Figure 3.

Phylogenetic tree of 57 Hox/paraHox HD sequences inferred by ML analysis where 242,075 of the 677,040 possible quartets of sequences (35.8%) were unresolved, leading to a multifurcating tree with a Log likelihood value of −3,656.89. Numbers above the branches correspond to the quartet puzzling support values; numbers under branches indicate percentages of 1,000 bootstrap replicates for NJ analysis of the same dataset. Ten sequences from non-Hox families (NK2, Msx, Not, and Emx) were used as an outgroup. Shaded boxes as in Fig. 2.