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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.
Supplementary phylogenetic trees of Babesia bigemina based on partial sequences of both genes Rap-1a and gp45, with SH-aLRT support values (%), aBayes support, and ultrafast bootstrap support (%).
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Datasets used in the papers: STree: A Single Multi-class Oblique Decision Tree Based on Support Vector Machines & ODTE - An ensemble of multi-class SVM-based oblique decision trees
<p>These are the 49 datasets used in the benchmark. 45 of them are from the UCI machine learning repository, while the other 4 correspond to a problem about fecundity estimation for fisheries</p>
FIGURE 4. Maximum likelihood tree established under TIM3e in Berteroa physocarpa (Brassicaceae), a new species from NW Turkey based on morphological and molecular data
FIGURE 4. Maximum likelihood tree established under TIM3e+G model of DNA substitution in W-IQ-TREE in an analysis of 14 ITS sequences from 11 taxa. Ultrafast bootstrap values are indicated from 1000 replicates.
Figure 3. Phylogenomic tree estimated from a in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 3. Phylogenomic tree estimated from a concatenated dataset of 1680 orthogroups of 28 litostomateans and two spirotricheans
Figure 3. Phylogenomic tree estimated from a in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 3. Phylogenomic tree estimated from a concatenated dataset of 1680 orthogroups of 28 litostomateans and two spirotricheans by maximum likelihood (ML) and Bayesian inference (BI) methods. Sequences from the present study are in bold. Ŋe numbers at the nodes are the bootstrap values of ML out of 1000 pseudoreplicates and the posterior probability of Bayesian analysis* respectively. Ŋe black dots represent full support values both in the ML and in the BI trees. º* subclass ºrichostomatia; H* subclass Haptoria; R* subclass Rhynchostomatia.
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
Data from: A trait-based trade-off between growth and mortality: evidence from 15 tropical tree species using size-specific RGRs
A life-history trade-off between low mortality in the dark and rapid growth in the light is one of the most widely accepted mechanisms underlying plant ecological strategies in tropical forests. Differences in plant functional traits are thought to underlie these distinct ecological strategies; however, very few studies have shown relationships between functional traits and demographic rates within a functional group. We present 8 years of growth and mortality data from saplings of 15 species of Dipterocarpaceae planted into logged-over forest in Malaysian Borneo, and the relationships between these demographic rates and four key functional traits: wood density, specific leaf area (SLA), seed mass, and leaf C:N ratio. Species-specific differences in growth rates were separated from seedling size effects by fitting nonlinear mixed-effects models, to repeated measurements taken on individuals at multiple time points. Mortality data were analyzed using binary logistic regressions in a mixed-effects models framework. Growth increased and mortality decreased with increasing light availability. Species differed in both their growth and mortality rates, yet there was little evidence for a statistical interaction between species and light for either response. There was a positive relationship between growth rate and the predicted probability of mortality regardless of light environment, suggesting that this relationship may be driven by a general trade-off between traits that maximize growth and traits that minimize mortality, rather than through differential species responses to light. Our results indicate that wood density is an important trait that indicates both the ability of species to grow and resistance to mortality, but no other trait was correlated with either growth or mortality. Therefore, the growth mortality trade-off among species of dipterocarp appears to be general in being independent of species crossovers in performance in different light environments.
Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
FIGURE 1. Bayesian phylogenetic tree inferred from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 1. Bayesian phylogenetic tree inferred from 621 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene sampled from the Rhamphus specimens originated from Italy. Bayesian a posteriori probabilities are shown above/below branches (values below 0.7 are omitted). Abbreviation: oxy = R. oxyacanthae; bav = R.bavierai n. sp.; ham = R. hampsicora n. sp.; mon = R. monzinii.
Data from: Survival strategy of the endangered tree Acer catalpifolium Rehd., based on 13C fractionation
<p>We conducted a field investigation and evaluation of 13C natural abundance to determine the growth habit and propagation strategy of Acer catalpifolium Rehd., a tree species native to China that is highly endangered. The results showed that A. catalpifolium is a K-selected strategist and pioneer species. Its narrow ecological range limits its geographical distribution, and poor fecundity limits its population size. The analysis of 13C natural abundance showed that A. catalpifolium does not use organic matter for reproduction when its stand volume is less than 1.08×106 cm3 or it is less than 18.6 m tall, but it does use this strategy when it has a sufficient 1.08×106 cm3 stand volume or more or is taller than 18.6 m. If environmental conditions are not conducive (e.g., severe human disturbance, cliff edges, or fierce interspecific competition) to the continued growth of the tree, A. catalpifolium may allocate organic matter for reproduction. Human disturbance seems to promote the population expansion of A. catalpifolium. We provide our suggestions for the promotion and protection of A. catalpifolium as a species.</p>
FIGURE 2. Bayesian phylogenetic tree for 60 in Taxonomic reexamination of Portulaca okinawensis (Portulacaceae) in the Ryukyu Archipelago of Japan based on molecular and morphological data
FIGURE 2. Bayesian phylogenetic tree for 60 OTUs of Portulaca with three outgroups based on internal transcribed spacer (ITS) sequence. The topology of the maximum parsimony (MP) strict consensus tree was highly compatible with the Bayesian tree. Bayesian posterior probabilities (left) and bootstrap percentages in the MP analysis (right) are shown [see the Table 1 for the localities collection of the four ITS types (A–D) of P. okinawensis].
FIGURE 5. Bayesian tree, 50 in Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and web-based tools
FIGURE 5. Bayesian tree, 50% majority rule consensus using Saitoh et al. (2006) outgroups (Appendix III) recovered from 15,002 trees. Nodal values indicate posterior probabilities.
Figure 50. A tree based upon the analysis that generated Figure 48 in On the history, osteology, and systematic position of the Wealden (Hastings group) dinosaur Hypselospinus fittoni (Iguanodontia: Styracosterna)
Figure 50. A tree based upon the analysis that generated Figure 48, with particular nodes and stems named (see text for discussion/explanation). Abbreviations: CI, consistency index; RC, rescaled consistency index; RI, retention index.
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
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
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K in A phylogenetic study of the relationships within Mirinae subfamily (Insecta: Heteroptera: Miridae) based on specimens from Northern Iran: Insight into analyses of genera complexes
FIGURE. 2. Most parsimonious tree obtained from the analysis using implied weights, K= 8. Node numbers correspond to nodes in the results section. Filled circles represent non-homoplasious characters, and open circles represent homoplasious characters.
LiDAR-derived voxel-based leaf area density distribution data of urban trees
<p>This dataset includes 3D tree models and radiative transfer codes used in a paper entitled "Simulating the 3D distribution of absorbed shortwave radiation in a tree crown: comparison of simplified and Monte Carlo models" submitted to the JGR: Atmospheres.</p>
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.