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

Authors

Benjamin N. Sacks, University of California, Davis
Zachary T. Lounsberry, University of California, Davis
Halie M. Rando, College of Agricultural, Consumer and Environmental SciencesFollow
Kristopher Kluepfel, University of California, Davis
Steven R. Fain, US Fish and Wildlife National Forensics Laboratory
Sarah K. Brown, University of California, Davis
Anna V. Kukekova, College of Agricultural, Consumer and Environmental Sciences

Author ORCID Identifier

Benjamin Sacks: 0000-0003-0143-6589

Halie M. Rando: 0000-0001-7688-1770

Steven R. Fain: 0000-0002-9748-7745

Anna V. Kukekova: 0000-0001-7027-3715

Document Type

Article

Publication Date

1-1-2021

Publication Title

Genes

Abstract

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.

Keywords

Target capture, V. vulpes, Vulpes fulva, Y chromosome

Volume

12

Issue

1

First Page

1

Last Page

10

DOI

10.3390/genes12010097

Comments

Archived as published.

Recommended Citation

Sacks, Benjamin N.; Lounsberry, Zachary T.; Rando, Halie M.; Kluepfel, Kristopher; Fain, Steven R.; Brown, Sarah K.; and Kukekova, Anna V., "Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative Snp Markers and Glimpse Male-Specific Trans-Pacific Phylogeography" (2021). Computer Science: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/csc_facpubs/416