1,720,969 research outputs found
Whole genome sequencing data provide a landscape picture of genetic variability in sea cucumber species.
No full textHolothuria or sea cucumber is a genus of marine invertebrates, belonging to the group Echinodermata, commonly called sea cucumbers. Holothuria species are detritivores, raking sand into their mouth with oral tentacles, extracting and digesting the bacteria, animal and vegetal particles, and voiding the sand through the anus. In this way they churn up significant areas of the seabed, playing a central role in the habitat these species live. Holothuria species have been seen as a promising candidate for aquaculture, as they are resistant to handling and adapt easily to captivity conditions. The interest in Holothuria for aquaculture began in Asia and reached the European market, making it a potentially valuable species for European aquaculture. The genus counts more than 160 species, many of which are uncharacterised at the genome level. However, very recently, few genome drafts became available, allowing to conduct genomic analyses on these species. Here, we provide a first comparative genome analysis of two species of sea cucumber that are common along Italian shores, Holoturia polii (HP) and Holoturia tubulosa (HT) utilizing the reference genome of Holothuria glaberrima (HG) in the comparison, the only reference genome so far available. The reference genome is composed of 89,105 scaffolds, most of them (54,676) with scaffolds below 10 kbp in size. Scaffolds over 10 kbp represent 1.067Gb of the predicted 1.1Gb. We produced whole genome sequencing datasets using Illumina paired-end read for a few HP and HT samples. About 300 million reads per sample were filtered and then mapped to the HG reference genome with standard options. Variant calling was performed considering all samples together. The genome coverage from the datasets of HP and HT was 56% and 58%, respectively. This relatively low coverage is probably linked to the drafted genome assembly for HG, which is highly fragmented. Variant calling produced 72,217,418 single nucleotide polymorphisms (SNPs), mostly on the longer scaffolds that will constitute the core of the analyses. This information has been used to estimate the genetic relationship among the three species and detect genomic regions of high genetic divergence that might be useful to define specific genome regions that characterize different Holothuria species.
Acknowledgements
This study was supported by HOLOTHURIA project funded by Italian Ministry of Agriculture, Food Sovereignty and Forestry (MASAF) grant n. J56J20000150001
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
An integrated genetic and morphological approach to clarify the conservation status of the threatened Italian endemic species Alburnus albidus (Cypriniformes: Cyprinidae)
No full textThe Italian bleak, Alburnus albidus, is a
freshwater species endemic of southern Italy, that was
recently classified as vulnerable in the IUCN Red List,
due to the impact of introduced species. In this study, a
combined genetic (mitochondrial cyt b and nuclear
ITS1 DNA markers) and morphometric approach was
applied to five populations from the whole range of A.
albidus. Data were compared with those for the
alborella A. arborella, an introduced species native
to northern Italy. The results indicate a dramatic threat
to A. albidus, as 39% of the specimens examined are
the result of hybridization with other introduced
cyprinids, mainly A. arborella. Hybrid individuals
suggest bi-directional hybridization, but introgressed
individuals exclusively show A. albidus nuclear
genomes and A. arborella mitochondrial haplotypes.
Morphological data discriminate the two parental
Alburnus but not their hybrids or introgressed individuals.
Genetic variability between the species is
greater than the morphological variability. Ofanto
River shows the most compromised situation suggesting
the occurrence of multiple introductions, while
Agri and Trigno populations are the most conserved,
and deserve priority conservation actions. Given this,
an update of the conservation status is recommended
A shape distance based on the Fisher–Rao metric and its application for shapes clustering
No full textIn the clustering of shapes, which is a longstanding challenge in the framework of geometric morphometrics and shape analysis, is crucial the selection and application of a suitable and appropriate measurement of distance among observations (i.e. individuals). The aim of this study is to model shapes from complex systems using Information Geometry tools.
It is well-known that the Fisher information endows the statistical manifold, defined by a family of probability distributions, with a Riemannian metric, called the Fisher–Rao metric. With respect to this, geodesic paths are determined, minimizing information in Fisher sense. The geodesic distance induced by the Fisher–Rao metric can be used to define a shape metric which enables us to quantify differences between shapes.
The discriminative power of the proposed Fisher–Rao distance is tested in the context of shapes clustering on both simulated and real data sets. Results show a better ability in recovering the true cluster structure with respect to the standard Kendall’s shape metric
Variations on the Author
Get PDF“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
The consumption of farmed and organic fish in italy
No full textThis tool offers insights about the creation of the consumer survey and the results which offer valuable insights for the organic aquaculture sector in Italy but also Europe as a whole
Organic aquaculture - Weaknesses and opportunities in the sector
No full textThe tool offers information about the state of organic aquaculture in Europe, and specifically in Italy. You can also find information about the main certification bodies in Italy, insights from producers, specific breeds for organic aquaculture and information about certain EU regulations
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe 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
Get PDFWe 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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