A phylogenetic analysis of monocotyledons based on the chloroplast gene rps4, using parsimony and a new numerical phenetics method.

We have sequenced the chloroplast gene rps4 of 72 species; the sequence of 6 more species was found in the databanks. The 78 species were chosen so as to be representative of two taxonomic levels: the family, with 39 Poaceae, and the class, with 28 additional monocot species. Eleven dicots and other land plants were used as outgroups to the monocots. The 78 sequences were aligned by eye. Phylogenetic reconstruction was performed using the Wagner parsimony method: our first results were in contradiction with classical systematics, due to a local minimum. We then used the results obtained with the new distance method Anataxis to redraw a new tree and carry on further the parsimony calculations starting from this Anataxis tree. Up to 20,000 most parsimonious trees were thus obtained. The robustness of our results was checked by the bootstrap test and decay analyses. The Anataxis and the strict consensus tree fitted the general features of land plant evolution. Some of our results concerning relationships within the monocots corroborated those obtained with the chloroplast gene rbcL. Both genes raise questions concerning the monocot superorders as defined in a previous classification. This study proves the rps4 gene to be a useful phylogenetic tool within the Poaceae family and the Monocotyledonae order.