Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes

Analyses of complete cytochrome b sequences from all species of cranes(Aves: Gruidae) reveal aspects of sequence evolution in the early stages ofdivergence. These DNA sequences are > or = 89% identical, but expecteddepartures from random substitution are evident. Silent, third- positionpyrimidine transitions are the dominant substitution type, withtransversion comprising only a small fraction of sequence differences.Substitution patterns are not clearly manifested until divergence hasreached a moderate level (> 3%), as expected for a stochastic process.Variation in the frequency of mismatch types among lineages decreases atlarger divergences, but the level of bias does not decay. Divergence variesup to fivefold among gene regions but is not correlated with structuraldomain. All protein structural domains except extramembrane 4 display <20% variable residues. Regions corresponding to putative functional domainsshow the excepted conservation of amino acids, although the C-terminalportion of the Q0 reaction center displays several nonconservativereplacements. Phylogenetic analyses incorporating substitution asymmetriesproduced mixed results. Distances estimated with multiple parameters(transition, codon-position, composition, and pyrimidine-transition biases)yielded identical additive tree topologies with comparable bootstrapvalues, all consistent with uncontroversial species relationships. Maximumlikelihood analysis incorporating these biases, as well as equally weightedparsimony analysis, produced similar results. Static, differentialweighting for parsimony did not improve the phylogenetic signal butproduced unusual trees with low bootstraps. The overall rate of nucleotidesubstitution varies slightly but significantly among cranes, andcalibration of distances against fossil dates suggests divergence rates of0.7%-1.7% per million years.