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

McDevitt, A; Coscia, I; Browett, SS; Ruiz‐González, A; Statham, MJ; Ruczyńska, I; Roberts, L; Stojak, J; Frantz, AC; Norén, K; Ågren, EO; Learmount, J; Basto, M; Fernandes, C; Stuart, P; Tosh, DG; Sindicic, M; Andreanszky, T; Isomursu, M; Panek, M; Korolev, A; Okhlopkov, IM; Saveljev, AP; Pokorny, B; Flajšman, K; Harrison, SWR; Lobkov, V; Ćirović, D; Mullins, J; Pertoldi, C; Randi, E; Sacks, BN; Kowalczyk, R; Wójcik, JM

Abstract

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using Genotyping-by-Sequencing (GBS)) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. 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). 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 that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to an increased mammalian fauna on the island in the early post-glacial period. 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 evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Citation

McDevitt, A., Coscia, I., Browett, S., Ruiz‐González, A., Statham, M., Ruczyńska, I., …Wójcik, J. (2022). Next‐generation phylogeography resolves post‐glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe. Molecular Ecology, 31(3), 993-1006. https://doi.org/10.1111/mec.16276

• Journal Article Type: Article
• Acceptance Date: Nov 8, 2021
• Online Publication Date: Nov 14, 2021
• Publication Date: Feb 1, 2022
• Deposit Date: Nov 16, 2021
• Publicly Available Date: Nov 14, 2022
• Journal: Molecular Ecology
• Print ISSN: 0962-1083
• Electronic ISSN: 1365-294X
• Publisher: Wiley
• Volume: 31
• Issue: 3
• Pages: 993-1006
• DOI: https://doi.org/10.1111/mec.16276
• Publisher URL: https://doi.org/10.1111/mec.16276
• Related Public URLs: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-294X
• Additional Information: Additional Information : A pre-print version of this paper is available in the bioRxiv server at https://doi.org/10.1101/2020.02.21.954966; Access Information : This is the peer reviewed version of the following article: McDevitt, A.D., Coscia, I., Browett, S.S., Ruiz-González, A., Statham, M.J., Ruczyńska, I., Roberts, L., Stojak, J., Frantz, A.C., Norén, K., Ågren, E.O., Learmount, J., Basto, M., Fernandes, C., Stuart, P., Tosh, D.G., Sindicic, M., Andreanszky, T., Isomursu, M., Panek, M., Korolev, A., Okhlopkov, I.M., Saveljev, A.P., Pokorny, B., Flajšman, K., Harrison, S.W.R., Lobkov, V., Ćirović, D., Mullins, J., Pertoldi, C., Randi, E., Sacks, B.N., Kowalczyk, R. and Wójcik, J.M. (2021), Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe.. Mol Ecol., which has been published in final form at https://doi.org/10.1111/mec.16276. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.; Funders : National Science Centre, Poland; Grant Number: DEC-2012/05/B/NZ8/00976