Lo Pei-Chun, Liu Shu-Hui, Nor Siti Azizah Mohd, Chen Wei-Jen
Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia.
PLoS One. 2017 Apr 28;12(4):e0176623. doi: 10.1371/journal.pone.0176623. eCollection 2017.
The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.
石首鱼科，即人们所知的黄花鱼或鼓鱼，是鲈形目鱼类中最大的科之一。最近一项基于多基因的研究，对全球石首鱼科鱼类的系统发育和生物地理学进行了调查，结果显示，该科的起源和早期分化发生在晚渐新世 - 早中新世的热带美洲地区，之后其分布范围扩展到包括印度 - 西太平洋在内的其他海域，而在该海域观察到了较高的物种丰富度。尽管对该科的整体进化历史有了这样的明确认识，但由于缺乏对所有分类单元的全面调查，关于印度 - 西太平洋地区特有的石首鱼属的分类学和系统发育的知识仍然有限。在本研究中，我们采用基于DNA的方法来研究印度 - 西太平洋分支内石首鱼物种/属的进化关系、探索物种多样性，并阐明其分类地位。为实现上述目标，本文构建了三个数据集：一个由一个核基因（RAG1）和一个线粒体基因（COI）组成的联合数据集（来自45个目前已确认物种的248个样本）；仅包含RAG1基因序列的数据集（来自44个目前已确认物种的245个样本）；以及仅包含COI基因序列的数据集（来自51个目前已确认物种的308个样本）。后者主要用于通过两种不同的物种界定方法（自动条形码间隙发现法，ABGD和广义混合尤尔合并法，GMYC）进行生物多样性探索。借助四个物种界定的补充标准（遗传相似性、从单个基因和联合数据树推断的单系性、地理分布和形态学）对结果进行了进一步评估。我们的最终结果证实了32个目前已确认物种的有效性，并识别出了几个有待正式描述的潜在新物种。我们还重新审视了鳓属、黄姑鱼属、白姑鱼属和大棘黄姑鱼属的分类地位，并建议对黄姑鱼属进行修订，同时提出了一个新属——拟鳓属。
