ABSTRACT
In this contribution, we will review how much is currently known about fungal evolution, and how well phylogenetic hypotheses are supported by the data that were used for these inferences. We will start with the controversial question of how fungi should be classified as an organismal group, using molecular evolutionary criteria, instead of the classical taxonomic and morphological ones, and the extent to which more recent molecular evolutionary results are compatible with the classical views. We will then introduce recent developments in phylogenetics and genomics research that promise to take us another step forward in revolutionizing our understanding of the Fungi, and of eukaryotes in general. By combining information on fungal and other eukaryotic genomes (comparative and evolutionary genomics), genome-wide expression data on mRNAs and structural RNAs (ribonomics or transcriptomics) and proteins (proteomics), and by adding the current knowledge about the interactions of all proteins, RNAs and other molecules (interactomics), fungi have become the best-understood eukaryotic models. In addition, the relatively small genomes of fungi are rapidly deciphered at a moderate cost (e.g., compared to metazoan and plant genomes), and specific genes and gene products are easily analyzed using genetics, reverse genetics, and biochemical techniques that are becoming available for an increasing number of fungi. However, it should be kept in mind that their value as eukaryotic model systems might be limited. Particularly, the intensely studied ascomycete fungi are adapted to rather specialized saprophytic life styles as reflected by their highly reduced gene sets (e.g., compared to animals). It is nonetheless possible that species from other fungal lineages have significantly higher coding capacities that more closely reflect those of other eukaryotes. Through systematic studies of complete fungal genomes from all four fungal phyla we will be able to address this question, as well as further advance the understanding of eukaryotic evolution, of which fungi constitute a substantial portion.
