Recent human effective population size estimated from linkage disequilibrium
Open accessAbstract
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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Estimates of effective population sizes of the ancestral Homo sapiens population range from 700 to about 7000 individuals.
“Estimates of effective population sizes of the ancestral Homo sapiens population range from 700 (Zhivotovsky et al., 2003) to about 7000 individuals (Tenesa et al., 2007).”
From The Challenge of Evolution to Religion (2019) · cites this paper as Tenesa et al., 2007
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- Authors
- Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D. L., Clarke, G. M., Goddard, M. E., & Visscher, P. M.
- Affiliations
- Western General Hospital (GB)
- University of Edinburgh (GB)
- QIMR Berghofer Medical Research Institute (AU)
- Centre for Human Genetics (GB)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-03-09
- Volume
- 17
- Issue
- 4
- Pages
- 520-526
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC1832099
- OpenAlex
- W2127055349
- Cited by
- 438
- References
- 1
- Citations by year
- 2026: 7 · 2025: 15 · 2024: 14 · 2023: 16 · 2022: 25 · 2021: 20 · 2020: 25 · 2019: 30 · 2018: 19 · 2017: 13 · 2016: 15 · 2015: 31 · 2014: 31 · 2013: 35 · 2012: 42
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion)
- Funders
- Wellcome Trust
- Cancer Research UK
- Directorate for Biological Sciences
- Medical Research Council
- National Health and Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- effective population size, linkage disequilibrium, human population history, population bottleneck, out-of-Africa migration, recombination rate, HapMap, Yoruba, Japanese, Han Chinese, X chromosome, autosomes, genetic drift
- MeSH terms
- Algorithms, Female, Gene Frequency, Genetics, Population, Haplotypes, Humans, Male, Models, Genetic, Population Density, Linkage Disequilibrium, Genome, Human, Polymorphism, Single Nucleotide
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