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.

<b>文件列表：</b>
数据集S1：包含ddRAD序列位点比对结果的分区nexus格式文件。
数据集S2：用于BPP多物种溯祖分析的序列文件。
数据集S3：pajek格式的共祖矩阵，为infomap聚类算法的输入文件。
数据集S4：用于化石出生-死亡分化定年的输入文件。
数据集S5：整合于单个Excel电子表格中的补充表格。
数据集S6：裸鼹鼠属（*Heterocephalus*）分布点位的气候与土壤数据。
数据集S7：所用生物样本概况。
数据集S8：细胞色素b（*CYTB*）基因与核基因的原始序列。
<b>摘要：</b>
裸鼹鼠（*Heterocephalus*）是分布于非洲之角的无毛地下啮齿类。其因合作繁殖行为、变温特性、超长寿命、抗癌能力以及疼痛与低氧耐受能力等特征，广受科学界关注。传统上，裸鼹鼠属仅被视为单一物种——*H. glaber*。本研究基于其分布范围内的线粒体与核基因组数据，证实存在三个高度分化的支系。其中一支被定为*H. phillipsi* Thomas 1885，该支系分化尤为显著，应被认定为独立物种，其分化时间可追溯至410万年前，早于哺乳动物典型的物种级分化时长。形态学上，*H. phillipsi*同样具有独特特征，尤以第三臼齿退化为典型标志。另外两支此前分别被定为亚种*H. g. glaber* Rüppell 1842与*H. g. ansorgei* Thomas 1903，二者的分化时间约为230万年前。尽管这两支系在系统发育上同样存在分化，但其遗传与形态差异相对较弱。本次发现的三个深度分化支系分别占据不同的生境条件——尤其是*H. phillipsi*栖息于极端恶劣的生境中——这为包括生物医学在内的多个研究领域开辟了新的研究方向，同时提升了裸鼹鼠作为模式生物的研究价值。