Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, Milano, Italy.
PLoS One. 2012;7(9):e43256. doi: 10.1371/journal.pone.0043256. Epub 2012 Sep 10.
Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting). DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences.
METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy). The core barcode markers (plastidial rbcL and matK), plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios.
CONCLUSIONS/SIGNIFICANCE: Our results show that the core barcode markers univocally identify most species of our local flora (96%). The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant biodiversity surveys.
鉴定钥匙是决策树，它要求在过程的每一步都观察生物体的一个或多个形态特征。虽然现代数字钥匙可以克服经典纸质钥匙的几个限制，但它们的性能并非无错误的。此外，当标本缺乏某些形态特征（例如由于季节、发育不完全或采集不当）时，鉴定可能无法完成。DNA 条形码已被证明在植物鉴定方面具有巨大潜力，而对于某些密切相关的分类群，它可能无效，因为相对较短的进化距离没有在核心条形码序列中产生差异。
方法/主要发现：在本文中，我们研究了 DNA 条形码如何支持现代数字方法来鉴定生物体，使用 Mt.Valerio 的本地植物群作为案例研究，这是位于意大利东北部的的里雅斯特市中心附近的一个小山丘。核心条形码标记物（质体 rbcL 和 matK），加上额外的 trnH-psbA 区域，用于鉴定维管束植物标本。我们在三个独立的模拟场景中测试了 DNA 条形码数据在增强数字识别钥匙性能方面的有用性。
结论/意义：我们的结果表明，核心条形码标记物可以唯一地识别我们本地植物群的大多数物种（96%）。trnH-psbA 数据提高了 DNA 条形码在密切相关的植物分类群之间的区分能力。在多参数数字钥匙中，DNA 条形码数据提高了识别成功率；在我们的模拟中，DNA 数据克服了某些形态特征的缺失，达到了 100%的物种正确识别。用于生成数字钥匙的 FRIDA 软件具有结合不同数据源的潜力：我们建议利用这一特性来包括分子数据，为植物生物多样性调查创建一个集成的识别系统。
