Analysis of human accelerated DNA regions using archaic hominin genomes

Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans....

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Published inPloS one Vol. 7; no. 3; p. e32877
Main Authors Burbano, Hernán A, Green, Richard E, Maricic, Tomislav, Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Kelso, Janet, Pollard, Katherine S, Lachmann, Michael, Pääbo, Svante
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 07.03.2012
Public Library of Science (PLoS)
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Summary:Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations.
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Conceived and designed the experiments: HAB REG SP. Performed the experiments: TM. Analyzed the data: HAB ML. Contributed reagents/materials/analysis tools: HAB REG TM CL-F MdlR AR JK KSP ML SP. Wrote the paper: HAB KSP SP.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0032877