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5. Assess Reliability

123456789. taxa1. CGATCGTTA. taxa2. CAATGATAG. taxa3. CGCTGATAA. CGCTGATCG. taxa4. Dataset1: 729338554. Dataset2: 631981282. …. Dataset1: 1-3-56789. Dataset2: 12-45678-. …. 5. Assess Reliability. Resampling to produce pseudo-dataset (random weighting). 100. 73. I. Bootstrap.

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5. Assess Reliability

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  1. 123456789 taxa1 CGATCGTTA taxa2 CAATGATAG taxa3 CGCTGATAA CGCTGATCG taxa4 Dataset1: 729338554 Dataset2: 631981282 … Dataset1: 1-3-56789 Dataset2: 12-45678- … 5. Assess Reliability Resampling to produce pseudo-dataset (random weighting) 100 73 I. Bootstrap Sampling with replacement II. Jacknife Random deletion of sub-dataset Randomize dataset to build null likelihood distribution III. Permutation test

  2. Reconstructed ancestral sequences to infer environment • Was the ancestor of bacteria a thermophile? • Reconstructed EF-Tu at key nodes (Gaucher et al., 2003) • All ancestral types have high Topt

  3. Genetic exchange in bacteria/archaea • Transformation • Used by Griffiths, and later Avery to show DNA is genetic material • Some bacteria naturally competent • Transduction • Generalized & specialized • Conjugation • High-frequency recombinants (Hfr) • All are partial and unidirectional

  4. Detecting HGT from genomes: atypical nt composition • Recent transfers often have unique signature • “Molecular archaeology” of E. coli(Lawrence & Ochman, 1998) • 17.6% HGT, but amelioration since • Calculated age distribution based on average rate of divergence (Hacker & Carniel, 2001)

  5. HGT genes often clustered • HGT genes often clustered in large islands encoding related function • Could HGT itself drive operon formation? • Selfish operon theory (Lawrence & Roth, 1996) • Linkage increases chance of co-transfer of cluster • Recent analysis (Price et al., 2005) • Identified HGT events and new operons in E. coli • No particular enrichment of HGT in new operons • Role of co-regulation instead?

  6. Detecting HGT: incongruent phylogeny/synteny • Any incongruent phylogeny could be explained by HGT or independent gene loss Ex: glycerol-3-P DH HGT only Loss only (Koonin, 2003)

  7. Detecting HGT: H4MPT pathway • Tree based upon concatenated sequences (bootstrap = distance/parsimony; Kalyuzhnaya et al., 2005)

  8. Detecting HGT: H4MPT pathway different (Kalyuzhnaya et al., 2005) similar

  9. Detecting HGT: H4MPT pathway New C1 genes found due to clustering different (Kalyuzhnaya et al., 2005) similar

  10. Detecting HGT: H4MPT pathway (Kalyuzhnaya et al., 2005) Scenarios for pathway evolution (Chistoserdova et al., 2004)

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

  12. Detecting HGT: differential gene content • Analysis of three E. coli(Welch et al., 2002) • Shared genes >95% similarity • Each genome only ~½ core genes • Combination of HGT & differential loss • Identity of non-core genes? • Unusually AT-rich & short (Daubin & Ochman, 2004) • Tend to be more environment-specific (Pál et al., 2005)

  13. Detecting HGT: differential gene content • Analysis of three E. coli(Welch et al., 2002) • Shared genes >95% similarity • Each genome only ~½ core genes • Combination of HGT & differential loss • Identity of non-core genes? • Unusually AT-rich & short (Daubin & Ochman, 2004) • Tend to be more environment-specific and “attach” to network periphery (Pál et al., 2005)

  14. Measurements of natural horizontal gene transfer (HGT) • Method for in situ plasmid transfer (Sørensen et al., 2005) • 20-100x higher rate than culture-dep. method

  15. Measurements of natural horizontal gene transfer (HGT) • Sort via FACS, amplify 16S rRNA & sequence • Visualize in situ on leaf

  16. Limitations to HGT • Environmental parameters: conjugation in ocean? • Phage appear to be major vectors for exchange amongst Prochlorococcus(Lindell et al., 2004) • Some encode unstable photosynthesis proteins that are expressed during infection (Lindell et al., 2005)

  17. Limitations to HGT • Environmental parameters: conjugation in ocean? • Phage appear to be major vectors for exchange amongst Prochlorococcus(Lindell et al., 2004) • Some encode unstable photosynthesis proteins that are expressed during infection (Lindell et al., 2005) • Fate and process of incorporating HGT genes into network?

  18. Can gene histories be retraced? • trp operon (Xie et al., 2004)

  19. Can gene histories be retraced? • “Highways of gene sharing” (Bieko et al., 2005) • >220000 proteins from 144 genomes

  20. Can gene histories be retraced? • “Net of life” (Kunin et al., 2005)

  21. Is there still a tree?: (Daubin et al., 2003)

  22. Is there still a tree?: (Daubin et al., 2003)

  23. Is there still a tree?: (Doolittle & Bapteste, 2007)

  24. “Automated TOL”(Ciccarelli et al., 2006)

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