Population Genetics Models of Local Ancestry
Open accessAbstract
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright–Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of “European” gene flow significantly improves the modeling of both tract lengths and ancestry variances.
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Both the paper's ancestry segments and prior results supported a model with an earlier date of Native American admixture.
“Both our ancestry segments and prior results supported a model with an earlier date of Native American admixture.25,47”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [47]
The Abstract describes Native American ancestry as an example of a source-population label, but does not date Native American admixture. The Tract lengths section tests admixture models in African-American samples using European and West African reference panels; it does not report prior results supporting an earlier date of Native American admixture. Searches for that date and for Native American admixture timing found no supporting passage. (LLM, conf=0.76)
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- Authors
- Gravel, S.
- Affiliations
- Stanford University (US)
- Corresponding author
- Gravel, Simon
- ORCID
- Gravel, Simon
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-06-01
- Volume
- 191
- Issue
- 2
- Pages
- 607-619
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC3374321
- OpenAlex
- W2154940281
- Cited by
- 311
- References
- 3
- Citations by year
- 2026: 17 · 2025: 17 · 2024: 10 · 2023: 17 · 2022: 51 · 2021: 23 · 2020: 24 · 2019: 27 · 2018: 30 · 2017: 14 · 2016: 18 · 2015: 19 · 2014: 23 · 2013: 16 · 2012: 5
- FWCI
- 11.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U01HG005715)
- National Institute of General Medical Sciences (R01GM090087)
- 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 › Race, Genetics, and Society
- Keywords
- local ancestry, population structure, gene flow, migration rate, population genetic models
- MeSH terms
- Algorithms, Black or African American, Computer Simulation, Humans, Models, Genetic, Population Dynamics, White People, Gene Flow, HapMap Project
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