Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
Open accessAbstract
We present an expanded data set of 50 unlinked autosomal noncoding regions, resequenced in samples of Hausa from Cameroon, Italians, and Chinese. We use these data to make inferences about human demographic history by using a technique that combines multiple aspects of genetic data, including levels of polymorphism, the allele frequency spectrum, and linkage disequilibrium. We explore an extensive range of demographic parameters and demonstrate that our method of combining multiple aspects of the data results in a significant reduction of the compatible parameter space. In agreement with previous reports, we find that the Hausa data are compatible with demographic equilibrium as well as a set of recent population expansion models. In contrast to the Hausa, when multiple aspects of the data are considered jointly, the non-Africans depart from an equilibrium model of constant population size and are compatible with a range of simple bottleneck models, including a 50–90% reduction in effective population size occurring some time after the appearance of modern humans in Africa 160,000–120,000 years ago.
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The demographic model most compatible with the data for European and East Asian populations is a bottleneck scenario, with stronger genetic drift in East Asian populations than European populations.
“Recent studies have shown that the demographic model most compatible with the data for European and East Asian populations is a bottleneck scenario, with stronger genetic drift in East Asian populations than European populations (Schaffner et al. 2005;Voight et al. 2005).”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Voight et al. 2005
The Discussion concludes that simple bottleneck models can explain the non-African data. In “Testing Bottleneck Models in the Non-African Data” (page unavailable), the Chinese sample admits slightly more severe bottlenecks than the Italian sample under a 40,000-year onset, but the compatible ranges are similar and milder Chinese bottlenecks cannot be rejected under an 80,000-year onset. The paper therefore does not establish stronger genetic drift in East Asians as an unqualified finding, or identify a single most-compatible model. (LLM, conf=0.85)
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- Authors
- Voight, B. F., Adams, A. M., Frisse, L. A., Qian, Y., Hudson, R. R., & Di Rienzo, A.
- Affiliations
- University of Chicago (US)
- Harvard University (US)
- Committee on Genetics and Departments of Human Genetics and Ecology and Evolution, University of Chicago, Chicago, IL 60637
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2005-12-13
- Volume
- 102
- Issue
- 51
- Pages
- 18508-18513
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1311907
- OpenAlex
- W2028704045
- Cited by
- 262
- References
- 51
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 1 · 2023: 1 · 2021: 4 · 2020: 3 · 2019: 7 · 2018: 7 · 2017: 1 · 2016: 11 · 2015: 10 · 2014: 18 · 2013: 23 · 2012: 25
- FWCI
- 11.86
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Education
- DePaul University
- National Institutes of Health (5r01hg002098-03)
- National Human Genome Research Institute (R01 HG02772, R01 HG02098, F32 HG00219, R01HG002772, F32HG000219)
- National Institute of General Medical Sciences (T32GM07197, T32GM007197)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK 55889, R01DK055889)
- 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
- demographic history, population growth, population bottleneck, allele frequency spectrum, linkage disequilibrium, non-coding regions, Hausa language, Italian, Chinese, effective population size, parameter space reduction, modern human origins
- MeSH terms
- Cameroon, China, Gene Frequency, Humans, Italy, Models, Genetic, Population Density, Time Factors, Genetic Variation
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