Detecting past changes of effective population size

• Published in: Evolutionary Applications
• Main Authors: Nikolic, Natacha, Chevalet, Claude
• Other Authors: Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse ENSAT, Laboratoire de Genetique Cellulaire at INRA (Toulouse)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2014
• Subjects: Atlantic salmon; effective population size; past demography; microsatellites; [SDV]Life Sciences [q-bio]; [INFO]Computer Science [cs]
• Online Access: https://hal.inrae.fr/hal-02641586; https://hal.inrae.fr/hal-02641586/document; https://hal.inrae.fr/hal-02641586/file/Nikolic_et_al-2014-Evolutionary_Applications_1.pdf; https://doi.org/10.1111/eva.12170

International audience 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.