Bayesian analyses using the higher evolutionary rate of 11 17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum.
By reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa.
Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var.
However, species-wide samples are not suitable for investigating population processes of divergence, demographic change, and local adaptation.
Selection and population demographic changes drive divergence of populations during isolation.
A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees.
We next used a program (IMa2) based on the isolation-with-migration model [ 49- 51, 63] to estimate multiple demographic parameters (including divergence time, migration rate and effective population sizes of derived populations and their ancestral populations) using MCMC simulation.
The IM model uses a Markov chain Monte Carlo (MCMC) method to estimate the posterior probability densities of six demographic parameters: the divergence time (t), bidirectional migration rates (m1 and m2), and the effective population sizes of the ancestral (θA) and descendent populations (θ1 and θ2).
The networks, single demographic expansion patterns, and divergence estimates based on nuclear and mitochondrial DNA are consistent with intermediate divergence and postglacial isolation.
This approach has the advantage of explicitly incorporating divergence and demographic processes, which can otherwise confound assessment of selection.
