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Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure
Author(s) -
PETER BENJAMIN M.,
WEGMANN DANIEL,
EXCOFFIER LAURENT
Publication year - 2010
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/j.1365-294x.2010.04783.x
Subject(s) - panmixia , biology , population , bottleneck , approximate bayesian computation , population model , population bottleneck , range (aeronautics) , evolutionary biology , bayesian probability , population size , sample (material) , subdivision , econometrics , statistics , genetic diversity , genetic structure , computer science , mathematics , genetics , demography , geography , microsatellite , allele , materials science , chemistry , archaeology , sociology , composite material , embedded system , chromatography , gene
Although most natural populations are genetically subdivided, they are often analysed as if they were panmictic units. In particular, signals of past demographic size changes are often inferred from genetic data by assuming that the analysed sample is drawn from a population without any internal subdivision. However, it has been shown that a bottleneck signal can result from the presence of some recent immigrants in a population. It thus appears important to contrast these two alternative scenarios in a model choice procedure to prevent wrong conclusions to be made. We use here an Approximate Bayesian Computation (ABC) approach to infer whether observed patterns of genetic diversity in a given sample are more compatible with it being drawn from a panmictic population having gone through some size change, or from one or several demes belonging to a recent finite island model. Simulations show that we can correctly identify samples drawn from a subdivided population in up to 95% of the cases for a wide range of parameters. We apply our model choice procedure to the case of the chimpanzee ( Pan troglodytes ) and find conclusive evidence that Western and Eastern chimpanzee samples are drawn from a spatially subdivided population.