genetics.
Here, we discuss aspects of population genetics that have embraced methods from
physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo
methods, among others, have been used to study polygenic evolution, rates of adaptation
and range expansions. These applications indicate that evolutionary biology can
further benefit from interactions with other areas of statistical physics; for
example, by following the distribution of paths taken by a population through
time'
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: de Vladar H, Barton NH. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002
apa: de Vladar, H., & Barton, N. H. (2011). The contribution of statistical
physics to evolutionary biology. Trends in Ecology and Evolution. Cell
Press. https://doi.org/10.1016/j.tree.2011.04.002
chicago: Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell
Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002.
ieee: H. de Vladar and N. H. Barton, “The contribution of statistical physics to
evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8.
Cell Press, pp. 424–432, 2011.
ista: de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary
biology. Trends in Ecology and Evolution. 26(8), 424–432.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical
Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol.
26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002.
short: H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2021-01-12T07:43:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/j.tree.2011.04.002
ec_funded: 1
intvolume: ' 26'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1104.2854
month: '08'
oa: 1
oa_version: Submitted Version
page: 424 - 432
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '3216'
quality_controlled: '1'
scopus_import: 1
status: public
title: The contribution of statistical physics to evolutionary biology
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2011'
...
---
_id: '3784'
abstract:
- lang: eng
text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal
trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005.
Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage
phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology
is described and illustrated. This constitutes the second complete description
of a Scyllaridae phyllosoma with its specific identity being validated by molecular
techniques (the first was S. pygmaeus). These results also solved a long lasting
taxonomic anomaly of several species assigned to the ancient genus Phyllosoma
Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of
S. arctus shows closer affinities with the American scyllarid Scyllarus depressus
or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its
sympatric species S. pygmaeus.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda:
Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological
description. Journal of the Marine Biological Association of the United Kingdom.
2011;91(2):485-492. doi:10.1017/S0025315410000287'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus
(Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis,
with morphological description. Journal of the Marine Biological Association
of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus
Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by
DNA Analysis, with Morphological Description.” Journal of the Marine Biological
Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description,” Journal of the Marine Biological Association of
the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492,
2011.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description. Journal of the Marine Biological Association of the
United Kingdom. 91(2), 485–492.'
mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae)
Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.”
Journal of the Marine Biological Association of the United Kingdom, vol.
91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological
Association of the United Kingdom 91 (2011) 485–492.
date_created: 2018-12-11T12:05:09Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1017/S0025315410000287
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf
month: '03'
oa: 1
oa_version: Published Version
page: 485 - 492
publication: Journal of the Marine Biological Association of the United Kingdom
publication_status: published
publisher: Cambridge University Press
publist_id: '2443'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma
identified by DNA analysis, with morphological description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2011'
...
---
_id: '3290'
abstract:
- lang: eng
text: 'Analysis of genomic data requires an efficient way to calculate likelihoods
across very large numbers of loci. We describe a general method for finding the
distribution of genealogies: we allow migration between demes, splitting of demes
[as in the isolation-with-migration (IM) model], and recombination between linked
loci. These processes are described by a set of linear recursions for the generating
function of branch lengths. Under the infinite-sites model, the probability of
any configuration of mutations can be found by differentiating this generating
function. Such calculations are feasible for small numbers of sampled genomes:
as an example, we show how the generating function can be derived explicitly for
three genes under the two-deme IM model. This derivation is done automatically,
using Mathematica. Given data from a large number of unlinked and nonrecombining
blocks of sequence, these results can be used to find maximum-likelihood estimates
of model parameters by tabulating the probabilities of all relevant mutational
configurations and then multiplying across loci. The feasibility of the method
is demonstrated by applying it to simulated data and to a data set previously
analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila
simulans and D. melanogaster. Our results suggest that such likelihood calculations
are scalable to genomic data as long as the numbers of sampled individuals and
mutations per sequence block are small.'
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Richard
full_name: Harrison, Richard
last_name: Harrison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods
under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569
apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating
likelihoods under the coalescent process. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.111.129569
chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method
for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics
Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.
ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating
likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics
Society of America, pp. 977–987, 2011.
ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods
under the coalescent process. Genetics. 189(3), 977–987.
mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the
Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America,
2011, pp. 977–87, doi:10.1534/genetics.111.129569.
short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.
date_created: 2018-12-11T12:02:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
intvolume: ' 189'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/
month: '11'
oa: 1
oa_version: Submitted Version
page: 977 - 987
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3355'
quality_controlled: '1'
scopus_import: 1
status: public
title: A general method for calculating likelihoods under the coalescent process
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3380'
abstract:
- lang: eng
text: Linkage between markers and genes that affect a phenotype of interest may
be determined by examining differences in marker allele frequency in the extreme
progeny of a cross between two inbred lines. This strategy is usually employed
when pooling is used to reduce genotyping costs. When the cross progeny are asexual,
the extreme progeny may be selected by multiple generations of asexual reproduction
and selection. We analyse this method of measuring phenotype in asexual progeny
and examine the changes in marker allele frequency due to selection over many
generations. Stochasticity in marker frequency in the selected population arises
due to the finite initial population size. We derive the distribution of marker
frequency as a result of selection at a single major locus, and show that in order
to avoid spurious changes in marker allele frequency in the selected population,
the initial population size should be in the low to mid hundreds.
article_processing_charge: No
article_type: original
author:
- first_name: Sayanthan
full_name: Logeswaran, Sayanthan
last_name: Logeswaran
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using
changes in marker allele frequency. Genetical Research. 2011;93(3):221-232.
doi:10.1017/S0016672311000115
apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual
progeny using changes in marker allele frequency. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672311000115
chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits
in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research.
Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.
ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency,” Genetical Research, vol. 93,
no. 3. Cambridge University Press, pp. 221–232, 2011.
ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency. Genetical Research. 93(3), 221–232.
mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in
Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research,
vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.
short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-05-18T00:00:00Z
date_updated: 2021-01-12T07:43:05Z
day: '18'
department:
- _id: NiBa
doi: 10.1017/S0016672311000115
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf
month: '05'
oa: 1
oa_version: Published Version
page: 221 - 232
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '3227'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping Mendelian traits in asexual progeny using changes in marker allele
frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2011'
...
---
_id: '3778'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206.
doi:10.1038/hdy.2010.67
apa: Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature
Publishing Group. https://doi.org/10.1038/hdy.2010.67
chicago: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity.
Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67.
ieee: N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106,
no. 2. Nature Publishing Group, pp. 205–206, 2011.
ista: Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.
mla: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol.
106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67.
short: N.H. Barton, Heredity 106 (2011) 205–206.
date_created: 2018-12-11T12:05:07Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T07:52:08Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2010.67
external_id:
pmid:
- '20502479'
intvolume: ' 106'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/
month: '02'
oa: 1
oa_version: Submitted Version
page: 205 - 206
pmid: 1
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2449'
scopus_import: 1
status: public
title: Estimating linkage disequilibria
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2011'
...
---
_id: '3395'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies aiming to evaluate the genetic health of the exploited populations. The
present study is based on a set of ten nuclear markers amplified in 331 individuals
from ten different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and instead showed a large and stable
historical effective size. This result could be accounted for by specific life-history
traits (reproduction and longevity) and the limitations of molecular markers in
covering recent timescales for nontemporal samples. The findings of the present
study emphasize the need to integrate information on effective population sizes
and life-history parameters when evaluating population connectivity levels from
genetic data.
acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the
Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded
by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors
are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the
Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418.
doi:10.1111/j.1095-8312.2011.01728.x
apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas. Biological Journal of the
Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x
chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic
Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal
of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.
ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas,” Biological Journal of the
Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.
ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2),
407–418.
mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on
the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.”
Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell,
2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological
Journal of the Linnean Society 104 (2011) 407–418.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2023-02-23T14:07:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
intvolume: ' 104'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 407 - 418
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3212'
quality_controlled: '1'
related_material:
record:
- id: '9762'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of oceanographic barriers and overfishing on the population genetic
structure of the European spiny lobster Palinurus elephas
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 104
year: '2011'
...
---
_id: '9762'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies to evaluate the genetic health of the exploited populations. The present
work is based on a set of 10 nuclear markers amplified in 331 individuals from
10 different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and showed a large and stable historical
effective size instead. This result could be accounted for by specific life history
traits (reproduction and longevity) and the limitations of molecular markers in
covering very recent timescales for non temporal samples. Our study emphasizes
the necessity of integrating information on effective population sizes and life
history parameters when evaluating population connectivity levels from genetic
data.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8'
apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas). IST Austria.
https://doi.org/10.5061/dryad.299h8'
chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population
Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria,
2011. https://doi.org/10.5061/dryad.299h8.'
ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.'
ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from:
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.'
mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and
Overfishing on the Population Genetic Structure of the European Spiny Lobster
(Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.'
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).
date_created: 2021-08-02T07:11:19Z
date_published: 2011-05-12T00:00:00Z
date_updated: 2023-02-23T11:25:25Z
day: '12'
department:
- _id: NiBa
doi: 10.5061/dryad.299h8
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.299h8
month: '05'
oa: 1
oa_version: Published Version
publisher: IST Austria
related_material:
record:
- id: '3395'
relation: used_in_publication
status: public
status: public
title: 'Data from: Effect of oceanographic barriers and overfishing on the population
genetic structure of the European spiny lobster (Palinurus elephas)'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2011'
...
---
_id: '3375'
abstract:
- lang: eng
text: 'By exploiting an analogy between population genetics and statistical mechanics,
we study the evolution of a polygenic trait under stabilizing selection, mutation
and genetic drift. This requires us to track only four macroscopic variables,
instead of the distribution of all the allele frequencies that influence the trait.
These macroscopic variables are the expectations of: the trait mean and its square,
the genetic variance, and of a measure of heterozygosity, and are derived from
a generating function that is in turn derived by maximizing an entropy measure.
These four macroscopics are enough to accurately describe the dynamics of the
trait mean and of its genetic variance (and in principle of any other quantity).
Unlike previous approaches that were based on an infinite series of moments or
cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined
approximation procedure. We apply the framework to abrupt and gradual changes
in the optimum, as well as to changes in the strength of stabilizing selection.
Our approximations are surprisingly accurate, even for systems with as few as
five loci. We find that when the effects of drift are included, the expected genetic
variance is hardly altered by directional selection, even though it fluctuates
in any particular instance. We also find hysteresis, showing that even after averaging
over the microscopic variables, the macroscopic trajectories retain a memory of
the underlying genetic states.'
article_processing_charge: No
article_type: original
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: de Vladar H, Barton NH. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society
Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438
apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic
character under stabilizing selection mutation and drift. Journal of the Royal
Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438
chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of
a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438.
ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift,” Journal of the Royal Society
Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.
ista: de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character
under stabilizing selection mutation and drift. Journal of the Royal Society Interface.
8(58), 720–739.
mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a
Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal
of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp.
720–39, doi:10.1098/rsif.2010.0438.
short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011)
720–739.
date_created: 2018-12-11T12:02:58Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2023-10-18T06:39:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1098/rsif.2010.0438
ec_funded: 1
external_id:
pmid:
- '21084341'
intvolume: ' 8'
issue: '58'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/
month: '05'
oa: 1
oa_version: Submitted Version
page: 720 - 739
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of the Royal Society Interface
publication_status: published
publisher: The Royal Society
publist_id: '3232'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The statistical mechanics of a polygenic character under stabilizing selection
mutation and drift
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2011'
...
---
_id: '3393'
abstract:
- lang: eng
text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread
throughout a species range once introduced anywhere, “bistable” variants, such
as chromosome translocations, have two alternative stable frequencies, absence
and (near) fixation. Analogous to populations with Allee effects, bistable variants
tend to increase locally only once they become sufficiently common, and their
spread depends on their rate of increase averaged over all frequencies. Several
proposed manipulations of insect populations, such as using Wolbachia or “engineered
underdominance” to suppress vector-borne diseases, produce bistable rather than
Fisherian dynamics. We synthesize and extend theoretical analyses concerning three
features of their spatial behavior: rate of spread, conditions to initiate spread
from a localized introduction, and wave stopping caused by variation in population
densities or dispersal rates. Unlike Fisherian variants, bistable variants tend
to spread spatially only for particular parameter combinations and initial conditions.
Wave initiation requires introduction over an extended region, while subsequent
spatial spread is slower than for Fisherian waves and can easily be halted by
local spatial inhomogeneities. We present several new results, including robust
sufficient conditions to initiate (and stop) spread, using a one-parameter cubic
approximation applicable to several models. The results have both basic and applied
implications.'
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic
and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75.
doi:10.1086/661246'
apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable
dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist.
The University of Chicago Press. https://doi.org/10.1086/661246'
chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with
Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American
Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.'
ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects,” American Naturalist,
vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.'
ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics:
Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3),
E48–E75.'
mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable
Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist,
vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.'
short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2023-10-18T08:01:43Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/661246
file:
- access_level: open_access
checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:31Z
date_updated: 2020-07-14T12:46:11Z
file_id: '4692'
file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf
file_size: 629130
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 178'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: E48 - E75
publication: American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: The University of Chicago Press
publist_id: '3214'
pubrep_id: '554'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues
of Allee effects'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2011'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
intvolume: ' 186'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3337'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2010'
...
---
_id: '3604'
abstract:
- lang: eng
text: We investigated temporal changes in hybridization and introgression between
native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on
the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples
of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that
either the proportion of recent hybrids, or the levels of introgression had changed
over the study period. Nevertheless, in one population where the two species have
been in contact since ∼1970, 44% of individuals sampled during the study were
hybrids. This suggests that hybridization between these species can proceed fairly
rapidly. By analysing the number of alleles that have introgressed from polymorphic
red deer into the genetically homogenous sika population, we reconstructed the
haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization
events could account for all the recently hybridized sika-like individuals found
across a large section of the Peninsula. Although we demonstrate that low rates
of F1 hybridization can lead to substantial introgression, the progress of hybridization
and introgression appears to be unpredictable over the short timescales.
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal
changes in hybridisation and introgression between invasive sika (Cervus nippon)
and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular
Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x
apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010).
Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x
chicago: Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine
Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010.
https://doi.org/10.1111/j.1365-294X.2009.04497.x.
ieee: H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,”
Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.
ista: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland.
Molecular Ecology. 19(5), 910–924.
mla: Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell,
2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.
short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology
19 (2010) 910–924.
date_created: 2018-12-11T12:04:12Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T07:44:36Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2009.04497.x
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 910 - 924
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2779'
quality_controlled: '1'
scopus_import: 1
status: public
title: Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2010'
...
---
_id: '3783'
abstract:
- lang: eng
text: MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that
facilitates several tasks when scoring microsatellites. It implements new subroutines
in R and PERL and takes advantage of features provided by previously developed
freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification
through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite
markers according to their multiplex group, fluorochrome type, and size range.
After peak selection, binning of alleles can be carried out 1) automatically through
AlleloBin or 2) by manual bin definition through Binator. In both cases, several
features for quality checking and further binning improvement are provided. The
genotype table can then be converted into input files for several population genetics
programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence
intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT
is the only freely available public-domain software that facilitates full multiplex
microsatellite scoring, from electropherogram files to user-defined text files
to be used with population genetics software. MICROSATELIGHT has been created
for the Windows XP operating system and has been successfully tested under Windows
7. It is available at http://sourceforge.net/projects/microsatelight/.
acknowledgement: "Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635).
M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya.
F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel
Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us
pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat
de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous
referees for their valuable comments. These comments certainly helped to improve
the manuscript."
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Fernando
full_name: González Candelas, Fernando
last_name: González Candelas
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite
microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111
apa: Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight
– Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford
University Press. https://doi.org/10.1093/jhered/esq111
chicago: Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight
– Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford
University Press, 2010. https://doi.org/10.1093/jhered/esq111.
ieee: F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline
to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no.
2. Oxford University Press, pp. 247–249, 2010.
ista: Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline
to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.
mla: Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite
Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press,
2010, pp. 247–49, doi:10.1093/jhered/esq111.
short: F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010)
247–249.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-12-02T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '02'
department:
- _id: NiBa
doi: 10.1093/jhered/esq111
intvolume: ' 102'
issue: '2'
language:
- iso: eng
month: '12'
oa_version: None
page: 247 - 249
publication: Journal of Heredity
publication_status: published
publisher: Oxford University Press
publist_id: '2444'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microsatelight – Pipeline to expedite microsatellite analysis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2010'
...
---
_id: '4134'
abstract:
- lang: eng
text: 'All species are restricted in their distribution. Currently, ecological models
can only explain such limits if patches vary in quality, leading to asymmetrical
dispersal, or if genetic variation is too low at the margins for adaptation. However,
population genetic models suggest that the increase in genetic variance resulting
from dispersal should allow adaptation to almost any ecological gradient. Clearly
therefore, these models miss something that prevents evolution in natural populations.
We developed an individual-based simulation to explore stochastic effects in these
models. At high carrying capacities, our simulations largely agree with deterministic
predictions. However, when carrying capacity is low, the population fails to establish
for a wide range of parameter values where adaptation was expected from previous
models. Stochastic or transient effects appear critical around the boundaries
in parameter space between simulation behaviours. Dispersal, gradient steepness,
and population density emerge as key factors determining adaptation on an ecological
gradient. '
acknowledgement: We are very grateful to Nick Barton.
author:
- first_name: Jon
full_name: Bridle, Jon
last_name: Bridle
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Masakado
full_name: Kawata, Masakado
last_name: Kawata
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological
margins? New insights from individual-based simulations. Ecology Letters.
2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x
apa: Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation
prevented at ecological margins? New insights from individual-based simulations.
Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x
chicago: Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is
Adaptation Prevented at Ecological Margins? New Insights from Individual-Based
Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x.
ieee: J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented
at ecological margins? New insights from individual-based simulations,” Ecology
Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010.
ista: Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented
at ecological margins? New insights from individual-based simulations. Ecology
Letters. 13(4), 485–494.
mla: Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New
Insights from Individual-Based Simulations.” Ecology Letters, vol. 13,
no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x.
short: J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010)
485–494.
date_created: 2018-12-11T12:07:08Z
date_published: 2010-03-15T00:00:00Z
date_updated: 2021-01-12T07:54:45Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/j.1461-0248.2010.01442.x
ec_funded: 1
intvolume: ' 13'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 485 - 494
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Ecology Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1987'
quality_controlled: '1'
scopus_import: 1
status: public
title: Why is adaptation prevented at ecological margins? New insights from individual-based
simulations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2010'
...
---
_id: '4243'
abstract:
- lang: eng
text: We investigate a new model for populations evolving in a spatial continuum.
This model can be thought of as a spatial version of the Lambda-Fleming-Viot process.
It explicitly incorporates both small scale reproduction events and large scale
extinction-recolonisation events. The lineages ancestral to a sample from a population
evolving according to this model can be described in terms of a spatial version
of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence
and uniqueness in law for the model. We then investigate the asymptotic behaviour
of the genealogy of a finite number of individuals sampled uniformly at random
(or more generally `far enough apart') from a two-dimensional torus of sidelength
L as L tends to infinity. Under appropriate conditions (and on a suitable timescale)
we can obtain as limiting genealogical processes a Kingman coalescent, a more
general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local
coalescence mechanism).
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum.
Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741
apa: Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution
in a spatial continuum. Electronic Journal of Probability. Institute of
Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model
for Evolution in a Spatial Continuum.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a
spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7.
Institute of Mathematical Statistics, pp. 162–216, 2010.
ista: Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial
continuum. Electronic Journal of Probability. 15(7), 162–216.
mla: Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.”
Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical
Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741.
short: N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15
(2010) 162–216.
date_created: 2018-12-11T12:07:48Z
date_published: 2010-02-03T00:00:00Z
date_updated: 2021-01-12T07:55:34Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1214/EJP.v15-741
file:
- access_level: open_access
checksum: bab577546dd4e8f882e9a9dd645cd01e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:21Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5140'
file_name: IST-2015-369-v1+1_741-2535-1-PB.pdf
file_size: 450171
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 162 - 216
publication: Electronic Journal of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '1863'
pubrep_id: '369'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new model for evolution in a spatial continuum
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2010'
...
---
_id: '3776'
abstract:
- lang: eng
text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling
questions in biology. The most compelling general explanation is that recombination
facilitates selection by breaking down the negative associations generated by
random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of
HRI owing to: deleterious mutation, balancing selection and selective sweeps on:
neutral diversity, rates of adaptation and the mutation load. These effects are
mediated primarily by the density of deleterious mutations and of selective sweeps.
Sequence polymorphism and divergence suggest that these rates may be high enough
to cause significant interference even in genomic regions of high recombination.
However, neither seems able to generate enough variance in fitness to select strongly
for high rates of recombination. It is plausible that spatial and temporal fluctuations
in selection generate much more fitness variance, and hence selection for recombination,
than can be explained by uniformly deleterious mutations or species-wide selective
sweeps.'
acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would
like to thank Brian Charlesworth and Sally Otto for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569.
doi:10.1098/rstb.2010.0106
apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2010.0106
chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.
ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1552. Royal Society, pp. 2559–2569, 2010.
ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.
mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 2559–2569.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
file:
- access_level: open_access
checksum: 4d8aade10db030124ab158b622e337e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:40Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5093'
file_name: IST-2016-555-v1+1_RS2009_revised.pdf
file_size: 250255
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 365'
issue: '1552'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 2559 - 2569
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2450'
pubrep_id: '555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic linkage and natural selection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3773'
abstract:
- lang: eng
text: If distinct biological species are to coexist in sympatry, they must be reproductively
isolated and must exploit different limiting resources. A two-niche Levene model
is analysed, in which habitat preference and survival depend on underlying additive
traits. The population genetics of preference and viability are equivalent. However,
there is a linear trade-off between the chances of settling in either niche, whereas
viabilities may be constrained arbitrarily. With a convex trade-off, a sexual
population evolves a single generalist genotype, whereas with a concave trade-off,
disruptive selection favours maximal variance. A pure habitat preference evolves
to global linkage equilibrium if mating occurs in a single pool, but remarkably,
evolves to pairwise linkage equilibrium within niches if mating is within those
niches--independent of the genetics. With a concave trade-off, the population
shifts sharply between a unimodal distribution with high gene flow and a bimodal
distribution with strong isolation, as the underlying genetic variance increases.
However, these alternative states are only simultaneously stable for a narrow
parameter range. A sharp threshold is only seen if survival in the 'wrong' niche
is low; otherwise, strong isolation is impossible. Gene flow from divergent demes
makes speciation much easier in parapatry than in sympatry.
acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish
Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He
also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n"
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001
apa: Barton, N. H. (2010). What role does natural selection play in speciation?
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001
chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.
ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.
ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547),
1825–1840.
mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1825–1840.
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
pmid:
- '20439284'
intvolume: ' 365'
issue: '1547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20439284
month: '06'
oa: 1
oa_version: Submitted Version
page: 1825 - 1840
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2455'
quality_controlled: '1'
scopus_import: 1
status: public
title: What role does natural selection play in speciation?
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3777'
abstract:
- lang: eng
text: 'Under the classical view, selection depends more or less directly on mutation:
standing genetic variance is maintained by a balance between selection and mutation,
and adaptation is fuelled by new favourable mutations. Recombination is favoured
if it breaks negative associations among selected alleles, which interfere with
adaptation. Such associations may be generated by negative epistasis, or by random
drift (leading to the Hill-Robertson effect). Both deterministic and stochastic
explanations depend primarily on the genomic mutation rate, U. This may be large
enough to explain high recombination rates in some organisms, but seems unlikely
to be so in general. Random drift is a more general source of negative linkage
disequilibria, and can cause selection for recombination even in large populations,
through the chance loss of new favourable mutations. The rate of species-wide
substitutions is much too low to drive this mechanism, but local fluctuations
in selection, combined with gene flow, may suffice. These arguments are illustrated
by comparing the interaction between good and bad mutations at unlinked loci under
the infinitesimal model.'
acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this
special issue, and the Royal Society and Wolfson Foundation for their support. Also,
A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Mutation and the evolution of recombination. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294.
doi:10.1098/rstb.2009.0320
apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2009.0320
chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.
ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.
ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544),
1281–1294.
mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1281–1294.
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
pmid:
- '20308104'
intvolume: ' 365'
issue: '1544'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20308104
month: '04'
oa: 1
oa_version: Submitted Version
page: 1281 - 1294
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2451'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutation and the evolution of recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3774'
abstract:
- lang: eng
text: 1. Hybridisation with an invasive species has the potential to alter the phenotype
and hence the ecology of a native counterpart. 2. Here data from populations of
native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland
is used to assess the extent to which hybridisation between them is causing phenotypic
change. This is done by regression of phenotypic traits against genetic hybrid
scores. 3. Hybridisation is causing increases in the body weight of sika-like
deer and decreases in the body weight of red-like females. Hybridisation is causing
increases in jaw length and increases in incisor arcade breadth in sika-like females.
Hybridisation is also causing decreases in incisor arcade breadth in red-like
females. 4. There is currently no evidence that hybridisation is causing changes
in the kidney fat weight or pregnancy rates of either population. 5. Increased
phenotypic similarity between the two species is likely to lead to further hybridisation.
The ecological consequences of this are difficult to predict.
acknowledgement: "This project was funded through a NERC studentship to HVS which
was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission
Scotland rangers for all their help with providing the larder data for and samples
from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice
and Steve Albon for helpful comments on the manuscript."
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal
Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x
apa: Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010).
Phenotypic correlates of hybridisation between red and sika deer (genus Cervus).
Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x
chicago: Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine
Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus
Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.
ieee: H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic
correlates of hybridisation between red and sika deer (genus Cervus),” Journal
of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.
ista: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology.
79(2), 414–425.
mla: Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and
Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell,
2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.
short: H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal
Ecology 79 (2010) 414–425.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-2656.2009.01633.x
external_id:
pmid:
- '20002231'
intvolume: ' 79'
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
page: 414 - 425
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2453'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2010'
...
---
_id: '3772'
article_number: e1000987
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics.
2010;6(6). doi:10.1371/journal.pgen.1000987
apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987
chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.
ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics,
vol. 6, no. 6. Public Library of Science, 2010.
ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics.
6(6), e1000987.
mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.
short: N.H. Barton, PLoS Genetics 6 (2010).
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
file:
- access_level: open_access
checksum: 5c14de2680ab483cb835096c99ee734d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:24Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5075'
file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF
file_size: 349965
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '2454'
pubrep_id: '524'
quality_controlled: '1'
scopus_import: 1
status: public
title: Understanding adaptation in large populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '3787'
abstract:
- lang: eng
text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean
tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown
that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors
impede PCR success when dealing with formalin-fixed material. Instead, amplification
success from formalin-fixed tissue appears to depend on the presence of unmodified
DNA in the extracted sample. A staining method that facilitates the targeting
of samples with a high content of unmodified DNA is provided.
acknowledgement: "The authors would like to thank two anonymous reviewers for their
remarks, which helped to improve the manuscript. This project was supported by the
Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract
no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology
Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal
Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government
of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS
Project http://www.synthesys. info/ which is financed by European Community Research
Infrastructure Action under the FP6 “Structuring the European Research Area” Programme.
Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical
point drying, P.Crabb for helping with the UV-light photography setting and our
colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology
NHM \r\n\r\n"
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Sally
full_name: Hall, Sally
last_name: Hall
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: Jackie
full_name: Mackenzie Dodds, Jackie
last_name: Mackenzie Dodds
- first_name: Sven
full_name: Thatje, Sven
last_name: Thatje
citation:
ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction
from formalin-fixed tissue: new light from the deep sea. Scientia Marina.
2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465'
apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &
Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the
deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas.
https://doi.org/10.3989/scimar.2010.74n3465'
chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie
Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones
Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.'
ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje,
“DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia
Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp.
465–470, 2010.'
ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010.
DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia
Marina. 74(3), 465–470.'
mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de
Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.'
short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje,
Scientia Marina 74 (2010) 465–470.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:11Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
intvolume: ' 74'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.soton.ac.uk/68731/
month: '09'
oa: 1
oa_version: Submitted Version
page: 465 - 470
publication: Scientia Marina
publication_status: published
publisher: Consejo Superior de Investigaciones Científicas
publist_id: '2440'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2010'
...
---
_id: '3786'
abstract:
- lang: eng
text: Four rare palinurid phyllosoma larvae, one mid-stage and three final stage,
were found among the unclassified collections in the Crustacea Section, Natural
History Museum, London. Detailed morphological analysis of the larvae indicated
that they belong to several Palinustus species given the presence of incipient
blunt-horns, length of antennula, length ratio of segments of antennular peduncle,
distribution of pereiopod spines, and shape of uropods and telson. Moreover, the
size of the final-stage larvae agrees with that expected given the size of the
recently described puerulus stage of Palinustus mossambicus. This constitutes
the first description of a complete phyllosoma assigned to Palinustus species.
The phyllosoma described in the present study include the largest Palinuridae
larva ever found.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma
of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage
Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata:
Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press,
2010. https://doi.org/10.11646/zootaxa.2403.1.4.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of
Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The
first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press,
pp. 42–58, 2010.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus
A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first
complete description. Zootaxa. 2403(1), 42–58.'
mla: 'Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards,
1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.”
Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2022-03-21T08:22:58Z
day: '19'
department:
- _id: NiBa
doi: 10.11646/zootaxa.2403.1.4
intvolume: ' 2403'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 42 - 58
publication: Zootaxa
publication_status: published
publisher: Magnolia Press
publist_id: '2441'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda:
Achelata: Palinuridae)-The first complete description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2403
year: '2010'
...
---
_id: '474'
abstract:
- lang: eng
text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale
patterns; they predict much more genetic diversity than is observed; and they
assume that loosely linked genetic loci evolve independently. We propose a new
model that deals with these problems. Extinction events kill some fraction of
individuals in a region. These are replaced by offspring from a small number of
parents, drawn from the preexisting population. This model of evolution forwards
in time corresponds to a backwards model, in which ancestral lineages jump to
a new location if they are hit by an event, and may coalesce with other lineages
that are hit by the same event. We derive an expression for the identity in allelic
state, and show that, over scales much larger than the largest event, this converges
to the classical value derived by Wright and Malécot. However, rare events that
cover large areas cause low genetic diversity, large-scale patterns, and correlations
in ancestry between unlinked loci.'
acknowledgement: This work has made use of the resources provided by the Edinburgh
Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative.
NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant
EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization
in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715.
doi:10.1111/j.1558-5646.2010.01019.x'
apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x'
chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model
for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.”
Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.'
ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography,” Evolution,
vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.'
ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and
recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9),
2701–2715.'
mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization
in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no.
9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.'
short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.
date_created: 2018-12-11T11:46:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T08:00:52Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2010.01019.x
intvolume: ' 64'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2701 - 2715
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A new model for extinction and recolonization in two dimensions: Quantifying
phylogeography'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2010'
...
---
_id: '3779'
abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T14:07:34Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
file:
- access_level: open_access
checksum: ee1ce2fb283a6b4127544ae532d0b4a1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5060'
file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf
file_size: 1089530
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2448'
pubrep_id: '366'
quality_controlled: '1'
related_material:
record:
- id: '9764'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cryptic variation between species and the basis of hybrid performance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '9764'
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the
drift load. 2010. doi:10.1371/journal.pbio.1000429.s003
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010.
https://doi.org/10.1371/journal.pbio.1000429.s003.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis
and the drift load.” Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis
and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.
mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.s003.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).
date_created: 2021-08-02T09:45:39Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T11:42:17Z
day: '20'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '3779'
relation: used_in_publication
status: public
status: public
title: Heterosis and the drift load
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2010'
...
---
_id: '3785'
abstract:
- lang: eng
text: Most fisheries involving spiny lobsters of the genus Palinurus have been over
exploited during the last decades, so there is a raising concern about management
decisions for these valuable resources. A total of 13 microsatellite DNA loci
recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave
amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus
barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth
distribution was taken into account, shallower waters pecies consistently showed
larger historical effective population sizes than their deeper-water counterparts. This
could explain why deeper-water species are more sensitive to overfishing, and
would indicate that overexploitation may have a larger impact on their long-term
genetic diversity.
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: E.
full_name: Macpherson, E.
last_name: Macpherson
- first_name: C.
full_name: Matthee, C.
last_name: Matthee
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1'
apa: 'Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010).
Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus
(Decapoda: Achelata). Journal of Crustacean Biology. Oxford University
Press. https://doi.org/10.1651/09-3192.1'
chicago: 'Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual.
“Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus
(Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University
Press, 2010. https://doi.org/10.1651/09-3192.1.'
ieee: 'F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic
diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda:
Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University
Press, pp. 658–663, 2010.'
ista: 'Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity
levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata).
Journal of Crustacean Biology. 30(4), 658–663.'
mla: 'Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny
Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean
Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.'
short: F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean
Biology 30 (2010) 658–663.
date_created: 2018-12-11T12:05:09Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-10-16T09:51:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1651/09-3192.1
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '10'
oa_version: None
page: 658 - 663
publication: Journal of Crustacean Biology
publication_identifier:
eissn:
- 1937-240X
issn:
- 0278-0372
publication_status: published
publisher: Oxford University Press
publist_id: '2442'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genetic diversity levels in fishery-exploited spiny lobsters of the Genus
Palinurus (Decapoda: Achelata)'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2010'
...
---
_id: '3780'
abstract:
- lang: eng
text: Why are sinistral snails so rare? Two main hypotheses are that selection acts
against the establishment of new coiling morphs, because dextral and sinistral
snails have trouble mating, or else a developmental constraint prevents the establishment
of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in
which sinistrals are rare, and populations of Partula suturalis, in which sinistrals
are common, as well as a mathematical model, to understand the circumstances by
which new morphs evolve. The main finding is that the sinistral genotype is associated
with reduced egg viability in L. stagnalis, but in P. suturalis individuals of
sinistral and dextral genotype appear equally fecund, implying a lack of a constraint.
As positive frequency-dependent selection against the rare chiral morph in P.
suturalis also operates over a narrow range (< 3%), the results suggest a model
for chiral evolution in snails in which weak positive frequency-dependent selection
may be overcome by a negative frequency-dependent selection, such as reproductive
character displacement. In snails, there is not always a developmental constraint.
As the direction of cleavage, and thus the directional asymmetry of the entire
body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans,
sipunculids and nemerteans), it remains an open question as to whether this is
because of a constraint and/or because most taxa do not have a conspicuous external
asymmetry (like a shell) upon which selection can act.
acknowledgement: We owe a great debt to Jim Murray for his many contributions to the
study of Partula, in the field, in the laboratory, in the interpretation of data,
and in generating new ideas about evolution. With pleasure and respect we dedicate
this paper to him. Jim Murray played a leading role in making the collections used
here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with
collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift
of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund
Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis.
Comments from an anonymous referee, A. Richard Palmer and the editorial board improved
the manuscript. Work in the field was supported by the Royal Society, The Carnegie
Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research
Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society
and the University of Nottingham supported work in the laboratory.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Bryan
full_name: Clarke, Bryan
last_name: Clarke
citation:
ama: 'Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype
on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications
for the evolution of sinistral snails. Journal of Evolutionary Biology.
2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x'
apa: 'Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality
phenotype and genotype on the fecundity and viability of Partula suturalis and
Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal
of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x'
chicago: 'Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality
Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and
Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal
of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.'
ieee: 'A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype
and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails,” Journal of Evolutionary
Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.'
ista: 'Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and
genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails. Journal of Evolutionary Biology.
22(8), 1624–1635.'
mla: 'Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on
the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications
for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology,
vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.'
short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009)
1624–1635.
date_created: 2018-12-11T12:05:08Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1420-9101.2009.01770.x
file:
- access_level: open_access
checksum: f70c15c6ab9306121d4153a3be0d2346
content_type: application/pdf
creator: dernst
date_created: 2019-02-22T09:21:44Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6044'
file_name: Davison_JEB_v31_2009.pdf
file_size: 2583812
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 1624 - 1635
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley
publist_id: '2447'
pubrep_id: '553'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The effect of chirality phenotype and genotype on the fecundity and viability
of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral
snails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2009'
...
---
_id: '4136'
abstract:
- lang: eng
text: 'Populations living in a spatially and temporally changing environment can
adapt to the changing optimum and/or migrate toward favorable habitats. Here we
extend previous analyses with a static optimum to allow the environment to vary
in time as well as in space. The model follows both population dynamics and the
trait mean under stabilizing selection, and the outcomes can be understood by
comparing the loads due to genetic variance, dispersal, and temporal change. With
fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform
along the environmental gradient and that responds to the moving optimum as expected
for panmictic populations and when the spatial gradient is sufficiently steep,
and (2) a population with limited range that adapts more slowly than the environmental
optimum changes in both time and space; the population therefore becomes locally
extinct and migrates toward suitable habitat. We also use a population‐genetic
model with many loci to allow genetic variance to evolve, and we show that the
only solution now has uniform adaptation.'
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Glenn
full_name: Marion, Glenn
last_name: Marion
citation:
ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and
time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958'
apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation
in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958'
chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range:
Adaptation in Space and Time.” American Naturalist. University of Chicago
Press, 2009. https://doi.org/10.1086/605958.'
ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in
space and time,” American Naturalist, vol. 174, no. 5. University of Chicago
Press, pp. E186–E204, 2009.'
ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space
and time. American Naturalist. 174(5), E186–E204.'
mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American
Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204,
doi:10.1086/605958.'
short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.
date_created: 2018-12-11T12:07:09Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/605958
external_id:
pmid:
- ' 19788353'
intvolume: ' 174'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1086/605958
month: '11'
oa: 1
oa_version: Published Version
page: E186 - E204
pmid: 1
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1986'
pubrep_id: '552'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/659642
scopus_import: 1
status: public
title: 'Species'' range: Adaptation in space and time'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2009'
...
---
_id: '4242'
abstract:
- lang: eng
text: 'Felsenstein distinguished two ways by which selection can directly strengthen
isolation. First, a modifier that strengthens prezygotic isolation can be favored
everywhere. This fits with the traditional view of reinforcement as an adaptation
to reduce deleterious hybridization by strengthening assortative mating. Second,
selection can favor association between different incompatibilities, despite recombination.
We generalize this “two allele” model to follow associations among any number
of incompatibilities, which may include both assortment and hybrid inviability.
Our key argument is that this process, of coupling between incompatibilities,
may be quite different from the usual view of reinforcement: strong isolation
can evolve through the coupling of any kind of incompatibility, whether prezygotic
or postzygotic. Single locus incompatibilities become coupled because associations
between them increase the variance in compatibility, which in turn increases mean
fitness if there is positive epistasis. Multiple incompatibilities, each maintained
by epistasis, can become coupled in the same way. In contrast, a single-locus
incompatibility can become coupled with loci that reduce the viability of haploid
hybrids because this reduces harmful recombination. We obtain simple approximations
for the limits of tight linkage, and strong assortment, and show how assortment
alleles can invade through associations with other components of reproductive
isolation.'
acknowledgement: "This work was supported by a Royal Society/Wolfson Research Merit
award, and by a grant from the Natural Environment Research Council.\r\nWe are very
grateful for insightful comments from S. P. Otto, and for helpful suggestions from
the referees and the Associate Editor, Maria Servedio."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: De Cara, Maria
last_name: De Cara
citation:
ama: Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution;
International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x
apa: Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive
isolation. Evolution; International Journal of Organic Evolution. Wiley.
https://doi.org/10.1111/j.1558-5646.2009.00622.x
chicago: Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution. Wiley,
2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x.
ieee: N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,”
Evolution; International Journal of Organic Evolution, vol. 63, no. 5.
Wiley, pp. 1171–1190, 2009.
ista: Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation.
Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.
mla: Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution, vol.
63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x.
short: N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution
63 (2009) 1171–1190.
date_created: 2018-12-11T12:07:48Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:55:33Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2009.00622.x
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intvolume: ' 63'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 1171 - 1190
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley
publist_id: '1866'
pubrep_id: '551'
quality_controlled: '1'
scopus_import: 1
status: public
title: The evolution of strong reproductive isolation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2009'
...
---
_id: '3675'
abstract:
- lang: eng
text: "Sex and recombination have long been seen as adaptations that facilitate
natural selection by generating favorable variations. If recombination is to aid
selection, there must be negative linkage disequilibria—favorable alleles must
be found together less often than expected by chance. These negative linkage disequilibria
can be generated directly by selection, but this must involve negative epistasis
of just the right strength, which is not expected, from either experiment or theory.
Random drift provides a more general source of negative associations: Favorable
mutations almost always arise on different genomes, and negative associations
tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
can understand how recombination aids adaptation by determining the maximum possible
rate of adaptation. With unlinked loci, this rate increases only logarithmically
with the influx of favorable mutations. With a linear genome, a scaling argument
shows that in a large population, the rate of adaptive substitution depends only
on the expected rate in the absence of interference, divided by the total rate
of recombination. A two-locus approximation predicts an upper bound on the rate
of substitution, proportional to recombination rate.\r\n\r\nIf associations between
linked loci do impede adaptation, there can be substantial selection for modifiers
that increase recombination. Whether this can account for the maintenance of high
rates of sex and recombination depends on the extent of selection. It is clear
that the rate of species-wide substitutions is typically far too low to generate
appreciable selection for recombination. However, local sweeps within a subdivided
population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
(GR/ T11753/01)
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
doi:10.1101/sqb.2009.74.030'
apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor
Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030
chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor
Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory
Press, 2009. https://doi.org/10.1101/sqb.2009.74.030.
ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–195.
ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. vol. 74, 187–195.'
mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–95, doi:10.1101/sqb.2009.74.030.
short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
Spring Harbor Laboratory Press, 2009, pp. 187–195.
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
intvolume: ' 74'
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Why sex and recombination? '
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2009'
...
---
_id: '3775'
abstract:
- lang: eng
text: There is a close analogy between statistical thermodynamics and the evolution
of allele frequencies under mutation, selection and random drift. Wright's formula
for the stationary distribution of allele frequencies is analogous to the Boltzmann
distribution in statistical physics. Population size, 2N, plays the role of the
inverse temperature, 1/kT, and determines the magnitude of random fluctuations.
Log mean fitness, View the MathML source, tends to increase under selection, and
is analogous to a (negative) energy; a potential function, U, increases under
mutation in a similar way. An entropy, SH, can be defined which measures the deviation
from the distribution of allele frequencies expected under random drift alone;
the sum View the MathML source gives a free fitness that increases as the population
evolves towards its stationary distribution. Usually, we observe the distribution
of a few quantitative traits that depend on the frequencies of very many alleles.
The mean and variance of such traits are analogous to observable quantities in
statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures
the volume of allele frequency space that is consistent with the observed trait
distribution. The stationary distribution of the traits is View the MathML source;
this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are
distinct, but converge when there are so many alleles that traits fluctuate close
to their expectations. Populations tend to evolve towards states that can be realised
in many ways (i.e., large SΩ), which may lead to a substantial drop below the
adaptive peak; we illustrate this point with a simple model of genetic redundancy.
This analogy with statistical thermodynamics brings together previous ideas in
a general framework, and justifies a maximum entropy approximation to the dynamics
of quantitative traits.
acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by
grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates,
H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jason
full_name: Coe, Jason
last_name: Coe
citation:
ama: Barton NH, Coe J. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019
apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics
to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019
chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009.
https://doi.org/10.1016/j.jtbi.2009.03.019.
ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary
biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp.
317–324, 2009.
ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 259(2), 317–324.
mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no.
2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.
short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
date_created: 2018-12-11T12:05:06Z
date_published: 2009-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '21'
department:
- _id: NiBa
doi: 10.1016/j.jtbi.2009.03.019
intvolume: ' 259'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00554594/document
month: '07'
oa: 1
oa_version: Submitted Version
page: 317 - 324
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2452'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the application of statistical physics to evolutionary biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2009'
...
---
_id: '4231'
abstract:
- lang: eng
text: The evolution of quantitative characters depends on the frequencies of the
alleles involved, yet these frequencies cannot usually be measured. Previous groups
have proposed an approximation to the dynamics of quantitative traits, based on
an analogy with statistical mechanics. We present a modified version of that approach,
which makes the analogy more precise and applies quite generally to describe the
evolution of allele frequencies. We calculate explicitly how the macroscopic quantities
(i.e., quantities that depend on the quantitative trait) depend on evolutionary
forces, in a way that is independent of the microscopic details. We first show
that the stationary distribution of allele frequencies under drift, selection,
and mutation maximizes a certain measure of entropy, subject to constraints on
the expectation of observable quantities. We then approximate the dynamical changes
in these expectations, assuming that the distribution of allele frequencies always
maximizes entropy, conditional on the expected values. When applied to directional
selection on an additive trait, this gives a very good approximation to the evolution
of the trait mean and the genetic variance, when the number of mutations per generation
is sufficiently high (4Nμ > 1). We show how the method can be modified for
small mutation rates (4Nμ → 0). We outline how this method describes epistatic
interactions as, for example, with stabilizing selection.
acknowledgement: "N.B. was supported by the Engineering and Physical Sciences Research
Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to
Ellen Baake for helping to initiate this project and for her comments on this manuscript.
We also thank Michael Turelli for his comments on the manuscript and I. Pen for
discussions and support in this project. This project was a result of a collaboration
supported by the European Science Foundation grant “Integrating population genetics
and conservation biology.” "
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
citation:
ama: Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309
apa: Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution
of polygenic quantitative traits. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.108.099309
chicago: Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the
Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society
of America, 2009. https://doi.org/10.1534/genetics.108.099309.
ieee: N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of
polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society
of America, pp. 997–1011, 2009.
ista: Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 181(3), 997–1011.
mla: Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution
of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics
Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309.
short: N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.
date_created: 2018-12-11T12:07:44Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T07:55:29Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.108.099309
intvolume: ' 181'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 997 - 1011
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1882'
quality_controlled: '1'
scopus_import: 1
status: public
title: Statistical mechanics and the evolution of polygenic quantitative traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2009'
...
---
_id: '517'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: ' 89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...