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PMID: 22883142 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea.

American journal of human genetics ·Vol. 91 ·No. 2 ·2012-08-10 ·Pages 265-74

Mendez FL, Watkins JC, Hammer MF

Abstract

Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (~80 thousand years ago) and is found throughout Eurasia at an average frequency of ~5%. Interestingly, N is found in Melanesian populations at ~10-fold higher frequency (~54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2-all of which are part of the same 250 kb introgressive haplotype-as good candidates.

MeSH Terms
Adaptation, Biological/genetics Animals Base Sequence Evolution, Molecular Gene Components Genetics, Population Genotype Haplotypes/genetics Humans Linkage Disequilibrium Molecular Sequence Data Mutation/genetics Neanderthals/genetics Papua New Guinea Phylogeny Receptor, ErbB-3/genetics STAT2 Transcription Factor/genetics Selection, Genetic Sequence Analysis, DNA
Chemicals
STAT2 Transcription Factor STAT2 protein, human Receptor, ErbB-3
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Mendez Fernando L
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Watkins Joseph C
Hammer Michael F
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Article Info
Journal
American journal of human genetics
Abbr.
Am J Hum Genet
ISSN
1537-6605
DOI
10.1016/j.ajhg.2012.06.015
Published
2012-08-10
Pages
265-74
Language
English
Region
United States
NLM ID
0370475
PMCID
PMC3415544
Subset
IM
Databases
GENBANK
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External Links
PubMed source DOI: 10.1016/j.ajhg.2012.06.015 PMC Full Text View journal details
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