Genomic and fitness consequences of inbreeding in an endangered carnivore

Abstract

Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well‐documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome‐wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.

Runs of homozygosity in killer whale genomes provide a global record of demographic histories

“…After x subsequent generations, the ROH is either further broken up by recombination if subsequent recombination from generations F1 to F x occur within lineage B. If instead the F1 mates within lineage A then the F2 offspring could inherit the blue IBD tract from both parents, re‐establishing the same ROH within the F2 generation (see for example Hasselgren et al, 2021; Robinson et al, 2019)…”

Genomic erosion in the assessment of species extinction risk and recovery potential

“…Genomic erosion is manifested as: (1) a loss of genetic diversity, (2) an elevated realised load (that is, the component of genetic load whose fitness effects is expressed 9 , and which is caused by an increased number of homozygous loci with recessive deleterious alleles), (3) a mismatch between genetic adaptations and the prevailing environmental conditions (i.e., maladaptation), and (4) genetic introgression due to hybridisation. All four aspects of genomic erosion can reduce individual fitness and undermine viability of populations, both in the short-and long-term 8,29,37,38,39,40 . Although genomic erosion is rarely the primary cause for species extinction, it is tightly coupled to other (external) threats.…”

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

“…kakapo [ 85 ]; rattle snakes [ 86 ]; wolves [ 83 ]; killer whales [ 87 ]), while some studies show that decreased survival and population growth rate are correlated with higher inbreeding and mutation load (e.g. see arctic foxes [ 88 ] and alpine ibex [ 89 ]). Unfortunately, our understanding of the functional effects of specific mutations and their impacts on fitness in endangered species remains poor.…”