| Abstract: | Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of
Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties
of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining
trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account.
Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical
criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated
from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly
favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitution patterns
in plastid-encoded proteins and should be useful in future ML inferences using such data. A second rate matrix, called cpREV*,
based on a weighted sum of rate matrices from different trees, is also considered.
Received: 3 June 1999 / Accepted: 26 November 1999 |
