1,720,968 research outputs found
DNA barcoding e tassonomia integrata per lo studio della biodiversità in taxa animali ad elevata diversità criptica
No full textThe study of biodiversity is still a hot research topic today. DNA barcoding, proposed by Hebert et al. (2003), has proven to be a powerful and rapid tool for sample identification and species discovery. This molecular approach finds applications in various fields including community ecology, conservation biology, public health monitoring, pharmacognosy, food industry, and forensic medicine. The success of DNA barcoding relies on two main premises: (i) the barcoding gap, which separates intra-specific genetic divergences from inter-specific genetic divergences, allowing to distinguish conspecific samples from those belonging to different species; (ii) the availability of reference sequence libraries associated with accurately identified samples by expert taxonomists. In cases where DNA barcoding analyses fails to provide certain identifications (often due to gaps in the reference library), it become necessary an integrative taxonomic investigation, incorporating independent characters sets such as morphology, ecology, and biogeography, for species validation and identification. Starting from preliminary taxonomic hypotheses, based on species delimitation methods to define molecular operational taxonomic units (MOTUs), integrative taxonomic studies can allow reaching robust taxonomic conclusions and in-depth understanding of biodiversity.
The aim of the PhD thesis is to combine DNA barcoding and integrative taxonomy to assess the taxonomic diversity of two selected animal groups for which morphological diagnosis can be extremely challenging. The two animal groups selected as study model are the flea beetles (tribe Alticini Newman, 1834) and the true oysters, that belong to the families Chrysomelidae Latreille, 1802 and Ostreidae Rafinesque, 1815, respectively. Alticini are characterized by high diversity with approximately 10,000 species distributed across 601 genera. This group exhibits well-defined taxonomy; however, taxonomic experts on regional faunas are often required for correct identification at species-level. In contrast, the Ostreidae family, composed of 78 species distributed worldwide, has a poorly defined taxonomy. Taxonomic identification of most species is hampered by their phenotypic plasticity and the absence of reliable diagnostic characters.
In the first part, the thesis develops studies on the biodiversity of Alticini. The DNA barcoding approach was applied by generating a reference library for 99 species belonging to 21 genera based on morphological identification and sequencing of 278 samples from 119 sites along the entire Apennine chain. The rate of correct identification of these samples based on available BOLD and GB sequence libraries was high (88%). However, 684 cases of misidentification were found in the BOLD-GB library for the studied species, which were subsequently corrected based on the reference library generated in the thesis. This study substantiates the importance of accurate reference libraries and the key role of taxonomists both in generating libraries and in their posterior validation. The solid taxonomy available for Alticini makes DNA barcoding an efficient tool for molecular species identification, with a limited number of groups requiring taxonomic reassessment. Subsequently, an integrated taxonomy approach was applied in the thesis to the Longitarsus candidulus species group. In this case, the validity of three morphologically very similar species was confirmed using a multi-locus phylogenetic approach. In particular, the species L. laureolae and L. leonardii show a peculiar disjunct Apennine-Pyrenean distribution, likely reflecting a speciation event during the Pleistocene associated with a period of severe climate change in Europe.
In the second part of the thesis, the study of global oysters’ diversity was developed through the analysis of 813 samples deposited in two of the world's major collection
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
Mediterranean spreading of the bicolor purse oyster, Isognomon bicolor, and the chicken trigger, Malleus sp., vs. the Lessepsian prejudice
Full text linkThe introduction rate of alien species in the Mediterranean Sea is rapidly growing, and their taxonomical identification is increasingly challenging. This uncertain identification often leads to an incorrect estimation of the number of alien species, their route of introduction, and their potential negative effects. This is particularly true for some bivalves, which are characterized by high variation in their shells, resulting in uncertain morphological identification. This is the case for two alien bivalves, i.e., an Isognomonidae and a Malleidae species, both characterized by confused historical colonization records in the Mediterranean Sea, misidentifications, and controversial and changing nomenclatures that have insofar negatively affected our knowledge on their geographical distributions. In this respect, molecular approaches provide a strategy that is especially useful when traditional taxonomy fails, and DNA barcoding is a powerful and well-known tool to obtain reliable identifications through efficient molecular markers. In this work, we used the 16S rRNA marker to assess the preliminary identification of Isognomon sp. and Malleus sp. specimens from different localities in the Southern Mediterranean Sea. Bayesian inference (BI) and maximum likelihood (ML) methods were applied to test the monophyly of the phylogenetic linages and to clarify their taxonomic positions, allowing a complete overview of the colonization and spreading of these two alien bivalves in the Mediterranean Sea. In particular, the Isognomon sp. specimens were identified as the Atlantic I. bicolor, highlighting that previously suggested invasive migration patterns, (i.e., the Lessepsian migration), must be reconsidered with stronger critical attention in light of currently occurring global changes
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Identification of Dipteran species inhabiting Tuber aestivum (the summer truffle) ascomata
No full textTuber spp. (Ascomycota) forms hypogeous fruiting bodies (truffles) that host many microbial species as well as invertebrates which feed on them. Despite the larvae and adults of Diptera and Coleoptera are commonly found to inhabit truffles, molecular investigations assessing their occurrence are still few and the number of species is probably underestimated. In this study, 52 larvae and adults of Diptera from 23 T. aestivum ascomata collected in two provinces of northern and central Italy were molecularly characterized. The sequences fell into four Diptera families, and four taxa were identified as Cheilosia soror, Phaonia cf. trimaculata, Drosophila subobscura, and Suillia gigantea. Morphology of adults belonging to these species confirmed their identity. Additional three taxa belonging to the Helomyzidae remained unclassified. The study highlighted the coexistence of different Diptera species in the same ascoma, suggesting potential lack of competitive exclusion. Geographical distribution analysis reveals non-site specificity for most species. This research contributes insights into the diversity of Dipteran species and their interactions with truffles and lays the groundwork for their monitoring, at a time where truffle resources are threatened by anthropic and environmental factors
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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