Additional File 1 : it contains Sample details and GenBank accession number from Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a wide-spread habitat generalist

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 million years and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to the Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.

背景 栗猫（Catopuma badia）为婆罗洲特有种；其姊妹物种亚洲金猫（Catopuma temminckii）的分布范围涵盖喜马拉雅山脉、中国南部，经中南半岛、马来半岛至苏门答腊。基于形态学数据，亚洲金猫曾被划分为至多5个亚种，但目前仍缺乏整合分子数据与形态特征的分类学评估。
结果 本研究整合分子数据（线粒体全基因组（whole mitochondrial genomes））、形态学数据（被毛特征（pelage））与物种分布预测（species distribution projections，追溯至晚更新世（Late Pleistocene）），探究过去12万年间环境变化对这对姊妹物种分布格局的影响。分子分析基于3只栗猫与40只亚洲金猫的测序线粒体基因组（mitogenomes），样本主要来源于馆藏样本（archival samples）。分子数据显示，两个物种的分化时间约为316万年前，且亚洲金猫种群的核苷酸多样性（nucleotide diversity）极低，这一结果支持该种群近期发生过种群扩张（population expansion）。
讨论 亚洲金猫极低的核苷酸多样性提示其曾经历种群瓶颈（population bottleneck）事件，该事件可能由苏门答腊北部多巴火山（Toba volcano，约7.4万年前）的喷发引发，随后在晚更新世/全新世（Holocene）早期持续发生种群扩张。物种分布预测、种群历史重建（reconstruction of the demographic history）、遗传距离隔离（genetic isolation-by-distance）模式以及被毛特征的渐变式变异，均支持亚洲金猫在多巴火山喷发后，从中国南部/中南半岛向马来半岛与苏门答腊进行种群扩张的假说。本研究结果不支持当前将亚洲金猫划分为5个亚种的分类方案，而是支持其为单型种（monotypic species），或划分为2个亚种：（1）巽他金猫（C. t. temminckii），分布于克拉地峡（Isthmus of Kra）以南区域；（2）印支、印度、喜马拉雅与中国金猫（C. t. moormensis），分布于克拉地峡以北区域。