Data from: Phylogeography of the small Indian civet and origin of introductions to western Indian Ocean islands

The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (i) establish a time-calibrated phylogeography across the species’ native range and (ii) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified three geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2 – 2.3 Mya, with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6 – 1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single vs. multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene – Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East and Southeast Asia. Later Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species’ current natural distribution. Our molecular data supported the delineation of only four subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of pre-first millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.

上新世-更新世（Plio-Pleistocene）时期作用于印度次大陆、东亚及东南亚的生物地理动态，造就了极为复杂的生物多样性格局。
本研究针对89份历史与现代样本开展线粒体基因组（mitogenome）、细胞色素b（cytochrome b）及控制区（control region）测序，以此解析小灵猫（Viverricula indica）的分子生物地理学特征，具体研究目标为：（i）在该物种的原生分布范围内构建时间校准的系统地理框架；（ii）验证其向西印度洋岛屿的物种引入假说。
贝叶斯系统发育分析（Bayesian phylogenetic analyses）结果显示，小灵猫可划分为3个地理支系：东亚支系、与印度次大陆+中南半岛北部支系互为姐妹群的东南亚支系，支系分化时间介于3.2~2.3百万年前，未检测到显著的种群历史扩张信号。在东南亚支系内部，巴厘岛种群与其余种群的分化时间为2.6~1.3百万年前。西印度洋种群隶属于印度次大陆+中南半岛北部支系，其线粒体多样性水平最低。近似贝叶斯计算（Approximate Bayesian computation）未能区分单次引入与多次引入两种演化假说。
小灵猫的早期分化可能由上新世晚期-更新世早期的湿润气候期驱动，当时形成的常绿雨林屏障在印度次大陆、东亚及东南亚地区催生了多个种内特有分布区域。更新世后期，南亚与东南亚地区的干旱环境可能促进了物种扩散，最终形成该物种当前的自然分布范围。
本研究的分子数据支持将小灵猫划分为4个亚种，其中包含一个特有巴厘支系。此外，本研究还证实了公元第一个千年之前小灵猫向西印度洋岛屿的引入事件，推测当时印度及/或阿拉伯商人出于获取灵猫香的目的，将该物种引入了上述岛屿。