Bayesian identification of admixture events using multilocus molecular markers

Abstract

Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals' genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Genetic structuring in three closely related circumpolar plant species: AFLP versus microsatellite markers and high-arctic versus arctic–alpine distributions

“…The usual advantage of using codominant markers such as microsatellites compared with dominant ones such as AFLPs is therefore reduced. Most importantly, genetic structure analyses such as STRUCTURE and BAPS may be influenced by deviations from Hardy-Weinberg equilibrium and lead to overestimation of the number of groups (Pritchard et al, 2000;Falush et al, 2003;Corander and Marttinen, 2006).…”

“…Genetic structuring was analyzed for each data set using the Bayesian clustering approach implemented in STRUCTURE 2.2 (Pritchard et al, 2000;Falush et al, 2007) and BAPS 3.1 (Corander and Marttinen, 2006). The microsatellite data sets were converted into STRUCTURE format with the software CONVERT (Glaubitz, 2004), and AFLP data sets were converted with the script AFLPdat (Ehrich, 2006).…”

Pleistocene genetic legacy suggests incipient species of Sebastes mentella in the Irminger Sea

“…In addition, the samples from 1996 to 1995 from shallow-and deep-mesopelagic-zones grouped with the recent samples from the same zones (Figure 3; Tables 1 and 2 The programs STRUCTURE (Pritchard et al, 2000) and BAPS (Corander and Marttinen, 2006) were used to estimate individual q's, that is, the estimated proportion of an individual's genotype originating from one or the other of the two populations of origin. segregated before the last glacial maximum (18 kyr BP) in the Northern Hemisphere.…”

Geographic patterns of inversion polymorphisms in a wild African rodent, Mastomys erythroleucus

“…Where appropriate, the FDR (false discovery rate) correction for multiple tests was implemented following the procedure detailed in Verhoeven et al (2005, p. 644). Population genetic structure was assessed using the Bayesian clustering algorithm implemented in the software BAPS4.14 (Corander and Marttinen, 2006), which partitioned the populations into an optimal number of clusters with associated values of the Bayes factor.…”