1,721,143 research outputs found
Molecular taxonomy in 2D: A novel ITS2 rRNA sequencestructure approach guides the description of the oystersâ subfamily Saccostreinae and the genus Magallana (Bivalvia: Ostreidae)
Full text linkMolecular approaches have contributed to a drastic reconsideration of organismsâ systematics and evolution especially in some groups of bivalves where high levels of phenotypic plasticity have hampered morphology-based assessments. However, these insights have rarely been integrated into taxonomy and classification due to the challenge of taxon description based on DNA data alone. In this study we used, for the first time, an approach based on ITS2 rRNA sequence-structure for the diagnosis and description of new oyster taxa identified based on multi-locus phylogenetic analyses including new molecular data for Striostrea Vialov, 1936. Phylogenetic analyses and diagnostic ITS2 sequence-structure characters supported Ostreidae Rafinesque, 1815 with four subfamilies: Crassostreinae Scarlato & Starobogatov, 1979 (including Crassostrea Sacco, 1897, Talonostrea Li & Qi, 1994, and Magallana gen. nov.), Saccostreinae subfam. nov. (including Saccostrea Dollfus & Dautzenberg, 1920), Striostreinae Harry, 1985 (including Striostrea) and Ostreinae Rafinesque, 1815 (including the remaining genera). We provide a formal description of the subfamily Saccostreinae subfam. nov. and the genus Magallana gen. nov., a diagnosis for the subfamily Striostreinae, and suggest the reclassification of Striostrea circumpicta (Pilsbry, 1904) and Crassostrea zhanjiangensis Wu, Xiao & Yu, 2013 as Ostrea circumpicta and Talonostrea zhanjiangensis comb. nov., respectively. This study demonstrates the suitability of ITS2 sequence-structure characters for taxonomic diagnosis and description. The advantages of such an approach in the context of DNA taxonomy of cryptic taxa are discussed
Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia
No full textIn this study, we analyzed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum likelihood and Bayesian trees based on primary sequences were congruent with (profile-) neighbor-joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, providing a phylogenetic signal comparable to (mitochondrial/nuclear) gene fragments 2-5 times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves. © 2012 Elsevier Inc
Reptiles of sardinia: Updating the knowledge on their distribution
No full textSardinia shows a clear lack of herpetological data due to an evident paucity of herpetological surveys. Tis gap of knowledge is worthy of attention, since Sardinia hosts a rich herpetofauna with a large proportion of endemic species, and distribution data are crucial for targeting conservation eforts. In this paper we provide new distribution data for Sardinian reptiles, with the aim of updating our knowledge on their specifc distribution. Data were opportunistically recorded during ten years of feld research in Sardinia, carried out in more than twenty campaigns from April 1999 to June 2009. All the eighteen reptile species belonging to the Sardinian fauna were recorded. A total amount of 293 faunistic data were collected from 178 diferent localities covering the entire study area. Within this dataset, 137 faunistic data fall outside known species' ranges as reported in the Atlas of Italian amphibians and reptiles. In conclusion, data presented here produced a remarkable increase of knowledge on Sardinian reptiles' distribution. Nevertheless, it should be evidenced that, notwithstanding the present updating, the knowledge of Sardinian reptiles' distribution is probably still far from being exhaustive. Tus, further investigations are strongly required for obtaining a complete picture and identifying conservation priorities in terms of isolated species/populations and areas of high diversity and endemicity. © Firenze University Press
Figure 2 in Revision shock in Pacific oysters taxonomy: the genus Magallana (formerly Crassostrea in part) is well-founded and necessary
No full textFigure 2. Phylogeny of Ostreidae based on mitochondrial gene order data. The phylogenetic tree was inferred using the maximum-likelihood approach based on genome rearrangements (transpositions, duplications, insertions and losses) of 16 complete mitochondrial genomes retrieved from previous studies (see text for references). Bootstrap support over 1000 replicates is reported for the main nodes. On the right, the tRNA and rRNA duplications and the tRNA transpositions that distinguish Magallana from Crassostrea oysters are mapped on to the mitochondrial genome of M. gigas and C. virginica.Published as part of Salvi, Daniele & Mariottini, Paolo, 2021, Revision shock in Pacific oysters taxonomy: the genus Magallana (formerly Crassostrea in part) is well-founded and necessary, pp. 43-58 in Zoological Journal of the Linnean Society 192 (1) on page 51, DOI: 10.1093/zoolinnean/zlaa112, http://zenodo.org/record/530118
Molecular characterization and phylogenetic position of the giant deep-sea oyster Neopycnodonte zibrowii Gofas, Salas & Taviani, 2009
No full textThe giant deep-sea oyster Neopycnodonte zibrowii Gofas, C. Salas & Taviani, 2009 is a keystone deep-sea habitat builder species. Discovered about fifteen years ago in the Azores, it has been described and assigned to the genus Neopycnodonte Fischer von Waldheim, 1835 based on morphological features. In this study, we generated DNA sequence data for both mitochondrial (COI and 16S) and nuclear (ITS2 and 28S) markers based on the holotype specimen of N. zibrowii to establish a molecular phylogenetic framework for the systematic assessment of this species and to provide a reliable (i.e., holotype-based) reference sequence set for multilocus DNA barcoding approaches. Molecular data provide compelling evidence that the giant deep-sea oyster is a distinct species, rather than a deep-water ecophenotype of Neopycnodonte cochlear (Poli, 1795), with extremely high genetic divergence from any other gryphaeid. Multilocus phylogenetic analyses place the giant deep-sea oyster within the clade “Neopycnodonte/Pycnodonte” with closer affinity to N. cochlear rather than to P. taniguchii Hayami & Kase, 1992, thus supporting its assignment to the genus Neopycnodonte. Relationships within this clade are not well supported because mitochondrial variation is inflated by saturation that eroded phylogenetic signal, implying an old split between taxa within this clade. Finally, the set of reference barcode sequences of N. zibrowii generated in this study will be useful for a wide plethora of barcoding applications in deep-sea biodiversity surveys. Molecular validation of recent records of deep-sea oysters from the Atlantic Ocean and the Mediterranean Sea will be crucial to clarify the distribution of N. zibrowii and assess the phenotypic variation and ecology of this enigmatic species
High phylogeographical complexity within Mediterranean islands: Insights from the Corsican fire salamander
No full textAim: Mediterranean islands have been the subject of intense phylogeographical investigation. While most studies have focused on the processes of colonization and dispersal between landmasses, the phylogeographical structures within islands have received less attention. Here, we investigate the Pleistocene evolutionary history of the fire salamander Salamandra corsica. Our main aim is to shed more light on the importance of intra-island micro-evolutionary processes in structuring the patterns of biodiversity on Mediterranean islands. Location: Corsica Island. Methods: We sampled 165 individuals across the entire range of S. corsica, and we sequenced two mitochondrial (cytb and cox1) and one nuclear (ßfib) gene fragments. We used Bayesian phylogeographical and historical demographic analyses based on DNA sequence data, together with species distribution modelling (SDM) under the present and past bioclimatic envelopes. Results: Bayesian phylogeographical analyses indicated that S. corsica (re)colonized its northern range during the Last Interglacial period from an ancestral area located in central-southern Corsica. According to these analyses and the SDM, S. corsica was already established throughout the island during the last glacial phase, although likely with a fragmented distribution. Historical demographic analyses suggested a post-glacial demographic expansion, probably associated with the climate-driven spatial and temporal dynamics of forested habitats. Main conclusions: Despite its restricted and insular distribution, S. corsica showed past demographic and range dynamics that are comparable to those of wide-ranging species on the continent. These dynamics are not consistent with temporal, spatial, and demographic patterns previously seen for other Corsican endemics. Such patterns of complex Pleistocene evolutionary histories and extensive phylogeographical discordance are also emerging from other insular systems. We conclude that island endemics should not be considered, a priori, as single populations and conservation units, and that the use of co-occurrence patterns of island populations as inferential tools in historical biogeography should also be carefully reconsidered
La "nazionalità" influenza la morfometria di Archaeolacerta bedriagae?
No full textThe oral communcation deals with some aspects of the geographic variation of the species which occurs in both Sardinia and Corsica and shows some differences in the morphometric character status
Nuovi sentieri di sviluppo per l'Appennino Marchigiano dopo il sisma del 2016
No full textIn questo volume, si dà conto di una ricerca condotta dalle 4 università marchigiane (Camerino, Macerata, Politecnica delle Marche e Urbino), con la collaborazione esterna dell’Università di Modena - Reggio Emilia, per l’individuazione di “Nuovi Sentieri di Sviluppo per le aree dell’Appennino Marchigiano colpite dal sisma del 2016”.
All’indomani dell’evento calamitoso, nella primavera del 2017, il Consiglio Regionale delle Marche percepisce che la sola ricostruzione fisica del patrimonio edilizio e infrastrutturale danneggiato, pur restando la grande emergenza cui far fronte, non potrà scongiurare l’abbandono di questi territori e la perdita di una straordinaria civiltà, quella della “terra di mezzo” del nostro Paese (Sargolini, 2017a).
Da questa premessa, nasce il lavoro del gruppo di ricerca che ho avuto il compito di coordinare e che ci ha portato, nei tempi previsti, a consegnare al Consiglio Regionale “undici sentieri di sviluppo”: undici strategie per la rigenerazione di un’area gravemente colpita dagli eventi sismici del 14 agosto 2016 e seguenti.
Ognuno dei ricercatori coinvolti penso abbia avuto chiara la sensazione di essere di fronte alla sfida più intensa e pregna di significati che il suo percorso accademico potesse offrire: quella di mettersi a disposizione della società civile per contribuire, con le proprie conoscenze e la capacità di costruire pensiero e strategie di attuazione, alla definizione di un sistema di supporto alle decisioni che le strutture di governo, ai diversi livelli, potessero usare per orientare la rinascita dell’Appennino Marchigiano.
Il volume restituisce il lavoro svolto e lo mette a disposizione del dibattito scientifico più allargato, delle comunità interessate, degli enti di governo ai diversi livelli, in primis, della Giunta Regionale Marche, affinché possa accoglierlo, emendarlo, integrarlo ove necessario, e tradurlo in progettazione esecutiva. È evidente che si è di fronte a scelte epocali che segneranno il futuro del Centro Italia in una direzione, piuttosto che in un’altra. Scelte che obbligano unanimità d’intenti, cooperazione e condivisione, in consessi il più possibile ampi e partecipati. Un’esigenza, quella della partecipazione delle comunità, alla definizione del progetto di rinascita del territorio da non considerarsi come un intralcio, un appesantimento, bensì come il valore fondante del processo
New distribution and genetic data extend the ranges of the spectacled salamanders, genus Salamandrina, in the Apulia region (South Italy)
No full textAdditional data on the distribution of the genus Salamandrina in the Apulia region (southern Italy) are provided. Based on fieldwork carried out from May to August 2011 in two new localities, Volturara Appula (Foggia province) and Spinazzola (Barletta province), the presence of Salamandrina species was recorded. Results from the genetic analyses of the 12S rRNA gene fragment from six individuals demonstrated that S. perspicillata occurs in Volturara Appula while S. terdigitata in the Spinazzola locality. The latter species is reported for the first time for the Apulia region. These new distribution data represent considerable range extensions for the Salamandrina species, indicating that more surveys are needed to complement the existing knowledge on their distribution as well as of the herpetofauna from the Apulia region. The conservation implications of our findings are also discussed. © Firenze University Press
The amphibians of the Circeo National Park, central Italy: distribution and aquatic habitat use
No full textAmphibians usually show pronounced variety in habitat use at different periods, selecting only part of the habitats available from their home range depending on the specific stage of the life cycle (larval, juvenile, adult) and the phenological phase (terrestrial, aquatic). The authors investigated the distribution and aquatic habitat use of seven species of amphibians occurring in Circeo National Park, central Italy. Aquatic habitats were inspected fortnightly in diurnal and nocturnal surveys from September 2009 to August 2010. Amphibians were found in 15 water bodies (three artificial and 12 natural) that differed in terms of hydro-morphology (size, depth, bottom substrate, turbidity), vegetation (aquatic, riparian and surrounding), and location (near lakes and riparian areas, fields or wooded areas). Analysis of the individuals detected was done to assess the reliability of presence/absence data and a PCA was performed for reducing dimensionality and decreasing redundancy of the environmental covariate data set. Logistic regression analysis produced significant habitat models for the anuran species (Bufo bufo, Bufotes balearicus, Hyla intermedia, two collectively evaluated Pelophylax taxa [lessonae and esculentus] and Rana dalmatina), whereas for both urodelan species (Lissotriton vulgaris and Triturus carnifex) it was not possible to derive statistically significant models. It is discussed how faunistic and ecological data appropriately analyzed could provide practical instruments for the amphibian conservation at a local scale by identifying priority species and biotopes that deserve strict management
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