Outgroup

Each tree contains one or more sequences from a whale (or other cetacean), cow, pig, and outgroup (usually rat). Tree I is traditional and groups cows with pigs. Tree II groups whales with cows, while tree III groups whales with pigs. The tree with the minimum number of steps in each case is underlined. 

Fig. 1.4. (cont d) Two main competing outgroups for the Neodermata are (a,c,e,g) a clade of parasitic turbellaria, which, with the obligate parasites, form the Mediofusata (see Fig. 1.3c) and (b,d,f,h) a clade of neoophoran turbellarians (see Fig. 1.3e). By mapping site of infection (ectoparasitic/endoparasitic) and identity of hosts used, few topologies offer unequivocal reconstructions of plesiomorphic states.

The ABPX-related protein PdivOBPI from the scarab beetle Phylloperta diversa (Acc. Num. BAA88061 Wojtasek et al., 1999) was used as outgroup... 

Fig. 9.2. (Continued) Supports for tree ((Eukarya, py-Proteobacteria), (a-Proteobacteria, outgroup)) obtained in quartet mapping and internal branch length analysis (see legendto Fig. 9.1) were 50% and 0.98, respectively. For other details see the legend to Fig. 9.1...

Sampling Error. In a reversal of the relative rate test, we can calculate a conservative estimate of the error inherent in the metric by assuming that rates of substitution are constant in different lineages and comparing the distance of several more closely related taxa to outgroups (Table II). The... 

Comparison of Multiple Taxa to Outgroups to Estimate Error Inherent in Two-Dimensional Protein Electrophoresis Metric"... 

Fig. 2. Schematic representation of phenetic or phylogenetic hypotheses tested immuno-logically. The immunological evidence indicated that the proteins from taxa B and C resemble one another more than they do the protein from taxon A (left-hand side of figure), whereas earlier hypotheses, based on nonmolecular evidence, had suggested the organismal relationships shown on the right-hand side, with C being the outgroup taxon. See Table III and text for examples.

Phylogenetic screening has been used successfully to isolate retroelements that have been active in recent evolutionary time. In a phi-screen of the white-footed mouse, Peromyscus leucopus, the retrovirus-like element mys was identified by virtue of its hybridization to Peromyscus DNA but its lack of hybridization to Mus (the outgroup) DNA.13 In a phi-screen of human DNA using Galago as an outgroup, both the 5 end of the LI element and the retrovirus-like element THE 1 hybridized differentially,... 

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.

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