Divergence Population Genetics of Chimpanzees

Abstract

The divergence of two subspecies of common chimpanzees (Pan troglodytes troglodytes and P. t. verus) and the bonobo (P. paniscus) was studied using a recently developed method for analyzing population divergence. Under the isolation with migration model, the posterior probability distributions of divergence time, migration rates, and effective population sizes were estimated for large multilocus DNA sequence data sets drawn from the literature. The bonobo and the common chimpanzee are estimated to have diverged approximately 0.86 to 0.89 MYA, and the divergence of the two common chimpanzee subspecies is estimated to have occurred 0.42 MYA. P. t. troglodytes appears to have had a larger effective population size (22,400 to 27,900) compared with P. paniscus, P. t. verus, and the ancestral populations of these species. No evidence of gene flow was found in the comparisons involving P. paniscus; however a clear signal of unidirectional gene flow was found from P. t. verus to P. t. troglodytes (2Nm = 0.51).

Extensive X-linked adaptive evolution in central chimpanzees

“…Using a much larger dataset, we confirm previous reports that central chimpanzees harbor two to three times more synonymous polymorphism than human populations and that the population has undergone expansion (18,33,34). We report here that purifying selection, as measured by the DFE (Fig.…”

High gene flow due to pelagic larval dispersal among South Pacific archipelagos in two amphidromous gastropods (Neritomorpha: Neritidae)

“…This value summarizes the effective number of migrants per generation that move between the populations after their time of splitting, but does not distinguish between constant migration and a few massive dispersal events. Therefore, because IM explicitly estimates genealogies with migration events between populations, we also used it to produce a histogram of the number of independent migration events inserted during each iteration of the Markov chain (Won and Hey, 2005). To get a heuristic estimate of the maximum amount of time since population divergence, we converted the divergence time, t, to years using a relatively slow divergence rate of 1% per million years (based on fossil-calibrated Molluscan rates, Marko, 2002).…”

Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin‐1 Receptor

“…For the Santa Ana and Makira populations, we used the ND2, Myo2, andTGFb2 sequence data in the program IM to simultaneously estimate six population genetic parameters, which were all scaled to the neutral mutation rate m: v melanic (population mutation rate of the melanic Santa Ana population), v chestnut (population mutation rate of the chestnut-bellied Makira population), v ancestral (population mutation rate of the ancestral population), t (time since divergence), (migration rate from the m melanicrchestnut melanic into the chestnut-bellied population), and (migration rate from the chestnut-bellied m chestnutrmelanic into the melanic population; Hey 2005). We performed initial IM runs with large, flat priors for each parameter (Won and Hey 2005). On the basis of the results of these preliminary runs, we defined narrower upper bounds for each prior that encompassed the entire posterior distribution for each parameter estimate (see table A4 and fig.…”