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.
Highlights
The most divergent mitochondrial split dates to approximately half a million years ago and separates a clade that evolved in North America south of the ice sheets prior to the last glaciation (Nearctic clade) and one that spans Eurasia and Alaska–western Canada, reflecting a secondary continental exchange event ~100 thousand years ago [2,4]
Little is known about red fox Y chromosome diversity
Microsatellites are useful for populationgenetic questions about contemporary gene flow and recent historical demography, more conserved mutations are needed for deeper reconstruction of Y chromosome phylogenies
Summary
The phylogeography of red fox (Vulpes vulpes) has been well-characterized in terms of mitochondrial and nuclear patterns of diversity over most of its global distribution [1,2,3,4,5,6,7]. Little is known about red fox Y chromosome diversity. Except for microsatellites, no markers exist for such investigations in red foxes [4,8]. Microsatellites are useful for populationgenetic questions about contemporary gene flow and recent historical demography, more conserved mutations are needed for deeper reconstruction of Y chromosome phylogenies
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