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Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa
Open accessAbstract
Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.
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“The increased variant count in African populations is consistent with the out-of-Africa model of human migration across the world, as well as the decreased genetic diversity in non-African populations as a result of the bottlenecks that occurred as humans moved into Eurasia, Oceania, and the Americas (Ramachandran et al. 2005; DeGiorgio et al. 2009; Li and Durbin 2011).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as DeGiorgio et al. 2009
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Metadata
- Authors
- DeGiorgio, M., Jakobsson, M., & Rosenberg, N. A.
- Affiliations
- Center for Computational Medicine and Bioinformatics and
- Uppsala University (SE)
- University of Michigan (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2009-09-22
- Volume
- 106
- Issue
- 38
- Pages
- 16057-16062
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2752555
- OpenAlex
- W2157535960
- Cited by
- 175
- References
- 32
- Citations by year
- 2026: 6 · 2025: 3 · 2024: 2 · 2023: 8 · 2022: 14 · 2021: 14 · 2020: 8 · 2019: 11 · 2018: 7 · 2017: 4 · 2016: 8 · 2015: 17 · 2014: 15 · 2013: 19 · 2012: 14
- FWCI
- 7.60
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Alfred P. Sloan Foundation
- Svenska Forskningsrådet Formas
- Vetenskapsrådet
- National Institutes of Health
- National Human Genome Research Institute (T32HG000040)
- National Institute of General Medical Sciences (T32GM070449, R01GM081441)
- 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
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- human genetic variation, coalescent, heterozygosity, linkage disequilibrium, allele frequency spectrum, genetic drift, archaic human admixture, East Africa
- MeSH terms
- Africa, Animals, Anthropology, Physical, Biological Evolution, Fossils, Genetics, Population, Heterozygote, Humans, Models, Genetic, Population Dynamics, Genetic Variation, Hominidae, Linkage Disequilibrium, Founder Effect, Evolution, Molecular
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