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501 results for “Phylogenetic tree”
FIGURE 1. Phylogenetic tree generated from a in Additions to the genus Periconia from northern Thailand
FIGURE 1. Phylogenetic tree generated from a maximum likelihood analysis based on a concatenated alignment of ITS, LSU, SSU, and TEF1-α sequences data in Periconiaceae. The tree is rooted with Morosphaeria ramunculicola (KH220) and M. velatispora (KH221). Bootstrap support values equal to or higher than 70% ML (left) or posterior probability values equal to or higher than 0.90 Bayesian PP (right) are indicated on the nodes. The newly generated sequences are in red, and type strains are in black/red bold.
FIGURE 7. Maximum likelihood trees. A in Descriptions of two new species of Armatoplana (Polycladida: Stylochoplanidae) from the coasts of Japan, with their phylogenetic positions in Leptoplanoidea
FIGURE 7. Maximum likelihood trees. A, ML tree based on Dataset 2 (32 terminal taxa, 2768 bp, 17% missing data); B, ML tree based on Dataset 3 (28 terminal taxa, 2776 bp, 9% missing data). The Armatoplana species in the tree are presented in bold. For clades that received either ≥70% ML bootstrap or ≥0.90 BI posterior probability, the support values are presented near the nodes.
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain).
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain).
Figure 3. The Bayesian tree inferred from the dataset 107 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 3. The Bayesian tree inferred from the dataset 107-taxon_PCG_nt12 using PhyloBayes, under the site-heterogeneous mixture model (CAT-GTR). Node numbers show the posterior probability values (> 0.90). The insect pictures are provided by Yuqiang Xi.
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 of Ochthebius with focus on subgenus Cobalius (purple shade) and quadricollis species group (green shade) (former subgenus 'Calobius'). Numbers at nodes represent posterior probabilities, and 95% highest posterior density are given in blue horizontal rectangles. Calibrations points used in analysis are specified by grey dots.
FIGURE 3. Phylogenetic tree topology for the 16S in Description of a new flat gecko (Squamata: Gekkonidae: Afroedura) from Mount Gorongosa, Mozambique
FIGURE 3. Phylogenetic tree topology for the 16S gene (identical for Bayes and ML) using Afroedura hawequensis as outgroup. Support values for posterior probabilities and bootstraps are indicated by circles (PP:>0.95 / ML:>70%): full black circles indicated support by both methods and full open circles indicate no strong support by either method.
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 in A new species of nurse-frog (Aromobatidae, Allobates) from the Madeira River basin with a small geographic range
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 bp fragment of the mitochondrial 16S rDNA sampled from six Allobates bacurau paratypes and other cryptically colored species of Allobates distributed in Brazil and across cis-Andean South America. Clade labels indicate bootstrap support values estimated from 5000 bootstrap replicates (only support values>80% are shown). Basal clades with low bootstrap support should not be considered to reflect the true evolutionary history between taxa. Locations described in parentheses indicate sequence samples obtained from voucher specimens that did not proceed from the species type locality.
FIGURE 3. Phylogenetic reconstruction for 30 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 3. Phylogenetic reconstruction for 30 specimens of Leptogomphus and three outgroup taxa using the combined COI+ITS dataset. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.
Figure 2. Phylogenetic trees obtained from Parsimony analyses. A, under equal weights. B in Revisiting the phylogeny of the scolebythid wasps (Hymenoptera: Aculeata) through Bayesian model evaluation and parsimony, with description of a new fossil family of Chrysidoidea
Figure 2. Phylogenetic trees obtained from Parsimony analyses. A, under equal weights. B, under implied weighting (k = 3).
Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 in A Taxonomic Revision of the Madagascar-Endemic Genus Bemangidia (Sapotaceae), with Description of a Second Species
Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 protein-coding genes. Note that ASTRAL calculates only internal branch lengths, and that tip lines are artificially fixed at the same length for all the specimens. The node labels represent ASTRAL support values given as posterior probabilities (PP). Specimen collector's numbers are indicated after the species name, except for Capurodendron and Sapoteae, which appear in Boluda et al. (2022). BioSample numbers for sequence accessions are given in Boluda et al. (2022), except for Bemangidia sp. nov. Randriatafika 813 (BioSample no. SAMN35983425), B. lowryi Gautier 5784 (BioSample no. SAMN35982381), B. lowryi Lowryi et al. 6657 (BioSample no. SAMN35983092), Northia seychellana Bernardi 14641 (BioSample no. SAMN35983402) and Tsebona sp. Andriamiarisoa 2582 (BioSample no. SAMN35983419).
FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P in A new species of Plumarella (Octocorallia: Calcaxonia: Primnoidae) from the Northeast Pacific, and the redescription of Plumarella longispina Kinoshita, 1908
FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P. williamsi (in bold), the redescribed species P. longispina (in red), the related taxa and rooted to outgroup genera. ML bootstrap support values>70% are shown above branches.
Supplementary Figure 1 for "A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees"
<p>Supplementary Figure 1 for "A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees"</p>
FIGURE 1. Maximum Likelihood tree with branch lengths, inferred from a 2,492 in A new species of Hyloscirtus (Anura, Hylidae) from the Colombian and Venezuelan slopes of Sierra de Perijá, and the phylogenetic position of Hyloscirtus jahni (Rivero, 1961)
FIGURE 1. Maximum Likelihood tree with branch lengths, inferred from a 2,492 bp fragment of the mitochondrial genes 12S rRNA, tRNA-Val, and 16S rRNA, depicting phylogenetic relationships of Hyloscirtus species. Bootstrap support values higher than 50% are presented for each node. Values of 100% are represented by an asterisk.
FIGURE 4. Phylogenetic tree for 6 in Madeirasquilla tuerkayi, a new genus and species of mantis shrimps from Madeira Island, eastern Atlantic (Crustacea: Stomatopoda: Nannosquillidae)
FIGURE 4. Phylogenetic tree for 6 selected stomatopod species of the family Nannosquillidae, with Squilla mantis (Squillidae) used as outgroup, obtained by Maximum Likelihood analysis of 16S rRNA sequences (GTR+I+Γ substitution model); bootstrap probability values shown in nodes.
Phylogenetic trees of archaea, bacteria, fungi and plants
<p>RData containing phylogenetic trees of archaea, bacteria, fungi and plants. Five independent phylogenetic trees per biological group are provided. </p> <p>Plant and fungal phylogenies were reconstructed after grafting our study species in a supertree derived from the literature. Archaeal and bacterial phylogenies were reconstructed from 16S rRNA sequences using maximum likelihood.</p>
FIGURE 77. Strict consensus tree resulting from 82 in A revision of the Neotropical spider genus Nops MacLeay (Araneae: Caponiidae) with the first phylogenetic hypothesis for the Nopinae genera
FIGURE 77. Strict consensus tree resulting from 82 most parsimonious trees using implied weights (k=2–6) (Lf=115, Ci=0.44, Ri=0.72), with unambiguous character optimizations shown for every branch. Empty and filled hashmarks represent homoplasious and non–homoplasious transformations respectively, with characters on top and states below. Numbers above branches with colored background are Jackknife percentages (left) and Bremer support values in units of fit (right). Jackknife values below 60 % were omitted.
FIGURE 1. Phylogenetic tree for Cyt b in A phylogenetic assessment of the meadow lizard Darevskia praticola (Eversmann, 1834) from Iran
FIGURE 1. Phylogenetic tree for Cyt b gene, aS BayeSian and ML analySeS Show Similar tree topologieS only the ML tree iS preSented. NumberS on brancheS are bootStrap Support valueS for ML (below) and poSterior probability valueS for BayeSian (above) analySeS. Only valueS greater than 70 and 0.7, reSpectively, are Shown
FIGURE 2. PhylOgenetic tree inFerring FrOm a in First record of the earthworm genus Pheretima Kinberg, 1867 sensu stricto in Vietnam, with description of a new species (Annelida: Clitellata: Megascolecidae)
FIGURE 2. PhylOgenetic tree inFerring FrOm a dataset OF 523 bp Fragment OF COI using MaXimum LikelihOOd and Bayesian InFerence analysis. BOOtstrap and BI values are shOWn at nOde; # are values less than 65% (ML) Or 0.7 BPP. Sequences With KU are FrOm Jeratthitikul et al. (2017); With KT are FrOm BlakemOre (2016); With MF are FrOm this study; With LC are FrOm Aspe et al. (2016); With KX are FrOm GenBank (unpublished). TWO spequences (MF481209, MF481210) are FrOm samples cOllected FrOm SOc Trang PrOvinve (CTU-EW.DNA.006.01) and Ba Ria—Vung Tau PrOvince (CTU-EW.DNA.006.02).
FIGURE 3. Phylogenetic tree for the four species under study. A in No more machismo in Callyntra (Coleoptera: Tenebrionidae): Callyntra femina, a new species discovered based on female genitalia and genetic evidence
FIGURE 3. Phylogenetic tree for the four species under study. A) Tree obtained using Bayesian Inference with mitochondrial COI and 16S genes combined. Number above the nodes correspond to the posterior probabilities. B) Clade G from the COI + 16S combined tree obtained by Zúñiga-Reinoso & Méndez (2018), highlighting the species under study with colorful branches. The colors are matching the species in both trees.
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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.