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How to use SNPs and other diagnostic diallelic genetic markers to identify the species composition of multi-species hybrids

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Abstract

Hybridization with non-native species is a threat to many taxa, but hybrids can be difficult to identify based on morphology. Genetic data is useful for estimating the ancestry of admixed populations, and diallelic markers such as single nucleotide polymorphisms are popular for such applications. When taxa are evolutionarily well diverged, loci frequently become fixed for different alleles in each taxa, and the degree of genetic admixture between two taxa can be estimated by counting diagnostic alleles for each taxa. However, when there is hybridization between more than two taxa, and loci have only two alleles, the origin of each allele cannot be assigned ambiguously to a taxon. In this note, I show how the expectation–maximization algorithm can be used to solve this problem. A computer program for implementing this approach is available at www.montana.edu/kalinowski.

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Acknowledgments

Funding for this work was provided by Montana Fish Wildlife and Parks and the National Science Foundation (DEB 071745). I thank two anonymous reviewers for suggestions that improved this paper.

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Authors and Affiliations

  1. Department of Ecology, 310 Lewis Hall Montana State University, Bozeman, MT, 59717, USA

    Steven T. Kalinowski

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  1. Steven T. Kalinowski
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Correspondence to Steven T. Kalinowski.

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Kalinowski, S.T. How to use SNPs and other diagnostic diallelic genetic markers to identify the species composition of multi-species hybrids. Conservation Genet Resour 2, 63–66 (2010). https://doi.org/10.1007/s12686-009-9146-0

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