Range-wide population structure of three tropical deepwater Eteline snappers across the Indo-Pacific basin

Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of three tropical deepwater snappers of the genus Etelis that reside at 100 – 400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for two of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these two species, as well as a recently proposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to management of these valuable food fishes. A total of 1,153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1,064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first two species were analyzed with mtDNA and 9 – 11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA FST= 0.010 (P=0.0007), with isolation of the Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA FST= 0.021 (P=0.0001), with low but significant levels of isolation for Hawaiʻi, and divergence between Tonga and Fiji. Etelis sp. had mtDNA FST= 0.018 (P=0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence, and isolation at the fringes of the Indo-Pacific basin in Hawaiʻi and the western Indian Ocean. While most shallow water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow water species. This population structure indicates capacity for widespread dispersal throughout the Indo-Pacific region.

Methods
The dataset includes the following, with a separate file for each of the three species in the study:

Fasta files with mitochondrial cytochrome b (cytb) DNA sequences for each sample used in this study.

Example Arlequin infiles with mitochondrial cytochrome b (cytb) DNA sequence data for each sample used in this study.

Text files with microsatellite genotypes for each sample used in this study.

深海生境可能塑造鱼类独特的扩散模式与种群动态特征，但针对此类环境中的鱼类开展相关种群遗传学分析的研究仍较为稀缺。本研究聚焦笛鲷属（Etelis）的3种热带深水笛鲷，它们栖息于100~400米水深海域，在印度-太平洋区域拥有广泛且重叠的分布范围。此前的研究显示，其中两个物种——闪光笛鲷（Etelis coruscans）与星斑笛鲷（E. carbunculus）——在夏威夷群岛内部的种群结构并不显著。本研究将采样范围拓展至每个物种的完整地理分布区，以解析这两个物种以及一个新近被提出的隐存物种（Etelis sp.）的种群遗传结构。本研究的两大目标：其一，探明深水笛鲷是否较浅水性鱼类具备更强的扩散能力；其二，探明亚中光带鱼类是否相较于受冰川海平面波动影响的浅海栖息物种，拥有更为古老且稳定的种群。这两项研究目标对于这类极具经济价值的食用鱼类的资源管理具有重要意义。本研究共分析了来自15个地理区域的1153尾闪光笛鲷样本、来自11个区域的1064尾星斑笛鲷样本，以及来自16个区域的590尾Etelis sp.样本。前两个物种采用线粒体DNA（mtDNA）与9~11个微卫星（microsatellite）位点进行遗传分析，而Etelis sp.仅采用线粒体DNA开展分析。闪光笛鲷的微卫星全局FST值无统计学显著性，但其线粒体DNA全局FST值为0.010（P=0.0007），表现为印度洋西部的塞舌尔种群出现遗传分化，同时夏威夷群岛存在间歇性的种群分化信号。星斑笛鲷的微卫星全局FST值同样无统计学显著性，而其线粒体DNA全局FST值为0.021（P=0.0001），夏威夷种群虽分化程度较低但仍具有统计学显著性，汤加与斐济种群间亦存在遗传分化。Etelis sp.的线粒体DNA FST值为0.018（P=0.0005），塞舌尔与汤加种群均呈现出显著的种群分化模式。整体而言，本研究观察到较低的种群遗传结构水平、较浅的线粒体DNA溯祖深度，且在印度-太平洋盆地边缘的夏威夷群岛与印度洋西部区域存在种群分化现象。与多数在生物地理省尺度上形成种群结构的浅水性物种不同，深水笛鲷的种群结构以大洋盆地为尺度形成，相较于浅水性物种，其种群特征更接近于远洋鱼类。这种种群结构模式表明，这类深水笛鲷具备在整个印度-太平洋区域广泛扩散的能力。

## 方法
本数据集包含以下内容，本研究涉及的3个物种各对应一个独立文件：
1. 本研究所用全部样本的线粒体细胞色素b（cytochrome b, cytb）DNA序列的Fasta格式文件
2. 本研究所用全部样本的线粒体细胞色素b（cytb）DNA序列数据的Arlequin输入文件示例
3. 包含本研究所用全部样本微卫星基因型的文本文件