1. Tree of Life: primary divisions OEB 192 – 11.09.12

2. Tree of Life: three “domains” Based on 16S rRNA (Woese, 1987):

3. Tree of Life: three “domains” Based on 16S rRNA (Pace, 1997):

4. Bacteria & Archaeal: all genomes as of 12 Feb., 2010 (Lee, Robinson & Marx, in prep)

5. Tree basics: meaning

6. Tree basics: rotation

7. Tree basics: shape

8. Microbial systematics Formerly Pseudomonas (partial list): Ralstonia, Burkholderia, Hydrogenophaga, Sphingomonas, Methylobacterium, Cellvibrio, Xanthomonas, Acidovorax, Hydrogenophillus, Brevundimonas, Pandoraea

9. 16S rRNA as phylogenetic marker Why a good molecule? 70S 30S 50S

10. Tree basics: clades & character changes

11. Key phylogenetic terms

12. Phenetics vs. cladistics

13. Maximum Parsimony Parsimony – shortest tree (fewest homoplasies)

14. Neutral theory Developed by Motoo Kimura, 1968

15. Wednesday (9/14): Molecular evolution & phylogenetic inference: case of HIV & comment…