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Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

1
Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA
2
Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
3
Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
4
U. S. Fish & Wildlife Service, National Forensics Laboratory, Ashland, OR 97520, USA
*
Author to whom correspondence should be addressed.
Genes 2021, 12(1), 97; https://doi.org/10.3390/genes12010097
Received: 9 December 2020 / Revised: 1 January 2021 / Accepted: 11 January 2021 / Published: 14 January 2021
(This article belongs to the Collection Tools for Population and Evolutionary Genetics)
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography. View Full-Text
Keywords: target capture; Vulpes fulva; V. vulpes; Y chromosome target capture; Vulpes fulva; V. vulpes; Y chromosome
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MDPI and ACS Style

Sacks, B.N.; Lounsberry, Z.T.; Rando, H.M.; Kluepfel, K.; Fain, S.R.; Brown, S.K.; Kukekova, A.V. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes 2021, 12, 97. https://doi.org/10.3390/genes12010097

AMA Style

Sacks BN, Lounsberry ZT, Rando HM, Kluepfel K, Fain SR, Brown SK, Kukekova AV. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes. 2021; 12(1):97. https://doi.org/10.3390/genes12010097

Chicago/Turabian Style

Sacks, Benjamin N., Zachary T. Lounsberry, Halie M. Rando, Kristopher Kluepfel, Steven R. Fain, Sarah K. Brown, and Anna V. Kukekova 2021. "Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography" Genes 12, no. 1: 97. https://doi.org/10.3390/genes12010097

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