Coalescence in a metapopulation with recurrent local extinction and recolonization

Abstract Many species exist as metapopulations in balance between local population extinction and recolonization. The effect of these processes on average population differentiation, within-deme diversity, and specieswide diversity has been considered previously. In this paper, coalescent simulations of Slatkin's propagule-pool and migrant-pool models are used to characterize the distribution of neutral genetic diversity within demes (π_s), diversity in the metapopulation a whole (TT_T), the ratio F _ST= (π_t–π_S)/π_T, Tajima's D statistic, and several ratios of gene-tree branch lengths. Using these distributions, power to detect differences in key metapopulation parameter values is determined under contrasting sampling regimes. The results indicate that it will be difficult to use sequence data from a single locus to detect a history of extinctions and recolonizations in a metapopulation because of high genealogical variance, the loss of diversity due to reductions in effective population size, and the fact that a genealogy of lineages from different demes under Slatkin's model differs from a neutral coalescent only in its time scale. Genetic indices of gene-tree shape that capture the effects of extinction/recolonization on both external branches and the length of the genealogy as a whole will provide the best indication of metapopulation dynamics if several lineages are sampled from several different demes.