Molecular Biology and Evolution, Vol 13, 21-30, Copyright © 1996 by Society for Molecular Biology and Evolution
C Krajewski and DG King
Analyses of complete cytochrome b sequences from all species of cranes
(Aves: Gruidae) reveal aspects of sequence evolution in the early stages of
divergence. These DNA sequences are > or = 89% identical, but expected
departures from random substitution are evident. Silent, third- position
pyrimidine transitions are the dominant substitution type, with
transversion comprising only a small fraction of sequence differences.
Substitution patterns are not clearly manifested until divergence has
reached a moderate level (> 3%), as expected for a stochastic process.
Variation in the frequency of mismatch types among lineages decreases at
larger divergences, but the level of bias does not decay. Divergence varies
up to fivefold among gene regions but is not correlated with structural
domain. All protein structural domains except extramembrane 4 display <
20% variable residues. Regions corresponding to putative functional domains
show the excepted conservation of amino acids, although the C-terminal
portion of the Q0 reaction center displays several nonconservative
replacements. Phylogenetic analyses incorporating substitution asymmetries
produced mixed results. Distances estimated with multiple parameters
(transition, codon-position, composition, and pyrimidine-transition biases)
yielded identical additive tree topologies with comparable bootstrap
values, all consistent with uncontroversial species relationships. Maximum
likelihood analysis incorporating these biases, as well as equally weighted
parsimony analysis, produced similar results. Static, differential
weighting for parsimony did not improve the phylogenetic signal but
produced unusual trees with low bootstraps. The overall rate of nucleotide
substitution varies slightly but significantly among cranes, and
calibration of distances against fossil dates suggests divergence rates of
0.7%-1.7% per million years.
ORIGINAL ARTICLE
Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes
Department of Zoology, Southern Illinois University at Carbondale 62901- 6501, USA.
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