Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations

Fernando L. Mendez, Joseph C Watkins, Michael F Hammer

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

Recent analysis of DNA extracted from two Eurasian forms of archaic human shows that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. Although these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We resequenced a 7-kb region encompassing the OAS1 gene in 88 individuals from six Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5′ region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 myr, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1,500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

Original languageEnglish (US)
Pages (from-to)1513-1520
Number of pages8
JournalMolecular Biology and Evolution
Volume29
Issue number6
DOIs
StatePublished - Jun 2012

Fingerprint

Haplotypes
genetic variation
Eurasia
haplotypes
gene
genome
Population
ancestry
Melanesia
introgression
common ancestry
Genome
Siberia
Genes
disequilibrium
loci
Indonesia
genes
Africa South of the Sahara
Linkage Disequilibrium

Keywords

  • Denisova
  • Human origins
  • Hybridization
  • Linkage disequilibrium
  • TMRCA

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. / Mendez, Fernando L.; Watkins, Joseph C; Hammer, Michael F.

In: Molecular Biology and Evolution, Vol. 29, No. 6, 06.2012, p. 1513-1520.

Research output: Contribution to journalArticle

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