Outgroup rooting

Fig. 7. Bootstrap analysis among characters in a parsimony analysis. The tree to the right of each matrix is the most parsimonious tree for that matrix. The final results of the bootstrap analysis are shown in the tree at the bottom. The number of times each branch was supported in the bootstrap replication is shown as a percentage. Outgroup rooting carries the assumption of ingroup monophyly, so no confidence interval can be assigned to the branch that unites the ingroup.

Figure 5.2 Neighbor-joining tree of sequence similarity in the 7TM domains of human monoamine-related GPCRs. The receptors are coded according to the SwissProt nomenclature scheme orphan receptors are coded with the prefix GPR followed by an index number. Distance corresponds to percent sequence identity, scale is indicated by a 5% bar. The tree is rooted by outgrouping the node of the H, and muscarinic receptors. The numbers on the branches are the result of bootstrap analysis (1 OCX) replicates). For further details see [60].

Figure 2 Backbone endophyte phylogeny based on combined tub2, tefl, and actl intron sequences. Major clades are labeled above branches as a-k. Tree is midpoint rooted (left edge). Position of the root, using outgroups Claviceps purpurea and Dussiella tuberiformis, is indicated by arrow 1.

Figure 14.2A shows the ML tree built for the 20 terebratulide brachiopods rooted by the three outgroup short-looped forms. The MP tree differed from the NJ (not shown) and ML trees only by showing less resolution of the deeper nodes (Fig. 14.2B). 

The unrooted strict consensus of the three equally most parsimonious cladograms obtained is illustrated in Fig. 26.1 A the first of the three cladograms rooted at the outgroups is shown in Fig. 26. IB. The other two cladograms differ only in the relative... 

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