Data from: RAD sequencing and genomic simulations resolve hybrid origins within North American Canis

• Main Authors: Rutledge, Linda Y., Devillard, S., Boone, J. Q., Hohenlohe, P. A., White, B. N.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2017
• Subjects: eastern wolf; Canis lycaon; Canis latrans; Canis lupus
• Online Access: https://doi.org/10.5061/dryad.pr318

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. MetaData_Quality_VCF This file contains 1) metadata that describes each sample used, 2) quality scores from sequencing on Illumina platform, and 3) an initial VCF file with individual genotypes compiled from the raw sequencing data (refer to methods in publication for a description of genotypes used to generate the PCA in the manuscript). Eastern Wolf Raw Data This file contains raw Illumina sequence data for the Eastern Wolves (Canis lycaon). Please check the metadata to confirm and cross-reference sample IDs. EasternWolfRawData.zip Eastern Coyote Raw Data This file contains raw Illumina sequence data for the Eastern Coyotes (Canis latrans var.). Please check the metadata to confirm and cross-reference sample IDs. EasternCoyoteRawData.zip Great Lakes ...