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2,052 results for “Species tree”
FIGURE 2. Bayesian Inference tree from 429 in A new species of Megophrys Kuhl & Van Hasselt (Amphibia: Megophryidae) from Borneo allied to M. nasuta (Schlegel, 1858)
FIGURE 2. Bayesian Inference tree from 429 bp of 16S rRNA gene, numbers above or below branches represent bootstrap support for Bayesian Inference posterior probability, Maximum Likelihood probability and Neighbour Joining probability, (BPP/ MLBP/ NJBP).
FIGURE 3. Ultrametric tree showing focal groups. Node bars indicate 95 in Diversification in the mountains: a generic reappraisal of the Western Ghats endemic gecko genus Dravidogecko Smith, 1933 (Squamata: Gekkonidae) with descriptions of six new species
FIGURE 3. Ultrametric tree showing focal groups. Node bars indicate 95% HPD. Slant arrow indicates the point of divergence between Dravidogecko and Hemidactylus. Key geological events are indicated on the timeline: KT- Cretaceous/Tertiary boundary, IA-India's collision with Laurasia.
Fig. 5 in Phylogeography of three closely related myrmecophytic pioneer tree species in SE Asia: implications for species delimitation
Fig. 5 Distribution of the different ant species on their respective host plants M. constricta, M. griffithiana, and M. motleyana (including data from Quek et al. 2007 = lineages A, B, D, K, and G/H)
Fig. 2 in Phylogeography of three closely related myrmecophytic pioneer tree species in SE Asia: implications for species delimitation
Fig. 2 Statistical parsimony network based on cpDNA haplotype data, generated with the TCS program (Clement et al. 2000). Each circle represents a unique haplotype (indicated by numbers). Circle sizes are proportional to the number of individuals carrying the respective
Fig. 2 Ultrametric tree showing the GMYC delimitation results obtained from the Cox1 in Focus on the details: morphological evidence supports new cryptic land flatworm (Platyhelminthes) species revealed with molecules
Fig. 2 Ultrametric tree showing the GMYC delimitation results obtained from the Cox1Del dataset. Threshold separating speciation and coalescent processes plotted as grey vertical line that delimits 18 entities (including 7 singletons)
Fig. 4 Bayesian tree for fragment 1 in The world's economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus)
Fig. 4 Bayesian tree for fragment 1 haplotypes (mtDNA: 12S rRNA) of Pelodiscus. For GenBank haplotypes, accession numbers shown. Dash indicates this branch not found by MP analysis. Sequences labelled as P. axenaria or P. sinensis by Chen et al. (2005) and by
Fig. 8 Bayesian tree for fragment 3 in The world's economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus)
Fig. 8 Bayesian tree for fragment 3 haplotypes (mtDNA: cyt b + tRNA-Thr) of Pelodiscus. For GenBank haplotypes, accession numbers shown. Sequences labelled as P. axenaria or P. sinensis by
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 in Trichoderma changiae (Hypocreales), a new species isolated from a native orchid in Taiwan
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 sequences using Maximum-likelihood analysis. The new species Trichoderma changiae is highlighted in bold blue. Bootstrap values above 50% from RAxML-HPC2 on XSEDE (left) and posterior probabilities above 0.95 from Bayesian analysis (right) are displayed at the nodes. The scale bar represents 0.05 substitutions per nucleotide position. Trichoderma vulgatum was used as the outgroup. "T" denotes type strains.
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 in A new species of Naematelia (Tremellales, Basidiomycota) from India
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 are indicated above branches. The new species is indicated in bold. Holotype is represented in red color. Cryptococcus depauperatus was set as the outgroup.
FIGURE 2. Magnolia corquinensis. A. Tree. B. Habitat. C. Trunk bark. D. Leaves. E. Leaves abaxially glaucous. F. Abaxial midvein base with pubescence. G. Abaxial midvein losing pubescence towards the apex. H. Internodes and leaf stipules. I in A new species, Magnolia corquinensis, and a new record of Magnolia quetzal (Magnoliaceae) for Honduras
FIGURE 2. Magnolia corquinensis. A. Tree. B. Habitat. C. Trunk bark. D. Leaves. E. Leaves abaxially glaucous. F. Abaxial midvein base with pubescence. G. Abaxial midvein losing pubescence towards the apex. H. Internodes and leaf stipules. I. Stipules adnate to the petiole. J. Flower bud with spathaceous bract and early axillary leaf buds. Photographs A–C, H & J by H. Vega; D–G & I by S. Morales.
FIGURES 16–19 in Oecanthus buxixu sp. nov. (Orthoptera: Grylloidea: Oecanthidae): A new species of tree cricket from Brazilian Amazon rainforest
FIGURES 16–19. Spectrogram of the calling song of Oecanthus buxixu sp. nov. 16, Sonogram of the calling song registered in the field; 17, Sonogram of the calling song registered in the Lab.; 18, Oscillogram of the calling song registered in the Lab; 19, peak frequency.
FIGURES 20–24 in Oecanthus buxixu sp. nov. (Orthoptera: Grylloidea: Oecanthidae): A new species of tree cricket from Brazilian Amazon rainforest
FIGURES 20–24. Photographs of Oecanthus buxixu sp. nov. in the field. 20, Adult male; 21, Adult female; 22, Nymph f; 23, Adult female feeding; 24, shrub Clidemia japurensis (buxixu). Photos by Mendes, D.M.M.
FIGURES 1–15 in Oecanthus buxixu sp. nov. (Orthoptera: Grylloidea: Oecanthidae): A new species of tree cricket from Brazilian Amazon rainforest
FIGURES 1–15. Male and Female morphological characteristics of Oecanthus buxixu sp. nov. after alcohol fixation. 1–3, Male in dorsal, ventral and lateral view; 4, Part of head in dorsal view, with scape and pedicel in ventral view; 5, Male terminalia in ventral view, showing subgenital plate and cerci; 6, Male supranal plate, dorsal view; 7, Female terminalia in dorsal view, showing supranal plate; 8, Tibia III serrulate, with four inner and three outer subapical spurs (*); 9, Tibia III apex, with three outer apical spurs (a, b, c); 10, Tibia III apex, with four inner apical spurs (d, e, f, g); 11, Ovipositor apex, ventral view; 12, Male metanotal gland, dorsal view; 13, Male right tegmina, ventral view; 14, Phallic sclerites, ventral view; 15, Phallic sclerites, dorsal view. Conventions: sp—scape, pd—pedicel, Sc—scutum, St—scutellum, pml—posterior median lobe, MLophi—median lophi of pseudepiphallus; PsAp—pseudepiphallic apodema; r—rami; Arc—ectophallic arc; EctF—ectophallic fold; EctVp— ectophallic invagination ventral projection; EctAp—ectophallic apodema; End—endophalus.
FIG. 2. Species tree for P in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 2. Species tree for P. brachyphona as estimated in ASTRAL. Numbers on the branches are local posterior probabilities/boostrap support values from RAxML (A). The identifiers are field numbers, followed by the ''I'' number (DNA sample identifier, see Table 1). State abbreviation and county where the sample was collected are also shown. The tree shows two well-supported clades, corresponding to P. brachyphona from the Northern and Southern distribution ranges, respectively. Pseudacris brimleyi and P. feriarum were included as outgroups. Branch lengths (B) are shown in the inset tree generated with RAxML.
Figure 4 in The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms
Figure 4. Majority rule consensus phylogenetic tree resulting from Bayesian inference for Hyla orientalis haplotypes. Grey branches indicate the backbone phylogeny with representatives for each Western Palearctic Hyla species; the relatively distinct H. meridionalis and H. carthaginiensis were used as outgroup and are not shown. The pink haplotype is newly identified in the Netherlands; black haplotypes have not been reported in the Netherlands. Haplotype labels correspond to supplementary table S1.
Figure 2 in The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms
Figure 2. Majority rule consensus tree resulting from Bayesian inference to allocate new Hyla haplotypes to species. Grey branches indicate the backbone phylogeny with representatives for each Western Palearctic Hyla species; the relatively distinct H. meridionalis and H. carthaginiensis were used as outgroup and are not shown. New haplotypes are coloured blue (H. arborea) or pink (H. orientalis). Haplotype labels correspond to supplementary table S1.
Figure 1 in The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms
Figure 1. Map of the Netherlands showing sampled localities for Hyla tree frogs. A rough outline of the natural tree frog distribution range is shaded grey. Pies are sampled localities. Pie slices are coloured according to haplotype and pie sizes reflect sample sizes. Previously identified haplotypes are labelled 'old' and those newly identified in this study 'new'. The five populations introduced in the coastal dunes are labelled with the (approximate) date of appearance. Sampling details are in supplementary table S1.
Figure 3 in The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms
Figure 3. Majority rule consensus phylogenetic tree resulting from Bayesian inference for Hyla arborea haplotypes. Grey branches indicate the backbone phylogeny with representatives for each Western Palearctic Hyla species; the relatively distinct H. meridionalis and H. carthaginiensis were used as outgroup and are not shown. Blue haplotypes are newly identified and orange haplotypes were previously reported haplotypes in the Netherlands; black haplotypes have not been reported in the Netherlands. Haplotype labels correspond to supplementary table S1.
Fig. 13. Neighbour-joining tree reconstructed using 22 in Lasioglossum dorchini (Hymenoptera: Apoidea: Halictidae) a new species of bee from Israel
Fig. 13. Neighbour-joining tree reconstructed using 22 barcode sequences (658bp) of the cytochrome oxidase c subunit I gene for specimens currently identified into the virens/littorale group of species. The tree is drawn to scale, with branch lengths representing p-distances (i.e. proportions of variable sites). Four barcodes sequences (shaded in grey) are used as outgroup for the phylogenetic tree: Lasioglossum morio and L. nitidulum. Each label corresponds to the study code (Table 1) or GenBank accession followed by the species name and the country of collection. The shaded colours on the tree correspond to morphological delineation except for the species identified as Lasioglossum littorale or aff. littorale which are left unshaded. Values at node correspond to bootstrap values (%).
SDM results for 10,590 tree species from "Regional uniqueness of tree species composition and response to forest loss and climate change"
<p>Output from species distribution models (SDMs) with geographic constraints to estimate the spatial distribution of tree species at the global level at a 30-arc second resolution, presented in the publication "Regional uniqueness of tree species composition and response to forest loss and climate change". </p> <h2>Data</h2> <p>This file contains the results for 10,590 tree species. The results for each species are contained in a directory with the species name connected by an underscore. For most species, the directory contains several .tif files that make up the tiles of the distribution maps for that species and a metadata file. The .tif files can be merged with the gdal_merge.py function to obtain a single .tif file per species (see example below). For some species, the directory contains a single .tif file which does not require merging. In all cases, the .tif files contain 9 bands that correspond to the predicted species distribution using climatic variables corresponding to various climate projections from Chelsa 2.1.</p> <h3>Band order</h3> <ol> <li>covariates_1981_2010: average of historical climate measurements from 1981 to 2010</li> <li>covariates_2011_2040_ssp126: average future climate projection for 2011-2040 under shared socioeconomic pathway (SSP) 1.26</li> <li>covariates_2011_2040_ssp370: average future climate projection for 2011-2040 under SSP 3.70</li> <li>covariates_2011_2040_ssp585: average future climate projection for 2011-2040 under SSP 5.85</li> <li>covariates_2041_2070_ssp126: average future climate projection for 2041-2070 under SSP 1.26</li> <li>covariates_2041_2070_ssp370: average future climate projection for 2041-2070 under SSP 3.70</li> <li>covariates_2041_2070_ssp585: average future climate projection for 2041-2070 under SSP 5.85</li> <li>covariates_2071_2100_ssp126: average future climate projection for 2071-2100 under SSP 1.26</li> <li>covariates_2071_2100_ssp370: average future climate projection for 2071-2100 under SSP 3.70</li> <li>covariates_2071_2100_ssp585: average future climate projection for 2071-2100 under SSP 5.85</li> </ol> <h3>Metadata</h3> <p>The metadata contains more information about the bands, as well as the following species-level properties:</p> <ul> <li>nobs: number of spatially distinct occurrence records used in model training</li> <li>precision: precision of binarised model output computed through 3-fold cross-validation</li> <li>threshold: threshold used to binarise probabilistic model output, determined as the threshold maximizing the true skill statistic (TSS) during 3-fold cross-validation</li> <li>f1: F1 score of binarised model output computed through 3-fold cross-validation</li> <li>auc: area under the ROC curve (AUC) of model output computed through 3-fold cross-validation</li> <li>prevalence: prevalence of presences (ie. occurrences records) throughout the training data which consisted of occurrence records and pseudo-absences</li> <li>tss: TSS of binarised model output computed through 3-fold cross-validation</li> <li>recall: recall of binarised model output computed through 3-fold cross-validation</li> <li>nativeness_info: indicates whether reported native countries were available for this species (possible values: "yes" or "no", should be "yes" for all species included)</li> <li>npa: number of pseudo-absences used in model training</li> <li>system:index: species name </li> </ul> <h3>Merging example</h3> <p>For example, the directory Abarema_barbouriana contains files Abarema_barbouriana_0.tif, Abarema_barbouriana_2.tif, ..., Abarema_barbouriana_9.tif and metadata.json. The tiles can be merged with the command "gdal_merge.py -o Abarema_barbouriana_merged.tif Abarema_barbouriana/Abarema_barbouriana_*.tif".</p>
ScienceDex guides
Understand access before you commit
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.