Conservation genomics in inbred Scandinavian wolves using bioinformatic methods

• Main Author: Smeds, Linnéa
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Uppsala universitet, Evolutionsbiologi 2024
• Subjects: conservation genomics; Canis lupus; bioinformatics; Y chromosome; admixture; genetic load; structural variation; GWAS; Evolutionary Biology; Evolutionsbiologi
• Online Access: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-517653

With the recent and unprecedented progress in retrieving DNA sequence information from a large number of individuals of any species, conservation genetic research has entered a new phase. Specifically, it has become possible to study how genomes of endangered species respond to reductions in population size. Using genomic and bioinformatic approaches, in this thesis I investigate the contemporary Scandinavian wolf population founded 40 years ago by only three individuals, after the original population had been extirpated some decades earlier. The origin of the founders has been the subject of controversy, so I aimed to trace their origin using first male-specific Y chromosome sequences, and then whole-genome sequence data. I compared Scandinavian wolves to wolves from the nearby Finnish-Russian population as well as to publicly available wolf and dog samples from around the northern hemisphere, and found that the Scandinavian founders shared Y-haplotypes only with Finnish wolves. Consistent with this observation, when assessing population structure on the genomic scale, founders clustered with Finnish and Russian wolves, and an admixture analysis showed no other ancestries, nor traces of introgression from dogs. Small populations tend to have less genetic variation than larger populations, which might reduce their adaptive potential and increase the risk for extinction. A common measure used to investigate the genetic health of small populations is the genetic load, which is the fitness reduction of individuals due to accumulation of deleterious variants. I assessed the genetic load in Scandinavian wolves, divided into the components masked load (comprised of deleterious mutations in heterozygous state) and realized load (comprised of deleterious mutations in homozygous state), using both putatively deleterious single nucleotides and structural variants. I found that the realized load increased with every generation of inbreeding but was alleviated after genetic rescue events when new immigrants entered the ...