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Research article2018Peer reviewedOpen access

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos, Marty; Akesson, Mikael; Fountain, Toby; Flagstad, Oystein; Liberg, Olof; Olason, Pall; Sand, Hakan; Wabakken, Petter; Wikenros, Camilla; Ellegren, Hans


Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F-ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors <= 10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F-P) was strongly correlated with realized inbreeding measured with the entire genome (r(2) = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F-ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F-P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.

Published in

Nature ecology & evolution
2018, Volume: 2, number: 1, pages: 124-131