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 sta ges of divergence. These DNA sequences are greater than or equal to 89 % identical, but expected departures from random substitution are evid ent. Silent, third-position pyrimidine transitions are the dominant su bstitution type, with transversions comprising only a small fraction o f sequence differences. Substitution patterns are not clearly manifest ed until divergence has reached a moderate level (>3%), as expected fo r a stochastic process. Variation in the frequency of mismatch types a mong lineages decreases at larger divergences, but the level of bias d oes not decay. Divergence varies up to fivefold among gene regions but is not correlated with structural domain. All protein structural doma ins except extramembrane 4 display <20% variable residues. Regions cor responding to putative functional domains show the excepted conservati on of amino acids, although the C-terminal portion of the Q(0) reactio n center displays several nonconservative replacements. Phylogenetic a nalyses incorporating substitution asymmetries produced mixed results. Distances estimated with multiple parameters (transition, codon-posit ion, composition, and pyrimidine-transition biases) yielded identical additive tree topologies with comparable bootstrap values, all consist ent with uncontroversial species relationships. Maximum likelihood ana lysis incorporating these biases, as well as equally weighted parsimon y analysis, produced similar results. Static, differential weighting f or parsimony did not improve the phylogenetic signal but produced unus ual trees with low bootstraps. The overall rate of nucleotide substitu tion varies slightly but significantly among cranes, and calibration o f distances against fossil dates suggests divergence rates of 0.7%-1.7 % per million years.