The molecular evolution of the amino acid sequences of the mature small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygense (Rubisco) was determined. The dataset for each subunit consisted of sequences from 39 different taxa of which 22 are represented with sequence information for both subunits. Phylogenetic trees were reconstructed using distance matrix, parsimony and simultaneous alignment and phylogeny methods. For the small subunit, the latter two methods produced similar trees that differed from the topology of the distance matrix tree. For the large subunit, each of the three tree-building methods yielded a distinct tree. Except for the distance matrix small subunit tree, the tree-building methods produced topologies for the small and large subunit sequences from the nonflowering plant taxa that, for the most part, agree with current taxonomic schemes. With the full datasets, the lack of consistency both among the various trees and with conventional taxonomic relationships was most evident with the Rubisco sequences from angiosperms. It is unlikely that current tree-building methods will be able to reconstruct an unambiguous molecular evolution of either of the Rubisco subunits. Molecular trees, regardless of methodology, showed similar topologies for the small and large subunits from the 22 taxa from which both subunits have been sequenced, indicating that the subunits have changed to the same extent over time. In this case, similar trees were formed because only 4 of the 22 taxa were from dicots. Key words: ribulose-1,5-bisphosphate carboxylase/oxygenase, amino acid sequence, molecular evolution, phyletic trees.
Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes
