Assessing habitat quality in relation to the spatial distribution of protected areas in Italy.

The conservation of species and habitats is increasingly threatened by anthropogenic impacts, particularly land use change, from local to global scales. Although many efforts have been carried out so far to halt or at least reduce the biodiversity loss (e.g., the establishment of protected areas' networks), there are still both knowledge and policy gaps slowing the conservation of species and habitats in complex environments, such as the Mediterranean region. In particular, the human-driven impacts and threats on biodiversity need more careful analysis. Accordingly, this paper aims to assess the habitat quality and degradation in Italy in relation with the spatial pattern of the current protected areas' network, mainly to identify priority areas of intervention, thus supporting large-scale conservation strategies. A survey of experts was conducted to identify the main threats for biodiversity from different land uses at the national scale. The InVEST software was then applied to assess and map habitat quality and degradation with a high spatial resolution (20 m). The relationship between habitat quality and degradation as well as their hotspots, and alternative PA categories were also explored. Results indicate that: (i) habitat quality and degradation depend on the location and intensity of the anthropogenic impacts and are sensitive to different protection levels; (ii) the combination of the survey of experts and the spatially-explicit assessment of habitat quality and degradation is useful to highlight variations of the current conditions of biodiversity and habitats; and (iii) the identification of hotspots allows one to identify priority areas for conservation. Accordingly, the proposed approach may be used to strengthen the conservation efforts in similar contexts, and thus support the implementation of the biodiversity-related policies over the long term.

Diversity of European habitat types is correlated with geography more than climate and human pressure.

Habitat richness, that is, the diversity of ecosystem types, is a complex, spatially explicit aspect of biodiversity, which is affected by bioclimatic, geographic, and anthropogenic variables. The distribution of habitat types is a key component for understanding broad-scale biodiversity and for developing conservation strategies. We used data on the distribution of European Union (EU) habitats to answer the following questions: (i) how do bioclimatic, geographic, and anthropogenic variables affect habitat richness? (ii) Which of those factors is the most important? (iii) How do interactions among these variables influence habitat richness and which combinations produce the strongest interactions? The distribution maps of 222 terrestrial habitat types as defined by the Natura 2000 network were used to calculate habitat richness for the 10 km × 10 km EU grid map. We then investigated how environmental variables affect habitat richness, using generalized linear models, generalized additive models, and boosted regression trees. The main factors associated with habitat richness were geographic variables, with negative relationships observed for both latitude and longitude, and a positive relationship for terrain ruggedness. Bioclimatic variables played a secondary role, with habitat richness increasing slightly with annual mean temperature and overall annual precipitation. We also found an interaction between anthropogenic variables, with the combination of increased landscape fragmentation and increased population density strongly decreasing habitat richness. This is the first attempt to disentangle spatial patterns of habitat richness at the continental scale, as a key tool for protecting biodiversity. The number of European habitats is related to geography more than climate and human pressure, reflecting a major component of biogeographical patterns similar to the drivers observed at the species level. The interaction between anthropogenic variables highlights the need for coordinated, continental-scale management plans for biodiversity conservation.

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions.

BACKGROUND: Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. RESULTS: The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11-2 and BRGC11-3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. CONCLUSIONS: We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.

A grid-based map for the Biogeographical Regions of Europe.

BACKGROUND: Biogeographical units are widely adopted in ecological research and nature conservation management, even though biogeographical regionalisation is still under scientific debate. The European Environment Agency provided an official map of the European Biogeographical Regions (EBRs), which contains the official boundaries used in the Habitats and Birds Directives. However, these boundaries bisect cells in the official EU 10 km × 10 km grid used for many purposes, including reporting species and habitat data, meaning that 6881 cells overlap two or more regions. Therefore, superimposing the EBRs vector map over the grid creates ambiguities in associating some cells with European Biogeographical Regions. NEW INFORMATION: To provide an operational tool to unambiguously define the boundaries of the eleven European Biogeographical Regions, we provide a specifically developed raster map of Grid-Based European Biogeographical Regions (GB-EBRs). In this new map, the borders of the EBRs are reshaped to coherently match the standard European 10 km × 10 km grid imposed for reporting tasks by Article 17 of the Habitats Directive and used for many other datasets. We assign each cell to the EBR with the largest area within the cell.

Archival biogenic micro- and nanostructure data analysis: Signatures of diagenetic systems.

The present data in brief article provides additional data and information to our research article "Micro- and nanostructures reflect the degree of diagenetic alteration in modern and fossil brachiopod shell calcite: a multi-analytical screening approach (CL, FE-SEM, AFM, EBSD)" [1] (Casella et al.). We present fibre morphology, nano- and microstructure, as well as calcite crystal orientations and textures found in pristine, experimentally altered (hydrothermal and thermal), and diagenetically overprinted brachiopod shells. Combination of the screening tools AFM, FE-SEM, and EBSD allows to observe a significant change in microstructural and textural features with an increasing degree of laboratory-based and naturally occurring diagenetic alteration. Amalgamation of neighbouring fibres was observed on the micrometre scale level, whereas progressive decomposition of biopolymers in the shells and fusion of nanoparticulate calcite crystals was detected on the nanometre scale. The presented data in this article and the study described in [1] allows for qualitative information on the degree of diagenetic alteration of fossil archives used for palaeoclimate reconstruction.

Highly anomalous accumulation rates of C and N recorded by a relic, free-floating peatland in Central Italy.

Floating islands mysteriously moving around on lakes were described by several Latin authors almost two millennia ago. These fascinating ecosystems, known as free-floating mires, have been extensively investigated from ecological, hydrological and management points of view, but there have been no detailed studies of their rates of accumulation of organic matter (OM), organic carbon (OC) and total nitrogen (TN). We have collected a peat core 4 m long from the free-floating island of Posta Fibreno, a relic mire in Central Italy. This is the thickest accumulation of peat ever found in a free-floating mire, yet it has formed during the past seven centuries and represents the greatest accumulation rates, at both decadal and centennial timescale, of OM (0.63 vs. 0.37 kg/m2/yr), OC (0.28 vs. 0.18 kg/m2/yr) and TN (3.7 vs. 6.1 g/m2/yr) ever reported for coeval peatlands. The anomalously high accretion rates, obtained using 14C age dating, were confirmed using 210Pb and 137Cs: these show that the top 2 m of Sphagnum-peat has accumulated in only ~100 years. As an environmental archive, Posta Fibreno offers a temporal resolution which is 10x greater than any terrestrial peat bog, and promises to provide new insight into environmental changes occurring during the Anthropocene.

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.

BACKGROUND: In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. RESULTS: In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). CONCLUSIONS: We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.