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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 †.

publicAug 2024View details →

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Combined alignment fasta file used for the phylogenetic analysis of Micropsalliota

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Fig. 6 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

Fig. 6. Distribution of Winitia in Thailand. Winitia expansa Chaowasku (■), Winitia longipes (Craib) Chaowasku & Aongyong comb. nov. (●), and Winitia thailandana Chaowasku & Aongyong sp. nov. (▲).

Fig. 3 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

Fig. 3. Flowers and floral organs of Winitia cauliflora (Scheff.) Chaowasku (A, C, E, G) and Winitia longipes (Craib) Chaowasku & Aongyong comb. nov. (B, D, F, H). A–B. Flowers. C–D. Male flowers with petals removed. E–F. Stamens, abaxial (left) and adaxial (right) sides. G–H. Female flowers with petals removed. A, C, E, G from Chaowasku 185 (CMUB); B from Gardner et al. ST1665 (L); D, F, H from Aongyong 8 (CMUB). Photographs by T. Chaowasku (A) and S. Gardner (B).

Fig. 1 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

Fig. 1. Phylogram derived from maximum likelihood analysis, with support values shown: SR/BS/PP. Maximally supported clades are represented by thick branches without support values shown; strongly supported clades are represented by thick branches with support values shown; branches without support values shown signify SR <50%, BS <50%, and PP <0.85. ** signifies SR/BS <50%. Scale bar unit = substitutions per site. MAL. = Malmeeae; MON. = Monocarpieae.

Fig. 4 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

Fig. 4. Flowers and floral organs of Winitia thailandana Chaowasku & Aongyong sp. nov. A–B. Flower. C. Flower with petals removed. D. Stamen, abaxial (above) and adaxial (below) sides. E. Back side of flower, showing sepals (abaxial side). A, B from Gardner & Sidisunthorn ST0817 (L), photographs by S. Gardner; C–E from Aongyong 9 (CMUB).

Fig. 2 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand

Fig. 2. Part of multiple sequence alignment of trnL-trnF intergenic spacer, showing an indel (arrow) potentially diagnostic for generic discrimination in Miliuseae.

opencc-zeroDec 2008View details →

Data from: Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics

A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree, lacking several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets that identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis; comparative analysis of trees recovered from resampled data sets and the application of a randomization test. The results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, and we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the ML criteria is the most discriminating approach for the combined sequences. The results indicate that the caeliferan Pneumoroidea and Pamphagoidea (as previously suggested) are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.

opencc-zeroDec 2017View details →

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.

publicMay 2009View details →

Data from: Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics

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publicJun 2009View details →

Data from: Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences

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publicJun 2009View details →

Data from: Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes

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