1. First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )

2. Horizontal Gene transfer 1.Atypical nucleotide composition Lawrence and Ochman paper 2. Presence/absence of genes Welch et al 2002 3. Incongruent Phlyogenies

3. Genetic exchange in bacteria/archaea Transformation Transduction Conjugation Often detected by atypical nucleotide composition

4. Detecting HGT from genomes: atypical nt composition (Lawrence & Ochman, 1997)

5. Detecting HGT from genomes: atypical nt composition

7. (Lawrence & Ochman, 1998)

8. Molecular archaeology of the Escherichia coli genome (Lawrence & Ochman, 1998)

9. Horizontal Gene transfer 1.Atypical nucleotide composition Lawrence and Ochman paper 2. Presence/absence of genes Welch et al 2002 3. Incongruent Phlyogenies

10. Detecting HGT from genomes: atypical nt composition

11. Detecting HGT: differential gene content (Welch et al., 2002) (Pál et al., 2005)

12. Horizontal Gene transfer 1.Atypical nucleotide composition Lawrence and Ochman paper 2. Presence/absence of genes Welch et al 2002 3. Incongruent Phlyogenies

13. Detecting HGT: incongruent phylogeny/synteny HGT onlyLoss only (Koonin, 2003) Ex: glycerol-3-P DH

14. Detecting HGT: plants!?! Rafflesia (Malpighiales) (Davis & Wurdack, 2004)

15. Detecting HGT: bacteria to insects!?! (Hottop et al., 2007)

16. Can gene histories be retraced? (Xie et al., 2004)

17. Can gene histories be retraced? (Kunin et al., 2005)

18. Is there still an organismal tree? (Daubin et al., 2003)

19. Is there still an organismal tree? (Daubin et al., 2003)

20. Limitations to HGT

21. Decrease in recombination w/ sequence divergence (Fraser et al., 2007) Bacillus subtilis Bacillus mojavensis Streptococcus pneumoniae E. coli

22. Next week…. Are there species? Or is it just a continuum?