DOI: 10.5061/dryad.kp79t
title: Data from: Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia

description: Species are generally described from morphological features, but there is
 growing recognition of sister forms that show substantial genetic
 differentiation without obvious morphological variation and may therefore
 be considered ‘cryptic species’. Here, we investigate the field vole
 (Microtus agrestis), a Eurasian mammal with little apparent morphological
 differentiation but which, on the basis of previous sex-linked nuclear and
 mitochondrial DNA (mtDNA) analyses, is subdivided into a northern and a
 southern lineage, sufficiently divergent that they may represent two
 cryptic species. These earlier studies also provided limited evidence for
 two major mtDNA lineages within Iberia. In our present study we extend
 these findings through a multilocus approach. We sampled 160 individuals
 from 46 localities, mainly in Iberia, and sequenced 7 loci, maternally,
 paternally and bi-parentally inherited. Our results show that the mtDNA
 lineage identified in Portugal is indeed a distinct third lineage on the
 basis of other markers as well. In fact, multilocus coalescent based
 methods clearly support three separate evolutionary units which may
 represent cryptic species: Northern, Southern and Portuguese. Divergence
 among these units was inferred to have occurred during the last glacial
 period; the Portuguese lineage split occurred first (estimated at ca. 70
 000 years BP) and the Northern and Southern lineages separated at around
 the Last Glacial Maximum (estimated at ca. 18 500 years BP). Such recent
 formation of evolutionary units that might be considered species has
 repercussions in terms of understanding evolutionary processes and the
 diversity of small mammals in a European context.
description: Sample_dataNew sequence data and sequence data retrieved from GenBank for all loci analysed. Details on sampling locality are given for each specimen analysed. Haplotype names as well as GenBank accession numbers are detailed for each loci per specimen, as well as source of previously published data. Information on where samples are held in is also displayed.sample_data.txtBRCA1_genotype_alignmentAlignment of BRCA1 genotypes of all individuals used for species tree inference. This data set corresponds to the largest non-recombining blocks obtained with software IMgc (Woener et al. 2007). Two sequences are given per individual.BRCA1_haplotype_alignmentAlignment of BRCA1 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003). Dataset used for gene tree inference.DBX5_genotype_alignmentAlignment of DBX5 genotypes of all individuals used for species tree inference.DBX5_haplotype_alignmentAlignment of DBX5 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.CYTB_haplotype_alignmentAlignment of cytochrome b haplotypes used for gene tree inference.DBX6_genotype_alignmentAlignment of DBX6 genotypes of all individuals used for species tree inference.DBX6_haplotype_alignmentAlignment of DBX6 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.DBY7_genotype_alignmentAlignment of DBY7 sequences of all individuals used for species tree inference.DBY7_haplotype_alignmentAlignment of DBY7 haplotypes used for gene tree inference.RAG1_genotype_alignmentAlignment of RAG1 genotypes of all individuals used for species tree inference. This data set corresponds to the largest non-recombining blocks obtained with software IMgc (Woener et al. 2007). Two sequences are given per individual.RAG1_haplotype_alignmentAlignment of RAG1 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003). Dataset used for gene tree inference.SMCY7_genotype_alignmentAlignment of SMCY7 sequences of all individuals used for species tree inference.SMCY7_haplotype_alignmentAlignment of SMCY7 haplotypes used for gene tree inference.CYTB_genotype_alignmentAlignment of cytochrome b sequences of all individuals used for species tree inference.