title: Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent inFicedulaFlycatcher Genome Sequences.
abstract: Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287Ficedulaflycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate. However, this pattern was substantially weaker when ROH were mapped using genetic rather than physical single nucleotide polymorphism (SNP) coordinates in the genome. Empirical results and simulations suggest that high ROH abundance in regions of low recombination was partly caused by increased power to detect the very long IBD segments typical of regions with a low recombination rate. Simulations also showed that hard selective sweeps (but not soft sweeps or background selection) likely contributed to variation in the abundance of ROH across the genome. Comparisons of the abundance of ROH among several study populations indicated that the Spanish pied flycatcher population had the smallest historical effective population size (Ne) for this species, and that a putatively recently founded island (Baltic) population had the smallest historicalNeamong the collared flycatchers. Analysis of pairwise IBD in Baltic collared flycatchers indicated that this population was founded <60 generations ago. This study provides a rare genomic glimpse into demographic history and the mechanisms underlying the genome-wide distribution of ROH.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236, Sweden martykardos@gmail.com hans.ellegren@ebc.uu.se.|Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Polson, Montana 59860.
authors.forename: Marty
authors.initials: M
authors.lastname: Kardos
authors.affiliation: Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Qvarnström
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236, Sweden martykardos@gmail.com hans.ellegren@ebc.uu.se.
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D018703:Founder Effect; D016678:Genome; D006720:Homozygote; D007178:Inbreeding; D046109:Passeriformes / Q000235:genetics*; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide
keywords: effective population size; population genomics; runs of homozygosity