Timing of branching events on “significant” nodes (bootstrap>95) on the Maximum likelihood tree (Figure 1).

<p>Timing of branching events on “significant” nodes (bootstrap>95) on the Maximum likelihood tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030043#pone-0030043-g001" target="_blank">Figure 1</a>).</p

Maximum likelihood phylogenetic tree showing the relationship between 41 samples of blind mole rats plus one outgroup <i>Acomys cahirinus</i>.

<p>Numerical values represent bootstrap values out of 1000 reiterations. The nodes marked by capital letters represent internal and external branches supported by bootstrap values higher than 95%. The clades are referred to by Roman numerals: I “Spalax”, II “vasvarii”, III “leucodon”, IV “xanthodon” and V “ehrenbergi” (a). Taxonomic nomenclature is according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030043#pone.0030043.s001" target="_blank">Table S1</a>; Neighbour-net graph showing an agreement in the major splits with the ML tree (b).</p

Maximum likelihood phylogram of blind mole rates constructed by means of PhyMl.

<p>Branch values indicate the rate of heterogeneity (a). Neighbor-net graph showing relationship between clades “<i>vasvarii”,</i> “<i>leucodon”</i> and “<i>xanthodon”</i>. It shows that the clades are significantly separated (indicated by 100% bootstrap), but that among them some speciation-related processes such as hybridization or introgression could take place (b).</p

Sampling points covering the distribution area of blind mole rats ranging from the Carpathian Basin to the East Mediterranean.

<p>For numerical symbols see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030043#pone.0030043.s001" target="_blank">Table S1</a>.</p

mitochondrial_alignment_for_starbeast

An alignment of concatenated Cyt-b and COI genes (in FASTA) used in a *BEAST analysis for inferring the divergence processes within the Murina gracilis complex. The XML input file of *BEAST is also provided

microsat_flanking_regions_for_networks

Alignments of phased sequences (in FASTA) at two microsatellite flanking regions used in constructions of median-joining networks

IMa2_input

The input of multi-taxon IMa2 which is used to infer the divergence processes within the Murina gracilis complex

microsat_flanking_regions_for_starbeast

Alignments of phased sequences (in FASTA) at ten microsatellite flanking regions used in *BEAST analyses for inferring the divergence processes within the Murina gracilis complex. Prior to *BEAST analyses, all alignments except for that for the locus A122-2 are trimmed to be free from recombination. XML input files of *BEAST separately prepared for analyses with different demographic models are also provided