Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status.

Elizabeth Heppenheimer,Roland Kays,Tyler Wheeldon,Klaus-Peter Koepfli,John F Benson,Paul A Hohenlohe,Ryan J Harrigan,Linda Y Rutledge,Bridgett M Von Holdt,Brent R Patterson,Alexandra L Decandia,Kristin E Brzeski

doi:10.3390/genes9120606

Abstract

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.

Highlights

Neutral theory provides a strong foundation for the application of conservation genetics, which identifies evolutionary distinct lineages that are vulnerable to genetic erosion or extinction due to reductions in population sizes [1,2,3]
Given the potential for widespread hybridization, introgression, and dispersal across the region, we evaluated contemporary population genetic dynamics and conservation value to expand on the study of Rutledge et al [35] by using a similar genomic approach across a broader representation of canids
We identified a total of 16,587 single nucleotide polymorphism (SNP) loci in 304 canids from the Great Lakes region and central Ontario

Summary

Introduction

Neutral theory provides a strong foundation for the application of conservation genetics, which identifies evolutionary distinct lineages that are vulnerable to genetic erosion or extinction due to reductions in population sizes [1,2,3]. Conservation studies have had to rely on a small number of neutral loci for genetic surveillance, even though the consequences of reduced effective population sizes may manifest genome-wide (e.g., [4]). Island species have been used as archetypal evolutionary models representing the consequences of isolated populations that can persist despite low effective population sizes [5,6,7,8]. These examples represent the simplest of scenarios, where closely related, potentially hybridizing congeners are rarely a factor contributing to loss of genomic diversity. Assuming the isolated population is of management concern (i.e., threatened/endangered species), the consequences of natural source-sink dynamics can result in challenges for species protection regulations

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