Distribution of gene order changes have been used successfully for estimating phylogenies within and among various land plant groups. However, such chloroplast DNA structural characters remain largely untested for phylogenetic inference at very high taxonomic levels such as between Chlorophytes and Streptophytes or among major lineages of photosynthetic organisms. When chloroplast genomes of these more distantly related organisms are compared, computational difficulties increase dramatically. Challenges include unequal gene content and high rates of change relative to the number of genes available as landmarks. We have been developing and testing a variety of methods for reconstructing phylogenies based on gene order data (see abstracts by Jansen et al and Moret et al). Here we will compare results of our methods when analyzing highly divergent gene orders. We have determined gene orders, from complete genome sequence information available in genbank, for chloroplast genomes of eleven organisms. In our data, we represent the free-living cyanelle, Cyanophora, "red algae" (Cyanidium, Porphyra), "green algae" (Chlorophytes: Chlorella, Mesostigma, Nephroselmis and Streptophytes: Marchantia and tobacco), and presumed secondary endosymbionts (putative red algal derivatives: Guillardia, Odontella and putative green algal derivative: Euglena). To analyze these data we have utilized GRAPPA and other approaches based on breakpoint and inversion distance as well as cladistic analyses using shared rearrangement endpoints as characters.

Key words: chloroplast phylogeny, comparative genomics, gene order rearrangement, photosynthetic eukaryotes, phylogenetic methods