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
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.