1. BIOS E-127 – 08.09.29

2. Phenetics vs. cladistics

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

4. Maximum Parsimony

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

6. Molecular phylogenetics Zuckerkandl & Pauling. 1965. Molecules as documents of evolutionary history. J Theor Biol. 8:357-366. Neutral theory (Motoo Kimura, 1968)

7. 16S rRNA as phylogenetic marker Why a good molecule?

8. 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 Ortholog vs. paralog?

9. CGGATAAAC CGGATAGAC CGCGATAAAC CGGATAAC taxa1 taxa2 taxa3 taxa4 Alignment

10. Example: Neighbor Joining (NJ) Taxa Characters Species A ATGGCTATTCTTATAGTACG Species B ATCGCTAGTCTTATATTACA Species C TTCACTAGACCTGTGGTCCA Species D TTGACCAGACCTGTGGTCCG Species E TTGACCAGTTCTCTAGTTCG A B C D E Choose methods: distance-based A B C D E Species A ---- 4 10 9 8 Species B ---- 8 11 10 Species C ---- 3 8 Species D ---- 5 Species E ---- A B C D E Species A ---- 4 10 9 8 Species B -19.3 ---- 8 11 10 Species C -10 -14.7 ---- 3 8 Species D -10.7 -11.3 -16 ---- 5 Species E -12.7 -13.3 -12 -14.7 ---- M(AB)=d(AB) -[(r(A) + r(B))/(N-2)]

11. Ancestral Sequences Observed Sequences ? Model Choose “model”

12. Maximum Parsimony (MP): Model: Evolution goes through the least number of changes Maximum Likelihood (ML): L (data| model) Bayesian Inference Markov chain Monte Carlo (MCMC) method for sampling from posterior probability distribution Discrete character methods

13. I. Bootstrap Re-sampling to produce pseudo-dataset (random weighting) II. Jacknife Sampling with replacement III. Permutation test Random deletion of sub-dataset Randomize dataset to build null likelihood distribution CGATCGTTA CAATGATAG CGCTGATAA CGCTGATCG taxa1 taxa2 taxa3 taxa4 123456789 Dataset1: 729338554 Dataset2: 631981282 … Dataset1: 1-3-56789 Dataset2: 12-45678- … 100 73 Assess reliability

14. Reconstructed ancestral sequences to infer paleoenvironment (Gaucher et al., 2003)

15. Signs of selection (Sawyer & Malik, 2006)

16. 5. Assess Reliability Molecular clock: HIV-1 origin (Korber et al., 2000)

17. Genetic exchange in bacteria/archaea

18. Detecting HGT from genomes: atypical nt composition (Hacker & Carniel, 2001)

19. Monday (10/6): Microbial species, biogeography & population genetics II.