Recent human effective population size estimated from linkage disequilibrium

被引:326
作者
Tenesa, Albert
Navarro, Pau
Hayes, Ben J.
Duffy, David L.
Clarke, Geraldine M.
Goddard, Mike E.
Visscher, Peter M. [1 ]
机构
[1] Univ Edinburgh, Inst Evolut biol, Edinburgh EH9 3JT, Midlothian, Scotland
[2] Univ Edinburgh, Western Gen Hosp, Colon Canc Genet Grp, Edinburgh EH4 2XU, Midlothian, Scotland
[3] Western Gen Hosp, MRC Human Genet Unit, Edinburgh EH4 2XU, Midlothian, Scotland
[4] Victorian Inst Anim Sci, Attwood, Vic 3049, Australia
[5] Royal Brisbane Hosp, Queensland Inst Med Res, Brisbane, Qld 4006, Australia
[6] Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England
[7] Univ Melbourne, Inst Land & Food Resources, Parkville, Vic 3010, Australia
基金
英国惠康基金;
关键词
D O I
10.1101/gr.6023607
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Effective population size (N-e) 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 similar to 3100, whereas the estimate for the YRI was similar to 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 similar to 10,000 to 200,000 years ago.
引用
收藏
页码:520 / 526
页数:7
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