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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.Second, as with any model, Coal HMM makes several simplifying assumptions whose consequences we need to understand in the context of realistic demography. Using a rate of 10 mutations per bp per year, derived from fossil calibration of the human–macaque sequence divergence and as used in previous calculations, Coal HMM’s results would correspond to speciation time estimates T—to be hominins, and therefore to postdate the human–chimpanzee split (Fig. Indeed, the relationship between molecular and fossil evidence has remained difficult to resolve despite the accumulation of genetic data, potentially in better agreement with the fossil record.However, this timetable for hominine speciation must also be reconciled with older events, such as the speciation of orang-utan, which is thought to have occurred no earlier than the Middle Miocene (12–16 Myr ago), as fossil apes before that differ substantially from what we might expect of an early great ape in the common ancestor of great apes, decreasing to lower values in all extant species (Fig. Comparable changes in mutation rate have been observed previously in primate evolution on larger timescales, including an approximately 30% branch length decrease in humans compared to baboons since their common ancestor.Two issues need to be addressed in interpreting the results from Coal HMM (Supplementary Table 4.2).First, the results themselves are obtained in units of sequence divergence rather than years, and so need to be scaled by an appropriate yearly mutation rate.
Outside repeat masked regions and away from contig ends, the total rate of single-base and indel errors is 0.13 per kbp. We also collected less extensive sequence data for three other gorillas, to enable a comparison of species within the Gorilla genus.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).However we note that Sahelanthropus and Chororapithecus remain difficult to incorporate in this model, and can be accommodated as hominin and gorillin genera only if most of the decrease occurred early in great ape evolution.An alternative explanation for the apparent discrepancy in fossil and genetic dates (leaving aside the issue of whether fossil taxa have been correctly placed) is that ancestral demography may have affected the genetic inferences.
Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera.