1. February 11, 2012 Seth Bordenstein Departments of Biological Sciences & Pathology, Microbiology, and Immunology s.bordenstein@vanderbilt.edu Seth Bordenstein Departments of Biological Sciences & Pathology, Microbiology, and Immunology s.bordenstein@vanderbilt.edu

3. Gene loss / Genome reduction How do bacterial genomes change during symbiosis? Single nt mutations Insertions of DNA from foreign sources; Duplications

4. The Genome Sizes of Life

5. Rule 1: Genome Size Variation Correlates with Gene Number Variation Genome Size (Mb) Protein Coding Genes

6. Rule 2: Bacterial Ecology Alters Genome Evolution Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001. Trends Genet 17, 589-96. DNA Inflow DNA Outflow Eukaryotic cell Mutation bias for DNA deletions Relaxed selection on redundant genes between bacteria and host Reduced exposure to novel gene pools

7. BacteriophageTransposonPlasmid Rule 3: Bacterial Mobile DNAs Are The Agents of Open Source Evolution

8. Ecology Affects Mobile DNA Abundance Exposure to other microbes Horizontal Gene Transfer Mobile DNA Reduced exposure to other microbes Genome Reduction Genome Stability Free-living Bacteria Obligate Intracellular Bacteria

9. Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001. Trends Genet 17, 589-96. DNA Inflow DNA Outflow Eukaryotic cell DNA Inflow? Mobile DNA? DNA Inflow? Mobile DNA?

10. Three Questions How variable are mobile DNA contents in Bacteria? Does this variation statistically associate with phylogeny, genome size, or ecology? How do mobile elements survive and flourish in obligate, intracellular bacteria?

11. The Genomes of Life

12. How variable are mobile DNA contents in Bacteria? % Transposon % Prophage% Plasmid Newton & Bordenstein 2011

13. Is Mobile DNA Gene Density Independent of Phylogeny?

14. 16S rRNA Tree & Mobile DNA % K statistic Full dataset, K = 0.0024 K > 1 is significant association Mobile DNA % is scattered randomly across the tree K statistic Full dataset, K = 0.0024 K > 1 is significant association Mobile DNA % is scattered randomly across the tree Newton & Bordenstein 2011

15. Do Constraints in Ecology Vary with Mobile DNA Gene Density?

16. Facultative Intracellular world Facultative Extracellular Free-living world Obligate Intracellular Three Bacterial Ecotypes

17. >> P < 0.001 P < 0.005 N = 270N = 74N = 40 Newton & Bordenstein 2011 Facultative Intracellular world Free-living world Obligate Facultative Extracellular