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Open Access Publications from the University of California


Biogeographia – The Journal of Integrative Biogeography is the scientific journal of the Italian Biogeography Society (SIB, [in Italian only]). Since 1970, it publishes original research and reviews on any topic in biogeography.


DNA Barcodes of the animal species occurring in Italy under the European “Habitats Directive” (92/43/EEC): a reference library for the Italian National Biodiversity Network

The present paper reports the development of a public project addressed to build up and publish a DNA barcode reference library for the animal species occurring in Italy listed in the II, IV and V Annexes of the “Habitats Directive” 92/43/EEC. DNA barcoding is a global standard, namely a procedure based on a gene sequence located in a standardized genome region as a diagnostic biomarker for species. DNA barcodes data have been either produced in our laboratories or collected from the literature and international gene databases. They were subsequently used to assemble a database containing both genetic data and information related to the origin of the data. This project represents the first pilot store of DNA sequence data built-in interoperability within the portal of the National Network of Biodiversity of the Italian Ministry of the Environment. The archive, called "DNA Barcode Database of Italian Nature 2000 animal species" (owned by the Zoology and Evolutionary Biology group at Tor Vergata University), was implemented in a relational DBMS with a free license program (PostgreSQL v9.3.4), mapped using the schema ABCD and the extension DNA, and then made interoperable using the software BioCASE (v3.6.0).

Tracking the invasion of the red swamp crayfish Procambarus clarkii (Girard, 1852) (Decapoda Cambaridae) in Sicily: a “citizen science” approach

The first record of the red swamp crayfish in Sicily dates back to 2003 and, since then, the species seemed to be confined to a few localities in western Sicily. A small “citizen science” project carried out from November 2016 onwards led to the creation of the “Sicilian Procambarus working group” (SPwg), which aims at monitoring the distribution and impact of the species in Sicily. To date, the SPwg found the red swamp crayfish in five new sites on the island, thus doubling the number of local sites of occurrence. The new Procambarus clarkii sites lie in different river basins, some of them located several hundred kilometres from the invaded areas known to date, suggesting the existence of multiple independent releases of the species in the wild. The need of better informing the local population on the risks exerted by invasive species on biological diversity, and of carefully monitoring the impact of P. clarkii on the Sicilian inland water biota is briefly stressed.

Cave exploitation by an usual epigean species: a review on the current knowledge on fire salamander breeding in cave

The fire salamander (Salamandra salamandra) is a relatively common epigean amphibian, widely distributed throughout Europe, which usually gives birth to aquatic larvae. Even if epigean streams represent the most common places in which the species breeds, in some countries caves with underground waters are also used. To improve our understanding of the habitat features allowing successful breeding of salamanders in underground sites, we combined an exhaustive review of the available literature, especially the grey one, with direct observations performed from 2008 to 2017 in several natural and artificial caves of Lombardy, Liguria and Tuscany (Italy), Ariège and Provence (France). We provide a synthesis of published and unpublished caves in which the fire salamander breeding has been observed, along with a synthesis of the investigated ecological, behavioural and morphological traits. The use of underground sites is reported in several published papers and appears to be a common phenomenon not limited to single karst areas. The absence of predators, the relative stability of the aquatic habitats and the possibility to exploit new ecological resources are environmental factors that favour the breeding of the fire salamander. Our synthesis suggests that breeding of fire salamanders in caves is not a random event, but a widespread phenomenon that may be linked to specific biogeographical factors. Further insights may be obtained by performing genetic analyses on both cave and epigean populations, and considering larger landscape scales for ecological studies as well. Gene flow between salamanders that breed in caves and in streams probably occurs, but on the other hand, assortative mating might limit it, thus allowing the conservation of local adaptations driving successful cave colonisation.

Endemism in historical biogeography and conservation biology: concepts and implications

Endemism is often misinterpreted as referring to narrow distributions (range restriction). In fact, a taxon is said to be endemic to an area if it lives there and nowhere else. The expression “endemic area” is used to identify the geographical area to which a taxon is native, whereas “area of endemism” indicates an area characterized by the overlapping distributions of two or more taxa. Among the methods used to identify areas of endemism, the optimality criterion seems to be more efficient than Parsimony Analysis of Endemism (PAE), although PAE may be useful to disclose hierarchical relationships among areas of endemism. PAE remains the best explored method and may represent a useful benchmark for testing other approaches. Recently proposed approaches, such as the analysis of nested areas of endemism, networks and neighborjoining, are promising, but need to be more widely tested. All these methods attempt to identify biogeographically homogeneous sets of areas characterized by shared species, without any attempt to evaluate their relative importance for conservation purposes. Analyses based on weighted endemism methods identify areas of endemism according to specie distributional rarity and phylogenetic position, being thus appropriate for conservation purposes. The proportion of endemic species to the total number of species living a given area is the most frequently used measure to rank areas according to their relative endemism. However, proportions obscure differences in raw numbers that can be important in conservation biology. Because the number of (endemic) species tends to increase with area, some authors proposed to model the endemics-area relationship and to consider the areas displaced above the fitting curve (i.e. those having a positive residual) as hotspots. However, the use of residuals may lead to areas being identified as hotspots for almost every size class of richness. Thus, it is important to evaluate the ability of the hotspots recovered by these procedures to really conserve total (endemic) species diversity.

An historical and geographic data set on the distribution of macroinvertebrates in Italian mountain lakes

Macroinvertebrates play a key role in freshwater food webs, acting as major links between organic matter resources, primary consumers (such as bacteria), and secondary consumers (, amphibians, birds, and reptiles). In this paper we present a data set encompassing all geographic and historical data available on macroinvertebrates of the Italian mountain lakes from 1902 to 2016. The data set, divided per Italian mountain range (Alps and Apennines) and administrative region, covers more than a century of studies of many foreign and Italian scientists. The data set includes 2372 records and shows macroinvertebrate occurrence data in 176 Alpine and in 13 Apennine lakes, of which 178 of natural origin, 5 reservoirs, and 6 artificially extended. The data set lists 605 taxa, updated on the basis of their current taxonomic position. Only 353 taxa are identified at species level, highlighting the still poorly investigated biodiversity of Italian mountain lake macroinvertebrates. Since they function as key elements to characterize lake ecological status, our data set emphasizes the huge taxonomic effort that still has to be undertaken to fully characterize these ecosystems. The data set is available in csv (comma-separated values) format.

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