Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin anc...

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Published inScience (American Association for the Advancement of Science) Vol. 352; no. 6282; pp. 235 - 239
Main Authors Vernot, Benjamin, Tucci, Serena, Kelso, Janet, Schraiber, Joshua G., Wolf, Aaron B., Gittelman, Rachel M., Dannemann, Michael, Grote, Steffi, McCoy, Rajiv C., Norton, Heather, Scheinfeldt, Laura B., Merriwether, David A., Koki, George, Friedlaender, Jonathan S., Wakefield, Jon, Pääbo, Svante, Akey, Joshua M.
Format Journal Article
LanguageEnglish
Published United States American Association for the Advancement of Science 08.04.2016
The American Association for the Advancement of Science
Subjects
Animals
Deoxyribonucleic acid
DNA
DNA - genetics
Genetic Variation
Genome, Human - genetics
Genomes
Hominids
Humans
Melanesia
Neanderthals - genetics
Pacific Island People - genetics
Sequence Analysis, DNA
Melanesia
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Abstract Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.
AbstractList Modern humans carry remnants of DNA from interbreeding events with archaic lineages, such as Neandertals. However, people from Oceania also retain genes from a second ancient lineage, the Denisovans. Vernot et al. surveyed archaic genomic sequences in a worldwide sample of modern humans, including 35 individuals from the Melanesian Islands. All non-African genomes surveyed contained Neandertal DNA, but a significant Denisovan component was found only in the Melanesians. Reconstruction of this genetic history suggests that Neandertals bred with modern humans multiple times, but Denosivans only once, in ancestors of modern-day Melanesians. Science , this issue p. 235 Neandertal and Denisovan DNA live on in modern day Melanesians. Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.
Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.
Modern humans carry remnants of DNA from interbreeding events with archaic lineages, such as Neandertals. However, people from Oceania also retain genes from a second ancient lineage, the Denisovans. Vernot et al. surveyed archaic genomic sequences in a worldwide sample of modern humans, including 35 individuals from the Melanesian Islands. All non-African genomes surveyed contained Neandertal DNA, but a significant Denisovan component was found only in the Melanesians. Reconstruction of this genetic history suggests that Neandertals bred with modern humans multiple times, but Denosivans only once, in ancestors of modern-day Melanesians. Science, this issue p. 235 Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.
Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.
Author Merriwether, David A.
Vernot, Benjamin
Schraiber, Joshua G.
Koki, George
Kelso, Janet
Norton, Heather
Wolf, Aaron B.
Tucci, Serena
Dannemann, Michael
Akey, Joshua M.
Wakefield, Jon
McCoy, Rajiv C.
Pääbo, Svante
Gittelman, Rachel M.
Friedlaender, Jonathan S.
Grote, Steffi
Scheinfeldt, Laura B.
AuthorAffiliation 1 Department of Genome Sciences, University of Washington, Seattle, Washington, USA
6 Department of Anthropology, Binghamton University, Binghamton, NY, USA
9 Department of Statistics, University of Washington, Seattle, Washington, USA
2 Department of Life Sciences and Biotechnology, University of Ferrara, Italy
5 Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
4 Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA
7 Institute for Medical Research, Goroka, Eastern Highlands Province, Papua New Guinea
3 Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
8 Department of Anthropology, Temple University, Philadelphia PA, USA
AuthorAffiliation_xml – name: 1 Department of Genome Sciences, University of Washington, Seattle, Washington, USA
– name: 4 Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA
– name: 7 Institute for Medical Research, Goroka, Eastern Highlands Province, Papua New Guinea
– name: 2 Department of Life Sciences and Biotechnology, University of Ferrara, Italy
– name: 5 Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
– name: 6 Department of Anthropology, Binghamton University, Binghamton, NY, USA
– name: 8 Department of Anthropology, Temple University, Philadelphia PA, USA
– name: 9 Department of Statistics, University of Washington, Seattle, Washington, USA
– name: 3 Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
Author_xml – sequence: 1
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  surname: Vernot
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– sequence: 2
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  fullname: Gittelman, Rachel M.
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  fullname: Dannemann, Michael
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  fullname: McCoy, Rajiv C.
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  fullname: Scheinfeldt, Laura B.
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– sequence: 17
  givenname: Joshua M.
  surname: Akey
  fullname: Akey, Joshua M.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/26989198$$D View this record in MEDLINE/PubMed
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Snippet Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors...
Modern humans carry remnants of DNA from interbreeding events with archaic lineages, such as Neandertals. However, people from Oceania also retain genes from a...
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SubjectTerms Animals
Deoxyribonucleic acid
DNA
DNA - genetics
Genetic Variation
Genome, Human - genetics
Genomes
Hominids
Humans
Melanesia
Neanderthals - genetics
Pacific Island People - genetics
Sequence Analysis, DNA
Title Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
URI https://www.jstor.org/stable/24744207
https://www.ncbi.nlm.nih.gov/pubmed/26989198
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