RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org

Biodiversity and structure of spider communities along a metal pollution gradient

The objective of the study was to determine whether long-term metal pollution affects communities of epigeal spiders (Aranea), studied at three taxonomic levels: species, genera, and families. Biodiversity was defined by three indices: the Hierarchical Richness Index (HRI), Margalef index (DM) and Pielou evenness index (J). In different ways the indices describe taxa richness and the distribution of individuals among taxa. The dominance pattern of the communities was described with four measures: number of dominant species at a site, percentage of dominant species at a site, average dominant species abundance at a site, and the share of the most numerous species (Alopecosa cuneata) at a site. Spiders were collected along a metal pollution gradient in southern Poland, extending ca. 33 km from zinc and lead smelter to an uncontaminated area. The zinc concentration in soil was used as the pollution index.The study revealed a significant effect of metal pollution on spider biodiversity as described by HRI for species (p = 0.039), genera (p = 0.0041) and families (p = 0.0147), and by DM for genera (p = 0.0259) and families (p = 0.0028). HRI correlated negatively with pollution level, while DM correlated positively. This means that although broadly described HRI diversity decreased with increasing pollution level, species richness increased with increasing contamination. Mesophilic meadows were generally richer. Pielou (J) did not show any significant correlations. There were a few evidences for the intermediate disturbance hypothesis: certain indices reached their highest values at moderate pollution levels rather than at the cleanest or most polluted sites

Upper molar morphology, homologies and evolutionary patterns of chinchilloid rodents (Mammalia, Caviomorpha)

Chinchilloidea are a clade of caviomorph rodents that includes seven living species, the Dinomyidae Dinomys branickii, the Chinchillidae Lagostomus maximus, two species of Chinchilla and three species of Lagidium. In addition, two extinct families are traditionally considered chinchilloids – Neoepiblemidae and Cephalomyidae. The phylogeny of the Chinchilloidea has so far not been well established and is based on partial analyses. Studying the anatomy and ontogeny of extinct and extant taxa, we propose homologies for the upper molars of Chinchilloidea for which these homologies have not been previously proposed: that is the Chinchillidae Prolagostomus, Lagostomus, Lagidium and Chinchilla, and the Neoepiblemidae Neoepiblema and Phoberomys. We identify patterns of occlusal simplification within Chinchilloidea and evaluate its importance in an evolutionary context. A phylogenetic analysis recovered Dinomyidae, Chinchillidae and Neoepiblemidae as clades. ‘Cephalomyidae’ have not been not recovered as a monophyletic group and ‘cephalomyids’ are closely related to Neoepiblemidae. Branisamys is not included within the Dinomyidae and appears to be a basal chinchilloid.Fil: Rasia, Luciano Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; ArgentinaFil: Candela, Adriana Magdalena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentin

New toxodontid (Notoungulata) from the Early Miocene of Mendoza, Argentina

We describe a new toxodontid species, Nesodon taweretus sp. nov., from the Aisol Formation in Mendoza Province, central-west Argentina. Nesodon is a frequently found Toxodontidae, member of the Notoungulata, an extinct endemic group of Cenozoic South American mammals that are ecologically similar to current hoofed ungulates. The holotype of N. taweretus sp. nov. is a skull, and we tentatively assign some mandibular fragments and postcranial bones. N. taweretus sp. nov. differs from the other Nesodon species in several cranial and dental features, and close comparisons were made with the Patagonian Nesodon imbricatus, common in the Santa Cruz Formation (Santacrucian Age, Early Miocene). The material is of a similar size to N. imbricatus, with a body mass estimation of about 550 kg. The phylogenetic analysis groups N. taweretus sp. nov. with other species of Nesodon. The absolute age of the Aisol Formation has been established at ca 19.480 ± 0.025 Ma (Burdigalian; Early Miocene) by means of U–Pb zircon dating. The vertebrate association is encompassed by the Santacrucian Age. Latitudinal separation between Mendoza and Patagonia in the south would have favored taxonomic differences, as reflected in the species of Nesodon. = Wir beschreiben eine neue Art der Toxodontiden, Nesodon taweretus sp. nov., aus der Aisol-Formation in der Provinz Mendoza, im Zentralwesten von Argentinien. Nesodon ist ein häufig vorkommendes Taxon der Toxodontidae, die zu den Notoungulaten, einer ausgestorbenen Gruppe von endemischen Säugetieren des Känozoikums in Südamerika, gehören und den rezenten gehuften Ungulata ökologisch ähnlich waren. Der Holotyp von N. taweretus sp. nov. ist ein Schädel, dem wir vorläufig einige Unterkieferfragmente und postkraniale Knochen zuweisen. N. taweretus sp. nov. unterscheidet sich von den anderen Nesodon-Arten in mehreren Merkmalen des Schädels und der Bezahnung. Enge Vergleiche wurden mit dem aus Patagonien stammenden und in der Santa-Cruz-Formation (Santacruzium, frühes Miozän) verbreiteten Nesodon imbricatus gemacht. Das Material ist von ähnlicher Grösse wie N. imbricatus, Schätzungen der Körpermasse ist etwa 550 kg. Die phylogenetische Analyse gruppiert N. taweretus sp. nov. mit anderen Arten von Nesodon. Das absolute Alter der Aisol-Formation wurde mittels der U–Pb Zirkondatierung auf etwa 19.480 ± 0.025 Ma (Burdigalium, Unteres Miozäns) gesetzt. Die Wirbeltiervergesellschaftung in das Santacruzium eingeschlossen worden. Latitudinale Trennung zwischen Mendoza und Patagonien im Süden hätte taxonomischen Unterschiede begünstigt, wie das anhand der Arten von Nesodon widergegeben ist