A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances

Citation
Oe. Gaggiotti et L. Excoffier, A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances, P ROY SOC B, 267(1438), 2000, pp. 81-87
Citations number
43
Categorie Soggetti
Experimental Biology
Journal title
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES
ISSN journal
09628452 → ACNP
Volume
267
Issue
1438
Year of publication
2000
Pages
81 - 87
Database
ISI
SICI code
0962-8452(20000107)267:1438<81:ASMORT>2.0.ZU;2-4
Abstract
In this paper, we derive the expectation of two popular genetic distances u nder a model of pure population fission allowing for unequal population siz es. Under the model, we show that conventional genetic distances are not Pr oportional to the divergence time and generally overestimate it due to uneq ual genetic drift and to a bottleneck effect at the divergence time. This b ias cannot be totally removed even if the present population sizes are know n. Instead, we present a method to estimate the divergence times between po pulations which is based on the average number of nucleotide differences wi thin and between populations. The method simultaneously estimates the diver gence time, the ancestral population size and the relative sizes of the der ived populations. A simulation study revealed that this method is essential ly unbiased and that it leads to better estimates than traditional approach es for a very wide range of parameter values. Simulations also indicated th at moderate population growth after divergence has little effect on the est imates of all three estimated parameters. An application of our method to a comparison of humans and chimpanzee mitochondrial DNA diversity revealed t hat common chimpanzees have a significantly larger female population size t han humans.