A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

Daniel J. Lawson, Lucy van Dorp, Daniel Falush

Research output: Contribution to journalArticle

33 Citations (Scopus)

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.

Original languageEnglish
Article number3258
Pages (from-to)1-11
JournalNature Communications
Volume9
Issue number1
Early online date14 Aug 2018
DOIs
Publication statusPublished - 1 Dec 2018

Fingerprint

plots
History
histories
Genetic Drift
Clustering algorithms
African Americans
Population
Cluster Analysis
admixtures
Genetic algorithms
Demography
goodness of fit
inference
genetic algorithms
products

Keywords

  • African Continental Ancestry Group/genetics
  • Algorithms
  • Asian Continental Ancestry Group/genetics
  • Computer Simulation
  • Genetics, Population
  • Humans
  • Internationality

Cite this

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. / Lawson, Daniel J.; van Dorp, Lucy; Falush, Daniel.

In: Nature Communications, Vol. 9, No. 1, 3258, 01.12.2018, p. 1-11.

Research output: Contribution to journalArticle

Lawson, Daniel J. ; van Dorp, Lucy ; Falush, Daniel. / A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. In: Nature Communications. 2018 ; Vol. 9, No. 1. pp. 1-11.
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