Data from: A late Pleistocene marine glacial refugium in the south-west of Hainan Island, China: Phylogeographical insights from the brown alga Sargassum polycystum

Aim: Hainan Island, southern China, is characterized by rich diversity and endemism of marine organisms, yet the underpinning mechanisms and processes contributing to speciation and diversification are poorly understood. Here, the brown alga Sargassum polycystum is used as a model to identify putative marine glacial refugia and explore biogeographical patterns driven by climate change in the late Pleistocene ice ages.
Location: South-East Asia.
Methods: Mitochondrial cox1 and cox3 and nuclear internal transcribed spacer-2 (ITS2) were obtained from 310, 325 and 313 individuals of S. polycystum (23 localities), respectively. Phylogenetic trees (maximum likelihood and Bayesian inference) and haplotype/ribotype networks were constructed to elucidate phylogeographical patterns. Analysis of molecular variance (AMOVA), neutrality tests (Tajima's D and Fu & Li's D*), current (θπ) and historical (θw) genetic diversities and extended Bayesian skyline plots (EBSP) were used to estimate historical demography.
Results: The populations from the south-west of Hainan Island harboured much higher genetic diversity and unique endemism in comparison with other populations in the distribution range. Sargassum polycystum experienced relatively long-term stable population size followed by a continued period of demographic expansion in the late Pleistocene.
Main conclusions: Our phylogeographical evidence revealed the existence of a previously unidentified marine refugium specific to S. polycystum in the south-west of Hainan Island, China (the Central Depression of the Yinggehai Basin), along with a possible secondary refugium around the Bali Island, Indonesia. These biogeographical findings provide important insights regarding speciation, adaptation and evolution of marine organisms in South-East Asia and the conservation of unique biodiversity under climate change.

研究目的：中国海南岛拥有丰富的海洋生物多样性与特有性，但学界对支撑其物种形成与多样化的内在机制及过程仍知之甚少。本研究以马尾藻（Sargassum polycystum）为模式物种，旨在识别潜在的海洋冰期避难所，并探索更新世晚期冰期气候变化驱动的生物地理格局。
研究区域：东南亚。
研究方法：本研究分别从覆盖23个采样点的310、325及313份马尾藻样本中，获取了线粒体cox1、cox3基因与核内转录间隔区2（ITS2）序列。通过构建最大似然法与贝叶斯推断系统发育树，以及单倍型/核糖体型网络，以阐明其系统地理格局。本研究采用分子方差分析（Analysis of Molecular Variance, AMOVA）、中性检验（Tajima's D及Fu & Li's D*）、当前遗传多样性（θπ）与历史遗传多样性（θw），以及扩展贝叶斯天际线图（EBSP）来估算历史种群动态。
研究结果：海南岛西南部的种群相较于分布区内其他种群，具有更高的遗传多样性与独特的特有性。该物种在更新世晚期经历了长期稳定的种群规模，随后进入持续的种群扩张阶段。
主要结论：本研究的系统地理学证据显示，在中国海南岛西南部（莺歌海盆地中央坳陷）存在一处此前未被报道的马尾藻特异性海洋避难所，同时在印度尼西亚巴厘岛周边存在一处潜在的次级避难所。上述生物地理学发现，为东南亚海洋生物的物种形成、适应与演化研究，以及气候变化背景下独特生物多样性的保护工作提供了重要的科学启示。