Figure 1. Phylogenetic tree (evolutionary distance dendrogram in this case) of bacterial and archaeal diversity, derived from analysis of 16S rRNA gene sequences, demonstrating the major phylum (division) level lineages in each major prokaryote domain. Phyla are displayed as wedges with dimensions reflecting the known degree of divergence within each lineage. Phyla with any cultivated representatives are in red, whereas those known only from environmental sequences are blue, and are named after the first clones found within the group. Phylum level lineages indicated by upper case letters and numbers were first described by sequencing clone libraries prepared from DNA of uncultured microbial communities, e.g. Obsidian Pool in Yellowstone National Park, USA in the case of OP divisions. Archaeal kingdoms Euryarcheota and Crenarcheota are abbreviated to ‘Eury’ and ‘Cren,’ respectively, and placed as suffixes to phylum names. Updated version of tree from Hugenholtz (2002). Courtesy of Phil Hugenholtz, Joint Genome Institute.

Figure 2. Conservation secondary structure diagrams for 16S rRNA molecules of (a) Archaea and (b) Bacteria, showing overall similarities in secondary structure of 16S rRNA from species in the two prokaryotic domains of life, and the degree of conservation of sequence in different structural regions of 16S rRNA found when many sequences are compared e.g. most nucleotides are more than 98% conserved between positions 500 and 550 whether in Archaea or Bacteria (only the Bacteria positions are numbered) while in a variable region, such as that between positions 600 and 650, most positions are less than 80% conserved. Modified from diagrams available at the Comparative RNA Web Site – rRNA Conservation Diagrams (Public) (http://www.rna.ccbb.utexas.edu/).

Figure 3. Alignments for (a) pyruvate kinase (pyk) gene sequence and (b) 16S rRNA gene sequence for three strains of the genus Streptococcus: two strains of Streptococcus pyogenes (strains M1GAS and MGAS8232) and one of Streptococcus pneumoniae (TIGR4), illustrating that the separate species S. pneumoniae differs from both S. pyogenes strains to a much greater extent in the case of pyruvate kinase protein gene sequence than when 16S rRNA sequences are compared, and demonstrating the greater utility of some protein genes for species distinction. Only the first 360 nucleotides of each alignment are shown. ClustalX software was used to produce alignments. Key to sequences: NC_002737=S. pyogenes M1GAS (strain SF370); NC_003485=S. pyogenes MGAS8232; NC_003028=S. pneumoniae strain TIGR4. Sequences are from the National Center for Biotechnology Information (NCBI) microbial database. Alignments were generated by the author.

Figure 4. Genetic map of representatives of the mitis group of the genus Streptococcus, based on concatenated sequences of six genes used in the multi-locus sequence typing (MLST) approach as applied to streptococci. Red dots represent S. pneumoniae, yellow dots Streptococcus pseudopneumoniae, purple dots Streptococcus mitis, and brown dots Streptococcus oralis. The three light blue dots represent strains for which named species status could not be assessed. Reproduced from Fraser et al. (2007). http://www.sciencemag.org/ Readers may view, browse, and/or download material for temporary copying purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed, published, or sold in whole or in part, without prior written permission from the publisher.