DNA Barcoding as an Effective Tool in Improving a Digital Plant Identification System: A Case Study for the Area of Mt. Valerio, Trieste (NE Italy)

Background

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.     

A federated database of taxon pages in the Italian Biodiversity Network

Primary biodiversity data are often organised in federated databases in the framework of big international projects and initiatives. Other data are normally organised into isolated resources: ecological, morphological and morpho-anatomic databases, checklists, archives of digital identification tools, etc. These data, which do not refer specifically to one specimen or observation, but to a taxon, can be addressed to as “taxon-related data”. In the framework of the Italian Biodiversity Network, taxon-related data have been aggregated by using a federated approach, with the creation of a network of data providers, which required the development of a communication protocol, the species-related data (SRD) protocol and of a simple data format (the SRD format). The SRD federated database aggregates currently ca. 70,000 taxon pages for several groups of organisms: vascular plants, lichens, mosses, algae, freshwater fishes and butterflies. All these resources can be queried by using one simple interface in the web portal of the Italian Biodiversity Network (http://www.naturaitalia.it/nnb/).     

From Local Checklists to Online Identification Portals: A Case Study on Vascular Plants

Checklists, the result of time-consuming exploration and painstaking bibliographic research, can be easily converted into online databases, which have the advantage of being updatable online in real time, and of reaching a much wider audience. However, thousands of local checklists (Natural Parks, protected areas, etc.) are still available on paper only, and most of those published online appear as dry lists of latin names, which strongly reduces their outreach for a wider audience. The University of Trieste has recently started the publication of several local checklists in a way that may be more appealing for the general public, by linking species'' names to archives of digital resources, and especially to digital identification tools produced by software FRIDA (FRiendly IDentificAtion). The query interfaces were developed on the basis of feedback from a wide range of users. The result is no longer a simple list of names accessible on the Web, but a veritable multimedial, interactive portal to the biodiversity of a given area. This paper provides an example of how relevant added value can be given to local lists of taxa by embedding them in a complex system of biodiversity-related resources, making them usable for a much wider audience than a restricted circle of specialists, as testified by the almost 1.000.000 unique visitors reached in 2014. A critical mass of digital resources is also put at disposal of the scientific community by releasing them under a Creative Commons license.     

Sharing Italian Botanic Gardens’ living collections: The role of the National Biodiversity Network

This paper presents the role of the Italian National Biodiversity Network in making available biodiversity data from Italian Botanic Gardens at a national and international level. The case study of the Botanic Garden of Rome is presented explaining procedures and methods for collecting georeferenced data on living plant species and making them available through web-based applications.     

An information system on Italian liverworts,hornworts and mosses

The checklist of hornworts, liverworts and mosses of Italy is available online as a federated database, which can be queried by combining taxonomic and distributional information. Several digital identification keys have been included in the system, which will be part of the forthcoming Italian Biodiversity Network.     

Testing the predictivity of ecological indicator values. A comparison of real and `virtual' relevés of lichen vegetation

A complex database on the lichens of Italy was used to combine ecological indicator values assigned to each species (pH, eutrophication, light and aridity), in such a way as to simulate `virtual habitats' from a beech forest of northern Italy. For each habitat, a list of species was obtained (`virtual relevé'). A matrix of real and virtual relevés was submitted to classification and ordination, obtaining six main community-types, all of which include both real and virtual relevés. Two ordinations of species were carried out, one on the matrix of real relevés, the other on that of virtual relevés: their comparison shows that the consistency and the resolving power of the indicator values was high, but it also permits to detect and correct some errors. The results indicate a high predictivity of the indicator values for constructing ecological scenarios.     

JellyWeb: an interactive information system on Scyphozoa,Cubozoa and Staurozoa

Identification of organisms is traditionally based on the use of “classic” identification keys, normally printed on paper. These keys have several drawbacks: they are mainly based on the systematics, requiring identification of orders, families and genera at first; they are written by experts for other experts, in a specific scientific jargon; they have a “frozen” structure (sequence of theses/antitheses); once published, they cannot be changed or updated without printing a new edition. Due to the use of computers, it is now possible to build new digital identification tools, which: 1) can be produced automatically, if the characters are stored in a database; 2) can be freed from the traditional systematics, giving priority to easy-to-observe characters, incl. those usually uncommon to the classical keys, such as ecology and distribution; 3) can be updated in real time once published on-line; 4) can be available on different media, and on mobile devices. An important feature of these new digital tools is their “collaborative” nature. They can be enriched by the contribution of several researchers, which can cooperate while maintaining rights and property of the resources and data they contribute to the system. JellyWeb, the information system on Scyphozoa, Cubozoa and Staurozoa has been developed in Trieste since 2010. The system was created with the aim of – potentially – becoming a starting point for a wide collaborative effort in developing a user-friendly worldwide digital identification system for jellyfishes.     

Botanical gardens and citizen science: An (as yet) under-exploited potential

Participation of citizens to research activities probably began with a “Christmas bird count” in 1900. Citizen science (CS) activities can aim at several purposes: long-term monitoring, environmental education, preservation of traditional ecological knowledge. Citizen scientists can collect data, support scientists in the field, involve decision-makers, plan new research activities, etc. While CS may have critical issues, especially as far as data quality is concerned, it has several relevant advantages as well (reduced costs, production of “big data”, awareness raising, etc.). However, especially in Europe, there is still an under-exploited potential for botanical gardens to act as drivers for CS initiatives.     

Botanical information in the Italian Biodiversity Network: One year of data aggregation and future perspectives

Since its formal institution in May 2012, the Italian Biodiversity Network is aggregating data from several research centres, for a total of ca. 1.5 million records. Botanical data made ca. 50% of the total, and range from primary biodiversity data to ecological, morpho-anatomical and taxonomical information. However, this is only a small portion of the total amount of botanical data which could be aggregated and exposed to the scientific community, professionals and citizens. In this paper we present the current status of data aggregation of the Network and its impact on digitalisation of biodiversity data, research, conservation and environmental management and education in Italy.