Data from: Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.

系统地理学（phylogeography）研究表明，部分浅海海洋生物（如部分珊瑚礁鱼类）在大洋尺度上不存在空间种群结构，尽管各珊瑚礁之间以及其他扩散障碍之间存在广阔的远洋生境间隔。然而，这些具有扩散能力的广布类群在其物种分布范围内是否长期处于泛交种群（panmictic population）状态，目前仍不明确。传统的系统地理学推断往往难以区分长期泛交（panmixia）与受基因交流连接的集合种群（metapopulation）。此外，众所周知海洋生物的有效种群规模极大，这会干扰种群结构的检测。因此，海洋种群在何种空间尺度上会形成独立的进化轨迹并最终发生物种分化，目前仍无定论。
本研究针对广布印度-太平洋海域的珊瑚礁鱼类六棘鼻鱼（Naso hexacanthus）及其姊妹种蓝带鼻鱼（Naso caesius），采用2个线粒体DNA（mtDNA）标记与2个核DNA（nDNA）标记开展系统地理学研究。本研究的目标分为两部分：其一，在贝叶斯统计框架下，通过将数据拟合至多种系统地理学模型，检验六棘鼻鱼是否存在大洋尺度的泛交种群结构；其二，探究这两种广泛同域分布物种之间的遗传分化模式。
研究结果表明，六棘鼻鱼在印度-太平洋海域几乎不存在种群结构，全域长期泛交种群模型与数据的拟合度最优。因此，该物种目前在热带印度洋与太平洋的大部分区域内，均属于单一进化单元。线粒体DNA标记分析显示，六棘鼻鱼与蓝带鼻鱼并不存在相互单系（reciprocally monophyletic）关系，但二者在两个核内含子区域呈现出不同程度的种群水平分化。总体而言，研究结果符合经历一段隔离期后发生次生基因渗入（introgression）的模式，这一现象可能与更新世中晚期的海洋环境条件相关——该时期正是这两个物种的分化时段。