Inferring weak population structure with the assistance of sample group information
Open accessAbstract
Genetic clustering algorithms require a certain amount of data to produce informative results. In the common situation that individuals are sampled at several locations, we show how sample group information can be used to achieve better results when the amount of data is limited. New models are developed for the structure program, both for the cases of admixture and no admixture. These models work by modifying the prior distribution for each individual's population assignment. The new prior distributions allow the proportion of individuals assigned to a particular cluster to vary by location. The models are tested on simulated data, and illustrated using microsatellite data from the CEPH Human Genome Diversity Panel. We demonstrate that the new models allow structure to be detected at lower levels of divergence, or with less data, than the original structure models or principal components methods, and that they are not biased towards detecting structure when it is not present. These models are implemented in a new version of structure which is freely available online at http://pritch.bsd.uchicago.edu/structure.html.
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STRUCTURE determines the number and composition of subpopulations based on Hardy-Weinberg equilibrium and linkage equilibrium.
“This method attempts to determine the number and composition of subpopulations based on Hardy-Weinberg equilibrium and linkage equilibrium (Hubisz et al., 2009; Zhang et al., 2014).”
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- Authors
- HUBISZ, M. J., FALUSH, D., STEPHENS, M., & PRITCHARD, J. K.
- Affiliations
- Howard Hughes Medical Institute (US)
- University College Cork (IE)
- Corresponding author
- HUBISZ, MELISSA J.
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2009-08-12
- Volume
- 9
- Issue
- 5
- Pages
- 1322-1332
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- PMC
- PMC3518025
- OpenAlex
- W2060891246
- Cited by
- 3,475
- References
- 18
- Citations by year
- 2026: 83 · 2025: 109 · 2024: 162 · 2023: 148 · 2022: 192 · 2021: 239 · 2020: 245 · 2019: 239 · 2018: 265 · 2017: 236 · 2016: 298 · 2015: 282 · 2014: 250 · 2013: 259 · 2012: 210
- FWCI
- 89.77
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular Ecology Resources (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- population structure inference, genetic clustering, admixture, prior distributions, population assignment, small sample size, microsatellite data, principal component analysis
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