Bayesian inference of population expansions in domestic bovines

Abstract

The past population dynamics of four domestic and one wild species of bovine were estimated using Bayesian skyline plots, a coalescent Markov chain Monte Carlo method that does not require an assumed parametric model of demographic history. Four domestic species share a recent rapid population expansion not visible in the wild African buffalo (Syncerus caffer). The estimated timings of the expansions are consistent with the archaeological records of domestication.

Figure 1

Neighbour-joining trees drawn using (a) 110 water buffalo, (b) 24 mithan, (c) 71 yak; (d) 84 cattle and (e) 195 African buffalo sequences. The scale bar indicates units of genetic distance. The cattle and water buffalo phylogenies show phylogenetically distinct clusters indicative of population expansions. The phylogenies of the yak, mithan and African buffalo samples are more complex and difficult to interpret.

Figure 2

A comparison of (a) the median values and (b) 95% HPDs of the posterior distribution of N_e estimates for four domesticated and one wild bovine species. Note that only the HPDs should be considered for robust inference of change in population size. Time is plotted linearly; N_e is presented on a logarithmic scale. The HPDs of the domestic species show rapid recent population expansions since the time of domestication, while the African buffalo show a gradual population expansion followed by a decline.