Data from: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika

We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.

本研究从坦噶尼喀湖（Lake Tanganyika, LT）沿岸带（littoral zone）的96个形态种（morphospecies）慈鲷中，获取了398条细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I）条形码序列。本研究采用物种鉴定（species identification）与物种划分（species delineation）两类方法，评估了DNA条形码（DNA barcoding）在该类群鱼类中的应用潜力。采用最佳匹配（best match, BM）与最佳近邻匹配（best close match, BCM）方法评估整体鉴定成功率，共分析了三类样本库，其中标本以三种不同方式被划分为操作分类单元（Operational Taxonomic Units, OTU）：（A）包含未描述种在内的形态学区分物种，（B）有效物种，以及（C）形态相似或近缘物种复合体。三类样本库A、B、C经BM方法的正确鉴定率分别为73%、73%与96%，经BCM方法的正确鉴定率则分别为72%、70%与94%。此外，本研究还测试了两种物种划分方法的应用潜力。广义混合尤尔合并模型（General Mixed Yule Coalescent, GMYC）分析提示存在70个假想物种，而自动条形码间隙发现（Automatic Barcode Gap Discovery, ABGD）方法则识别出115个推定物种。尽管ABGD方法存在过度拆分的倾向，但其在物种还原效果上优于GMYC分析。在多数ABGD提示过度拆分的案例中，该现象源于种内地理变异。GMYC方法无法还原多数物种的原因，可归因于线粒体基因树（mitochondrial gene trees）与坦噶尼喀湖慈鲷物种进化历史之间的不一致性。坦噶尼喀湖沿岸带慈鲷具有复杂的进化历史，涵盖杂交、基因渐渗（introgression）与快速成种（rapid speciation）等事件。尽管DNA条形码在物种鉴定中的应用仅局限于物种复合体层级，但其在慈鲷辐射演化类群（cichlid radiations）的物种发现中仍具备应用潜力。