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较低的物种。这一现象被推测为距今10000至12000年前的种群瓶颈事件所致，同时也使得学界此前假设各已描述亚种间仅存在微小的遗传差异。然而，本研究对该物种绝大多数历史分布范围内的猎豹样本进行线粒体DNA（mitochondrial DNA）与微卫星（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，且多数方法估算的分化时间早于此前推测的种群瓶颈事件发生时间。线粒体DNA单系性与整体遗传分化水平均支持东北非猎豹（Acinonyx jubatus soemmeringii）的独特分类地位。此外，通过整合考古动物学（archaeozoology）样本与现代样本，本研究证实亚洲猎豹（Acinonyx jubatus venaticus）与非洲各亚种间存在明确的遗传分化。基于线粒体DNA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）的分化事件发生时间处于32000至67000年前；若采用人类微卫星突变率，则分化时间为4700至44000年前。猎豹在全球范围内均被列为易危物种，而其亚洲分布种群则处于极危状态：全球仅存的70至110头猎豹均栖息于伊朗境内。本研究证实：现存伊朗猎豹属于本土起源的单系种群，亦是亚洲猎豹亚种（A. j. venaticus）的最后存续类群。本研究呼吁：保护策略应充分考量未被揭示的亚洲猎豹与非洲猎豹，以及部分非洲亚种间各自独立的演化历史。此举将有助于兼顾两大核心保护目标：维持本地适应的生态型与保护遗传多样性。