Abstract
BackgroundIdentification 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 FindingsIn 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/SignificanceOur 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.
Highlights
In biology, the identification process consists of assigning an existing taxon name to a specimen
Amplification and sequencing success were achieved for all samples except Hieracium racemosum for rbcL, Koeleria lobata for matK, and Cistus salvifolius, Hieracium racemosum, and Stellaria media for psbA-trnH
The matK and trnH-psbA showed a certain degree of intraspecific variability, but Kimura 2-parameter (K2P) values were consistently lower than 2%, as was expected in the case of a strongly heterogeneous local flora
Summary
The identification process consists of assigning an existing taxon name to a specimen. The constraints of a paper-printed publication forced most authors to organize data according to the hierarchical scheme of biological classification, so that most classical identification keys first lead to families, to genera, and to species [3]. Paper-printed keys are made of a series of identification steps fixed by the author(s), which must be followed entirely to obtain a correct identification. Digital identification keys can overcome these drawbacks. When they are based upon matrices of taxa and characters, they prevent users from following a fixed sequence of identification steps, and/or difficult characters. Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. 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
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