Majority rule consensus trees

Repeat resampling 1000 times compute majority-rule consensus tree i... 

FIGURE 6.4 Fifty percent majority rule consensus tree of 2348 most parsimonious trees (L = 808, Cl = 54, RI = 79) of analysis of 86 terminals. Jackknife (in italics) and Bremer support values are shown below branches those clades that appear also in the strict consensus topology are shown with 100 above the branch. 

In Bayesian analysis GTR+I+G model of nucleotide substitutions with four rate categories was used. Four Metropolis-coupled MCMC chains were run from randomly chosen starting trees for 3000000 generations, trees were saved once every 10 generations, 114000 first trees were ignored. The other options retained default values. Majority-rule consensus trees were constructed and Bayesian posterior probabilities as branch support values were calculated. This analysis will be referred to as MB144 where based on dataset 1, and as MB135 where based on dataset 2. 

Note Node numbers correspond to those on the chronogram (Figure 17.1). Point estimates are from analyses of the all-compatible majority rule consensus tree and posterior probability values are rep ted. The Mode value represents the most likely divergence lime value under the specified model (obtained by local density estimation calculated over the 100 random frees drawn from the posterior distribution of trees and parameters), and the HPD values limits the confidence interval for the estimates. ( node constrained j age estimates show bimodal distribution across the 100 random trees > age distribution with a pronounced right tail across the 100 random frees)... 

PAUP 3.1.1 (Swofford 1993) (b) simplified SO per cent majority-rule consensus tree (c) one of the shortest trees. See Appendix 3 for the characters supporting the numbered nodes. 

Figure 9.7 50 per cent majority-rule consensus bootstrap trees based on the mitochondrial tRNA data set using the lamprey as outgroup. Numbers indicate bootstrap values based on 100 pseudo-replications. The mitochondrial tRNA sequence data set was subjected to MP (bootstrap values upper of each triplet of numbers), NJ (bootstrap values in the middle of each triplet of numbers), and ML (bootstrap values lower of each triplet of numbers) analyses. 

Figure 9.9 50 per cent majority-rule consensus bootstrap trees based on the mitochondrial protien data on the set using lamprey and hagfish as outgroup. 

Consensus tree Consensus DNA/Protein Compute consensus tree by majority rule... 

Figure 14.2 Phylogenetic analysis cox I amino acid sequences to determine relationship within the long-looped terebratulides. (A) ML tree with LBPs estimated by ProtML, using the three outgroup short-looped forms. Branch length refers to the estimates number of substitutions per 100 sites. (B) MP consensus tree based on 50% majority-rule. A total of 500 bootstrap replicates were performed.

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