Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The . gov means it’s official. Federal government websites often end in . gov or . mil VSports app下载. Before sharing sensitive information, make sure you’re on a federal government site. .

Https

The site is secure V体育官网. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely. .

. 2007 Apr;17(4):520-6.
doi: 10.1101/gr.6023607. Epub 2007 Mar 9.

"VSports最新版本" Recent human effective population size estimated from linkage disequilibrium

Albert Tenesa  1 , Pau Navarro, Ben J Hayes, David L Duffy, Geraldine M Clarke, Mike E Goddard, Peter M Visscher
Affiliations

Recent human effective population size estimated from linkage disequilibrium

Albert Tenesa et al. Genome Res. 2007 Apr.

Abstract

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 VSports手机版. 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 approximately 3100, whereas the estimate for the YRI was approximately 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 N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago. .

PubMed Disclaimer

Figures (VSports最新版本)

Figure 1.
Figure 1.
Reciprocal of r2 plotted against physical distance for each of the 22 autosomes for the CEU population. The X-axis shows the physical distance in kilobases and the Y-axis shows 1/mean(r2). The mean value of r2 was calculated in 1 kb bins.
Figure 2.
Figure 2.
Comparison of the estimate of Ne from each of the labeled 23 chromosomes for the JPT and HCB population (Method 1). The X-axis shows the effective population size for each autosome and the X chromosome estimated from the JPT sample using a nonlinear regression of r2 on physical distance between pairs of SNPs. The Y-axis shows the estimates of Ne for each chromosome from HCB sample. The fitted linear regression line fits nearly perfectly, presumably reflecting common ancestry of the two populations.
Figure 3.
Figure 3.
Ancestral population size estimated from 22 autosomes of the CEU (A) and YRI (B) data (Method 1). For each chromosome and for each SNP recombination distance bin (0.001 cM spacing), Ne was estimated from the mean r2, using E(r2) = 1/(α + 4Nec). The number of generations in the past was calculated as 1/(2c), and was truncated at 5000. Effective population size has increased dramatically in the last ∼1000 generations (20,000 yr), from a fairly constant ancestral size of ∼2500 (CEU) and ∼7000 (YRI).
See this image and copyright information in PMC

References

    1. Altshuler D., Brooks L.D., Chakravarti A., Collins F.S., Daly M.J., Donnelly P., Brooks L.D., Chakravarti A., Collins F.S., Daly M.J., Donnelly P., Chakravarti A., Collins F.S., Daly M.J., Donnelly P., Collins F.S., Daly M.J., Donnelly P., Daly M.J., Donnelly P., Donnelly P. A haplotype map of the human genome. Nature. 2005;437:1299–1320. - PMC - PubMed
    1. Barrett J.C., Fry B., Maller J., Daly M.J., Fry B., Maller J., Daly M.J., Maller J., Daly M.J., Daly M.J. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–265. - PubMed
    1. Clarke G.M., Cardon L.R., Cardon L.R. Disentangling linkage disequilibrium and linkage from dense single-nucleotide polymorphism trio data. Genetics. 2005;171:2085–2095. - PMC - PubMed
    1. Eller E. Estimating relative population sizes from simulated data sets and the question of greater African effective size. Am. J. Phys. Anthropol. 2001;116:1–12. - PubMed
    1. Erlich H.A., Bergstrom T.F., Stoneking M., Gyllensten U., Bergstrom T.F., Stoneking M., Gyllensten U., Stoneking M., Gyllensten U., Gyllensten U. HLA sequence polymorphism and the origin of humans. Science. 1996;274:1552–1554. - "VSports手机版" PubMed

Publication types

V体育官网入口 - LinkOut - more resources