www.melkonian.uni-koeln.de

What is Phylogeny?

The word "phylogeny" has its roots in ancient Greek and is a combination of phylon = stem and genesis = coming into being, origin. Phylogeny is the science of the relationships among the different lifeforms. The relationships of the organisms are described in phylogenetic trees similar to the family trees in genealogy. In phylogeny, the relatedness is inferred from comparisons of morphological (e.g. the skeleton of vertebrates), biochemical (antigenic epitopes, metabolites) and/or molecular (DNA, proteins) characters. The evolutionary history of a group of organisms can be deduced from a phylogenetic tree, thus phylogeny and evolutionary research are interconnected. Most phylogeneticists specialize on groups of organisms, as in our algae phylogeny group, but one goal of phylogenetic research is the reconstruction of the evolution of life from its origins and to gather the results of the phylogenetic research from different laboratories in the huge tree of life project. The knowledge about the relationships is a prerequisite for systematics, because the classification into families, genera, species etc. should reflect the evolutionary history of the organisms.

Why Molecular Phylogeny?

For many decades, phylogenetic hypotheses were based exclusively on structural characters and their comparison between organisms. This method implies many problems, e.g. convergent evolution, character losses, and the (usually) low number of comparable structural characters. Especially in protists and unicellular algae, only few characters are available for higher-level phylogeny and classification, e.g. the ultrastructure of the flagellar apparatus. However, many non-flagellated algae have even lost the whole flagellar apparatus (e.g. in the green alga Chlorella) and their phylogenetic position remained unresolved. In contrast, molecular phylogeny uses DNA- or protein-sequence data to compare organisms and to evaluate their relationship. If genes of universal occurrence (for example, many genes involved in the transcription- or translation-apparatus, or house-keeping genes) are examined, the phylogeny of all organisms can be analysed including those with reduced morphology (Chlorella in the green algae, yeast in the Fungi). The homology of molecular characters (every nucleotide in a gene is considered a separate character) is unambiguously evaluated in a multiple alignment (one gene, many organisms). Finally, the number of available molecular characters is usually very large - probably the most important advantage over structural characters. On the other hand, molecular phylogeny is also confronted with many problems: lateral gene transfers between unrelated organisms, extremely high sequence conservation or high variability, unequal base compositions, unequal rates of evolution (in different organisms, gene regions or times) and long-branch artefacts.
In our lab, most projects use the nuclear-encoded SSU rRNA gene (encoding the rRNA of the small subunit of the cytoplasmic ribosome); other projects analyse the ITS-regions, the LSU rRNA gene or the plastid-encoded rbcL gene (for the large subunit of Ribulose-Bisphosphate Carboxylase/Oxygenase).

The Figure shows the ribosomal operon. It is called an operon, because all genes on it are read and translated as one large piece of RNA at once. The ITS regions are then cut out to get the mature ribosomal RNAs. In a nuclear genome, usually multiple copies of ribosomal operons are distributed among several chromosomes and contribute to the nucleolus. The ribosomal RNAs are needed in the ribosomes, the large ribonucleo-protein complexes that perform protein synthesis in the cells. Thus, every living cell needs the genes of the ribosomal operon.