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

• Published in: Molecular Ecology
• Main Authors: Leblois, Raphaël, Slatkin, Montgomery
• Other Authors: Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Department of Integrative Biology, University of California Berkeley (UC Berkeley), University of California (UC), United States Department of Health & Human Services, National Institutes of Health (NIH) - USA, NIH National Institute of General Medical Sciences (NIGMS) : R01-GM40282
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2007
• Subjects: coalescent theory; founder effect; gene genealogy; linkage disequilibrium; maximum-likelihood estimation; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Canis lupus
• Online Access: https://hal.inrae.fr/hal-02929790; https://doi.org/10.1111/j.1365-294X.2007.03288.x

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.