---
_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: 2025-09-29T11:38:51Z
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.'
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T12:00:19Z
date_published: 2012-11-06T00:00:00Z
date_updated: 2025-09-29T13:28:52Z
day: '06'
department:
- _id: NiBa
doi: 10.1017/S1473550412000407
external_id:
isi:
- '000312526700008'
intvolume: ' 12'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2025-09-30T08:06:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
isi:
- '000310793900018'
pmid:
- '22960215'
intvolume: ' 192'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 192
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. "
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: 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: 2025-09-30T08:04:03Z
day: '01'
ddc:
- '570'
- '579'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05700.x
ec_funded: 1
external_id:
isi:
- '000308634300016'
file:
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checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:47Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5304'
file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf
file_size: 235820
relation: main_file
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checksum: f00afc5b887c8222014b57375b8caece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:48Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5305'
file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf
file_size: 41975
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file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 4605 - 4617
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3746'
pubrep_id: '296'
quality_controlled: '1'
related_material:
record:
- 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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: 2025-09-30T08:04:02Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.0G0FS
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.0g0fs
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2968'
relation: used_in_publication
status: public
status: public
title: 'Data from: A likelihood-based comparison of population histories in a parasitoid
guild'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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"
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:46:48Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2025-09-30T08:33:55Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/j.1752-4571.2012.00284.x
external_id:
isi:
- '000312808900013'
file:
- access_level: open_access
checksum: 233007138606aca5a2f75f7ae1742f43
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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
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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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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: 2025-09-29T13:25:35Z
day: '14'
department:
- _id: NiBa
doi: 10.5061/dryad.274b1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.274b1
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2944'
relation: used_in_publication
status: public
status: public
title: 'Data from: Approximate Bayesian computation for modular inference problems
with many parameters: the example of migration rates'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '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. '
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: 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.
corr_author: '1'
date_created: 2018-12-11T12:01:31Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2025-09-30T07:58:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05643.x
external_id:
isi:
- '000306478800002'
intvolume: ' 21'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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).
corr_author: '1'
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-07T00:00:00Z
date_updated: 2025-09-30T07:56:48Z
day: '07'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1002740
ec_funded: 1
external_id:
isi:
- '000305961000014'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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'
article_processing_charge: No
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).
corr_author: '1'
date_created: 2018-12-11T12:01:46Z
date_published: 2012-02-10T00:00:00Z
date_updated: 2025-09-30T07:51:20Z
day: '10'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1186/1745-6150-7-6
ec_funded: 1
external_id:
isi:
- '000305269300001'
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'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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.
corr_author: '1'
date_created: 2018-12-11T12:02:25Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2024-10-09T20:54:39Z
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: '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: 2025-09-30T08:42:31Z
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: '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.'
article_processing_charge: No
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: 2025-09-30T09:21:06Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
external_id:
isi:
- '000297020800022'
intvolume: ' 189'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 189
year: '2011'
...
---
_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.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Abbot, Patrick
last_name: Abbot
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: John
full_name: Alcock, John
last_name: Alcock
- first_name: Samuel
full_name: Alizon, Samuel
last_name: Alizon
- first_name: Joao
full_name: Alpedrinha, Joao
last_name: Alpedrinha
- first_name: Malte
full_name: Andersson, Malte
last_name: Andersson
- first_name: Jean
full_name: Andre, Jean
last_name: Andre
- first_name: Minus
full_name: Van Baalen, Minus
last_name: Van Baalen
- first_name: Francois
full_name: Balloux, Francois
last_name: Balloux
- first_name: Sigal
full_name: Balshine, Sigal
last_name: Balshine
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Leo
full_name: Beukeboom, Leo
last_name: Beukeboom
- first_name: Jay
full_name: Biernaskie, Jay
last_name: Biernaskie
- first_name: Trine
full_name: Bilde, Trine
last_name: Bilde
- first_name: Gerald
full_name: Borgia, Gerald
last_name: Borgia
- first_name: Michael
full_name: Breed, Michael
last_name: Breed
- first_name: Sam
full_name: Brown, Sam
last_name: Brown
- first_name: Redouan
full_name: Bshary, Redouan
last_name: Bshary
- first_name: Angus
full_name: Buckling, Angus
last_name: Buckling
- first_name: Nancy
full_name: Burley, Nancy
last_name: Burley
- first_name: Max
full_name: Burton Chellew, Max
last_name: Burton Chellew
- first_name: Michael
full_name: Cant, Michael
last_name: Cant
- first_name: Michel
full_name: Chapuisat, Michel
last_name: Chapuisat
- first_name: Eric
full_name: Charnov, Eric
last_name: Charnov
- first_name: Tim
full_name: Clutton Brock, Tim
last_name: Clutton Brock
- first_name: Andrew
full_name: Cockburn, Andrew
last_name: Cockburn
- first_name: Blaine
full_name: Cole, Blaine
last_name: Cole
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Leda
full_name: Cosmides, Leda
last_name: Cosmides
- first_name: Iain
full_name: Couzin, Iain
last_name: Couzin
- first_name: Jerry
full_name: Coyne, Jerry
last_name: Coyne
- first_name: Scott
full_name: Creel, Scott
last_name: Creel
- first_name: Bernard
full_name: Crespi, Bernard
last_name: Crespi
- first_name: Robert
full_name: Curry, Robert
last_name: Curry
- first_name: Sasha
full_name: Dall, Sasha
last_name: Dall
- first_name: Troy
full_name: Day, Troy
last_name: Day
- first_name: Janis
full_name: Dickinson, Janis
last_name: Dickinson
- first_name: Lee
full_name: Dugatkin, Lee
last_name: Dugatkin
- first_name: Claire
full_name: El Mouden, Claire
last_name: El Mouden
- first_name: Stephen
full_name: Emlen, Stephen
last_name: Emlen
- first_name: Jay
full_name: Evans, Jay
last_name: Evans
- first_name: Regis
full_name: Ferriere, Regis
last_name: Ferriere
- first_name: Jeremy
full_name: Field, Jeremy
last_name: Field
- first_name: Susanne
full_name: Foitzik, Susanne
last_name: Foitzik
- first_name: Kevin
full_name: Foster, Kevin
last_name: Foster
- first_name: William
full_name: Foster, William
last_name: Foster
- first_name: Charles
full_name: Fox, Charles
last_name: Fox
- first_name: Juergen
full_name: Gadau, Juergen
last_name: Gadau
- first_name: Sylvain
full_name: Gandon, Sylvain
last_name: Gandon
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Michael
full_name: Gardner, Michael
last_name: Gardner
- first_name: Thomas
full_name: Getty, Thomas
last_name: Getty
- first_name: Michael
full_name: Goodisman, Michael
last_name: Goodisman
- first_name: Alan
full_name: Grafen, Alan
last_name: Grafen
- first_name: Rick
full_name: Grosberg, Rick
last_name: Grosberg
- first_name: Christina
full_name: Grozinger, Christina
last_name: Grozinger
- first_name: Pierre
full_name: Gouyon, Pierre
last_name: Gouyon
- first_name: Darryl
full_name: Gwynne, Darryl
last_name: Gwynne
- first_name: Paul
full_name: Harvey, Paul
last_name: Harvey
- first_name: Ben
full_name: Hatchwell, Ben
last_name: Hatchwell
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Heikki
full_name: Helantera, Heikki
last_name: Helantera
- first_name: Ken
full_name: Helms, Ken
last_name: Helms
- first_name: Kim
full_name: Hill, Kim
last_name: Hill
- first_name: Natalie
full_name: Jiricny, Natalie
last_name: Jiricny
- first_name: Rufus
full_name: Johnstone, Rufus
last_name: Johnstone
- first_name: Alex
full_name: Kacelnik, Alex
last_name: Kacelnik
- first_name: E Toby
full_name: Kiers, E Toby
last_name: Kiers
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Jan
full_name: Komdeur, Jan
last_name: Komdeur
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Daniel
full_name: Kronauer, Daniel
last_name: Kronauer
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
- first_name: Laurent
full_name: Lehmann, Laurent
last_name: Lehmann
- first_name: Timothy
full_name: Linksvayer, Timothy
last_name: Linksvayer
- first_name: Sébastien
full_name: Lion, Sébastien
last_name: Lion
- first_name: Bruce
full_name: Lyon, Bruce
last_name: Lyon
- first_name: James
full_name: Marshall, James
last_name: Marshall
- first_name: Richard
full_name: Mcelreath, Richard
last_name: Mcelreath
- first_name: Yannis
full_name: Michalakis, Yannis
last_name: Michalakis
- first_name: Richard
full_name: Michod, Richard
last_name: Michod
- first_name: Douglas
full_name: Mock, Douglas
last_name: Mock
- first_name: Thibaud
full_name: Monnin, Thibaud
last_name: Monnin
- first_name: Robert
full_name: Montgomerie, Robert
last_name: Montgomerie
- first_name: Allen
full_name: Moore, Allen
last_name: Moore
- first_name: Ulrich
full_name: Mueller, Ulrich
last_name: Mueller
- first_name: Ronald
full_name: Noë, Ronald
last_name: Noë
- first_name: Samir
full_name: Okasha, Samir
last_name: Okasha
- first_name: Pekka
full_name: Pamilo, Pekka
last_name: Pamilo
- first_name: Geoff
full_name: Parker, Geoff
last_name: Parker
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
- first_name: Ido
full_name: Pen, Ido
last_name: Pen
- first_name: David
full_name: Pfennig, David
last_name: Pfennig
- first_name: David
full_name: Queller, David
last_name: Queller
- first_name: Daniel
full_name: Rankin, Daniel
last_name: Rankin
- first_name: Sarah
full_name: Reece, Sarah
last_name: Reece
- first_name: Hudson
full_name: Reeve, Hudson
last_name: Reeve
- first_name: Max
full_name: Reuter, Max
last_name: Reuter
- first_name: Gilbert
full_name: Roberts, Gilbert
last_name: Roberts
- first_name: Simon
full_name: Robson, Simon
last_name: Robson
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Francois
full_name: Rousset, Francois
last_name: Rousset
- first_name: Olav
full_name: Rueppell, Olav
last_name: Rueppell
- first_name: Joel
full_name: Sachs, Joel
last_name: Sachs
- first_name: Lorenzo
full_name: Santorelli, Lorenzo
last_name: Santorelli
- first_name: Paul
full_name: Schmid Hempel, Paul
last_name: Schmid Hempel
- first_name: Michael
full_name: Schwarz, Michael
last_name: Schwarz
- first_name: Tom
full_name: Scott Phillips, Tom
last_name: Scott Phillips
- first_name: Janet
full_name: Shellmann Sherman, Janet
last_name: Shellmann Sherman
- first_name: Paul
full_name: Sherman, Paul
last_name: Sherman
- first_name: David
full_name: Shuker, David
last_name: Shuker
- first_name: Jeff
full_name: Smith, Jeff
last_name: Smith
- first_name: Joseph
full_name: Spagna, Joseph
last_name: Spagna
- first_name: Beverly
full_name: Strassmann, Beverly
last_name: Strassmann
- first_name: Andrew
full_name: Suarez, Andrew
last_name: Suarez
- first_name: Liselotte
full_name: Sundström, Liselotte
last_name: Sundström
- first_name: Michael
full_name: Taborsky, Michael
last_name: Taborsky
- first_name: Peter
full_name: Taylor, Peter
last_name: Taylor
- first_name: Graham
full_name: Thompson, Graham
last_name: Thompson
- first_name: John
full_name: Tooby, John
last_name: Tooby
- first_name: Neil
full_name: Tsutsui, Neil
last_name: Tsutsui
- first_name: Kazuki
full_name: Tsuji, Kazuki
last_name: Tsuji
- first_name: Stefano
full_name: Turillazzi, Stefano
last_name: Turillazzi
- first_name: Francisco
full_name: Úbeda, Francisco
last_name: Úbeda
- first_name: Edward
full_name: Vargo, Edward
last_name: Vargo
- first_name: Bernard
full_name: Voelkl, Bernard
last_name: Voelkl
- first_name: Tom
full_name: Wenseleers, Tom
last_name: Wenseleers
- first_name: Stuart
full_name: West, Stuart
last_name: West
- first_name: Mary
full_name: West Eberhard, Mary
last_name: West Eberhard
- first_name: David
full_name: Westneat, David
last_name: Westneat
- first_name: Diane
full_name: Wiernasz, Diane
last_name: Wiernasz
- first_name: Geoff
full_name: Wild, Geoff
last_name: Wild
- first_name: Richard
full_name: Wrangham, Richard
last_name: Wrangham
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
- first_name: David
full_name: Zeh, David
last_name: Zeh
- first_name: Jeanne
full_name: Zeh, Jeanne
last_name: Zeh
- first_name: Andrew
full_name: Zink, Andrew
last_name: Zink
citation:
ama: Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality.
Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831
apa: Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M.,
… Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature09831
chicago: Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte
Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature.
Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831.
ieee: P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature,
vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.
ista: Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339),
E1–E4.
mla: Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature,
vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831.
short: P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre,
M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie,
T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M.
Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn,
B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi,
R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen,
J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J.
Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R.
Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze,
H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers,
H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer,
S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock,
T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo,
G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H.
Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J.
Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann
Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez,
L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji,
S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West
Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J.
Zeh, A. Zink, Nature 471 (2011) E1–E4.
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-23T00:00:00Z
date_updated: 2025-09-30T08:58:00Z
day: '23'
department:
- _id: NiBa
doi: 10.1038/nature09831
external_id:
isi:
- '000288702200001'
pmid:
- '21430721'
intvolume: ' 471'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 471
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.
corr_author: '1'
date_created: 2018-12-11T12:02:58Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2025-09-30T08:55:17Z
day: '01'
department:
- _id: NiBa
doi: 10.1098/rsif.2010.0438
ec_funded: 1
external_id:
isi:
- '000289671700011'
pmid:
- '21084341'
intvolume: ' 8'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
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: 2026-06-18T18:45:27Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1017/S0016672311000115
external_id:
isi:
- '000291114300005'
intvolume: ' 93'
isi: 1
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: '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.'
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
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.
corr_author: '1'
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2025-09-30T08:44:55Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.127555
ec_funded: 1
external_id:
isi:
- '000293700000018'
intvolume: ' 188'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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'
article_processing_charge: No
arxiv: 1
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.
corr_author: '1'
date_created: 2018-12-11T12:03:04Z
date_published: 2011-08-01T00:00:00Z
date_updated: 2025-09-30T08:44:25Z
day: '01'
department:
- _id: NiBa
doi: 10.1016/j.tree.2011.04.002
ec_funded: 1
external_id:
arxiv:
- '1104.2854'
isi:
- '000293940800010'
intvolume: ' 26'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
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.'
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T12:03:05Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2025-09-30T08:42:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129817
ec_funded: 1
external_id:
isi:
- '000294721600018'
intvolume: ' 189'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 189
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.
corr_author: '1'
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2025-09-30T08:42:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
external_id:
isi:
- '000294902700013'
intvolume: ' 104'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 104
year: '2011'
...