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Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R - Nature (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.

ABSTRACT
Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. 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. 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. 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. 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. 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.

Show MeSH
Speciation of the great apesa, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orangutan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orangutan. 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. b, Great ape speciation and divergence times. 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. Blue blocks represent hominid fossil species: each has a vertical extent spanning the range of dates estimated for it in the literature13,50, 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). The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a mid-Miocene speciation for orangutan. Lower panel: estimates of the average mutation rate in present-day humans10-12; grey bars show 95% confidence intervals, with black lines at the means.
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Figure 1: Speciation of the great apesa, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orangutan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orangutan. 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. b, Great ape speciation and divergence times. 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. Blue blocks represent hominid fossil species: each has a vertical extent spanning the range of dates estimated for it in the literature13,50, 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). The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a mid-Miocene speciation for orangutan. Lower panel: estimates of the average mutation rate in present-day humans10-12; grey bars show 95% confidence intervals, with black lines at the means.

Mentions: Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasised by Darwin and Huxley in the first evolutionary accounts of human origins1. Molecular studies confirmed that we are closer to the African apes than to orangutans, and on average closer to chimpanzees than gorillas2 (Fig. 1a). Subsequent analyses have explored functional differences between the great apes and their relevance to human evolution, assisted recently by reference genome sequences for chimpanzee3 and orangutan4. Here we provide a reference assembly and initial analysis of the gorilla genome sequence, establishing a foundation for the further study of great ape evolution and genetics.


Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R - Nature (2012)

Speciation of the great apesa, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orangutan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orangutan. 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. b, Great ape speciation and divergence times. 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. Blue blocks represent hominid fossil species: each has a vertical extent spanning the range of dates estimated for it in the literature13,50, 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). The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a mid-Miocene speciation for orangutan. Lower panel: estimates of the average mutation rate in present-day humans10-12; grey bars show 95% confidence intervals, with black lines at the means.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3303130&req=5

Figure 1: Speciation of the great apesa, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orangutan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orangutan. 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. b, Great ape speciation and divergence times. 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. Blue blocks represent hominid fossil species: each has a vertical extent spanning the range of dates estimated for it in the literature13,50, 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). The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a mid-Miocene speciation for orangutan. Lower panel: estimates of the average mutation rate in present-day humans10-12; grey bars show 95% confidence intervals, with black lines at the means.
Mentions: Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasised by Darwin and Huxley in the first evolutionary accounts of human origins1. Molecular studies confirmed that we are closer to the African apes than to orangutans, and on average closer to chimpanzees than gorillas2 (Fig. 1a). Subsequent analyses have explored functional differences between the great apes and their relevance to human evolution, assisted recently by reference genome sequences for chimpanzee3 and orangutan4. Here we provide a reference assembly and initial analysis of the gorilla genome sequence, establishing a foundation for the further study of great ape evolution and genetics.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.

ABSTRACT
Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. 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. 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. 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. 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. 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.

Show MeSH