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-更新世期间，影响印度次大陆、东亚及东南亚的生物地理动态塑造了复杂的生物多样性格局。本研究通过对89份历史及现代样本进行线粒体基因组（mitogenome）、细胞色素b（cytochrome b）基因及控制区（control region）测序，评估了小灵猫（Viverricula indica）的分子生物地理学特征，旨在：① 明确该物种种原分布范围内经时间校准的系统发育地理格局；② 验证其向西印度洋岛屿的引入场景。贝叶斯系统发育分析（Bayesian phylogenetic analyses）结果显示，该物种存在3个地理支系：东亚支系，以及与东南亚支系和印度次大陆+中南半岛北部支系互为姊妹群的支系，三者分化时间为3.2~2.3百万年前（Mya），未检测到显著的古种群扩张信号。在东南亚范围内，巴厘岛种群与其他种群的分化时间为2.6~1.3百万年前（Mya）。西印度洋种群被划归至印度次大陆+中南半岛北部支系，且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场景。小灵猫的早期分化很可能受上新世晚期-更新世早期的湿润期影响——该时期形成的常绿雨林屏障，在印度次大陆、东亚及东南亚区域催生了多个种内特有分布区。更新世后期，南亚与东南亚区域的干旱环境或推动了种群扩散，进而形成该物种现今的自然分布格局。本研究的分子数据支持将小灵猫划分为4个亚种，其中包括1个巴厘岛特有支系。本研究同时揭示，公元第一个千年之前的引入事件对西印度洋岛屿产生了影响，印度及/或阿拉伯商人或为获取灵猫香而将该物种引入这些岛屿。