Data from: Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo-Australian Archipelago

Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea-level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo-Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterised the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf), and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia, and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of south-westward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.

阐明基因流的空间格局与种群遗传结构，对于海洋生态系统的保护至关重要。此前学界预测，现代洋流与更新世海平面波动引发的历史隔离效应，会对海洋种群的遗传结构产生影响。作为全球海洋生物多样性热点区域的印度-澳大利亚群岛（Indo-Australian Archipelago, IAA）中，海草是其核心生态组成部分，但目前相关种群遗传学研究信息仍十分匮乏。本研究基于单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记，重构了印度-澳大利亚群岛海域海神草（Thalassia hemprichii）的系统地理学格局；同时利用16个微卫星标记组合，解析了其种群遗传结构。本研究进一步探讨了历史隔离与现代洋流在塑造种群遗传结构格局中的相对重要性。单核苷酸多态性标记的分析结果显示，该海域海神草可划分为3个种群类群：印尼东部、印尼西部（巽他陆架，Sunda Shelf）以及印度洋海域；而微卫星标记则将其分为5个种群类群：印尼东部、巽他陆架、小巽他群岛、西澳大利亚以及印度洋海域。两类标记均显示，种群类群间存在不对称的基因流，且呈现出从印尼东部向西南方向迁移的趋势。种群遗传多样性整体以印尼东部区域为最高，并向西南方向逐渐降低。该种群的遗传结构与连通格局，部分归因于更新世海平面波动，现代洋流则对该格局产生了小幅调控影响。