![]() See Supplementary Information for further details. Outside repeat masked regions and away from contig ends, the total rate of single-base and indel errors is 0.13 per kbp. An assessment of assembly quality using finished fosmid sequences found that typical (N50 see Table 1 for definition) stretches of error-free sequence are 7.2 kbp in length, with errors tending to be clustered in repetitive regions. Table 1 summarizes the assembly and annotation properties. Genes, transcripts and predictions of gene orthologues and paralogues were annotated by Ensembl 5, and additional analysis found evidence for 498 functional long (>200-bp) intergenic RNA transcripts. We generated a reference assembly from a single female western lowland gorilla ( Gorilla gorilla gorilla) named Kamilah, using 5.4 × 10 9 base pairs (5.4 Gbp) of capillary sequence combined with 166.8 Gbp of Illumina read pairs (Methods Summary). Recent technological developments have substantially reduced the costs of sequencing, but the assembly of a whole vertebrate genome remains a challenging computational problem. Estimates were made by the 1000 Genomes Project for trios of European (CEU) and Yoruban African (YRI) ancestry. Lower panel, estimates of the average mutation rate in present-day humans 11, 12, 13 grey bars show 95% confidence intervals, with black lines at the means. 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. 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 9, 50, and a horizontal position at the maximum mutation rate consistent both with its proposed phylogenetic position and the CoalHMM estimates (including some allowance for ancestral polymorphism in the case of Sivapithecus). Upper panel, solid lines show how times for the HC and HCG speciation events estimated by CoalHMM vary with average mutation rate dashed lines show the corresponding average sequence divergence times, as well as the HO sequence divergence. b, Great ape speciation and divergence times. Below are mean nucleotide divergences between human and the other great apes from the EPO alignment. 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). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orang-utan. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.Ī, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orang-utan (O). 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. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. 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. Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Nature volume 483, pages 169–175 ( 2012) Cite this article Insights into hominid evolution from the gorilla genome sequence ![]()
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