Pre-Proof Version: Horizontal gene transfer and the formation of groups of microorganisms

3 Problems encountered in phylogenetic reconstruction 4 Towards a natural taxonomy 4 Gene transfer and phylogenetic reconstruction 5 HGT can create patterns indistinguishable from those created through shared ancestry 9 Plurality of pattern and process 9 A population genetic point of view for higher level taxonomic units 10 HGT and the creation of metabolic pathways 11 Categorizing gene transfer 11 Homologous and non-homologous recombination 11 Effects on fitness 12 HGT between distant relatives 13 HGT and the expansion of metabolic networks 14 Oxygen producing photosynthesis 15 Acetoclastic methanogenesis in Methanosarcina 17 Evolution of Na and H pumping ATPases/ATP synthase 18 Transferred genes as shared derived characters 20 HGT of aminoacyl tRNA synthetases 21 The origin of primary plastids 22 Correlating evolution across the domains of life 23 Conclusions 24 Acknowledgments 24 References 25 Horizontal gene transfer and the formation of groups. Page 3