Genomics of end-Pleistocene population replacement in a small mammal

Abstract

Current species distributions at high latitudes are the product of expansion from glacial refugia into previously uninhabitable areas at the end of the last glaciation. The traditional view of postglacial colonization is that southern populations expanded their ranges into unoccupied northern territories. Recent findings on mitochondrial DNA (mtDNA) of British small mammals have challenged this simple colonization scenario by demonstrating a more complex genetic turnover in Britain during the Pleistocene-Holocene transition where one mtDNA clade of each species was replaced by another mtDNA clade of the same species. Here, we provide evidence from one of those small mammals, the bank vole (), that the replacement was genome-wide. Using more than 10 000 autosomal SNPs we found that similar to mtDNA, bank vole genomes in Britain form two (north and south) clusters which admix. Therefore, the genome of the original postglacial colonists (the northern cluster) was probably replaced by another wave of migration from a different continental European population (the southern cluster), and we gained support for this by modelling with approximate Bayesian computation. This finding emphasizes the importance of analysis of genome-wide diversity within species under changing climate in creating opportunities for sophisticated testing of population history scenarios.

An amphibian species pushed out of Britain by a moving hybrid zone

“…However, the mid‐Holocene climate models raise the question if not a B. spinosus genetic footprint would also be found in other areas with past favourable climatic conditions including Cornwall, the coastal zone of Wales and parts of Scotland. Such observations might be aligned with Oceanic climate preferences and with the "Celtic fringe" pattern of intraspecific lineage replacement that has been postulated for several small mammals (Brace et al, ; Kotlík et al, ; Kotlík, Marková, Konczal, Babik, & Searle, ; Piertney et al, ; Searle et al, ). Of particular interest in this respect are the records for peripheral and isolated toad populations on Lundy Island and the Isles of Scilly and the possible presence of toads on the Isle of Man (NBNatlas, ).…”

Polish suture zone as the goblet of truth in post-glacial history of mammals in Europe

“…Over the last few decades, numerous phylogeographic studies concerning mammalian species have been conducted in western Europe using different molecular markers-short tandem repeats (STR, microsatellite DNA; e.g., Neumann et al 2005;Beysard and Heckel 2014;Herman et al 2019), single nucleotide polymorphisms (SNP; e.g., Kotlík et al 2018), the Y chromosome (e.g., Herman et al 2019;Jones and Searle 2015), and different fragments of mitochondrial DNA (mtDNA), such as the control region (D-loop) or cytochrome b gene (e.g., Haynes et al 2003;Deffontaine et al 2005;Heckel et al 2005;Neumann et al 2005;Saarma et al 2007;Braaker and Heckel 2009;Searle et al 2009;Skog et al 2009;Lebarbenchon et al 2010;Edwards et al 2012;Herman et al 2014;Martínkovà et al 2013;Kinoshita et al 2017;Herman et al 2019). However, only results from studies using maternally inherited mtDNA are accessible (for instance, in GenBank database) and useful for continental comparison.…”

High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end‐glacial refugia

“…A total of 833 bank voles representing all major genetic lineages from 103 localities across the species range in Europe were used (Figure 1; additional data Table in Appendix ). The samples were available prior to this study (Filipi et al., 2015; Kotlík et al., 2006; Kotlík, Marková, Konczal, Babik, & Searle, 2018; Strážnická, Marková, Searle, & Kotlík, 2018; Wójcik et al., 2010) and included spleen, liver, muscle and toe clips stored in 95% ethanol at 4°C. Genomic DNA treated with RNase A was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA).…”

“…Sanger reads were assembled against the bank vole reference mitochondrial genome (GenBank accession number KF918859) (Bendová, Marková, Searle, & Kotlík, 2016) using the CodonCode Aligner version 7.1.2 (CodonCode Corporation, Centerville, MA). For 29 voles, the sequences of the protein‐coding regions of the mitochondrial genome were assembled from previously available paired‐end Illumina (San Diego, CA) RNA‐seq data (Kotlík et al., 2018) by mapping reads from each vole to the reference using the CLC Genomics Workbench version 12.0 (CLC bio A/S, Aarhus, Denmark). A set of 28 genomes described by Filipi et al.…”