RAD sequencing and genomic simulations resolve hybrid origins within North American Canis.

L Y Rutledge,S Devillard,B N White,P A Hohenlohe,J Q Boone

doi:10.1098/rsbl.2015.0303

Abstract

Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.

Highlights

Carnivores are disappearing at an alarming rate, threatening top-down regulation, ecosystem resiliency and biodiversity worldwide [1]
To test the hypothesis that eastern wolves arose from grey wolf Â western coyote hybridization, we used RADSeq [18] of samples that are representative of the various Canis types to produce genotypes at 127 235 (127K) single-nucleotide polymorphisms (SNPs) based on a grey wolf genomic assembly
Simulated grey wolf Â western coyote hybrid genomes failed to overlap with any other Canis types when projected on the factorial map, but simulated grey wolf Â eastern wolf genomes overlapped with observed data for Great Lakes-boreal wolves and simulated eastern wolf Â western coyote genotypes overlapped with observed data for eastern coyotes

Summary

Introduction

Carnivores are disappearing at an alarming rate, threatening top-down regulation, ecosystem resiliency and biodiversity worldwide [1]. Resolving the evolutionary origins of eastern wolves from Algonquin Park and grey wolves from the Great Lakes states is a key factor in moving forward with wolf conservation in eastern North America.

Results

Conclusion