Molecular phylogenies of plastid origins and algal evolution

Abstract

An overview of recent molecular analyses regarding origins of plastids in algal lineages is presented. Since different phylogenetic analyses can yield contradictory views of algal plastid origins, we have examined the effect of two distance measurement methods and two distance matrix tree-building methods upon topologies for the ribulose-l,5-bisphosphate carboxylase/oxygenase large subunit nucleotide sequence data set. These results are contrasted to those from bootstrap parsimony analysis of nucleotide sequence data subsets. It is shown that the phylogenetic information contained within nucleotide sequences for the chloroplastencoded gene for the large subunit of ribulose-l,5-bisphosphate carboxylase/oxygenase, integral to photosynthesis, indicates an independent origin for this plastid gene in different plant taxa. This finding is contrasted to contrary results derived from 16S rRNA sequences. Possible explanations for discrepancies observed for these two different molecules are put forth. Other molecular sequence data which address questions of early plant evolution and the eubacterial origins of algal organelles are discussed.

The chaperone connection to the origins of the eukaryotic organelles

“…2) a situation that suggests in principle that the plastids in these eukaryotic lineages derive from separate events of endosymbiosis (from distinct lineages among the cyanobacteria). It is difficult to evaluate at this stage whether the discrepancies between the results presented here (or those based in rRNA analysis [ 1 l-131) with rbc-based sequence comparisons [5] represent either a differential retention of duplicated genes originally present in the ancestor of the plastids, lateral transfer/ replacement events (i.e. mosaic genomes) [2-61, or problems associated to current phylogenetic methods [2][3][4].…”

“…However, inferences based on ribulose bisphosphate carboxylase genes (rbc) indicate that plastids from non-green algae derive from the cc-or j?-Proteobacteria [5], again pointing to a scenario that includes ancestors from different eubacterial division lineages [336].…”

“…Explanations for some of these conflicting results include either lateral transfer of genes, paralogy, differential retention of duplicated operons present in a common ancestor of the endosymbionts, or limitations inherent to the assumptions on which phylogenetic methods are based [2-61. Concerning the latter, inferences based on a macromolecule which has evolved differentially in the various organisms under study may not necessarily re-fleet the true phylogeny of these lineages [2][3][4][5]. Therefore, as pointed out by several authors [2][3][4][5]14,, it is becoming increasingly evident that the resolution of the evolutionary history of organisms in general (and eukaryotic organelles in particular) will undoubtedly require of a comparative and critical analysis of data from different macromolecules, the fossil record (when available), and a correlation of the inferred phylogenies with the phenotypic traits of the organisms under consideration.…”

“…Therefore, as pointed out by several authors [2][3][4][5]14,, it is becoming increasingly evident that the resolution of the evolutionary history of organisms in general (and eukaryotic organelles in particular) will undoubtedly require of a comparative and critical analysis of data from different macromolecules, the fossil record (when available), and a correlation of the inferred phylogenies with the phenotypic traits of the organisms under consideration.…”

Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes.

“…Deduced amino acid sequences were aligned with the Genetics Computer Group package (14). Phylogenetic trees were constructed by the neighborjoining method (15), which has been shown to be very efficient in recovery of the correct topology under a variety of sequence parameters (16 (19).…”