Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times

Fifty-eight homologous protein sequences from the completely sequenced chloroplast genomes of Zea mays, Oryza sativa, Nicotiana tabacum, Pinus thunbergii, Marchantia polymorpha and Poryphyra. purpurea were investigated. Analyzed individually, only 40 of the 58 proteins gave the true, known topology for these species. Trees constructed from the concatenated 14295 amino acid alignment and from automatically generated subsets of the data containing successively fewer polymorphisms were used to estimate the Nicotiana-Zea and Pinus-angiosperm divergence times as 160 and 348 million years, respectively, with an uncertainty of about 10%. These estimates based upon phylogenetic analysis of protein data from complete chloroplast genomes are in much better accordance with current interpretations of fossil evidence than previous molecular estimates.