Recent human effective population size estimated from linkage disequilibrium

Tenesa, Albert, Navarro, Pau, Hayes, Ben J., Duffy, David L., Clarke, Geraldine M., Goddard, Mike E. and Visscher, Peter M. (2007) Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17 4: 520-526. doi:10.1101/gr.6023607

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Author Tenesa, Albert
Navarro, Pau
Hayes, Ben J.
Duffy, David L.
Clarke, Geraldine M.
Goddard, Mike E.
Visscher, Peter M.
Title Recent human effective population size estimated from linkage disequilibrium
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2007
Sub-type Article (original research)
DOI 10.1101/gr.6023607
Open Access Status File (Publisher version)
Volume 17
Issue 4
Start page 520
End page 526
Total pages 7
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Formatted abstract
Effective population size (Ne) determines the amount of genetic variation, genetic drift, and linkage disequilibrium (LD) in populations. Here, we present the first genome-wide estimates of human effective population size from LD data. Chromosome-specific effective population size was estimated for all autosomes and the X chromosome from estimated LD between SNP pairs <100 kb apart. We account for variation in recombination rate by using coalescent-based estimates of fine-scale recombination rate from one sample and correlating these with LD in an independent sample. Phase I of the HapMap project produced between 18 and 22 million SNP pairs in samples from four populations: Yoruba from Ibadan (YRI), Nigeria; Japanese from Tokyo (JPT); Han Chinese from Beijing (HCB); and residents from Utah with ancestry from northern and western Europe (CEU). For CEU, JPT, and HCB, the estimate of effective population size, adjusted for SNP ascertainment bias, was ∼3100, whereas the estimate for the YRI was ∼7500, consistent with the out-of-Africa theory of ancestral human population expansion and concurrent bottlenecks. We show that the decay in LD over distance between SNPs is consistent with recent population growth. The estimates of Ne are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred ∼10,000 to 200,000 years ago.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
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