CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

TLDR

Clustering individuals into populations based on multilocus genotypes is common in population genetics, but unsupervised algorithms such as BAPS, STRUCTURE, and TESS can yield multiple, distinct solutions due to label switching and genuine multimodality. The authors aim to provide algorithms that align multiple replicate clustering analyses of the same dataset. They developed three alignment algorithms and implemented them in the CLUMPP program, which processes replicate cluster membership coefficients. CLUMPP was demonstrated by aligning 100 replicate analyses of 600 chickens from 20 breeds, illustrating its practical utility. CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html (contact [e-mail]).

Abstract

Abstract Motivation: Clustering of individuals into populations on the basis of multilocus genotypes is informative in a variety of settings. In population-genetic clustering algorithms, such as BAPS, STRUCTURE and TESS, individual multilocus genotypes are partitioned over a set of clusters, often using unsupervised approaches that involve stochastic simulation. As a result, replicate cluster analyses of the same data may produce several distinct solutions for estimated cluster membership coefficients, even though the same initial conditions were used. Major differences among clustering solutions have two main sources: (1) ‘label switching’ of clusters across replicates, caused by the arbitrary way in which clusters in an unsupervised analysis are labeled, and (2) ‘genuine multimodality,’ truly distinct solutions across replicates. Results: To facilitate the interpretation of population-genetic clustering results, we describe three algorithms for aligning multiple replicate analyses of the same data set. We have implemented these algorithms in the computer program CLUMPP (CLUster Matching and Permutation Program). We illustrate the use of CLUMPP by aligning the cluster membership coefficients from 100 replicate cluster analyses of 600 chickens from 20 different breeds. Availability: CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html Contact: [e-mail]