Data from: Y-chromosome markers for the red fox

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated
the development of genomic tools for the species. Efforts to identify the
population history of red foxes in North America have previously been
limited by a lack of information about the red fox Y-chromosome sequence.
However, a megabase of red fox Y-chromosome sequence was recently
identified over 2 scaffolds in the reference genome. Here, these scaffolds
were scanned for repeated motifs, revealing 194 likely microsatellites.
Twenty-three of these loci were selected for primer development and, after
testing, produced a panel of 11 novel markers that were analyzed alongside
2 markers previously developed for the red fox from dog Y-chromosome
sequence. The markers were genotyped in 76 male red foxes from 4
populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland
(eastern United States), and 9 from the island of Great Britain, as well
as 48 foxes of known North American origin maintained on an experimental
farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes
among these red foxes, whereas the 2 previously known markers alone would
have identified only 10 haplotypes. The haplotypes from the 4 populations
clustered primarily by continent, but unidirectional gene flow from Great
Britain and farm populations may influence haplotype diversity in the
Maryland population. The development of new markers has increased the
resolution at which red fox Y-chromosome diversity can be analyzed and
provides insight into the contribution of males to red fox population
diversity and patterns of phylogeography.