Stefano Martellos

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.

Plant sciences and the Italian National Biodiversity Network

Abstract Several national and global initiatives aim to increase access to biodiversity information worldwide. The Italian National Biodiversity Network, started in the framework of the project “Sistema Ambiente 2010”, will organise and manage biodiversity data hosted by museums, universities and research centres in Italy, in order to make them widely available on the Web.

Identification keys on mobile devices: The Dryades experience

Abstract This article describes the experience of project Dryades, coordinated by the University of Trieste, in developing interactive identification keys in the form of applications for mobile devices (iPhone/iPad/iPodtouch). All of our keys were previously generated from a database of morpho-anatomical characters using software FRIDA. The applications for mobile devices, which were tested Europe-wide during the project KeyToNature, have proved to be useful in education, in the promotion of nature-aware tourism and in projects of citizen science. The first-generation apps were stand-alone packages which consisted into a sequence of stand-alone HTML pages, while those of the second generation do incorporate the digital key as a true database into the mobile device. All of the hitherto published applications are basically in the form of illustrated dichotomous keys. Future developments will also include a multi-entry query interface, and will be extended to devices which use the Android system.

New trends in biodiversity informatics

Abstract Plant Biosystems dedicated a special issue to present and discuss new trends in biodiversity and informatics. The definition and theoretical framework of this challenging and stimulating research field are delineated together with several examples that illustrate data collection, organisation, dissemination, analysis and application.

From a textual checklist to an information system: The case study of ITALIC, the Information System on Italian Lichens

Abstract Checklists are fundamental for accessing information about organisms known to occur in a given area. It is possible to convert textual, paper-printed checklists into structured digital formats. This process can eventually lead to the development of digital information systems, for which the output can be far more complex than a list of taxa. Digital information systems can be continuously updated by a constant flow of information, and their content can be exported in many other different formats, hence not only mobilising, but also making biodiversity data reusable on different platforms. The conversion of the Checklist of Italian Lichens into an information system is discussed, in order to provide some general guidelines of such a process.

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.

The distribution of the two chemical varieties of the lichen Pseudevernia furfuracea in Italy

ABSTRACT The Italian distribution of the two chemical varieties of the lichen Pseudevernia furfuracea (var. ceratea with olivetoric acid and var. furfuracea without olivetoric acid) was studied on the basis of 329 samples. Var. furfuracea is most common in the beech belt, under humid climatic conditions, var. ceratea in more continental areas, such as the subalpine belt of the Alps. Differences in substrata depend on the presence of different trees in humid and continental areas.

Distributional patterns of endemic, native and alien species along a roadside elevation gradient in Tenerife, Canary Islands

Invasion by alien plant species may be rapid and aggressive, causing erosion of local biodiversity. This is particularly true for islands, where natural and anthropogenic corridors promote the rapid spread of invasive plants. Although evidence shows that corridors may facilitate plant invasions, the question of how their importance in the spread of alien species varies along environmental gradients deserves more attention. Here, we addressed this issue by examining diversity patterns (species richness of endemic, native and alien species) along and across roads, along an elevation gradient from sea-level up to 2050 m a.s.l. in Tenerife (Canary Islands, Spain), at multiple spatial scales. Species richness was assessed using a multi-scale sampling design consisting of 59 T-transects of 150 m × 2 m, along three major roads each placed over the whole elevation gradient. Each transect was composed of three sections of five plots each: Section 1 was located on the road edges, Section 2 at intermediate distance, and Section 3 far from the road edge, the latter representing the “native community” less affected by road-specific disturbance. The effect of elevation and distance from roadsides was evaluated for the three groups of species (endemic, native and alien species), using parametric and non-parametric regression analyses as well as additive diversity partitioning. Differences among roads explained the majority of the variation in alien species richness and composition. Patterns in alien species richness were also affected by elevation, with a decline in richness with increasing elevation and no alien species recorded at high elevations. Elevation was the most important factor determining patterns in endemic and native species. These findings confirm that climate filtering reflected in varying patterns along elevational gradients is an important determinant of the richness of alien species (which are not adapted to high elevations), while anthropogenic pressures may explain the richness of alien species at low elevation.

User-generated content in the digital identification of organisms: the KeyToNature approach

In biology, proper identification is fundamental to retrieve information linked to the name of an organism. Digital identification keys can be easier than the traditional paper-printed keys. However, like the latter, they often cannot be modified by users. A research group of the European Project KeyToNature has developed a new open source software, the KeyToNature Open Key Editor, which permits to easily add digital user-generated content to almost any digital dichotomous or polytomous key with the use of any common web browser. The most interesting features of the Key Editor are discussed together with some of the possible scenarios in which it can be used.

Morpho-anatomical and physiological traits in saplings of drought-tolerant Mediterranean woody species

Key messageEasily measurable functional traits can be used as proxies in the selection of drought-tolerant saplings for reforestation in Mediterranean ecosystems.AbstractHeat and drought events—increasing both in frequency and severity—have led to forest decline, and are a serious threat for the Mediterranean biome. Whereas drought tolerance of adult trees of different Mediterranean species has been widely investigated, this is not the case for saplings and young trees. We analysed correlations and trade-offs among leaf (water potential at the turgor loss point, Ψtlp, modulus of elasticity, ε, osmotic potential at full turgor, π0, leaf capacitance, Cleaf_dw, leaf venation, VLA, leaf mass per area, LMA) and stem (wood capacitance and wood density, Cwood and Dwood, stem-specific conductivity and water potential inducing 50% loss of hydraulic conductance) functional traits of saplings for 14 woody species of the Mediterranean flora. The results support previously reported correlations among functional traits known to confer drought tolerance to plants. In particular, Ψtlp was positively correlated to π0, Cleaf_dw and VLA, while negatively correlated to ε and LMA. A highly significant correlation was highlighted between Cwood and Dwood. Overall, we observed surprisingly low symplastic and apoplastic resistance. We identify some easily measurable traits (π0 and LMA), which evidence seedlings’ ability to cope with drought, and which therefore could be used as proxies in the selection of drought-tolerant saplings for reforestation in Mediterranean areas.