Does a global DNA barcoding gap exist in Annelida?

Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications – false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for “Polychaeta”, “Oligochaeta”, and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 (“Polychaeta”), 3639 (“Oligochaeta”), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.

借助DNA条形码(DNA barcoding)技术精准鉴定未知标本，除其他因素外，依赖于DNA条形码间隙(DNA barcoding gap)的存在；若缺乏该间隙，则可能导致可疑的物种鉴定结果——即假阴性或假阳性。尽管若缺乏清晰且规模足够的条形码间隙，DNA条形码技术的应用价值将大幅降低，但目前针对全面采样数据的种内与种间遗传距离阈值，仍鲜有被深入检视。本研究旨在针对动物界环节动物门(Annelida)，全面阐明条形码技术的这一应用局限。本研究从基因银行(GenBank)中下载环节动物门，以及多毛纲(Polychaeta)、寡毛纲(Oligochaeta)和蛭纲(Hirudinea)各自的所有细胞色素c氧化酶亚基I序列（即cox1基因(cox1 gene)，动物DNA条形码的标准选定区域），并针对序列长度、覆盖度及潜在污染情况进行质控整理。最终数据集分别包含9782条环节动物门、5545条多毛纲、3639条寡毛纲以及598条蛭纲的cox1序列，这些序列要么直接用于自动化全局DNA条形码间隙检测分析，要么进一步开展遗传距离分析：先将序列按种内与种间比对进行分箱，再绘制成图表以可视化潜在的全局DNA条形码间隙。本研究共完成超过7000万次成对遗传比对，结果显示：尽管各类数据集均呈现出一定的序列分离趋势，但所有数据集均未存在清晰且规模足够的全局DNA条形码间隙，这意味着未来的条形码鉴定工作存在物种鉴定出错的风险（不过局部DNA条形码间隙仍可能存在，可用于较低分类阶元的物种鉴定）。这一点在蚯蚓类群中尤为明显：在所有显示0%遗传分歧度的种间比对中，蚯蚓类群占比高达35%。