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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

Figure 3

Maximum-likelihood tree for vertebrate Emx genes with either cyclostome species. These ML trees were reconstructed using 132 amino acid sites in the multiple alignment in Additional file 7 under the JTT model [49] with among-site rate heterogeneity taken into account by assuming the gamma distribution [50] with four rate categories (JTT + Γ4 model). To evaluate the effect of the choice of cyclostome sequences, we performed the analysis including sea lamprey (a) or hagfish (b), with a shape parameter of the gamma distribution α of 0.37 and 0.38, respectively. The numbers at nodes indicate bootstrap probabilities with 100 replicates for the ML and NJ methods, in order.

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