Bacterial Evolution

PERSPECTIVE ................................................................ 222 A Fruitless Search and Its Consequences ................................................................ 222 Three Ideas That Shape Our Concept of Bacterial Evolution .......................................................224 Procaryote-eucaryote dichotomy ............................................................... 224 Oparin Ocean scenario ............................................................... 224 Darwin's warm little pond ............................................................... 226 MEASUREMENT OF BACTERIAL PHYLOGENETIC RELATIONSHIPS ......................................226 Three-Dimensional and One-Dimensional Characters ............................................................... 226 The evolutionary clock ............................................................... 226 A missed opportunity ............................................................... 226 Nature of Molecular Chronometers ................................................................ 227 Clocklike behavior............................................................... 227 Phylogenetic range ............................................................... 227 Size and accuracy............................................................... 227 rRNAs, the Ultimate Molecular Chronometers ................................................................ 227 Why they are so good ............................................................... 227 Oligonucleotide cataloging............................................................... 228 Analysis of Sequence Alignments ............................................................... 228 Distance matrix methods................................................................ 228 Maximum parsimony analysis ............................................................... 228 Cluster analysis ............................................................... 228 DO BACTERIA HAVE A GENEALOGY AND A MEANINGFUL TAXONOMY9. .............................230 THE UNIVERSAL PHYLOGENETIC TREE ............................................................... 231 EUBACTERIAL PHYLOGENY ............................................................... 232 Background ..................................................... 232 Major Eubacterial Groups and Their Subdivisions ..................................................... 232 Purple Bacteria..................................................... 236 a-Purple bacteria ...................................................... 237 ,-Purple bacteria ..................................................... 238 ,y-Purple bacteria ..................................................... 238 8-Purple bacteria ...................................................... 238 Gram-Positive Eubacteria ..................................................... 240 Cyanobacteria ..................................................... 242 Green Sulfur Bacteria ..................................................... 243 Spirochetes ..................................................... 244 Bacteroides, Flavobacteria, and Their Relatives..................................................... 244 Planctomyces and Their Relatives ..................................................... 244 Chlamydiae..................................................... 245 Radiation-Resistant Micrococci and Their Relatives ..................................................... 245 Green Non-Sulfur Bacteria and Their Relatives ..................................................... 245 Other Eubacterial Phyla ..................................................... 245 Overall Structure of the Eubacterial Tree..................................................... 245 ARCHAEBACTERIAL PHYLOGENY ..................................................... 247 Unusual Nature of the Archaebacterial Phenotype..................................................... 247 Definition of the Major Archaebacterial Groups ...................................................... 247 Methanogens ..................................................... 248 Extreme halophiles ..................................................... 248 Extreme thermophiles ..................................................... 249 The Archaebacterial Tree: Its Branching Order and Root...................................................... 249 Main branches..................................................... 249 Thermococcus and Thermoplasma ..................................................... 251 Branching order among the methanogens and extreme halophiles..............................................251 A BRIEF LOOK AT EUCARYOTE PHYLOGENY ..................................................... 252 Implications of the Eucaryote Phylogenetic Tree ..................................................... 252 NATURE OF THE EVOLUTIONARY PROCESS IN BACTERIA ..................................................253 25 Relationship Between Evolution's Tempo and Its Mode ..............................................................253 Macroevolution at the Molecular Level: the Mycoplasmas and Their rRNAs...................................253