Genomic Inference of Inbreeding in Alexander Archipelago Wolves (Canis lupus ligoni) on Prince of Wales Island, Southeast Alaska

• Main Author: Zarn, Katherine Emily
• Format: Thesis
• Language: unknown
• Published: University of Montana 2019
• Subjects: runs of homozygosity; wildlife genomics; wildlife conservation; heterozygosity; hybridization capture; wildlife management; Bioinformatics; Genomics; Prince of Wales Island; Archipelago; Canis lupus; Alaska
• Online Access: https://scholarworks.umt.edu/etd/11497; https://scholarworks.umt.edu/context/etd/article/12574/viewcontent/Zarn_Katherine_Thesis.pdf

Habitat loss and climate change are increasingly resulting in reduction and fragmentation of wildlife populations. Populations that have experienced fragmentation and decreases in abundance are at heightened risk of inbreeding due to reduced opportunities to mate with unrelated conspecifics. Prolonged or extensive inbreeding can result in inbreeding depression via the exposure of deleterious alleles in long runs of homozygosity. Alexander Archipelago wolves (Canis lupus ligoni) on Prince of Wales Island (POW) in Southeast Alaska are a small, isolated population of conservation concern that have experienced habitat loss and high harvest rates, and present an ideal system in which to explore questions about inbreeding. We present a custom hybridization capture that generates 37,082 genome-wide single nucleotide polymorphism (SNP) genotypes and over 500,000 SNP genotype likelihoods, allowing us to characterize and understand the extent of genomic inbreeding. We found that FROH­ revealed different patterns of inbreeding across three populations of Alexander Archipelago wolves when compared to FH. Estimates of FH revealed no differences between the three populations, while FROH revealed that wolves in the southeast portion of the study area had the greatest total proportion of the genome in runs of homozygosity, including short runs from inbreeding in distant ancestors. Wolves on POW had more long runs of homozygosity, indicating more frequent mating between individuals with recent common ancestors, likely due to smaller recent historical population size on POW. We demonstrate the advantage of using genomics to assess inbreeding via FROH (versus FH), which allows for inference about the timing and severity of inbreeding. Wolves on POW exhibit similar inbreeding patterns as wolves in Isle Royale National Park, a population that was founded by two to three individuals and has demonstrated severe inbreeding depression. This result is important for management (e.g. informing habitat use, population targets, and harvest ...