A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

Abstract

We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

Speciation with gene flow in equids despite extensive chromosomal plasticity

“…We next used the coalescent hidden Markov model approach HMMCoal (30) to detect gene flow during the first divergence within Equus (SI Appendix, section 10.1). Our analysis suggests that noncaballine equids did not emerge after a founder event into the Old World, but rather maintained gene flow in North America with caballine equids.…”

“…The hidden Markov coalescent framework CoalHMM (30) was used to estimate the mode (allopatry or with gene flow) and times of the pairwise equine population splits. The demography parameters were estimated in 10-Mb nonoverlapping windows, and the Akaike information criterion (47) was used to determine the mode of the split.…”

Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes

“…The speciation of great apes is very dependent on geographical history and has been modeled recently [75]. For rodents we find an average of 17.3 non-synonymous substitutions since divergence from the common ancestor of primates and rodents ~75 million years ago, i.e.…”

Análise da estrutura populacional e do desequilíbrio de ligação de um painel de acessos de sorgo: uma abordagem usando teoria da coalescência

“…Palczewski and Beerli (2013) desenvolveram método aproximado para estimação de altas taxas de fluxo gênico em situações em que populações trocaram muitos alelos entre si. Além disso, taxas de fluxo gênico têm sido investigadas em modelos que consideram, pelo menos em princípio, outros processos, tais como recombinação (Becquet and Przeworski, 2007;Lohse et al, 2011;Mailund et al, 2012) e seleção .…”

“…Acredita-se que tal abordagem poderá ser desenvolvida em breve no contexto de coalescência, já que estudos recentes têm sido propostos para modelar processos conjuntamente (Lohse et al, 2011;Mailund et al, 2012).…”