Data from: Range-wide snow leopard phylogeography supports three subspecies

The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the Holocene (~8,000 years ago) coinciding with increased temperatures, precipitation, and upward treeline shift in the Tibetan Plateau. Multiple analyses supported three primary genetic clusters: (1) Northern (the Altai region), (2) Central (core Himalaya and Tibetan Plateau), and (3) Western (Tian Shan, Pamir, trans-Himalaya regions). Accordingly, we recognize three subspecies, P. u. irbis (Northern group), P. u. uncia (Western group), and P. u. uncioides (Central group) based upon genetic distinctness, low levels of admixture, unambiguous population assignment, and geographic separation. The patterns of variation were consistent with desert-basin "barrier effects" of the Gobi isolating the northern subspecies (Mongolia), and the trans-Himalaya dividing the central (Qinghai, Tibet, Bhutan, and Nepal) and western subspecies (India, Pakistan, Tajikistan, and Kyrgyzstan). Hierarchical Bayesian clustering analysis revealed additional subdivision into a minimum of six proposed management units: western Mongolia, southern Mongolia, Tian Shan, Pamir-Himalaya, Tibet-Himalaya, and Qinghai, with spatial autocorrelation suggesting potential connectivity by dispersing individuals up to ~ 400 km. We provide a foundation for global conservation of snow leopard subspecies, and set the stage for in-depth landscape genetics and genomic studies.

雪豹（Panthera uncia）是一种行踪隐秘的高海拔特化物种，栖息于亚洲范围内广袤且难以抵达的栖息地。本研究开展了全球首次基于非侵入式粪便调查（noninvasive scat surveys）的雪豹全分布区遗传评估。研究对70个个体的基因组进行了33个微卫星（microsatellites）位点的基因分型，并完成了总长683碱基对的线粒体DNA（mitochondrial DNA）测序。雪豹在微卫星位点上呈现较低的遗传多样性（等位基因平均数AN=5.8，观测杂合度H_O=0.433，期望杂合度H_E=0.568），线粒体DNA几乎无变异；其种群在全新世（约8000年前）经历了瓶颈事件，该事件与青藏高原的气温升高、降水增加以及林线上移的时间节点高度吻合。多项分析结果支持雪豹存在三个主要遗传簇：（1）北部簇（阿尔泰地区），（2）中部簇（喜马拉雅核心区与青藏高原），（3）西部簇（天山、帕米尔、跨喜马拉雅地区）。基于遗传分化特征、有限的基因交流水平、明确的种群归属以及地理隔离格局，我们将雪豹划分为三个亚种：北部亚种（P. u. irbis）、西部亚种（P. u. uncia）与中部亚种（P. u. uncioides）。该变异模式符合戈壁沙漠盆地的“屏障效应”：戈壁隔离了北部亚种（蒙古种群），而跨喜马拉雅山脉则分隔了中部亚种（青海、西藏、不丹与尼泊尔种群）与西部亚种（印度、巴基斯坦、塔吉克斯坦与吉尔吉斯斯坦种群）。分层贝叶斯聚类分析（hierarchical Bayesian clustering analysis）进一步揭示了至少6个候选管理单元的细分：西蒙古、南蒙古、天山、帕米尔-喜马拉雅、西藏-喜马拉雅以及青海；空间自相关（spatial autocorrelation）分析表明，扩散个体可实现最远约400公里的种群连通性。本研究为雪豹亚种的全球保护工作奠定了科学基础，并为后续深入开展景观遗传学与基因组学研究搭建了重要框架。