Detecting past changes of effective population size
Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires...
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ftarchimer:oai:archimer.ifremer.fr:30565 2023-05-15T15:31:24+02:00 Detecting past changes of effective population size Nikolic, Natacha Chevalet, Claude 2014-06 application/pdf https://archimer.ifremer.fr/doc/00194/30565/28986.pdf https://archimer.ifremer.fr/doc/00194/30565/29469.pdf https://doi.org/10.1111/eva.12170 https://archimer.ifremer.fr/doc/00194/30565/ eng eng Wiley-blackwell https://archimer.ifremer.fr/doc/00194/30565/28986.pdf https://archimer.ifremer.fr/doc/00194/30565/29469.pdf doi:10.1111/eva.12170 https://archimer.ifremer.fr/doc/00194/30565/ 2014 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. info:eu-repo/semantics/openAccess restricted use CC-BY Evolutionary Applications (1752-4571) (Wiley-blackwell), 2014-06 , Vol. 7 , N. 6 , P. 663-681 Atlantic salmon effective population size microsatellites past demography text Publication info:eu-repo/semantics/article 2014 ftarchimer https://doi.org/10.1111/eva.12170 2021-09-23T20:24:34Z Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff. Article in Journal/Newspaper Atlantic salmon Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Evolutionary Applications 7 6 663 681 |
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Open Polar |
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Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
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ftarchimer |
language |
English |
topic |
Atlantic salmon effective population size microsatellites past demography |
spellingShingle |
Atlantic salmon effective population size microsatellites past demography Nikolic, Natacha Chevalet, Claude Detecting past changes of effective population size |
topic_facet |
Atlantic salmon effective population size microsatellites past demography |
description |
Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff. |
format |
Article in Journal/Newspaper |
author |
Nikolic, Natacha Chevalet, Claude |
author_facet |
Nikolic, Natacha Chevalet, Claude |
author_sort |
Nikolic, Natacha |
title |
Detecting past changes of effective population size |
title_short |
Detecting past changes of effective population size |
title_full |
Detecting past changes of effective population size |
title_fullStr |
Detecting past changes of effective population size |
title_full_unstemmed |
Detecting past changes of effective population size |
title_sort |
detecting past changes of effective population size |
publisher |
Wiley-blackwell |
publishDate |
2014 |
url |
https://archimer.ifremer.fr/doc/00194/30565/28986.pdf https://archimer.ifremer.fr/doc/00194/30565/29469.pdf https://doi.org/10.1111/eva.12170 https://archimer.ifremer.fr/doc/00194/30565/ |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Evolutionary Applications (1752-4571) (Wiley-blackwell), 2014-06 , Vol. 7 , N. 6 , P. 663-681 |
op_relation |
https://archimer.ifremer.fr/doc/00194/30565/28986.pdf https://archimer.ifremer.fr/doc/00194/30565/29469.pdf doi:10.1111/eva.12170 https://archimer.ifremer.fr/doc/00194/30565/ |
op_rights |
2014 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. info:eu-repo/semantics/openAccess restricted use |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1111/eva.12170 |
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Evolutionary Applications |
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7 |
container_issue |
6 |
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663 |
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