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501 results for “Phylogenetic tree”
FIGURE 2. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 2. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Tricholomopsis species. ML bootstrap (BS>50%) are shown above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
FIGURE 1. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 1. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Boletinellus species. ML bootstrap (BS>50 %) are indicated above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus.
Extra Data for "Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial"
<p>This dataset includes extra data generated or used in the experiments of the paper "Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial".</p>
FIGURE 4. Phylogenetic tree for 56 in A small, new gerbil-mouse Eligmodontia (Rodentia: Cricetidae) from dunes at the coasts and deserts of north-central Chile: molecular, chromosomic, and morphological analyses
FIGURE 4. Phylogenetic tree for 56 Eligmodontia sequences and two outgroups resulting from the maximum-likelihood analysis of 1140 bp of the cytochrome b gene. Model of sequence evolution was HKY+G+I. Numbers above branches show the percentage values from 500 bootstrap iterations, and Bayesian posterior probabilities (>50 values).
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S in Lysobacter humi sp. nov., isolated from soil
Fig. 1. Neighbour-joining phylogenetic tree reconstructed using the 16S rRNA gene sequences of strains FJY8T and related taxa. Numbers at branch nodes present bootstrap values (>50 %) obtained as percentages of 1000 replicates. Filled circles indicate the corresponding nodes recovered by using the maximum-parsimony algorithm. Bar, 0.02 substitutions per nucleotide position.
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
FIGURE 6. Bayesian inference tree for the the combineid 965 in A new species of the subterranean millipede genus Antrokoreana Verhoeff, 1938 from the Nanatsuoguchi Mine, central Honshu, Japan, and insights into the phylogenetic position of Antrokoreana (Diplopoda, Julida, Nemasomatidae)
FIGURE 6. Bayesian inference tree for the the combineid 965 bp of nuclear 28S rRNA and mitochondrial 16S rRNA marker sequences. Numbers on nodes are the bootstrap values for maximum likelihood ≥ 60% and Bayesian posterior probabilities ≥ 0.95.
Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial
<p>This dataset includes code, used and generated data for the experiments in the paper Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial, and the supplementary material of the paper. The paper introduces representation and comparison methods for rooted unlabelled phylogenetic trees based on a tree lattice that serves as a coordinate system for rooted binary trees with branch lengths and a graph polynomial that fully characterizes tree shapes. The methods provide fast, accurate, likelihood-free, distance-based appraoches to analyzing phylogenetic trees and allow analysis for large trees with more than a thousand taxa. </p> <p>The dataset has three sections. The first section is the implementation of the introduced methods for phylogenetic tree analysis as an R package, inlcuding the source code and the binary of the package. This packege provides basic functions for tree analysis and can be used or edited for related analysis. The secoond section includes all code for analyses performed in the the paper, and all the data used and generated in the analyses. The third section contains the supplementary material for the paper, which includes supplememntary results and figures. For details, please refer to the paper and the README file.</p>
FIGURE 7. Phylogenetic trees reconstructed using the mtDNA 16S in Johnius sasakii, a new species of croaker (Perciformes: Sciaenidae) with a key to Johnius from East Malaysia, Borneo
FIGURE 7. Phylogenetic trees reconstructed using the mtDNA 16S genes of five Johnius (Johnius) species. Values above the branches are respective bootstrap values from 5000 replications for the Neighbour-Joining (NJ) and Maximum-Likelihood (ML) analyses. Bar indicates genetic distances of 0.02.
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a using the best-fit model (GTR+I+G) identified with JModeltest 2.1.10. Bayesian posterior probabilities values are depicted at the nodes. Included are our own sequences (PCR number next to the name) and those retrieved from GenBank (accession numbers next to the name), if specimens identify different taxa in the COI and ITS analysis they are considered hybrids. Haplotype analysis (TCS-network made in PopART 1.7) is shown in Figs. 5 and 6.
FIGURE 3. Overview tree from the ITS gene fragment. Bayesian inference tree using MrBayes 3.2.7a in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 3. Overview tree from the ITS gene fragment. Bayesian inference tree using MrBayes 3.2.7a using the best-fit model (HKY+G) identified with JModeltest 2.1.10. Bayesian posterior probabilities values are depicted at the nodes. Included are our isolated sequences (PCR number next to the name) and those retrieved from GenBank (accession numbers next to the name), if specimens identify different taxa in the COI and ITS analysis they are indicated hybrids.
Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes
We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000+ meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence-absence of tree species within plots with phylogenetic information, we analyzed: 1) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α-diversity); and 2) the replacement of lineages along the gradient using the PhyloSorensen metric (β-diversity). More specifically, we established 20 0.25-ha permanent tree inventory plots between 750 and 2802 m asl where all individuals with Diameter at Breast Height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic over-dispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β-diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra-tropical regions have significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests.
FIGURE 1. Maximum likelihood phylogenetic tree inferred from a in Additions to Fitzroyomyces (Stictidaceae, Ascomycota) from Yunnan Province, China
FIGURE 1. Maximum likelihood phylogenetic tree inferred from a combined dataset of LSU, ITS and mtSSU. The tree has been artificially rooted with Orceolina kerguelensis, Placopsis perrugosa and Trapelia placodioides sequences. Newly isolated strains are indicated in red bold font. Bootstrap support values for maximum likelihood (ML) equal to or higher than 60% and Bayesian Probability (BYPP) equal to or higher than 0.90 are mentioned above/below the branches.
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold. in Four new species of Entoloma (Entolomataceae, Agaricomycetes) subgenera Cyanula and Claudopus from Vietnam and their phylogenetic position
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold.
FIGURE 3. Phylogenetic tree inferred from a in A new species of Hystrignathus (Nematoda: Thelastomatoidea: Hystrignathidae) associated with the Bess Beetle Passalus Interruptus Linnaeus (Coleoptera: Passalidae) from The Peruvian Amazonia
FIGURE 3. Phylogenetic tree inferred from a Bayesian inference analysis of concatenated dataset of SSU and LSU partial sequences of Hystrignathidae and other Oxyuridomorpha. Values of posterior probability and bootstrap are shown at the nodes. New species in bold fonts. Clade of species found in Passalidae indicated in bold lines. The scale bar represents the number of nucleotide substitutions per site.
ITS and LSU sequences, phylogenetic trees
<p>Russula kashmiriana sp. nov (<em>subg. Tenellula, sect. Laricinae</em>) has been collected and described from Himalayan coniferous forest of Azad Jammu and Kashmir (AJ&K), Pakistan. The taxon is characterized by bright reddish orange pileus with cracked margins and obvious reddish orange circle on the pileus, yellow context and light olive to yellowish amyloid basidiospores. Micro and macroscopic features along with molecular phylogenetic analysis based on large subunit (LSU) and internal transcribed spacer (ITS) sequences data confirmed the status of <em>Russula kashmiriana</em> as a distinct species. AJ&K, LSU, Phylogeny, Russulaceae.</p>
FIGURE 1. ITS rDNA phylogenetic tree obtained with MrBayes v. 3.2.1 in Scleroderma furfuraceum (Boletales, Agaricomycetes)-a new species from the Russian Far East
FIGURE 1. ITS rDNA phylogenetic tree obtained with MrBayes v. 3.2.1 (Ronquist et al. 2012) under GTR+I+G model for 1 M generations. Posterior probability values are indicated on the branches. Novel species is indicated in a bold font in the green box; type specimen is indicated with an asterisk (*). GenBank accession numbers of sequences are indicated after the species names.
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
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Annotated Behaviour and Observability Dataset (ABODe)
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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.