Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.猎豹（Acinonyx jubatus）被认为是遗传变异水平极低的物种。此前学界普遍认为，这一特征源于10000~12000年前的种群瓶颈（demographic bottleneck）事件，并由此推测现有猎豹亚种间仅存在微弱的遗传差异。然而，本研究对覆盖该物种绝大多数历史分布范围的猎豹样本开展线粒体DNA（mitochondrial DNA）与微卫星标记（microsatellites）分析后发现，部分研究种群间存在较为显著的系统地理分化（phylogeographic breaks），且多数方法得到的分化时间估算结果均早于此前推测的种群瓶颈事件。线粒体DNA单系群性（mitochondrial DNA monophyly）与整体遗传分化水平均支持东北非猎豹（Acinonyx jubatus soemmeringii）的分类独立性。此外，结合考古动物学（archaeozoological）样本与现代样本，本研究证实亚洲猎豹（Acinonyx jubatus venaticus）与非洲猎豹亚种存在明确的遗传分化。基于线粒体与核基因数据的分化时间估算显示：若采用哺乳动物平均微卫星突变率，亚洲猎豹与南非猎豹（Acinonyx jubatus jubatus）的分化时间为32000~67000年前；若采用人类微卫星突变率，则分化时间为4700~44000年前。猎豹在全球范围内均属于易危物种，在其亚洲分布区则处于极危状态：目前仅存的70~110头个体仅存活于伊朗境内。本研究证实，现存的伊朗猎豹为本土单系群种群，亦是亚洲猎豹亚种（A. j. venaticus）的最后存续类群。我们主张，保护策略应充分考虑亚洲猎豹与非洲猎豹，以及部分非洲猎豹亚种间已被揭示的独立演化历史。这将有助于兼顾两大保护优先级：维持本地适应的生态型与保护遗传多样性。