Estimating the number of founder lineages from haplotypes of closely linked SNPs



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      Present address: Unité Origine, Structure et Evolution de la Biodiversité, Département Systématique et Evolution, Muséum National d’Histoire Naturelle, 16 Rue Buffon, 75005 Paris, France


    1. Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 9472-3140, USA
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Montgomery Slatkin, Fax: 510-643-6264; E-mail:


We consider an isolated population founded by a small number of individuals randomly chosen from a source population of known genetic composition at a known time in the past. We develop a Monte-Carlo maximum-likelihood method for estimating the number of founding individuals from the haplotype frequencies at several SNP (single nucleotide polymorphism) loci in a sample. We assume the isolated population was founded recently enough that that mutation can be ignored and that haplotype frequencies in the source population have not changed. We apply the method to simulated data and show that it is unbiased. With a reasonable number of individuals sampled, it is possible to estimate the number of founders within a factor of 2. We show that the performance of the method is not degraded substantially if the frequencies of the rare haplotypes in the source are not known precisely and if there is some recombination. We illustrate the use of our method by applying it to a previously published data set from a recently founded population of wolves (Canis lupus) in Scandinavia.