The evolution of prokaryotic ferredoxins--with a general method correcting for unobserved substitutions in less branched lineages.

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Abstract
Thirty-one bacterial type ferredoxins were examined by means of the parsimony method for their phylogenetic implications. The results show reasonable relationships in that photosynthetic, thermophilic, and desulfovibrio groups are identifiable; but a number of interesting anomalies occur. These include a methanogen sequence that clusters among the desulfovibrios. There are several differences from the phylogeny of Woese. At least two duplications producing paralogous genes are demonstrated, plus the probable existence of two more. The partial internal gene duplication that doubled the length of ferredoxin is confirmed by showing that the probability of the two ancestrally reconstructed halves possessing that much similarity by chance is 10(-7). Howard and co-workers proposed that the two halves of the Azotobacter vinelandii are reversed relative to most other sequences. A phylogeny, drawn with the halves of the azotobacter sequence (and its relatives) reversed produced a tree that had only three less nucleotide substitutions than did the tree without their halves reversed. This plus other evidence suggests that the significantly greater similarity observed across rather than within the halves is more likely the result of convergence.