1. OEB 192 – 10.09.13 “Evolutionary speculation constitutes a kind of metascience, which has the same intellectual fascination for some biologists that metaphysical speculation possessed for some mediaeval scholastics. It can be considered a relatively harmless habit, like eating peanuts, unless it assumes the form of an obsession; then it becomes a vice” (Stanier, 1970)

2. Tree of Life: primary divisions

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

4. 16S rRNA as phylogenetic marker Why a good molecule? 70S 30S 50S

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

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

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

8. Tree basics: meaning

9. Tree basics: rotation

10. Tree basics: shape

11. Tree basics: character change

12. Key phylogenetic terms

14. Phenetics vs. cladistics

15. Lysozyme amino acid changes in unrelated ruminants Phenetics vs. cladistics

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

17. Neutral theory Developed by Motoo Kimura, 1968

18. Good Dataset [A1, A2, A3, A4] [A1, B2, A3, A4] Bad Dataset A B species 1 species 2 species 3 species 4 A1 B1 A2 B2 A4 B4 A3 B3 1. Collect Sequence Data Ortholog vs. paralog?

19. 2. Sequence Alignment CGGATAAAC CGGATAGAC CGCTGATAAAC CGGATAC taxa1 taxa2 taxa3 taxa4 Alignment

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

21. Upcoming talks in (microbial) evolution… Wednesday, 9/15 11:00 AM Main Lecture Hall BioLabs Building OEB Weekly Seminar Series Gunter Wagner Yale University Transcription factor protein evolution and the origin of evolutionary novelties Host: Abzhanov Lab