Phylogenetic analyses of individual and combined (concatenated) sequence alignments bearing on the position of nematodes. V = vertebrate, A = arthropod, N = nematode, P = platyhelminth. Bootstrap values (>95%) are shown for neighbor-joining, maximum parsimony, and maximum likelihood, respectively; all are indicated for the node joining Homo and Drosophila (=Coelomata). Posterior probabilities are not shown (all highlighted nodes = 1.0). (A) Four-taxon analysis of 100 combined protein alignments (44,214 amino acids), using nematode Caenorhabditis elegans (Chromadorea, Rhabditida, Rhabditoidea, Rhabditidae); the nematode branch is approximately 16% longer than the vertebrate and arthropod branches. (B) Five-taxon analysis of 100 combined proteins includes planarian EST sequences (14,041 amino acids); the nematode branch is approximately 23% longer. Other trees show different representative nematodes. (C) Brugia (Chromadorea, Spirurida, Filarioidea, Onchocercidae), based on 18 combined proteins (4598 amino acids); nematode branch= 15% longer. (D) Trichinella (Enoplea, Trichocephalida, Trichinellidae), based on 6 combined proteins (2261 amino acids); nematode branch = 24% longer than the vertebrate branch and 5% shorter than the arthropod branch. (E) Proportion of individual protein analyses supporting each of the three possible topologies with differing numbers of phyla included (4 taxa = 124 proteins, 5 taxa= 107 proteins, 6 taxa= 66 proteins, >6 taxa = 12 proteins).