A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots

Abstract

Genetic clustering algorithms, implemented in popular 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 who are a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups which 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, available at github.com/danjlawson/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 based on genetic data.