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UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders
<p>The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus <i>Batrachuperus</i>, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six <i>Batrachuperus</i> species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern <i>B. karlschmidti</i> population has experienced admixture with <i>B. tibetanus</i>. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of <i>B. pinchonii</i> (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of <i>B. daochengensis</i> and <i>B. yenyuanensis</i> and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.</p>
FIGURE 2. Rhipidocladum arenicolum. A. Culm node with branch complement showing apsidate branching, B. Caryopsis, C. Floret showing persistent rachis internode, D. Branchlet bearing terminal synflorescence, E. Spikelet, F. Gynoecium, G in Three new species of Rhipidocladum (Poaceae: Bambusoideae: Arthrostylidiinae) from South America
FIGURE 2. Rhipidocladum arenicolum. A. Culm node with branch complement showing apsidate branching, B. Caryopsis, C. Floret showing persistent rachis internode, D. Branchlet bearing terminal synflorescence, E. Spikelet, F. Gynoecium, G. Node of geniculate synflorescence with pulvinus, H. Anther, I. Foliage leaf ligular area. Illustration by Eric Small based on Luteyn et al. 15520.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 1. Rubia pianmaensis. A. Flowering branch. B. Node with leaves and stipules. C. Stipule. D in A new species of Rubia (Rubiaceae) from western Yunnan, China
FIGURE 1. Rubia pianmaensis. A. Flowering branch. B. Node with leaves and stipules. C. Stipule. D. Flower (5-merous). E. Flower (6-merous). F. Dissected corolla showing stamens. G. Ovary and style. Drawn by Rongmei Zhang from the holotype.
Supplementary data for "Beyond radical-rebound: Methane oxidation to methanol catalyzed by iron species in metal–organic framework nodes"
<p>Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Beyond radical-rebound: Methane oxidation to methanol catalyzed by iron species in metal-organic framework nodes" (<a href="https://doi.org/10.1021/jacs.1c04766">https://doi.org/10.1021/jacs.1c04766</a>)</p>
FIGURE 1. Elaeagia coriacea a. Fruiting branch. b. Node with intrapetiolar stipules. c. Papillate leaf abaxial surface. d in Elaeagia coriacea (Condamineeae, Rubiaceae), a new species from Ecuador
FIGURE 1. Elaeagia coriacea a. Fruiting branch. b. Node with intrapetiolar stipules. c. Papillate leaf abaxial surface. d. Branch of infructescence. e. Open corolla, showing stamens. f. Fruit with persistent calyx, side and inner view. Drawn from J. Homeier 546 (MO). Illustration by Carlos Maldonado.
Figure 2 in Dark axils and nodes in various plant species may serve as defensive mimicry of beetle and beetle faeces
Figure 2. Brown nodal zones of indigenous grasses in Israel. (A) Avena sterilis, (B) Phalaris paradoxa, (C) Hordeum bulbosum. Scale bars: 5 mm.
Figure 1 in Dark axils and nodes in various plant species may serve as defensive mimicry of beetle and beetle faeces
Figure 1. (A) Spring shoot of Lycium chinense with dark axils. (B) Faeces and faeces-covered Lema decempunctata larvae (white arrows). (C) Lema decempunctata larvae feeding on a Lycium chinense leaf. Scale bars: (A), (B) 10 mm, (C) 3 mm.
Example workflow using KLIFS nodes in KNIME - identifying structures with similar molecules
<p>This is KNIME workflow created during the recording of the following <a href="https://www.youtube.com/channel/UCzSo1G_wyTv1vp42AhFDT8A">YouTube demonstration video</a>.</p> <p>Using this workflow, the user can draw a molecule and compare this molecule to all ligands from the KLIFS database (<a href="https://klifs.net">https://klifs.net</a>) to identify structures with molecules that are similar to the drawn molecule.</p> <p>In this workflow the follow steps are performed:</p> <ul> <li>Draw a molecule</li> <li>Collect all kinase ligands with a known structures from KLIFS</li> <li>Compare all KLIFS ligands to the drawn molecule using the ECFP-4 fingerprint and calculate a Tanimoto score </li> <li>Select the highest scoring three ligands and search for their PDB structures</li> <li>Collect the MOL2 files of the ligands as observed while binding in the PDB structures (note: all the PDB structures were first aligned by KLIFS)</li> </ul>
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana.
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella.
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai.
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella.
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella.
Figure 3 in Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics
Figure 3. Thin plate splines illustrating shape changes between selected nodes of the tree in Figure 4 based on weighted branch lengths.
Figure 4 in Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics
Figure 4. Reconstruction of shell shape and size based on weighted (above branches) and unweighted (below branches) branch lengths. The inset shows the tree shape based on COI sequence data evolved into the AFLP tree topology. Node numbers are in italic; size is expressed as centroid size; the colour of the centroid size values indicates shape changes.
FIGURE 2. Bothriochloa ewartiana under cultivation. A. Habit. B. Inflorescence. C. Leaf sheath. D. Channeled internode. E. Bearded node. F in Synopsis of the genus Bothriochloa (Poaceae: Andropogoneae) in India
FIGURE 2. Bothriochloa ewartiana under cultivation. A. Habit. B. Inflorescence. C. Leaf sheath. D. Channeled internode. E. Bearded node. F. Keeled sheath.
Figure 3. Alternative topologies for node A in A reanalysis of Parabuthus (Scorpiones: Buthidae) phylogeny with descriptions of two new Parabuthus species endemic to the Central Namib gravel plains, Namibia
Figure 3. Alternative topologies for node A (Fig. 2) retrieved by analysis with equal weights. See Table 2 for details.
Subnetwork representation learning for discovering network biomarkers in predicting lymph node metastasis in early oral cancer
<p>Dataset for the specified study.</p>
FIGURE. Bayesian tree of New Zealand spider orchids (Corybas) based on DNA sequence data from ITS, trnL-trnF and psbJ-petA. Major clades are indicated by open bars and capital letters, members of the C. trilobus aggregate are shaded, and posterior probabilities/ bootstrap percentages (≥50) indicated by numbers near each node. NI: North Island, SI: South Island, MCQI: Macquarie Island, CHI: Chatham Island in Five new species of Corybas (Diurideae, Orchidaceae) endemic to New Zealand and phylogeny of the Nematoceras clade
FIGURE. Bayesian tree of New Zealand spider orchids (Corybas) based on DNA sequence data from ITS, trnL-trnF and psbJ-petA. Major clades are indicated by open bars and capital letters, members of the C. trilobus aggregate are shaded, and posterior probabilities/ bootstrap percentages (≥50) indicated by numbers near each node. NI: North Island, SI: South Island, MCQI: Macquarie Island, CHI: Chatham Island
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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.