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133 results for “backbone”
Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data
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Scaling of biological rates with body size as a backbone in the assembly of metacommunity biodiversity
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Data for: CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range
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Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree
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Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)
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A phylogenomic backbone for gastropod molluscs
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Data from: Adaptation and constraint in the evolution of the mammalian backbone
Background: The axial skeleton consists of repeating units (vertebrae) that are integrated through their development and evolution. Unlike most tetrapods, vertebrae in the mammalian trunk are subdivided into distinct thoracic and lumbar modules, resulting in a system that is constrained in terms of count but highly variable in morphology. This study asks how thoracolumbar regionalization has impacted adaptation and evolvability across mammals. Using geometric morphometrics, we examine evolutionary patterns in five vertebral positions from diverse mammal species encompassing a broad range of locomotor ecologies. We quantitatively compare the effects of phylogenetic and allometric constraints, and ecological adaptation between regions, and examine their impact on evolvability (disparity and evolutionary rate) of serially-homologous vertebrae. Results: Although phylogenetic signal and allometry are evident throughout the trunk, the effect of locomotor ecology is partitioned between vertebral positions. Lumbar vertebral shape correlates most strongly with ecology, differentiating taxa based on their use of asymmetric gaits. Similarly, disparity and evolutionary rates are also elevated posteriorly, indicating a link between the lumbar region, locomotor adaptation, and evolvability. Conclusion: Vertebral regionalization in mammals has facilitated rapid evolution of the posterior trunk in response to selection for locomotion and static body support.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I in A new species of Dendrobates (Anura: Dendrobatidae) from the Amazonian lowlands in Perú
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I sequence data were available. Numbers indicate posterior probabilities from the Bayesian analysis. Species of the Ventrimaculatus group are denoted with s.s. (sensu stricto), s.l. (sensu lato) and sp. aff (species affinis).
Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al.
<p>Description of the parameterization strategy for phosphorothioate-modified therapeutic nucleic acids, and files related to the system preparation, MD trajectories and analysis.</p>
Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum
<p><b>Premise of the study: </b>Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in <i>Solanum,</i> one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.<b> </b></p> <p><b>Methods:</b> A densely sampled species-level phylogeny of <i>Solanum</i> is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, <i>waxy</i>, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of <i>Solanum </i>(Angiosperms353 probe set).</p> <p><b>Key results: </b>While the taxonomic framework of <i>Solanum </i>remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths<i>. </i>The strongest area of discordance, near the crown node of <i>Solanum, </i>could potentially represent a hard polytomy.</p> <p><b>Conclusions:</b> We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.</p>
Post-Translational Site-selective Protein Backbone α-Deuteration
<p>This folder TS_xyz contains all the TS structures from conformational sampling in .xyz format accompanying the paper</p> <p>"Post-Translational Site-selective Protein α-Deuteration: Protein Backbone Modification and Use as a Tool for Protein Mechanism" by Galan et al.</p> <p><br> Two subfolders, indicated by the identity of the base used int the studies, with the following substructures, can be found:</p> <p> <br> |------ THTCD_deprotonation: all TSs from deprotonation of tetrahydrothiophene ring<br> | <br> 1_hydroxide_base --------|------ intramolecular deprotonation: all TSs from intramolecular deprotonation by sulfonium ylid<br> |<br> |------ E2_deprotonation: all TSs from deprotonation of alpha-carbon of cysteine<br> |<br> |------ sulfonium_ylid_deprotonation: all TSs from sulfonium ylid decomposition via cycloreversion</p> <p> |------ THTCD_deprotonation: lowest (and the only found) TS for deprotonation of tetrahydrothiophene ring <br> | <br> 2_dihydrogen_phosphate_base --------|<br> |<br> |------ E2_deprotonation: all TSs from deprotonation of alpha-carbon of cysteine<br> </p>
Fig. 3 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 3. Metrics resulting from quartet sampling of the amino acid alignment over the phylogeny resulting from maximum likelihood analyses of amino acids. Clade support is depicted as: QC/QD/QI.
Fig. 1 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 1. Phylogeny of Heteroptera resulting from partitioned analysis of concatenated nucleotides. Clade support is based on bootstrap replicates and the scale bar is average substitutions per site.
Fig. 2 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 2. Metrics resulting from quartet sampling of the nucleotide alignment over the phylogeny resulting from maximum likelihood analyses of concatenated nucleotides. Clade support is depicted as: QC/QD/QI.
Fig. 4 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 4. Subtree of Pentatomomorpha based on the ML analysis of concatenated nucleotides and subsequent quartet sampling. Clade support is depicted as: QC/QD/QI.
Fig. 2 in A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata)
Fig. 2 Left. Bayesian inference of the phylogenetic tree based on the concatenated sequences of the nuclear marker 28S rRNA and the mitochondrial 16S rRNA, NADH dehydrogenase (ND1), 12S rRNA, and COI. Right. Phylogenetic tree based on the same analysis but imple-
FIGURE 7 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 7. Coniochaeta coluteae (from isotype culture MFLUCC 17-2299) a. Culture on MEA from above after 4 weeks. b. Culture on MEA from below after 4 weeks. c, d. Hyphal strands on the culture. e–j. Conidiogenous cells on hyphal cells (arrow heads: conidiogenesis). k. Conidia. Scale bars: c,d=200 μm, e–k=5 μm.
FIGURE 6 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 6. Coniochaeta coluteae (holotype TASM 6104) a, b. Ascomata on the substrate. c, d. Vertical section of ascoma. e, f. Ostiole. g. Section of peridium (in water). h. Section of peridium (in 5% KOH). i. Paraphyses. j. Ascus apex in Congo Red. k. Ascospores. l–n. Asci (arrowheads show germ slits in n). Scale bars: a=500 μm, b=200 μm, c=100 μm, d=50 μm, e, f=20 μm, g–i, l–n=10 μm, j, k=5 μm.
FIGURE 3 in Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan
FIGURE 3. Results of the PHI test of closely related species (a C. acaciae, b C. coluteae) using both LogDet transformation and splits decomposition. New species described in this study are indicated in red, type strains are in boldface.
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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.