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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.
Two issues need to be addressed in interpreting the results from Coal HMM (Supplementary Table 4.2).
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Lower panel, estimates of the average mutation rate in present-day humans Recent technological developments have substantially reduced the costs of sequencing, but the assembly of a whole vertebrate genome remains a challenging computational problem.
We generated a reference assembly from a single female western lowland gorilla (Gorilla gorilla gorilla) named Kamilah, using 5.4 × 10 base pairs (5.4 Gbp) of capillary sequence combined with 166.8 Gbp of Illumina read pairs (Methods Summary).
A decrease within the great apes is also a predicted consequence of the observed increase in body sizes over this time period and the association of small size with shorter generation times in other primates, and is consistent with deviations from a molecular clock seen in sequence divergences of the great apes and macaque (Supplementary Table 3.3).
We discuss these and other constraints on estimates of great ape speciation times in the Supplementary Information.Blue blocks represent hominid fossil species (key at top right): each has a vertical extent spanning the range of dates estimated for it in the literature, and a horizontal position at the maximum mutation rate consistent both with its proposed phylogenetic position and the Coal HMM estimates (including some allowance for ancestral polymorphism in the case of Sivapithecus).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.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.To the extent that this is plausible, for example as part of a non-allopatric speciation process, it constitutes an alternative explanation for the dating discrepancy without requiring a change in mutation rate.