Allison Patrick F, Pickich Emily T, Barnett Zanethia C, Garrick Ryan C
Department of Biology University of Mississippi University Mississippi USA.
Southern Research Station USDA Forest Service, Center for Bottomland Hardwoods Research Clemson South Carolina USA.
Ecol Evol. 2024 Jul 21;14(7):e70050. doi: 10.1002/ece3.70050. eCollection 2024 Jul.
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes ( ) per species, and another that focused on total number of sequences ( ; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (, , , and ), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the and datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.
DNA条形码技术常用于物种鉴定。尽管如此，尚未对小龙虾（十足目：螯虾科）中DNA条形码技术的实用性进行全面评估。在此，我们研究了小龙虾中局部条形码间隙（用于物种鉴定）和全局条形码间隙（用于物种发现）的存在程度，以及全局间隙是否符合先前提出的10倍阈值（种间平均差异比种内平均差异大10倍）。我们使用来自美国国立生物技术信息中心核苷酸数据库的公开线粒体COI序列数据来研究条形码间隙。我们创建了两个用于下游分析的COI数据集版本：一个侧重于每个物种的独特单倍型数量，另一个侧重于每个物种的序列总数（即包括冗余单倍型）。总共包括81个物种，其中螯虾科有58个物种和5个属，拟螯虾科有3个属的23个物种。仅在30个物种（20个螯虾科和10个拟螯虾科物种）中存在局部条形码间隙。我们仅在四个属（、、和）中检测到全局条形码间隙，均低于先前提出的10倍阈值（4.2倍至5.2倍）。我们建议约5倍阈值可能是物种发现更合适的工作假设。虽然和数据集产生了大致相似的结果，但存在一些不一致的推断。为了理解为什么有些物种缺乏局部条形码间隙，我们使用数据集对每个属进行了物种界定分析。这些结果表明，小龙虾目前的分类法可能不适用于大多数被研究的物种，并且即使存在局部条形码间隙的物种也可能需要进行分类修订。目前，DNA条形码技术在小龙虾物种鉴定和发现中的实用性相当有限，当使用基于线粒体的方法代替分类学专业知识时应谨慎。评估局部和全局条形码间隙的证据对于理解分子物种鉴定和发现的可靠性很重要，但结果取决于当前的分类学状态。随着分类学的改进（例如，通过解决物种复合体问题、可能将一些亚种提升到物种水平地位以及纠正自然历史和其他收藏中的标本错误鉴定），DNA条形码技术的实用性也将提高。
