Genomic consequences of intensive inbreeding in an isolated wolf population

Abstract

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 ). 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 ) was strongly correlated with realized inbreeding measured with the entire genome (r = 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 estimated with as few as 10,000 single nucleotide polymorphisms, than with F. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.

Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee

“…Our results show similar phenomenon to some other populations (wild wolves and laboratory planarians) that show heterozygosity throughout the genome despite many generations of inbreeding (Kardos et al., ) or selfing (Guo et al., )—though not clonal propagation as in the clone. However, it is important to note that the mating system of the honey bee differs markedly from these previously studied species.…”

A high‐quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal

“…Looking to the future, although ours and many other studies have quantified heterozygosity using microsatellites, simulations clearly indicate that tens of thousands of markers will outperform even very deep pedigrees at capturing inbreeding depression, particularly when they can be mapped to a reference genome to quantify ROH (Kardos et al., ; Wang, ). This is supported by a growing number of empirical studies of wild populations using approaches like restriction site‐associated DNA sequencing (Hoffman et al., ), high density SNP arrays (Chen et al., ; Huisman et al., ) and whole‐genome resequencing (Kardos et al., ). As the costs of these and related methods continue to fall, they are likely to become preferred approaches for studying inbreeding and its consequences in wild populations.…”

Do estimates of contemporary effective population size tell us what we want to know?

“…We have already mentioned hidden Markov models. Similarly, Kardos et al (2018), for example, measured inbreeding in Scandinavian wolves from "identical-by-descent" chromosome segments (runs of homozygosity), and also found that these estimates correlated surprisingly well with pedigree data and with estimates obtained from 500 single nucleotide polymorphisms (SNPs). Focusing on inbreeding rather than effective size could also help modelling in some situations.…”