PLoS Genet 8(12): e1003125. doi:10.1371/journal.pgen.1003125
A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species
Thomas Mailund et al.
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.
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"the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently".
ReplyDeleteThat doesn't really make sense unless 'recently' means some 10 million years. As far as I'm aware the gorilla and orang-utan have been geographically separated for at least that long.
"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".
Other researchers have also claimed that to be so, and it makes sense. The two species must have been in periodic contact for some time after an 'original' separation. The bonobo/chimp split is most likely a single split as the bonobo ancestors were able to cross the Congo River at some stage, never the two to meet again.