DOI: 10.5061/dryad.9fc86
title: Data from: Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole

description: Glacial refugia protected and promoted biodiversity during the
 Pleistocene, not only at a broader scale, but also for many endemics that
 contracted and expanded their ranges within refugial areas. Understanding
 the evolutionary history of refugial endemics is especially important in
 the case of endangered species to recognise the origins of their genetic
 structure and thus produce better informed conservation practices. The
 Iberian Peninsula is an important European glacial refugium, rich in
 endemics of conservation concern, including small mammals, such as the
 Cabrera vole (Microtus cabrerae). This near-threatened rodent is
 characterised by an unusual suite of genetic, life history and ecological
 traits, being restricted to isolated geographic nuclei in
 fast-disappearing Mediterranean sub-humid herbaceous habitats. To
 reconstruct the evolutionary history of the Cabrera vole, we studied
 sequence variation at mitochondrial, autosomal and sex-linked loci, using
 invasive and noninvasive samples. Despite low overall mitochondrial and
 nuclear nucleotide diversities, we observed two main well-supported
 mitochondrial lineages, west and east. Phylogeographic modelling in the
 context of the Cabrera vole's detailed fossil record, supports a
 demographic scenario of isolation of two populations during the Last
 Glacial Maximum (LGM) from a single focus in the southern part of the
 Iberian Peninsula. In addition, our data suggests subsequent divergence
 within the east, and secondary contact and introgression of the expanding
 western population, during the late Holocene. This work emphasises that
 refugial endemics may have a phylogeographic history as rich as that of
 more widespread species, and conservation of such endemics includes the
 preservation of that genetic legacy.
description: BRCA1_MC_TAlignment of 76 sequences from Cabrera vole tissue samples of the autossomal BRCA1 gene, exon 11.COPS7_MC_TAlignment of 77 sequences from Cabrera vole tissue samples of the autossomal COPS7A gene, intron 4.CYTB_MC_TNIAlignment of 284 sequences of Cabrera vole tissue samples and bones (from owl pellets) for the mitochondrial cyt-b gene.DBX5_MC_TAlignment of 79 sequences of Cabrera vole tissue samples for the sex-linked (X-chromossome) DBX gene, intron 5.DBX7_MC_TAlignment of 79 sequences of Cabrera vole tissue samples for the sex-linked (X-chromossome) DBX gene intron 7. There are two individuals with heterozygous indels, thus for those we provide phased sequences which are identified as "code" and "code+ii".IRBP_MC_TAlignment of 78 sequences of Cabrera vole tissue samples for the autossomal gene IRBP, exon 1.OSTA5_MC_TAlignment of 74 sequences of Cabrera vole tissue samples for the autossomal gene OSTA, intron 5.PNPO3_MC_TAlignment of 77 sequences of Cabrera vole tissue samples for the autossomal gene PNPO, intron 3.RAG1_MC_TAlignment of 70 sequences of Cabrera vole tissue samples for the autossomal gene RAG1, exon 1.SLC38_MC_TAlignment of 74 sequences of Cabrera vole tissue samples for the autossomal gene SLC38A7, intron 8.SMCY7_MC_TAlignment of 39 sequences of Cabrera vole tissue samples for the sex-linked (Y-chromossome) gene SMCY, intron 7.