Genomic Insights into Population Structure and Inbreeding of Alaska’s Kenai Peninsula Gray Wolves

Abstract

Inbreeding depression is a rising threat to wildlife as population sizes dwindle and habitats become increasingly fragmented. Inbreeding depression results from increased frequencies of deleterious alleles, and causes individual and population level fitness reductions. The gray wolf (Canis lupus) population of the Kenai Peninsula in Alaska may be at risk of suffering from inbreeding depression. The present-day population was established in the 1960s by a small number of immigrants from the mainland. Both topographic and anthropogenic barriers are predicted to limit dispersal onto this peninsula; gene flow with the mainland population is suspected to be minimal. This study used RAD-sequencing of 229 wolves from the Kenai Peninsula and nearby mainland population to explore the population structure and genetic diversity of this system. Analyses revealed significant genetic differentiation between mainland and Kenai populations. Individuals from the primary dispersal corridor between these populations exhibited mixed ancestry, consistent with patterns expected in a metapopulation. The inbreeding coefficient (FROH) of Kenai peninsula wolves was significantly higher than that of continental populations–including Isle Royale, a classic case study of the effects of long-term genetic isolation. Further analysis suggested that this elevated inbreeding coefficient is a result of historical founder effects, rather than a reflection of ongoing inbreeding. Pairwise genetic relatedness values of present-day Kenai individuals were very low, which is consistent with this finding. Together, these findings suggest that the Kenai population experiences infrequent gene flow. Despite this, it does not appear to be currently experiencing excessive inbreeding. The high inbreeding coefficients it presented with are most likely a lingering signature of its small founding population.