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Simulations (details in Supplementary Information) suggest that an ancestral population bottleneck would have had limited impact on the inference of T, its influence being captured largely by changes in the model’s effective population size.
Under conditions of genetic exchange between populations after the main separation of the chimpanzee and human lineages, the speciation time estimated by Coal HMM represents an average weighted by gene flow over the period of separation.
We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species.
The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.
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Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution.
Gorillas survive today only within several isolated and endangered populations whose evolutionary relationships are uncertain.
In addition to Kamilah, our analysis included two western lowland gorillas, Kwanza (male) and EB(JC) (female), and one eastern lowland gorilla, Mukisi (male). Filtering out low-quality regions of the chimpanzee assembly and regions with many alignment gaps, we obtained 2.01 Gbp of 1:1:1:1 great ape orthologous alignment blocks, to which we then applied a coalescent inference model, Coal HMM, to estimate the timescales and population sizes involved in the speciation of the hominines (African great apes; see Supplementary Table 1.1 for terminology), with orang-utan as an outgroup .
The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a middle Miocene speciation for orang-utan.Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasized by Darwin and Huxley in the first evolutionary accounts of human originsa, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orang-utan (O).Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orang-utan.Interior grey lines illustrate an example of incomplete lineage sorting at a particular genetic locus—in this case (((C, G), H), O) rather than (((H, C), G), O).Below are mean nucleotide divergences between human and the other great apes from the EPO alignment. Upper panel, solid lines show how times for the HC and HCG speciation events estimated by Coal HMM vary with average mutation rate; dashed lines show the corresponding average sequence divergence times, as well as the HO sequence divergence.