Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies

Molecular methods as applied to the biogeography of single species (phyloge ography) or multiple codistributed species (comparative phylogeography) hav e been productively and extensively used to elucidate common historical fea tures in the diversification of the Earth's biota. However, only recently h ave methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphi sm in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction be tween the gene divergence, the parameter that is typically recovered in mol ecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the ge ne divergence. Assuming that population sizes of ancestral species are dist ributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral spec ies can comprise from less than 10% to over 50% of the total divergence bet ween sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the num ber of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generall y smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Wh ereas the former variance can be reduced by further DNA sequencing at a sin gle locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal mo nophyly is in some ways more challenging than when allelic lines have not a chieved monophyly, because in the former case critical data on ancestral po pulation size provided by residual ancestral polymorphism is lost. In the f ormer case differences in coalescence time between species pairs can in pri nciple be explained entirely by differences in ancestral population size wi thout resorting to explanations involving differences in divergence time. F urthermore, the confidence limits on population divergence times are severe ly underestimated when those for number of substitutions per site in the DN A sequences examined are used as a proxy. This uncertainty highlights the i mportance of multilocus data in estimating population divergence times; mul tilocus data can in principle distinguish differences in coalescence time ( T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (theta) to T and t he effect of uncertainty in theta on estimates of population divergence (ta u) for single loci under reciprocal monophyly using a simple Bayesian exten sion of Takahata and Satta's and Yang's recent coalescent methods. The conf idence limits on tau decrease when the range over which ancestral populatio n size theta is assumed to be distributed decreases and when tau increases; they generally exclude zero when tau/(4N(e)) > 1. We also apply a maximum- likelihood method to several single and multilocus data sets. With multiloc us data, the criterion for excluding tau = 0 is roughly that l tau/(4N(e)) > 1, where l is the number of loci. Our analyses corroborate recent suggest ions that increasing the number of loci is critical to decreasing the uncer tainty in estimates of population divergence time.