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210 results for “Bayesian inference”
Figure 2. Phylogenies inferred from Maximum Parsimony and Bayesian inference. A in Morphological phylogenetics provide new insights into the classification and evolution of fossil soldier beetles from Mid-Cretaceous Burmese amber (Coleoptera: Cantharidae)
Figure 2. Phylogenies inferred from Maximum Parsimony and Bayesian inference. A, the majority consensus tree of two most-parsimonious trees obtained by implicit enumeration search under equal weighting (L = 96; CI = 73; RI = 84). Bootstrap values (BS> 49%) are shown near each of the corresponding nodes; B, the majority-rule consensus tree from the Bayesian analysis. Numbers at the nodes denote posterior probabilities.
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.
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.
StarBeast3: Adaptive parallelised Bayesian inference under the multispecies coalescent
<p><span><span>As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 -- a software package for efficient. Bayesian inference under the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and can achieve convergence on large datasets with hundreds of genes. StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.</span></span></p>
FIG. 9. Bayesian tree inferred using D2-D3 28S in Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus
FIG. 9. Bayesian tree inferred using D2-D3 28S rDNA sequences. Posterior probabilities (pp) exceeding 0.65 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank numbers are listed for each taxon. In bold: newly generated D2-D3 28S rDNA sequences. With regard to Telotylenchinae Clades (indicated in Roman figures) we adhered to Handoo et al. (2014)
FIG. 8. Bayesian tree inferred from 18S in Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus
FIG. 8. Bayesian tree inferred from 18S rDNA sequences. Posterior probabilities (pp) exceeding 0.65 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank numbers are listed for each taxon. In bold: newly generated 18S rDNA sequences. With regard to Telotylenchinae Clades (indicated in Roman figures) we adhered to Handoo et al. (2014).
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 1. Condensed Bayesian tree inferred from cyt b in Capoeta anamisensis, a new species from the Minab and Hasan Langhi River drainages in Iran (Teleostei: Cyprinidae)
FIGURE 1. Condensed Bayesian tree inferred from cyt b. Numbers right of the slash, indicate the posterior probabilities of the Bayesian analysis, using MrBayes, while numbers left of the slash are the bootstrap support for 10,000 replicates in the Maximum Likelihood tree, using RaxML. Asterisks (*) indicate less than 50% Maximum Likelihood support for the node.
FIGURE 2. Bayesian Inference Tree inferred from a in A review of Garra (Teleostei: Cypriniformes) from two rivers in West Yunnan, China with description of a new species
FIGURE 2. Bayesian Inference Tree inferred from a combined dataset (4,224 bp from COI, Cyt b, IRBP, and RAG1) for all species. The nodal numbers are posterior probability values. Only posterior probabilities greater than 50% are shown.
FIGURE 4. Bayesian tree inFerred From 28S in Ditylenchus sarvarae sp. n. (Tylenchina: Anguinidae) from Iran
FIGURE 4. Bayesian tree inFerred From 28S rDNA seqUences in Ditylenchus and newly seqUenced From Iran (Bold).
FIGURE 3. Bayesian tree inferred from mitochondrial cytochrome b in A review of the Barbatula loaches (Teleostei: Nemacheilidae) from north-eastern China, with the description of four new species
FIGURE 3. Bayesian tree inferred from mitochondrial cytochrome b gene sequences. Clade credibility values were given for nodes with bootstrap support for ML (below branch) and posterior probability for Bayesian inferences (above branch).
FIGURE 3. Cladogram using Bayesian inference with concatenated data from Cytochrome b, 12S in A review of the relationships of Xenochrophis cerasogaster Cantor, 1839 (Serpentes: Colubridae) to its congeners
FIGURE 3. Cladogram using Bayesian inference with concatenated data from Cytochrome b, 12S rRNA, and ND4 gene sequences with Coelognathus radiatus as the out-group. (Red: specimens from Northern Assam, Blue: Specimen from Southern Assam, Green: Specimen from Hyderabad)
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 1. Bayesian inference 50 in Reappraisal of Climacodon (Basidiomycota, Meruliaceae) and reinstatement of Donkia (Phanerochaetaceae) using multigene data
FIGURE 1. Bayesian inference 50 % majority rule consensus phylogram of the Phlebia clade from LSU-5.8S-SSU-RPB2-EF-RPB1 sequence data. Bayesian posterior probabilities (PP) ≥ 0.95 / Maximum Likelihood bootstrap values (ML-BP) ≥ 70 % are shown by nodes. Thickened branches received support by both ML-BP ≥ 70 % and PP ≥ 95 %. Recognized species are indicated by vertical bars.
FIGURE 1. Bayesian 50 in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 1. Bayesian 50% majority-rule consensus tree of Chamaesium and its related genus inferred from ITS(B) and plastid rpl16+rps16+trnT-trnL(A) using a GTR+G nucleotide substitution model. Values on the branches indicate its support (Bayesian posterior probability/ parsimony bootstrap). Short line denotes no support value. The tree is rooted with Bupleurum. The names of the clades identified are those of Zhou et al. (2008, 2009) and Downie et al. (2010).
FIGURE 2. Bayesian 50 in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 2. Bayesian 50% majority-rule consensus tree of Chamaesium and its related genus inferred from combined ITS and plastid rpl16+rps16+trnT-trnL using a GTR+G nucleotide substitution model. Values on the branches indicate its support (Bayesian posterior probability/ parsimony bootstrap). The tree is rooted with Bupleurum. The names of the clades identified are those of Zhou et al. (2008, 2009) and Downie et al. (2010).
FIGURE 2. Bayesian majority rule consensus tree inferred from the plastid DNA trnL-F in Evolutionary history of the tribe Astereae in the Flora Iranica area: Systematic implications
FIGURE 2. Bayesian majority rule consensus tree inferred from the plastid DNA trnL-F dataset. Numbers abovebranches are posterior probability (PP) and likelihood as well as parsimony bootstrap (BS) values, respectively. Values>50 % are shown.
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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.
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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
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