title: Recent human effective population size estimated from linkage disequilibrium.
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. 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.
authors.affiliation: Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK.
authors.forename: Albert
authors.initials: A
authors.lastname: Tenesa
authors.forename: Pau
authors.initials: P
authors.lastname: Navarro
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Hayes
authors.forename: David L
authors.initials: DL
authors.lastname: Duffy
authors.forename: Geraldine M
authors.initials: GM
authors.lastname: Clarke
authors.forename: Mike E
authors.initials: ME
authors.lastname: Goddard
authors.forename: Peter M
authors.initials: PM
authors.lastname: Visscher
mesh_terms: D000465:Algorithms; D005260:Female; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011156:Population Density