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39 results for “Bayesian analyses”
FIGURE 3. Bayesian 50 in Sobralia fugax (Orchidaceae: Sobraliae)-a new species from Colombia described on the basis of morphological study and phylogenetic analyses
FIGURE 3. Bayesian 50% majority-rule tree for Sobralieae from ITS1-5.8S-ITS2 sequences. Values above branches represent posterior probabilities (0.5). The GenBank numbers are shown next to the names of taxa; N denotes sequences obtained from Neubig et al. 2011.
Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 in A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and 'archaic' South American ungulates
Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 (H1) matrix. B, tip-dated topology constrained Bayesian phylogeny using hypothesis 1 (H1) matrix and constraining the node for the common ancestor of SANUs between the K/Pg boundary and the oldest age for the kollpaniines of Tiumpampa (66–65.075 Mya). The topological constraint in (B) was based on the topology of the undated Bayesian tree for H1. The trees in (A) and (B) represent a 50% majority rule in which tree support is indicated using Bayesian posterior probabilities in the nodes, and the node bars represent the 95% highest posterior density (HPD) for the estimated node ages. In (B), node support is only indicated for the node that was unconstrained (the undated tree presented a polytomy for that node). Litopterna is indicated with a star, but other nodes or tips of relevance are indicated in circles of different colours: blue, orders; black, families.
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 analyses 50 in Two new Oxalis (Oxalidaceae) species from the Richtersveld National Park, South Africa
FIGURE 1. Bayesian analyses 50% majority-rule consensus trees. Parsimony bootstrap support values> 70 % are shown above branches, Bayesian posterior probability values> 0.95 are shown below the branches. The O. pes-caprae clade is indicated. The two new species are indicated in bold. Bars below trees indicate expected number of substitutions per site. A) tree based on ITS data. B) tree based on trnSG data.
Data and code underpinning: "The association of smoking status with SARS-CoV-2 infection, hospitalisation and mortality from COVID-19: A living rapid evidence review with Bayesian meta-analyses (version 12)"
<p>No description provided.</p>
Figures 5–6. Optimal trees obtained under Bayesian analyses. Fig. 5. Mkv model. Fig. 6 in Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines
Figures 5–6. Optimal trees obtained under Bayesian analyses. Fig. 5. Mkv model. Fig. 6. MkvG model. Posterior probabilities values are indicated below branches.
Figure 61. Single marker phylograms from Bayesian analyses. See Figure 60 in The lace web spiders (Araneae, Phyxelididae) of Madagascar: phylogeny, biogeography and taxonomy
Figure 61. Single marker phylograms from Bayesian analyses. See Figure 60 for taxon names associated with specimen numbers. Posterior probabilities greater than or equal to 0.90 are labelled *. A, 28S. B, COI. C, 18S. D, H3.
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.
Script and results of the Bayesian analyses of environmental and phylogenetic effects of leaf composition
<p>These are the script and results of the Bayesian analysis of an article published in Ecology. In this study, we tested the suitability of biogeochemical niche hypothesis in a set of forestal tree rainforest species in a French Guiana forest. <span>Biogeochemical niche hypothesis (BN) aims to relate species/genotype elemental composition with its niche based </span>o<span>n the fact that different elements are involved differentially in distinct plant functions. </span></p> <p>These are the results of the models that allow us to analyze the effects of experimental independent variables (season, site and topography) on dependent variables (foliar traits) taking into account as random factors phylogeny of the distinct studied species and also taxonomy effects not linked to phylogeny such as convergence and divergence evolutive processes. <span>This script provides all the necessary information to conduct this type of analyses including the R-packages necessaries to conduct it.</span></p> <p><span>We observed strong legacy (phylogenic+species) signals in the species-specific foliar elemental composition (elementome) and, for the first time, provide empirical evidence for a relationship between species-specific foliar elementome and functional traits. Our study thus supports the BN hypothesis and confirm</span>s the<span> general niche segregation process through which the species-specific use of bio-elements drives the high levels of </span>a<span>-diversity in this tropical forest.</span></p>
Bayesian phylodynamic and phylogeographic analyses of invasive, hypervirulent Streptococcus agalactiae sequence type 283 dataset and R code
<p>Supplementary dataset S1, R code, and subsampled trees</p>
Data from: Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes
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Script and results of the Bayesian analyses of environmental and phylogenetic effects of leaf composition
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Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes
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Data from: Priors and posteriors in Bayesian timing of divergence analyses: the age of butterflies revisited
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Data from: Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range
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Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts
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Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample
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Bayesian inference of tree species using diffusion models: tabulated posterior statistics for SNAPP and SNAPPER analyses
<p>We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of datasets containing hundreds or thousands of individuals. The method, which we call \snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements and accuracy recovering known model parameters. A re-analysis of soybean SNP data demonstrates that the models implemented in \snapp and \snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP dataset sampled from 399 fresh water turtles in 41 populations.</p>
Bayesian inference of tree species using diffusion models: tabulated posterior statistics for SNAPP and SNAPPER analyses
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
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