Oxford Brookes University, Department of Social Sciences, Gipsy Lane, Oxford, OX3 0BP UK,
Centre for Functional Genomics, Oxford Brookes University, Oxford, OX3 0BP UK,
J Anthropol Sci. 2020 Dec 31;98. doi: 10.4436/JASS.98017.
Ambiguities within species description and identification may compromise research validity. Species identification has typically been based upon morphological characteristics, yet recent technological advances have led to identifications achieved via DNA approaches, including DNA barcoding. DNA barcoding studies typically use cytochrome c oxidase subunit I (COI) as the proposed universal molecular marker for animals. Here, we test 12 mitochondrial protein coding genes for the presence of a clear barcoding gap allowing us to unequivocally define species. Using the African Great Apes as our model group, we assess this at the species (Pan troglodytes), genus (Pan) and family (Hominidae) level. Based on 279 complete mitochondrial genomes, sequences were partitioned by gene for analysis and pairwise distances were calculated. No barcoding gap was observed at the within species level, i.e., the four recognised chimpanzee taxa were not distinguishable through DNA barcoding. However, NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit II (COII) produce the largest barcoding gaps at the genus (ND5 2%, COII 0.5%) and family (ND5 1.5%, COII 0.5%) level. Rather than focusing on COI, our analysis suggests that these two genes may be more, or at least as, appropriate markers in primate species delineation, with uses in the identification of extinct and extant species. Further use may be beneficial to taxonomists, providing additional evidence and new insights for these morphologically similar species.
物种描述和鉴定中的歧义可能会影响研究的有效性。物种鉴定通常基于形态特征，但最近的技术进步已经导致通过 DNA 方法进行鉴定，包括 DNA 条形码。DNA 条形码研究通常使用细胞色素 c 氧化酶亚基 I（COI）作为动物的拟议通用分子标记。在这里，我们测试了 12 个线粒体蛋白编码基因是否存在明确的条形码间隙，以便我们能够明确界定物种。我们以非洲大猿作为我们的模型组，在物种（黑猩猩）、属（人科）和科（人科）水平上评估这一点。基于 279 个完整的线粒体基因组，按基因进行序列分区，并计算成对距离。在种内水平上没有观察到条形码间隙，即四种公认的黑猩猩类群不能通过 DNA 条形码区分。然而，NADH 脱氢酶亚基 5（ND5）和细胞色素 c 氧化酶亚基 II（COII）在属（ND5 2%，COII 0.5%）和科（ND5 1.5%，COII 0.5%）水平上产生最大的条形码间隙。我们的分析表明，与其关注 COI，这两个基因可能更适合（或者至少与 COI 一样适合）在灵长类物种划分中作为标记基因，可用于鉴定已灭绝和现存物种。进一步的使用可能对分类学家有益，为这些形态相似的物种提供额外的证据和新的见解。
