Fig. 1.
The optimal MP and ML tree topology when all sites are included. Additionally, this topology represents the most parsimonious tree under a variety of data partitions including only first, second, and third positions. Branch lengths for branches A–J are in percent value and are Ka, Ks, and ML 1 and 2 distances. ML 1 distances are from the six datasets (Materials and Methods). Model parameters varied for different branches; however, the HKY+Γ model was always chosen as described in the text. ML 2 branch lengths are from the 90-kb dataset (Table 2) and were obtained by using the HKY+Γ model; α shape parameter = 0.3508. The names for the branches are: A, human terminal; B, chimpanzee terminal; C, gorilla terminal; D, orangutan terminal; E, OWM terminal; F, mouse terminal; G, human–chimpanzee stem; H, African ape stem; I, ape stem; and J, catarrhine stem extended to the primate–rodent mrca. Branches are not drawn to scale. Dates for the catarrhine mrca, African ape mrca, and human–chimpanzee mrca are averages and standard deviations of estimates obtained by global and local molecular clock models (see text and Table 4). Tree scores, bootstrap support values, and data partitions are shown in Table 2. *, Equally partitioned ML distances on branches F and J.