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FIG. 2. Phylogenetic trees based on concatenated protein sequences specified by loci of the 41-gene set. (A) Maximum-parsimony (MP) tree. (B) Neighbor-joining (NJ) tree. (C) Maximum-likelihood (ML) tree. Poisson-correction distance was used to draw the NJ tree. The JTT model was used to draw the ML tree. A uniform rate across amino acid positions was assumed in drawing the NJ and ML trees. However, by assuming rate variation across positions, essentially the same phylogenetic trees were obtained by the NJ and ML methods. Tree length (TL) = 5894 and consistency index (CI) = 0.85 for Tree 1 (MP tree); TL = 5915, CI = 0.84 for Tree 2; TL = 5896, CI = 0.86 for Tree 3. Log-likelihood values were –60271.5, –60314.0, and –60291.3 for Trees 1, 2, and 3, respectively. The difference of the log-likelihood values for Tree 3 and Tree 1 and for Tree 3 and Tree 2 were not significant by the Kishino-Hasewaga test. The numbers on the branches are bootstrap probabilities in percent. The scale bar indicates the number of substitutions per sequence for the MP tree and the number of substitutions per positions for the NJ and ML trees
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