A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots
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Abstract
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry "palettes" estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.
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Our results suggest that both LINADMIX and PHCP are highly informative for individuals with ancestry sources similar to those analyzed here.
“Thus, although ADMIXTURE, the basis of LINADMIX, is known to have certain pitfalls as a tool for quantifying ancestry proportions (Lawson et al., 2018), in the case of individuals with ancestry sources similar to those we have analyzed here, our results suggest that both LINADMIX and PHCP are highly informative.”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Lawson et al., 2018
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- Authors
- Lawson, D. J., van Dorp, L., & Falush, D.
- Affiliations
- University of Bristol (GB)
- University of Bath (GB)
- Corresponding author
- Falush, Daniel
- Venue
- Nature Communications
- Published
- 2018-08-14
- Volume
- 9
- Issue
- 1
- Pages
- 3258-3258
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6092366
- OpenAlex
- W2950373858
- Cited by
- 560
- References
- 34
- Citations by year
- 2026: 88 · 2025: 62 · 2024: 58 · 2023: 52 · 2022: 63 · 2021: 66 · 2020: 63 · 2019: 48 · 2018: 33 · 2017: 18 · 2016: 8 · 2013: 1
- FWCI
- 31.70
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (104125/Z/14/Z, WT104125AIA)
- Medical Research Council (MR/M501608/1, MR/L015080/1, MR/M501608/2)
- Engineering and Physical Sciences Research Council (1357822)
- 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
- structure, admixture, genetic clustering, bar charts, overinterpretation, ancestry inference, model goodness of fit, genetic drift, demographic inference
- MeSH terms
- Algorithms, Black or African American, Computer Simulation, Genetics, Population, Humans, Internationality, Black People, Asian People
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