Investigating the Comparative Biology of the Heterokonts with Nucleic Acids1

During the last decade investigations of heterokont protists utilizing molecular methods have challenged established biosystematic concepts. Most investigations emphasized the chloroplast genome or sequences from nuclear-encoded, ribosomal genes. Refinement of DNA isolation protocols, advent of “universal primers” and the polymerase chain reaction, automated sequencing and increased accessibility of DNA sequence databases have expanded data-gathering efficiency and increased dataset sizes. Because independent datasets have been easier to obtain, the testing of specific phylogenetic hypotheses has been facilitated, altering relationship concepts, primarily at phylum/class levels, and perceptions of cellular evolution. New approaches have emphasized ecological studies and extended studies to genus/species levels and poorly investigated genomes. This paper reviews studies documenting these impacts and identifies some current limitations. Additionally, new DNA sequence data from our laboratory on nuclear-encoded rDNA internal transcribed spacers and the chloroplast-encoded psb A gene suggest that these regions will provide taxonomic resolution for the Synu-rophyceae, at the class/order level and subspecies level, respectively.