Biased estimation of divergence time and population sizes in case of admixture.

<p>(A) Model of population divergence and admixture: one of two populations having diverged <i>T_Div</i> generations ago has received a fraction <i>a</i> of its genes from another unsampled population that diverged 14,000 generations ago (350,000 y assuming a generation time of 25 y). All populations sizes are assumed to consist of <i>N</i> = 20,000 haploids. (B) Estimated divergence time as a function of initial admixture rate <i>a</i>. (C) Estimated admixed population size for different divergence times and admixture rates. Simulated data consisted of 400,000 segments of 50 bp, thus totalling a 20-Mb DNA sequence. Parameters are estimated by maximizing the probability of the observed joint site frequency spectrum (SFS) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002837#pgen.1002837-Adams1" target="_blank">[68]</a>, where the expected SFS is estimated by simulation following the approach of Nielsen et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002837#pgen.1002837-Nielsen1" target="_blank">[69]</a>.