Ancestral components of admixed genomes in a Mexican cohort
Open accessAbstract
For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study "virtual genomes" of admixed individuals. We apply this approach to a cohort of 492 parent-offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations-Africa, Europe, and America-vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10-15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.
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In previous work on admixed populations from Mexico, accurate local ancestry estimates can be obtained using imperfect ancestral populations (including CEU and YRI), as long as the haplotype phasing is accurate.
“in previous work on admixed populations from Mexico [24], we have found that accurate local ancestry estimates can be obtained using imperfect ancestral populations (including CEU and YRI), as long as the haplotype phasing is accurate.”
From Genetic Architecture of Skin and Eye Color in an African-European Admixed Population (2013) · cites this paper as [24]
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- Authors
- Johnson, N. A., Coram, M. A., Shriver, M. D., Romieu, I., Barsh, G. S., London, S. J., & Tang, H.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- Pennsylvania State University (US)
- Instituto Nacional de Salud Pública (MX)
- National Institutes of Health (US)
- Corresponding author
- Barsh, Gregory S.
- Tang, Hua
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-12-15
- Volume
- 7
- Issue
- 12
- Pages
- e1002410
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3240599
- OpenAlex
- W1984534730
- Cited by
- 114
- References
- 41
- Citations by year
- 2026: 1 · 2025: 1 · 2023: 2 · 2022: 6 · 2021: 8 · 2020: 3 · 2019: 10 · 2018: 6 · 2017: 15 · 2016: 13 · 2015: 11 · 2014: 17 · 2013: 14 · 2012: 7
- FWCI
- 7.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- U.S. Department of Health and Human Services
- Alfred P. Sloan Foundation
- National Institutes of Health
- National Human Genome Research Institute (T32HG000044)
- National Institute of General Medical Sciences (GM073059, R01GM073059)
- NHLBI Division of Intramural Research
- 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
- admixture, biogeographic ancestry, Native American ancestry, African ancestry, European ancestry, Yucatán Peninsula, Mayans, African Americans, selection signatures, candidate loci, parent-offspring trios, population structure
- MeSH terms
- Black or African American, Demography, Ethnicity, Haplotypes, Hispanic or Latino, Humans, Mexico, Population, Selection, Genetic, Cohort Studies, Genome, Human, Evolution, Molecular, Polymorphism, Single Nucleotide, Principal Component Analysis, Black People, White People, American Indian or Alaska Native
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