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Fig. 5 in A Comprehensive Phylogeny of Tettigoniidae (Orthoptera: Ensifera) Reveals Extensive Ecomorph Convergence and Widespread Taxonomic Incongruence
Fig. 5. BEAST tree consisting of 235 ingroup taxa (continued). Posterior probabilities over 90 are marked with a circle at the node. Asterisks denote taxa that were recovered in a different position than in the phylogenetic analysis (Figs. 2 and 3). Colored branches indicate the biogeographic region. Vertical lines are based on fossil calibrations with each line indicating 50 million years.
Traversing the Great Lakes: Post-glacial colonization by a widespread terrestrial salamander
<p><strong>Aims:</strong> Glacial retreat at the end of the Pleistocene epoch opened vast expanses of emergent habitat in the northern hemisphere that were colonized by opportunistic taxa. However, species that undergo post-glacial expansion may have originated from one or several glacial refugia. We inferred the post-glacial expansion history of the Eastern Red-backed Salamander (<em>Plethodon cinereus</em>), a fully terrestrial species with a vast distribution despite severe dispersal limitations. Previous studies indicated populations south of the glacial boundary at the eastern and western limits of the distribution were closely related, suggesting either multiple refugia or an extraordinary post-glacial expansion event.</p> <p><strong>Location:</strong> Eastern North America.</p> <p><strong>Taxon:</strong> <em>Plethodon cinereus</em> (Green, 1818), Caudata: Plethodontidae.</p> <p><strong>Methods: </strong>We collected ddRAD-seq data from 106 individuals throughout the distribution of <em>P. cinereus</em>. We estimated phylogeographic structure, including finer-scale structure among the post-glacial populations. To test the origins and routes of colonization, we used ecological niche modeling, population trees, and analyses of directional range expansion.</p> <p><strong>Results: </strong>Analyses supported our hypothesis of a southeastern glacial refugium, with northward expansion along the Eastern Seaboard prior to westward invasion into the Great Lakes region, including southwestern expansion into unglaciated areas at the western end of the distribution. However, a distinct subgroup in the northwestern portion of the range raises the possibility of a second refugium near the ice-free Driftless Area.</p> <p><strong>Main conclusions:</strong> Based on our results, we hypothesize a southeastern refugium from which most of today's northern populations undertook extensive post-glacial colonization. Our results indicate a geographically non-linear colonization history for <em>P. cinereus</em>.</p>
nad1 alignment in Description of three widespread new Peronospora species parasitising Caryophyllales
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COX2/cox2-1 spacer/COX1 alignment in Description of three widespread new Peronospora species parasitising Caryophyllales
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ITS alignment in Description of three widespread new Peronospora species parasitising Caryophyllales
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hsp90 alignment in Description of three widespread new Peronospora species parasitising Caryophyllales
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RPS10 alignment in Description of three widespread new Peronospora species parasitising Caryophyllales
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qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps
<p>Benchmark dataset and prospective cases tested for the development of <em>qFit-ligand</em>. Files included: refined single conformer models, un-refined qFit-ligand multiconformer models, and refined qFit-ligand multiconformer models. </p>
Supplementary material 1 from: Potapov G, Kondakov A, Kolosova Y, Tomilova A, Filippov B, Gofarov M, Bolotov I (2018) Widespread continental mtDNA lineages prevail in the bumblebee fauna of Iceland. ZooKeys 774: 141-153. https://doi.org/10.3897/zookeys.774.26466
Table S1 : Explanation note: List of additional COI sequences of Bombus species obtained from GenBank or BOLD, including taxon, accession number, specimen code, locality information and data source.
Supplementary material 1 from: van Nieukerken EJ, Gilrein DO, Eiseman CS (2018) Stigmella multispicata Rociene. & Stonis, an Asian leafminer on Siberian elm, now widespread in eastern North America (Lepidoptera, Nepticulidae). ZooKeys 784: 95-125. https://doi.org/10.3897/zookeys.784.27296
Specimen data of Stigmellamultispicata and other Ulmus mining Nepticulidae : Explanation note: The 288 records are the records of specimens examined and records obtained from online sources, of the taxa treated in this paper and supplement the presented Material examined.
Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae)
<p>Datasets and supplementary material</p>
Fig. 1 in Northern origin and diversification in the central lowlands? - Complex phylogeography and taxonomy of widespread day geckos (Phelsuma) from Madagascar
Fig. 1 Distribution map of current nominal taxa and major mtDNA lineages of the Phelsuma lineata subgroup. The information on distribution areas is based on Glaw and Vences (2007), Hallmann et al. (2008), Schönecker (2008), Gehring et al. (2010), and our own results. a Distribution of P. dorsivittata and P. lineata ssp. (sensu lato), with
Fig. 2 in Northern origin and diversification in the central lowlands? - Complex phylogeography and taxonomy of widespread day geckos (Phelsuma) from Madagascar
Fig. 2 Median-joining network of 16S haplotypes in the P. lineata subgroup (consensus network of all the shortest trees). Black dots and squares with numbers represent median vectors and presumed unsampled or missing intermediates. Numbers denote haplotypes (for a detailed list assigning haplotypes to localities, see SI); colors are in accordance with major mtDNA clades as identified by phylogenetic analysis; size is proportional to their frequencies. Geographical location of the sampled populations and their haplotype composition are given in
Fig. 3 in A dragonfly in the desert: genetic pathways of the widespread Trithemis arteriosa (Odonata: Libellulidae) suggest male-biased dispersal
Fig. 3 Bayesian analysis of the nuclear genetic structure of T. arteriosa populations based on eight microsatellite loci. Each vertical bar represents an individual and is partitioned into one to three coloured segments indicating the individual membership in the three genetic
Fig. 8 in Integrated evidence sheds light on the taxonomy of the widespread Tantilla melanocephala species complex (Serpentes: Colubridae) and indicates the existence of a new species from southern South America
Fig. 8 Overview of South American Tantilla species. a T. selmae; b T. boipiranga; c T. melanocephala, Surinam pattern (above), Brazilian Cerrado pattern (middle), and transAndean pattern (bellow); d T. capistrata; e T. petersi. Illustrations by Lucas Kias
Fig. 4 in Integrated evidence sheds light on the taxonomy of the widespread Tantilla melanocephala species complex (Serpentes: Colubridae) and indicates the existence of a new species from southern South America
Fig. 4 Boxplots for selected variables based on the dataset D1, demonstrating the morphological differences among OTUs of the Tantilla melanocephala complex. Number of ventral scales in (a) females and (b) males; number of subcaudal scales in (c) females and (d) males. The thin (red) horizontal line within the box indicates the mean; the thick (black) horizontal line within the box indicates the median; the open circles are data points
Fig. 5 in Integrated evidence sheds light on the taxonomy of the widespread Tantilla melanocephala species complex (Serpentes: Colubridae) and indicates the existence of a new species from southern South America
Fig. 5 Specimens of Tantilla melanocephala complex from Brazil. a T. aff. melanocephala 1 from Bagé, RS, Brazil, IBSP 91713; b T. boipiranga from Morro do Pilar, MG, Brazil, IBSP 79060; c T. cf. melanocephala from Atibaia, SP, Brazil, IBSP 19376; d T. cf. melanocephala from Palmas, TO, Brazil, IBSP 65185; e T. cf. melanocephala from Aquidauana, MS, Brazil, IBSP 26757; f T. melanocephala from Belém, PA, Brazil, IBSP 15047
Fig. 7 in Integrated evidence sheds light on the taxonomy of the widespread Tantilla melanocephala species complex (Serpentes: Colubridae) and indicates the existence of a new species from southern South America
Fig. 7 Holotype of Tantilla selmae (IBSP 92724). Head views on the (a) dorsal, (b) right lateral, (c) left lateral, and (d) ventral. Body views on the (e) dorsal and (f) ventral. Horizontal scale bar: 2 mm. Vertical scale bar: 10 mm
Widespread naturally variable human exons aid genetic interpretation (Preprint)
<p>Supplemental files for Widespread naturally variable human exons aid genetic interpretation (<a href="https://www.biorxiv.org/content/10.1101/2024.09.09.612029v1">Preprint link</a>)</p> <p> </p> <p>For newest version, click here: <a href="https://zenodo.org/records/15790343">https://zenodo.org/records/15790343</a></p> <p> </p>
Fig. 4 in A widespread commensal loses its identity: suggested taxonomic revision for Indotyphlops braminus (Scolecophidia: Typhlopidae) based on molecular data
Fig. 4 The distributions of the three putative species, plotted on an annual precipitation layer (BIOCLIM 12) to indicate the wet zone
ScienceDex guides
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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.