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Data from: Diversity measures in environmental sequences are highly dependent on alignment quality—data from ITS and new LSU primers targeting basidiomycetes
The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used as a fungal marker in molecular ecology and systematics but cannot be aligned with confidence across genetically distant taxa. In order to study the diversity of Agaricomycotina in forest soils, we designed primers targeting the more alignable 28S (LSU) gene, which should be more useful for phylogenetic analyses of the detected taxa. This paper compares the performance of the established ITS1F/4B primer pair, which targets basidiomycetes, to that of two new pairs. Key factors in the comparison were the diversity covered, off-target amplification, rarefaction at different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of the method used to process the alignment to missing data and insecure positional homology, and the congruence of monophyletic clades with OTU assignments and BLAST-derived OTU names. The ITS primer pair yielded no off-target amplification but also exhibited the least fidelity to the expected phylogenetic groups. The LSU primers give complementary pictures of diversity, but were more sensitive to modifications of the alignment such as the removal of difficult-to align stretches. The LSU primers also yielded greater numbers of singletons but also had a greater tendency to produce OTUs containing sequences from a wider variety of species as judged by BLAST similarity. We introduced some new parameters to describe alignment heterogeneity based on Shannon entropy and the extent and contents of the OTUs in a phylogenetic tree space. Our results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.
Data from: New Zealand tree and giant wētā (Orthoptera) transcriptomics reveal divergent selection patterns in metabolic loci
Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of orthologue ratios of synonymous to non-synonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes and KEGG pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution
Data from: Fewer new species colonize at low frequency N addition in a temperate grassland
1. Biologically reactive nitrogen (Nr) enrichment threatens biodiversity in diverse ecosystems. Previous controlled N addition experiments may overestimate the effects of atmospheric Nr deposition on the rate of species loss, as it has been found that low frequency Nr additions, as used in traditional studies, lead to more rapid biodiversity loss. It remains unclear, however, whether the colonization of new species (gain) or extinction of old species (loss) is the cause of this difference. 2. By independently manipulating the frequency (twice vs. monthly additions yr–1) and the rate (from 0 to 50 g N m–2 yr–1) of NH4NO3 inputs for six years in a temperate grassland of northern China, we aimed to examine the contribution of gain and loss of species to the reduction in species richness under different regimes of Nr inputs. 3. Results showed that the gain of new species was higher at a high frequency of N addition than that at a low addition frequency, whilst loss of existing species was similar between the two frequencies of N addition. The number of new species gained decreased and old species lost increased with the increasing rate of Nr addition at both annual and five-year intervals. Cumulative gain of new species was negatively correlated with soil acidification, ammonium concentration and community biomass accumulation, whereas cumulative loss of old species was positively correlated with these variables. 4. Our results revealed lower new species colonization results in lower species richness at low frequency of Nr addition. Findings from this study highlight the important role of N addition frequency in regulating the effects of Nr addition on community dynamics. To assess the effects of atmospheric Nr deposition on ecosystem structure and functioning, it is necessary to assess not only the dose but also the frequency of N addition.
Data from: Preclinical toxicity and pharmacokinetics of a new orally bioavailable flubendazole formulation and the impact for clinical trials and risk/benefit to patients.
Background: Flubendazole, originally developed to treat infections with intestinal nematodes, has been shown to be efficacious in animal models of filarial infections. For treatment of filarial nematodes, systemic exposure is needed. For this purpose, an orally bioavailable amorphous solid dispersion (ASD) formulation was developed. As this formulation results in improved systemic absorption, the pharmacokinetic and toxicological profile of flubendazole administered with this formulation have been assessed to ensure human safety before clinical trials could be initiated. Methods & Findings: Safety pharmacology, toxicity and genotoxicity studies have been conducted with the flubendazole ASD formulation. In animals, flubendazole has good oral bioavailability from an ASD formulation ranging from 15 % in dogs, 276 % in rats to more than 100% in jirds. In in vivo toxicity studies with the ASD formulation, high systemic exposure to flubendazole and its main metabolites was reached. Flubendazole, up to high peak plasma concentrations, does not induce Cmax related effects in the CNS or cardiovascular system. In repeated dose toxicity studies in rats and dogs, flubendazole-induced changes were observed in haematological, lymphoid and gastrointestinal systems and in testes. In dog, the liver was an additional target organ. Upon treatment cessation, at least partial recovery was observed for these changes in the dog. In rat, the low dose was the No Observed Adverse Effect Level (NOAEL) was , i.e. 5 mg (as base)/kg body weight/day (mg eq./kg/day)mg eq./kg/day in males and 2.5 mg eq./kg/day in females. In dog, the NOAEL was lower than the low dose, 20 mg eq./kg/day. Regarding genotoxicity, flubendazole was negative in the Ames test but positive in the in vivo micronucleus test. Conclusions: Based on these results, in combination with previously described genotoxicity and reproductive toxicity data and the outcome of the preclinical efficacy studies, it was concluded that no flubendazole treatment regimen can be selected that would provide efficacy in humans at safe exposure.
Data from: Phylogeny of digitaria sections Trichachne and Trichophorae (Poaceae, Panicoideae, Paniceae): a morphological and molecular analysis. New circumscription and synopsis
The present study provides evidence for taxonomic delimitation of Digitaria sect. Trichachne based on morphological data (micro- and macromorphology) and molecular data. A phylogenetic analysis was performed using 121 morphological characters and ITS sequences of 22 species and one variety of Digitaria plus three outgroups. In all topologies (based on morphological, molecular, and combined data) Digitaria sect. Trichophorae was non-monophyletic and nested within D. sect. Trichachne. Digitaria sect. Trichophorae is thus synonymized under D. sect. Trichachne and the circumscription of D. sect. Trichachne is emended. Diagnostic morphological characters related to spikelet structure are described and documented with SEM. A key to taxa belonging to D. sect. Trichachne is provided, as well as a synopsis including synonymy, iconography, geographical distribution, and ecology. The neotype of Trichachne sacchariflora Nees is herein designated. Complete illustrations of Digitaria eggersii, D. hitchcockii, and D. patens are provided. The phylogenetic placement of the Australian species D. brownii differed among trees resulting from different data sets, thus it is provisionally not included in D. sect. Trichachne in spite of its morphological similarity. Furthermore, Megaloprotachne albescens is formally transferred to Digitaria, as Digitaria albescens .
Data from: Tricky Morphology: A new species of Chamaecrista (Leguminosae) shows strong morphological convergence among not closely related species found in similar habitat
<p>Plants from Brazilian <i>campos rupestres</i> usually present morphological strategies that allow them to survive in extreme environments. However, in <i>Chamaecrista </i>(Leguminosae, Caesalpinioideae), one of the most diverse genera in the <i>campos rupestres,</i> needle-like leaflets are rare. Reviewing the species that present such leaf morphology, we describe <i>Chamaecrista acicularis</i>, a new species, from the Canastra Range,<span> in the southwestern region of the state of Minas Gerais, Brazil. </span>Phylogenetic analyses revealed that <i>C. acicularis </i>is not closely related to other quite similar needle-like leafleted species and that this trait evolved convergently. We also present comments on the phylogenetic relationships of needle-like leafleted species as well as the evolution of the leaflet amplitude, and a detailed description of <i>C. acicularis </i>alongside illustrations, photos, geographical distribution, a key to the needle-like leafleted species and taxonomic notes on similar species. Additionally, we expand the description of <i>Chamaecrista strictifolia </i>and present a conservation status for all needle-like leafleted species.</p>
FIGURE 13 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURE 13. Eustigmaeus brevivestitus sp. n., female (holotype) right leg I, paraxial view.
FIGURE 4 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURE 4. Eustigmaeus formosus sp. n., female (holotype) ventral view.
FIGURE 10 in Two new free living mite species of Eustigmaeus (Actinedida: Raphignathoidea: Stigmaeidae) from Poland, with new data of some other rare species of the genus
FIGURE 10. Eustigmaeus brevivestitus sp. n., female (holotype) ventral view.
Figure 12 in Pseudonemesia tabiskey, a new species of Pseudonemesia Caporiacco 1955 and new ultramorphological data for the Microstigmatinae (Araneae: Microstigmatidae)
Figure 12. Map showing the known records of Pseudonemesia species.
FIGURE 22 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 22. Dorsal view of Aegla jundiai n. sp., female holotype (MZUSP 13493). Bar = 2.0 mm.
FIGURE 20 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 20. Dorsal view of Aegla jaragua n. sp., male holotype (MZUSP 34376). Bar = 3.0 mm.
FIGURE 18 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 18. Dorsal view of Aegla japi n. sp., male holotype (MZUSP 34374). Bar = 3.0 mm.
FIGURE 16 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status
FIGURE 16. Dorsal view of Aegla vanini n. sp., male holotype (MZUSP 34371). Bar = 3.0 mm.
FIGURE 7 in New data on millipedes of the family Julidae (Diplopoda, Julida) from Altai, Siberia
FIGURE 7. Sibiriulus profugus (Stuxberg, 1876), male. Gonopods, mesal view. Scale in mm.
FIGURE 2 in Two new genera and species of Eriococcidae (Hemiptera: Sternorrhyncha: Coccoidea) with new data on the family in Turkey
FIGURE 2. Adult female of Kotejacoccus turcicus Kaydan & Kozár sp. nov.
FIGURE 1 in Two new genera and species of Eriococcidae (Hemiptera: Sternorrhyncha: Coccoidea) with new data on the family in Turkey
FIGURE 1. Adult female of Borchseniococcus duzgunesae Kaydan & Kozár, sp. nov.
FIGURE 2 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from Malaysia including a literature survey of mensural and meristic data in the genus
FIGURE 2. Mental region of Cyrtodactylus stresemanni, holotype ZSM 249/1911.
FIGURE 1 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from Malaysia including a literature survey of mensural and meristic data in the genus
FIGURE 1. Nasal region of Cyrtodactylus stresemanni, holotype ZSM 249/1911.
FIGURE 4 in A new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from Malaysia including a literature survey of mensural and meristic data in the genus
FIGURE 4. Preanal groove of Cyrtodactylus stresemanni, holotype ZSM 249/1911.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.