Conference abstracts from the Colloqium Microbial Evolution: Concepts and Controversies organised by The Canada Research Chair in the history of biology at the Université du Québec à Montréal, from October 17 to 19 2002 Beyond neo-Darwinism: The Origins of Microbial Phylogenetics Jan Sapp Department fo History, Université du Québec à Montréal, CIRST Chairholder of the Canada Research Chair in the History of Biology The neo-Darwinian evolutionary synthesis of the 1930s and 1940s dealt with the evolution of plants and animals over the last 560 million years. It did not address the evolution of microorganisms and the previous 3000 million years of evolutionary change on earth. During the last two decades of the twentieth century, biologists developed new comparative molecular techniques and concepts to trace life back thousands of millions of years to investigate early microbial evolution with the aim to create a universal phylogeny. Studies of microbial phylogeny have brought about a conceptual revolution in the way in which evolutionary change occurs in microbes with the evidence for the fundamental importance of symbiotic mergers, fusions, and various other mechanisms for horizontal gene transfer. The scope and significance of these mechanisms remain subjects of controversy. The Origin of Intermediate Metabolism Harold Morowitz Krasnow Institute, George Mason University, Fairfax, VA 2030, USA The case is made for autotrophs preceding heterotrophs, chemoautorophs preceding photoautotrophs, and the reductive tricarboxylic acid cycle preceding the Calvin-Benson cycle. The acetyl Co-A pathway is less certain. A group of universal features of the primary chart of autotrophic metabolism is discussed. This includes the universal nitrogen entry point and the universal sulfur entry point. The ecological significance of universal features of primary metabolism is discussed. The existence of biological laws at various hierarchical levels is outlined. The Pauli Exclusion Principle is presented as an example of hierarchical laws. The anomalous features of Vitamin B12 are discussed. Molecular phylogeny of bacteria based on comparative sequence analysis of conserved genes 1 Karl Heinz Schleifer and Wolfgang Ludwig Department of Microbiology, Technical University Munich, Am Hochanger 4, D-85350 Freising; Germany Carl Woese and his coworkers achieved a breakthrough regarding the reconstruction of the phylogeny of prokaryotes by introducing rapid methods for comparative sequence analysis of small subunit rRNAs. Based on their data a phylogenetic tree of prokaryotes could be reconstructed for the first time. Currently more than 30000 small subunit rRNA sequences from pro- and eukaryotes are available in public databases. Due to the lack of comprehensive sequence data bases for other potential phylogenetic marker molecules, our view of the phylogeny of bacteria is mainly based on data derived from only one class of molecule, the 16S rRNA. Now in the era of genomics the rapidly increasing number of accessible full genome and further gene sequence data allows a sound evaluation of small subunit rRNA based phylogenetic conclusions. The comparative analysis of the available genome data showed that only a rather limited number of genes or gene products fulfils the criteria for phylogentic markers such as universal distribution as well as sufficient sequence conservation and complexity. The large subunit rRNA, elongation and initiation factors, subunits of proton translocation ATPase, RNA polymerase, DNA gyrase, recA, heat shock proteins, and amino acyl tRNA synthetases are among the most informative marker molecules. Comparative phylogenetic analyses of these markers are in good agreement with that of the small subunit rRNA, at least with respect to the major groups. However, local tree topologies often differ depending on the molecule analysed. This was to be expected. In a few cases there are also more drastic differences between phylogenetic trees derived from rRNA and protein genes. This, however, can mostly be explained by the presence of multiple genes which may originate from gene duplication or lateral gene transfer. Since functional consistency of multiple genes cannot be assumed for all variants, there may be the risk of comparing paralogous markers. The latter can only be recognized as such if there are genomes containing all variants of the multiple genes. This may complicate comparative phylogenetic analysis. However, with the availability of more full genome sequences it should be possible to handle such problems more properly.Despite the problems with multiple genes, the phylogenetic analyses based upon different alternative markers showed that small subunit rRNA derived trees globally reflect the phylogeny of the corresponding organisms, however, locally more their own history. Interactions between Horizontal Gene Transfer and the Environment. James Lake and R. Jain, M. Rivera, J. Moore Molecular Biology Institure, University of California, Los Angeles Horizontal gene transfer (HGT) is a process through which disparate prokaryotic groups can obtain foreign genetic material in response to a changing environment. It is an ancient process that has altered genomes since, at least, the last common ancestor of life and is influenced by abiotic factors such as temperature and pH. HGT is selective and preferentially favors the exchange of some gene types. Operational genes (mostly housekeeping genes) are readily incorporated through HGT, but informational genes (translation, transcription, and other genes) are less readily incorporated through this mechanism. HGT is also influenced by abiotic factors 2 such as temperature and pH. It has been suggested that the collection of organisms that exchange genes can be thought of as a globalorganism, having an immense population size and a correspondingly great potential for evolving novel genes. Here we ask whether the organisms which share genes truly share them on a global scale, or whether environmental factors can affect its scale. In other words, can geography and environment, or abiotic and biotic parameters, influence genetic exchange by HGT? Our analyses of some 20,000 genes in eight complete genomes show that environmental factors can significantly alter horizontal transfer among prokaryotes. Mountains and molehills what is at stake in the lateral gene transfer debate? W. Ford Doolittle Program in Evolutionary Biology, Canadian Institute for Advanced Research and Department of Biochemistry and Molecular Biology , Dalhousie University During the 1980s and 90s, microbiologists constructed, and came to believe in, a universal species tree based on sequences of a single gene (small subunit rRNA) even though they had known since the mid 1960s that some genes can be readily transferred between species. There were sound and unsound reasons for being optimistic about this enterprise, and many still endorse it, although complete prokaryotic genome sequences, ever more numerous and accessible, show that we had drastically underestimated the extent of transfer, over short and long evolutionary time scales. I will survey the current state of this debate over gene transfer the evidence, the arguments and the underlying reasons for the heat. CONTEMPORARY ISSUES IN MITOCHONDRIAL ORIGINS AND EVOLUTION Michael W. Gray Program in Evolutionary Biology, Canadian Institute for Advanced Research and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7 Questions about the origin of the mitochondrion and its subsequent evolution are intimately tied to the mitochondrial genome, for it is the latter that has provided the clearest indications of a bacterial (specifically a-Proteobacterial) origin for at least those functions (coupled oxidative phosphorylation, protein synthesis) that this genome partly encodes. One of the most remarkable features of the mitochondrial genome is its extreme structural and organizational diversity, which underpins a basically uniform genetic function. Mitochondrial DNAs (mtDNAs) in animals, plants, fungi and protists look very different from one another, and they evolve in radically different ways. Comparative sequence analysis, based on the determination of complete mtDNA sequences, has proven to be a powerful method for assessing the pathways and processes of mitochondrial genome evolution, and for making inferences about the origin of the mitochondrion. This approach has defined three general organizational patterns (designated ancestral, expanded ancestral and derived) into which mitochondrial genomes can be roughly classified, and has also identified the most gene-rich and eubacteria-like mitochondrial genomes yet known, providing our clearest picture to date of the ancestral mtDNA progenitor. Various types of data, including mitochondrial gene content, gene order and phylogenetic trees based on 3 concatenated mitochondrial protein-coding sequences, argue strongly in favour of a single origin of the mitochondrial genome. Although the mitochondrial genome is essential to the process of mitochondrial biogenesis, it encodes a relatively small number of the protein components of the mitochondrion: genes for the vast majority of mitochondrial proteins are carried by the nuclear genome. The availability of complete nuclear genome sequences (e.g., yeast) has provided an opportunity to assess the phylogenetic affiliations of nucleus-encoded mitochondrial proteins. A small proportion of these proteins can be traced unambiguously to the a-Proteobacterial