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Evolutionary Genomics of Samoans

55 Pages Posted: 7 Feb 2019 Publication Status: Review Complete

See all articles by Daniel N. Harris

Daniel N. Harris

University of Maryland - Institute for Genome Sciences

Michael D. Kessler

University of Maryland - Institute for Genome Sciences

Amol C. Shetty

University of Maryland - Institute for Genome Sciences

Daniel E. Weeks

University of Pittsburgh - Department of Human Genetics

Ryan L. Minster

University of Pittsburgh - Department of Human Genetics

Sharon Browning

University of Washington - Department of Biostatistics

Ethan E. Cochrane

University of Auckland - Department of Anthropology

Ranjan Deka

University of Cincinnati - Department of Environmental Health

Nicola L. Hawley

Yale University - Department of Epidemiology (Chronic Disease)

Muagututi‘a Sefuiva Reupena

Independent

Take Naseri

Government of Samoa - Ministry of Health

Trans-Omics for Precision Medicine (TOPMed) Consortium

Independent

TOPMed Population Genetics Working Group

Independent

Stephen T. McGarvey

Brown University

Timothy D. O’Connor

University of Maryland - Institute for Genome Sciences

More...

Abstract

Archaeological studies estimate the initial settlement of Samoa at 2,750-2,880 years ago, and identified only limited human modification to the landscape and settlement until about 1,000-1,500 years ago. A complex history of migration follows Samoa’s initial peopling; first with populations sharing ancestry with Papuan-speaking groups and more recently with Europeans, Africans, and East Asians due to European colonialism. Using 1,197 Samoan high coverage whole genomes, we identify population splits between the major Samoan islands, and detect asymmetrical gene flow to the capital city. Approximately, 25% of Samoan genomes come from Papuan related ancestry, which we find as the likely source of the archaic Denisovan haplotypes in Samoans. We also find that Samoans had an extreme bottleneck until about 1,000 years ago, followed by distinct expansions between the islands, and subsequent bottlenecks consistent with European colonization. These results give insights to an ongoing archaeological debate about the peopling of Samoa.

Keywords: Genetically Understudied Populations, Oceania, Austronesian, Polynesian, Rare Variants, Fine-scale Population Structure

Suggested Citation

Harris, Daniel N. and Kessler, Michael D. and Shetty, Amol C. and Weeks, Daniel E. and Minster, Ryan L. and Browning, Sharon and Cochrane, Ethan E. and Deka, Ranjan and Hawley, Nicola L. and Reupena, Muagututi‘a Sefuiva and Naseri, Take and Consortium, Trans-Omics for Precision Medicine (TOPMed) and Group, TOPMed Population Genetics Working and McGarvey, Stephen T. and O’Connor, Timothy D., Evolutionary Genomics of Samoans (February 6, 2019). Available at SSRN: https://ssrn.com/abstract=3329885 or http://dx.doi.org/10.2139/ssrn.3329885
This version of the paper has not been formally peer reviewed.

Daniel N. Harris

University of Maryland - Institute for Genome Sciences

College Park
College Park, MD 20742
United States

Michael D. Kessler

University of Maryland - Institute for Genome Sciences

College Park
College Park, MD 20742
United States

Amol C. Shetty

University of Maryland - Institute for Genome Sciences

College Park
College Park, MD 20742
United States

Daniel E. Weeks

University of Pittsburgh - Department of Human Genetics

135 N Bellefield Ave
Pittsburgh, PA 15260
United States

Ryan L. Minster

University of Pittsburgh - Department of Human Genetics

135 N Bellefield Ave
Pittsburgh, PA 15260
United States

Sharon Browning

University of Washington - Department of Biostatistics

Seattle, WA 98195
United States

Ethan E. Cochrane

University of Auckland - Department of Anthropology

Auckland, 1142
New Zealand

Ranjan Deka

University of Cincinnati - Department of Environmental Health

United States

Nicola L. Hawley

Yale University - Department of Epidemiology (Chronic Disease)

New Haven, CT 06520
United States

Take Naseri

Government of Samoa - Ministry of Health

Apia
Samoa

Stephen T. McGarvey

Brown University ( email )

Box 1860
Providence, RI 02912
United States

Timothy D. O’Connor (Contact Author)

University of Maryland - Institute for Genome Sciences ( email )

College Park
College Park, MD 20742
United States

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