Search results for "Taxonomic rank"

Metagenomics reveals our incomplete knowledge of global diversity

2008

Metagenomic sequencing obtains huge amounts of sequences from environmental and clinical samples, thus providing a glimpse of the global prokaryotic diversity of both species and genes in these sources. The current trend in metagenomic analysis follows the so-called gene-centric approach, focused on describing the environments by the study of the functional roles of the proteins encoded in the sequenced genes. In this way, it is clear that metagenomic analysis relies heavily on the accurate knowledge of the universe of proteins stored in the databases. Nevertheless, it is known that some biases exist in the composition of databases (which are rich in sequences from common, cultivable and ea…

2014

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-g…

Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses.

2005

AbstractSnails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host–parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is ev…

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

2013

Abstract Background The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data. Results We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different ass…

Benchmarking plant diversity of Palaearctic grasslands and other open habitats

2021

© 2021 The Authors.

Fossil echinoid (Echinoidea, Echinodermata) diversity of the Early Cretaceous (Hauterivian) in the Paris Basin (France).

2013

11 pages; International audience; This dataset inventories occurrence records of fossil echinoid specimens collected in the Calcaires à Spatangues Formation (CSF) that crops out in the southeast of the Paris Basin (France), and is dated from the Acanthodiscus radiatus chronozone (ca. 132 Ma, early Hauterivian, Early Cretaceous). Fossil richness and abundance of the CSF has attracted the attention of palaeontologists since the middle of the nineteenth century. This dataset compiles occurrence data (referenced by locality names and geographic coordinates with decimal numbers) of fossil echinoids both collated from the literature published over a century and a half, and completed by data from …

Fungal biodiversity and in situ conservation in Italy

2011

A remarkable increase in knowledge of fungal biodiversity in Italy has occurred in the last five years. The authors report up-to-date numbers of fungi (Basidiomycota and Ascomycota) by regions together with distributional and ecological data on hypogeous fungi. Specific case studies such as alpine fungi, orchid mycorrhizas symbionts, invasive species, and the use of macrofungi as food by red squirrels are analyzed. In situ conservation strategies carried out on target species and/or taxonomic groups are also indicated.

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

2010

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish beca…

Connectedness and connectivity of the Natura 2000 network of protected areas across country borders in the European Union

2012

Abstract We studied the spatial connectedness of Natura 2000 site boundaries and the functional connectivity of the Natura 2000 network across the 34 terrestrial borders of the European Union. Connectivity was measured by the dispersal success of 192 reptile, amphibian, invertebrate and plant species from Annex II of the European Union Habitats Directive, based on the presence of same species on both sides of the borders. Connectedness and connectivity varied greatly between state borders, with good and bad examples found in all parts of the European Union. Connectedness and connectivity were positively correlated. However, a few outlying examples showed that good connectedness is not neces…

Species–area relationships in continuous vegetation: Evidence from Palaearctic grasslands

2019

Aim Species-area relationships (SARs) are fundamental scaling laws in ecology although their shape is still disputed. At larger areas, power laws best represent SARs. Yet, it remains unclear whether SARs follow other shapes at finer spatial grains in continuous vegetation. We asked which function describes SARs best at small grains and explored how sampling methodology or the environment influence SAR shape. Location Palaearctic grasslands and other non-forested habitats. Taxa Vascular plants, bryophytes and lichens. Methods We used the GrassPlot database, containing standardized vegetation-plot data from vascular plants, bryophytes and lichens spanning a wide range of grassland types throu…