Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2000-04

AUTHORS

Jun Adachi, Peter J. Waddell, William Martin, Masami Hasegawa

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. More... »

PAGES

348-358

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s002399910038

DOI

http://dx.doi.org/10.1007/s002399910038

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1041828088

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/10795826


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