Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, Gwynedd, United Kingdom.
PLoS One. 2012;7(11):e49623. doi: 10.1371/journal.pone.0049623. Epub 2012 Nov 29.
DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.
METHODOLOGY/PRINCIPAL FINDINGS: Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32-4.82%) than mean estimates (0.24-0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata.
CONCLUSION/SIGNIFICANCE: This study confirms that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources.
DNA 条码通常集中在许多动物的细胞色素氧化酶 I 基因 (COI) 上，已被广泛用作物种鉴定工具。DNA 条码区分不同分类群物种的能力以及揭示隐种的能力已得到充分证明。尽管来自许多温带地区的鱼类 DNA 条码数据丰富，但来自东南亚地区的相对较少。在这里，我们以海洋鱼类鲹科为目标，该科是印度-马来群岛 (IMA) 最重要的商业鱼类家族之一，以生成初始参考 DNA 条码文库。
方法/主要发现：这里，对来自 IMA 水域的 36 种假定鲹科物种的 723 个个体进行了 COI 的 652bp 区域测序。在新生成的数据集内，三种已描述的物种表现出高达十倍的同物异形分化 (4.32-4.82%)，高于平均估计值 (0.24-0.39%)，表明与分配的形态分类鉴定存在差异，并且存在隐种。比较了种内和种间的线粒体 DNA COI 区域的变异性，以评估 COI 区域对物种鉴定的适用性。观察到的平均 K2P 距离范围趋势通常与基于分类层次的预期相符：种内个体之间为 0%-4.82%，属内物种之间为 0%-16.4%，属内科之间为 8.64%-25.39%。个体之间、属内物种之间和属内科之间的 Kimura 2-参数 (K2P) 平均距离分别为 0.37%、10.53%和 16.56%。尽管在印度-马来鲹科中检测到三种代表六个潜在隐种复合体的物种，但所有描述的物种都在邻接法系统发育树中形成单系聚类；Atule mate、Selar crumenophthalmus 和 Seriolina nigrofasciata。
结论/意义：这项研究证实 COI 是 IMA 鲹科物种鉴定的有效工具。在 IMA 的中心地区，假定种内存在中等程度的隐种多样性。然而，要解释 IMA 物种丰富度的假设，有必要在其广泛的地理范围内对整个家族进行采样。这些见解不仅有助于记录鲹科多样化和繁殖的机制，还为管理策略和商业重要渔业资源的保护提供了科学框架。
