ReptIslands: Mediterranean islands and the distribution of their reptile fauna

Aim: Analyses of biogeographical patterns and macroecology of islands require large datasets reporting the occurrence of species. The Mediterranean region is a biodiversity hotspot, which hosts a large number of reptile species and has been the focus of many studies. Nevertheless, comprehensive inventories describing the features and biodiversity of these environments are lacking. We gathered a dataset summarizing data on reptile distribution on islands of the Mediterranean basin and Macaronesia, also including detailed information on the geographical features. Location: Islands from the Mediterranean Basin, the Atlantic Ocean within the Mediterranean biogeographical region, and Macaronesia (Canary and Savage Islands, Azores, Madeira and Cape Verde). Time period: Present. Taxon: Reptiles (squamates and turtles). Methods: Initially, we developed a geographical database describing islands of the study region, then gathered information on reptile occurrences from 757 bibliographical sources, including atlases, published papers and the grey literature. Through a critical review of these sources, we also obtained information on the status of populations (native, island endemic or non-native) and on the reliability of occurrence data. Results: We obtained basic geographical information from 1875 islands covering the whole study region and with a very broad range of geographical features. We gathered >4150 records of reptile occurrence on islands, referring to 198 taxonomic units (species or species complexes); information on population status was available for 84.9% of records. Data are provided as comma-delimited text files. Main conclusions: The database provides a key resource for biogeographical analyses and can also serve as a backbone for conservation studies. The availability of a large database on island features can also be useful for biogeographers working on other taxonomic groups. Nevertheless, more data are required for some geographical areas, in order to ascertain the status (e.g., native vs. non-native) of many populations and to understand the interplay between natural and human-driven processes

Successful sequencing of Huntington’s disease CAG microsatellite orthologs from museum collection specimens

Huntington's Disease is an inherited neurodegenerative disorder affecting human and caused by the expansion of a CAG repeat microsatellite localized in the 5\u2019 end of the Huntingtin (Htt) gene, ultimately leading to neuronal loss in brain and motor and neuropsychiatric disturbances. To obtain information on Htt orthologous genes, a potential source of genomic DNA is represented by museum collections. Here we aimed at the characterization of orthologous sequences of the human microsatellite by assessing 141 specimens from Museo di Storia Naturale di Milano, Museo di Storia Naturale di Pavia and Acquario Civico di Milano. Samples belonged to four vertebrate groups: mammals (n=66), amphibians (n=1), fishes (n=22) and reptiles (n=52). Small fragments of tissues preserved in ethanol (n=52), stored frozen (n=79) and tissues that had undergone a tanning process (n=10) were used. These specimens ranged from recently collected to over 50-years-old specimens. Genomic DNA was extracted with two different commercial kits (Macherey-Nagel, Zymo Research) and its quality assessed by ultraviolet-visible spectrophotometry and gel electrophoresis. DNA extraction yielded fragments of highly variable length, probably depending on initial sample preservation conditions. Specific primers designed to encompass the CAG tract and targeting the most conservative regions of the different templates were used to amplify the sequences of interest. Amplicon length ranged from 100 to 250 base pairs. About 50% of the PCR reactions performed were successful and the relative products have been correctly sequenced. This study demonstrates that museum collections are a valuable resource of genomic material to amplify triplet repeat loci and restates the importance of specimens conservation for scientific research

Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5037926.”The behavior of defect chalcopyrite CdAl2S4 at high pressures and ambient temperature has been investigated in a joint experimental and theoretical study. High-pressure X-ray diffraction and Raman scattering measurements were complemented with theoretical ab initio calculations. The equation of state and pressure dependences of the structural parameters of CdAl2S4 were determined and compared to those of other AB(2)X(4) ordered-vacancy compounds. The pressure dependence of the Raman-active mode frequencies is reported, as well as the theoretical phonon dispersion curves and phonon density of states at 1 atm. Our measurements suggest that defect chalcopyrite CdAl2S4 undergoes a phase transition above 15 GPa to a disordered-rocksalt structure, whose equation of state was also obtained up to 25 GPa. In a downstroke from 25 GPa to 1 atm, our measurements indicate that CdAl2S4 does not return to the defect chalcopyrite phase; it partially retains the disordered-rocksalt phase and partially transforms into the spinel structure. The nature of the spinel structure was confirmed by the good agreement of our experimental results with our theoretical calculations. All in all, our experimental and theoretical results provide evidence that the spinel and defect chalcopyrite phases of CdAl2S4 are competitive at 1 atm. This result opens the way to the synthesis of spinel-type CdAl2S4 at near-ambient conditions.Financial support from the Spanish Consolider Ingenio 2010 Program (Project CSD2007-00045) is acknowledged. This work was also supported by Spanish MICCIN under Project MAT2010-21270-C04-03/04 and by Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time was provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. J.A.S. acknowledges the Juan de la Cierva fellowship program for financial support. AM. and P.R.-H. acknowledge S. Munoz Rodriguez for providing a data-parsing application.Sans Tresserras, JÁ.; Santamaría Pérez, D.; Popescu, C.; Gomis, O.; Manjón Herrera, FJ.; Vilaplana Cerda, RI.; Muñoz, A.... (2014). Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach. Journal of Physical Chemistry C. 118(28):15363-15374. https://doi.org/10.1021/jp5037926S15363153741182

Threatened and extinct amphibians and reptiles in Italian natural history collections are useful conservation tools

Natural history museums are irreplaceable tools to study and preserve the biological diversity around the globe and among the primary actors in the recognition of species and the logical repositories for their type specimens. In this paper we surveyed the consistency of the preserved specimens of amphibians and reptiles housed in the major Italian scientific collections, and verified the presence of threatened species according to the IUCN Red List, includ-ing the Extinct (EX), Extinct in the Wild (EW), Critically Endangered (CR), Endangered (EN), and Vulnerable (VU) categories. Altogether, we analyzed 39 Italian zoological collections. We confirmed the presence of one extinct reptile (Chioninia coctei) and five extinct or extinct in the wild amphibian species (Atelopus longirostris, Nectophrynoides asperginis, Pseudophilautus leucorhinus, P. nasutus, and P. variabilis). Seven CR amphibians, fourteen CR reptile species and the extinct skink C. coctei are shared by more than one institution. Museums which host the highest number of threatened and extinct amphibian species are respectively Turin (17 CR and 1 EX), Florence (13 CR and 1 EX), and Trento (15 CR and 1 EW), while for reptiles the richest museums are those from Genoa (15 CR and 1 EX), Florence (11 CR and 1 EX), and Pisa (7 CR). Finally, we discussed the utility of natural history museums and the strategies to follow for the implementation of their functionality. © Firenze University Press

Structural and vibrational study of pseudocubic CdIn2Se4 under compression

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5077565We report a comprehensive experimental and theoretical study of the structural and vibrational properties of a-CdIn2Se4 under compression. Angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy evidence that this ordered-vacancy compound with pseudocubic structure undergoes a phase transition (7 GPa) toward a disordered rocksalt structure as observed in many other ordered-vacancy compounds. The equation of state and the pressure dependence of the Raman-active modes of this semiconductor have been determined and compared both to ab initio total energy and lattice dynamics calculations and to related compounds. Interestingly, on decreasing pressure, at similar to 2 GPa, CdIn2Se4 transforms into a spinel structure which, according to calculations, is energetically competitive with the initial pseudocubic phase. The phase behavior of this compound under compression and the structural and compressibility trends in AB(2)Se(4) selenides are discussed.This study was supported by the Spanish government MEC under Grant Nos: MAT2013-46649-C4-3-P, MAT2013-46649-C4-2-P, MAT2010-21270-C04-03/04, and CTQ2009-14596-C02-01, by MALTA Consolider Ingenio 2010 Project (CSD2007-00045) and by Generalitat Valenciana (GVA-ACOMP-2013-1012). A.M. and P.R-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster, and also to S. Munoz-Rodriguez for providing a data-parsing application. J.A.S. acknowledges Juan de la Cierva fellowship program for financial support.Santamaría Pérez, D.; Gomis, O.; Pereira, ALJ.; Vilaplana Cerda, RI.; Popescu, C.; Sans Tresserras, JÁ.; Manjón Herrera, FJ.... (2014). Structural and vibrational study of pseudocubic CdIn2Se4 under compression. Journal of Physical Chemistry C. 118(46):26987-26999. https://doi.org/10.1021/jp5077565S26987269991184

Lattice dynamics study of HgGa2Se4 at high pressures

We report on Raman scattering measurements in mercury digallium selenide (HgGa2Se4) up to 25 GPa. We also performed, for the low-pressure defect-chalcopyrite structure, lattice-dynamics ab initio calculations at high pressures which agree with experiments. Measurements evidence that the semiconductor HgGa2Se4 exhibits a pressure-induced phase transition above 19 GPa to a previously undetected structure. This transition is followed by a transformation to a Raman-inactive phase above 23.4 GPa. On downstroke from 25 GPa until 2.5 GPa, a broad Raman spectrum was observed, which has been attributed to a fourth phase, and whose pressure dependence was followed during a second upstroke. Candidate structures for the three phases detected under compression are proposed. Finally, we also report and discuss the decomposition of the sample by laser heating at pressures close to 19 GPa. As possible products of decomposition, we have identified at least the formation of trigonal selenium nanoclusters and cinnabar-type HgSe.This study was supported by the Spanish government MEC under Grant No. MAT2010-21270-004-01/03/04, by MALTA Consolider Ingenio 2010 project (CSD2007-00045), by Generalitat Valenciana through project GVA-ACOMP-2013-012, and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0966 and UPV2011-0914). E.P.-G., J.L.-S., A.M., and P.R.-H. acknowledge computing time provided by Red Espanola de Super-computacion (RES) and MALTA-Cluster.Vilaplana Cerda, RI.; Gomis Hilario, O.; Manjón Herrera, FJ.; Ortiz, HM.; Pérez González, E.; López Solano, J.; Rodríguez Hernández, P.... (2013). Lattice dynamics study of HgGa2Se4 at high pressures. Journal of Physical Chemistry C. 117(30):15773-15781. https://doi.org/10.1021/jp402493rS15773157811173