Journal Article

Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range

Benjamin N Sacks, Zachary T Lounsberry and Mark J Statham

in Journal of Heredity

Published on behalf of American Genetic Association

Volume 109, issue 5, pages 573-584
Published in print June 2018 | ISSN: 0022-1503
Published online June 2018 | e-ISSN: 1465-7333 | DOI: https://dx.doi.org/10.1093/jhered/esy028

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  • Population Genetics
  • Phylogenetics

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Abstract

The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell’s foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.

Keywords: Population structure and phylogeography; Molecular systematics and phylogenetics; admixture; CanineHD BeadChip; phylogenomics; speciation; Vulpes fulva; V. vulpes

Journal Article.  7995 words.  Illustrated.

Subjects: Population Genetics ; Phylogenetics