DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae)

Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0–1.41%) when excluding <i>Pliocardia</i> sp.10 cf. <i>venusta</i> (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (<i>Abyssogena southwardae</i> and <i>Calyptogena rectimargo-starobogatovi</i>). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.

全球海洋的还原环境中均有深海蛤类（双壳纲：索足蛤科）分布，但由于该类群形态相似度高且可塑性强，其物种级及种以上阶元的分类学研究仍存在诸多混乱。本研究采集了线粒体细胞色素C氧化酶亚基I（COI）序列，以评估DNA条形码（DNA barcoding）在索足蛤科物种鉴定中的应用效能。基于COI序列的数据集共识别出56个支持度良好的候选物种/操作分类单元（OTUs），约占当前已记录索足蛤科物种数量的一半。其中OTU2为首次发现的类群，可能代表一新种。物种间平均遗传距离介于1.65%至29.64%之间，整体高于一般种内平均遗传距离（0%~1.41%）；若排除近似美丽纹蛤（Pliocardia sp.10 cf. venusta），该类群的种内平均遗传距离可达1.91%。在35个物种中，有33个存在局部条形码间隙（即最大种间遗传距离与最小种间遗传距离存在明显分界），仅两个类群例外：南深渊蛤（Abyssogena southwardae）和直壳铠蛤（Calyptogena rectimargo-starobogatovi）。条形码指数编号（BIN）系统为56个候选物种/OTUs中的41个分配了唯一的BIN，这表明这些类群的物种有效性得到了支持。另有3个物种被检测出拥有两个BIN，结合其较高的种内遗传变异水平，暗示这些类群内部存在隐存多样性。尽管本研究采集的16S rRNA序列数量较少，但得到了一致的研究结果：基于16S rRNA序列共鉴定出19个候选物种，且种内与种间遗传变异未出现重叠。本研究最后讨论了DNA条形码技术对索足蛤科分类学研究的启示。本研究的结果将为这一疑难蛤类类群的分类学修订提供重要依据，并为未来索足蛤科新物种的发现工作提供助力。