Molecular phylogeny of protists: origin and evolution of the Dinoflagellates

Abstract

Molecular sequence data have become prominent tools for phylogenetic relationship inference, particularly useful in the analysis of highly diverse taxonomic orders. Ribosomal RNA sequences provide markers that can be used in the study of phylogeny, because their function and structure have been conserved to a large extent throughout the evolutionary history of organisms. These sequences are inferred from cloned or enzymatically amplified gene sequences, or determined by direct RNA sequencing. The first step of the phylogenetic interpretation of nucleic acid sequence variations implies proper alignment of corresponding sequences from various organisms. Best alignment based on similarity criteria is greatly reinforced, in the case of ribosomal RNAs, by secondary structure homologies. Distance matrix methods to infer evolutionary trees are based on the assumption that the phylogenetic distance between each pair of organisms is proportional to the number of nucleotide substitution events. Computed tree inference methods usually take into consideration the possibility of unequal mutation rates among lineages. Divergence times can be estimated on the tree, provided that at least one lineage has been dated by fossil records. We have utilized this approach based on ribosomal RNA sequence comparison to investigate the phylogenetic relationship between dinoflagellated and other eukaryote protists, and to refine controverse phylogenies of the class Dinophycae.