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41 results for “Bayesian phylogenetic analysis”
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 9 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 9. Timing of dispersal of Otariidae into the Southern Hemisphere, as constrained by molecular clock (Yonezawa et al., 2009), fossil, and climatic data. Youngest ages of fossil taxa Hydrarctos lomasiensis (Muizon, 1978; Pilleri, 1990; Ehret et al., 2012) and Arctocephalus sp. nov. (Avery & Klein, 2011) indicated by circles, with possible oldest ages indicated by the dashed lines. Temperature data from Fedorov et al. (2013) and Rousselle et al. (2013) based on Ocean Deep-drilling Program sites 1021 (high latitude), 1010 (subtropical), and U1338 (tropical). Opal mass accumulation rates (MAR) from Farrell et al. (1995). Vertical red line indicates maximum sea surface temperature (SST) temperature tolerance reconstructed for ancestor of southern clade. Green horizontal bar indicates the most likely time period of dispersal into the Southern Hemisphere from the North Pacific, when subtropical SSTs were depressed and equatorial productivity was high.
Figure 8 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 8. Ancestral maximal sea surface temperature (SST) tolerance for Otariidae. Phylogeny used was the EX combined evidence phylogeny, which excludes fossil taxa with 50% or fewer cells coded for morphology. Fossil taxa are excluded. Extinct taxa are annotated with †.
Figure 7 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 7. Pattern of otariid dispersal based upon Bayesian ancestral area reconstruction presented in Figure 6. Numbers in circles represent major centres of origin, and with directions of dispersals indicated by arrows. Less certain dispersal routes are indicated by black dashed lines. 1, origin of Otariidae in North Pacific; 2, origin of Southern Hemisphere clade in eastern South Pacific; 3, dispersal of ancestor of Phocarctos to New Zealand; 4, dispersal of ancestor of Arctocephalus to South Africa; 5, tentative dispersal of Arctophoca tropicalis to Southern Ocean; 6, dispersal of Arctophoca gazella to Southern Ocean; 7, dispersal of Otaria and Arctophoca australis to Atlantic coastline of South America; 8, dispersal of Arctop. australis to New Zealand and Australia; 9, tentative dispersal of Arctocephalus to Australia from South Africa; 10, dispersal of Arctocephalus philippii to the west coast of North America; 11, dispersal of Zalophus to the Galapagos. Historic presence of sea lions (grey silhouettes) and fur seals (black silhouettes) on map indicated. Dispersal of Neophoca into Indian Ocean not shown.
Figure 6 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 6. Results of Bayesian (A) and maximum parsimony (B) ancestral area reconstruction. Phylogeny used was the EX combined evidence phylogeny, which excludes fossil taxa with 50% or fewer cells coded for morphology. Key in lower left corner is for both A and B. Extinct taxa indicated by †. RASP in figure key refers to the program used for Bayesian ancestral character state reconstruction.
Figure 4 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 4. Results of Bayesian phylogenetic analysis of molecules. Mitochondrial DNA (A) includes cytochrome b and d-loop sequences. Nuclear DNA (B) includes interphotoreceptor retinoid binding protein 3, growth hormone receptor, and feline sarcoma oncogene gene sequences. Fur seal icons in black represent members of Arctocephalinae and sea lion icons in grey represent members of Otariinae. Nodes with high support (posterior probability ≥ 0.95) are indicated by a black circle; nodes with moderate support (posterior probability = 0.90−0.94) are indicated by a white circle. Extinct taxa are annotated with †.
Figure 2 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 2. Results of prior analyses of otariid phylogeny using molecular data. Fur seal icons in black represent members of Arctocephalinae and sea lion icons in grey represent members of Otariinae.
Figure 3 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 3. Results of maximum parsimony phylogenetic analysis of morphological characters. Fur seal icons in black represent members of Arctocephalinae and sea lion icons in grey represent members of Otariinae. Nodes with high support (bootstrap ≥ 70) are indicated by a black circle; nodes with moderate support (bootstrap = 50–70) are indicated by a white circle. Extinct taxa are annotated with †.
Figure 1 in Colonization of the Southern Hemisphere by fur seals and sea lions (Carnivora: Otariidae) revealed by combined evidence phylogenetic and Bayesian biogeographical analysis
Figure 1. Results of prior analyses of otariid phylogeny using morphological data. Fur seal icons in black represent members of Arctocephalinae and sea lion icons in grey represent members of Otariinae. Extinct taxa are annotated with †.
Figure 1. Bayesian tree inferred from the 18S in A molecular analysis of the phylogenetic position of the suborder Cavernicola within the Tricladida (Platyhelminthes), with the description of a new species of stygobiont flatworm from Benin
Figure 1. Bayesian tree inferred from the 18S rDNA sequences showing the relationship of the new Novomitchellia species to other Tricladida species included in this analysis. Maximum likelihood (ML) yielded the same topology. Asterisks at nodes indicate posterior probabilities = 1/bootstrap values> 75% obtained respectively in the ML and Bayesian inference analyses. Scale bar: number of substitutions per nucleotide position.
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.
Data and code for "Spatial evolution of human cultures inferred through Bayesian phylogenetic analysis."
<p>Data and code for "Spatial evolution of human cultures inferred through Bayesian phylogenetic analysis."</p>
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Most of the outgroups are not shown. Above node numbers indicate posterior probability, bootstrap value for MP, and bootstrap value for ML. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %.
Data from: Bayesian phylogenetic analysis of combined data
The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.
FIGURE 2 in Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences
FIGURE 2. Phylogenetic tree obtained from the Bayesian inference analysis of the 16S rDNA dataset.
FIGURE 1 in Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences
FIGURE 1. Phylogenetic tree obtained from the Bayesian inference analysis of the 12S rDNA dataset.
Data from: Bayesian phylogenetic analysis of combined data
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Data from: Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees
Open the record for dataset details and reuse information.
FIGURE 3 in Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences
FIGURE 3. Phylogenetic tree obtained from the Bayesian inference analysis of the combined 12S and 16S rDNA dataset.
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrITS1-5.8S-ITS2 region 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 nrITS1-5.8S-ITS2 region 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.
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