Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach
Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach
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DOI：
10.1111/j.1755-0998.2009.02653.x
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发表时间：
2009-05-01
影响因子：
7.7
通讯作者：
Hanner, Robert H.
中科院分区：
文献类型：
--
作者：
Wong, Eugene H. -K.;Shivji, Mahmood S.;Hanner, Robert H.
全世界的鲨鱼渔业大多没有得到管理，但过去几十年来蓬勃发展的鱼翅业使监测这些动物的捕捞和贸易变得至关重要。作为一种分子物种鉴定的工具，DNA条形码提供了显着的潜力。然而，生命数据系统条形码所采用的基于遗传距离的物种鉴定方法可能经常缺乏需要明确鉴定结果的监管或法律的应用所需的特异性。这是因为这样的特异性通常不能通过查询序列与参考数据库中的条目使用遗传距离小于100%匹配来实现。虽然已经提出了各种分歧阈值来定义可接受的种内变异水平，但存在足够的例外情况，对使用基于距离的方法识别未知数的许多不完全匹配产生合理怀疑。另一种方法依赖于可用于明确诊断物种的离散分子特征的鉴定。本研究的目的是通过检查超过1000个DNA条形码（占所有已知板鳃类物种的近20%）来评估这些竞争方法之间的性能差异。我们的研究结果表明，基于字符的，核苷酸诊断（ND）的条形码识别方法是可行的，也提供了新的见解密切相关的鲨鱼物种之间的单倍型多样性的结构。还探讨了在应用领域中使用ND的考虑因素。
Shark fisheries worldwide are mostly unmanaged, but the burgeoning shark fin industry in the last few decades has made monitoring catch and trade of these animals critical. As a tool for molecular species identification, DNA barcoding offers significant potential. However, the genetic distance-based approach towards species identification employed by the Barcode of Life Data Systems may oftentimes lack the specificity needed for regulatory or legal applications that require unambiguous identification results. This is because such specificity is not typically realized by anything less than a 100% match of the query sequence to an entry in the reference database using genetic distance. Although various divergence thresholds have been proposed to define acceptable levels of intraspecific variation, enough exceptions exist to cast reasonable doubt on many less than exact matches using a distance-based approach for the identification of unknowns. An alternative approach relies on the identification of discrete molecular characters that can be used to unambiguously diagnose species. The objective of this study was to assess the performance differences between these competing approaches by examining more than 1000 DNA barcodes representing nearly 20% of all known elasmobranch species. Our results demonstrate that a character-based, nucleotide diagnostic (ND) approach to barcode identification is feasible and also provides novel insights into the structure of haplotype diversity among closely related species of sharks. Considerations for the use of NDs in applied fields are also explored.