ArticleGenome research2007
Recent human effective population size estimated from linkage disequilibrium.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers.
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Who cites it
229 citing papers in PubMed.
- Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2019Trial
- The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.PloS one · 2014Trial
- Genome-wide comparison of traditional and commercial Mehraban sheep populations reveals differences in genetic structure, linkage disequilibrium, and inbreeding patterns.BMC genomics · 2026Article
- Genetic and transcriptomic determinants of disseminated coccidioidomycosis identify a founder variant inmedRxiv : the preprint server for health sciences · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- High Rate of Mutation and Efficient Removal by Selection of Structural Variants From Natural Populations of Caenorhabditis Elegans.Genome biology and evolution · 2026Article
- Mutation rate estimate and population genomic analysis reveals decline of koalas prior to human arrival.Molecular biology and evolution · 2026Article
- Feed-forward neural networks for genomic selection: insights into varying levels of dominance heritability.BMC genomics · 2026Article
- Combining Multiple Genetic Estimates of NMolecular ecology resources · 2026Article
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
- The Importance of Effective Population Size in Conservation and Biodiversity Monitoring.Evolutionary applications · 2026Article
- Protein structure shapes natural genetic variation andbioRxiv : the preprint server for biology · 2025Article
- Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle.Veterinary medicine and science · 2025Article
- Genomic evidence for males of exceptional reproductive output (ERO) in apes and humans.National science review · 2025Article
- Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods.Nature communications · 2025Article
- The effectiveness of selection in a species affects the direction of amino acid frequency evolution.bioRxiv : the preprint server for biology · 2025Article
- Human deleterious mutation rate slows adaptation and implies high fitness variance.bioRxiv : the preprint server for biology · 2025Article
- Genetic Comparison and Selection of Reproductive and Growth-Related Traits in Qinchuan Cattle and Two Belgian Cattle Breeds.Animals : an open access journal from MDPI · 2025Article
- Genomic Rewilding of Domestic Animals: The Role of Hybridization and Selection in Wolfdog Breeds.Genes · 2025Article
- Genomic insights into runs of homozygosity, effective population size and selection signatures in Iranian meat and dairy sheep breeds.PloS one · 2025Article
169 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
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.
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