Figure 2. Phylogenetic tree of vertebrate and select plant CPs. The full alignment of CPs described in the legend to Fig. 1 was used, except that bovine cathepsin L was excluded, due to the incomplete C-terminal sequence. The PAUP 4b4a software package (Swofford, 2000) was used to search for trees by means of the distance optimality criterion and default parameters, and starting trees obtained by neighbor-joining. The tree shown is an unrooted 50% majority rule consensus tree obtained by the bootstrap method (500 replicates) with heuristic search. Values shown adjacent to branches are percentage support for a branch. The large arrow indicates the position of the presumptive root of the tree: CPs on the group of branches to the right of this point comprise Branch A, those to the left Branch B (see text for explanation of Branches A and B). The abbreviations used for species are: bo, bovine; ch, chicken; h, human; m, mouse; pig, pig; r, rat; ra, rabbit; rh, rhesus; sh, sheep; and zf, zebrafish.
