Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Abstract

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets.

Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

“…This early history of colonisation of the British Isles inferred here from whole-genome sequences and supported by SDM projections on past climatic features is apparently unique among terrestrial vertebrates, but it is far from the first to deviate from the most common colonisation route over Doggerland (e.g. Boston et al, 2015;Kelly et al, 2010;Snell et al, 2005;Stewart & Lister, 2001;Teacher et al, 2009) or to indicate an earlier colonisation than generally assumed (Martínková et al, 2007;McDevitt et al, 2020). The case of the stoat (Mustela erminea) is particularly interesting as it was found to have had an isolated glacial refugium also in now submerged land southwest of today's French coastline on the Bay of Biscay (Figure 4c -LGM; Martínková et al 2007).…”

Unexpected post‐glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

“…This early history of colonisation of the British Isles inferred here from whole‐genome sequences and supported by SDM projections on past climatic features is apparently unique among terrestrial vertebrates thus far, but it is far from the first to deviate from the most common colonisation route directly over Doggerland (e.g., Boston et al, 2015 ; Kelly et al, 2010 ; Snell et al, 2005 ; Stewart & Lister, 2001 ; Teacher et al, 2009 ) or to indicate an earlier colonisation than generally assumed (Martínková et al, 2007 ; McDevitt et al, 2020 ). Actually, it has often been conjectured that some organisms of the British Isles had an Iberian origin though this remained unconfirmed (e.g., Arntzen, 2019 ; Corbet, 1961 ; McDevitt et al, 2011 ).…”

Next‐generation phylogeography resolves post‐glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

“…Raw SNP data and data sets used for individual and population‐level analyses have been made available on Dryad (https://doi.org/10.5061/dryad.b2rbnzsb0; McDevitt et al, 2020).…”