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Estimating the number of founder lineages from haplotypes of closely linked SNPs
Author(s) -
LEBLOIS RAPHAËL,
SLATKIN MONTGOMERY
Publication year - 2007
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/j.1365-294x.2007.03288.x
Subject(s) - haplotype , biology , population , single nucleotide polymorphism , founder effect , genetics , population genetics , evolutionary biology , allele frequency , gene , demography , genotype , sociology
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.