Supplementary Datasets to "More than one species of the naked mole-rat, a new biomedical model"

<b>List of files:</b>Dataset S1 Partitioned nexus file with alignments of ddRAD sequence loci.Dataset S2 Sequence file for the multispecies coalescent analysis in BPP.Dataset S3 Coancestry matrix in pajek format, input for infomap clustering.Dataset S4 Input file for the fossilized birth-death divergence dating.Dataset S5 Supplementary Tables in a single Excel spreadsheet file.Dataset S6 Climatic and soil data at places with <i>Heterocephalus</i> presence.Dataset S7 Overview of biological samples used.Dataset S8 Raw sequences of <i>CYTB</i> and nuclear genes.<b>Abstract:</b> The naked mole-rat <i>Heterocephalus</i> is a hairless, subterranean rodent from the Horn of Africa. It has attracted scientific interest due to its cooperative breeding, poikilothermy, longevity, resistance to cancer, and tolerance to pain and hypoxia, among others. Traditionally, <i>Heterocephalus</i> has been considered a single species, <i>H. glaber</i>. Here, based on mitochondrial and nuclear genomic data across its distributional range, we report the existence of three highly divergent lineages. One of these, identified as <i>H. phillipsi</i> Thomas 1885, is especially distinct and warrants recognition as a full species. Its divergence dates back to 4.1 Ma, older than is typical for species-level splits in mammals. Morphologically, <i>H. phillipsi</i> is also distinct, notably by its reduced third molars. The split between the other two lineages, previously designated as the subspecies <i>H. g. glaber</i> Rüppell 1842 and <i>H. g. ansorgei</i> Thomas 1903, is estimated to have occurred around 2.3 Ma. While these lineages are also phylogenetically distinct, their genetic and morphological differentiation is less pronounced. The discovery of three deeply divergent lineages, each occupying different environmental conditions – particularly the presence of <i>H. phillipsi</i> in extremely harsh habitats – opens new research avenues and their value as a model organism across various fields, including biomedicine.