1. The phylogenetics project data revealed! October 4, 2010 BIOS E-127

2. Geographic Distribution Pathogen = Salmonella Typhi

3. Why so little turnover? Letters indicate antibiotic resistant haplotypes Selection less effective due to “carriers” with no symptoms!

4. Codon Usage Bias & Selection October 4, 2010 BIOS E-127

5. Degenerate Code

6. Codon Usage Bias Non-random usage of codons Rickettsia (bacteria) - Winkler 1988 Percent codon usage in family Codons for each amino acid Preferred arginine codon Unpreferred arginine codon

7. Why non-random codon usage? Let’s look at tRNA

8. Codons correspond to anticodons on tRNAs

9. Unequal numbers of tRNAs There are six leucine codons So, there are six corresponding tRNAs tRNA copy number differences E. Coli - Ikemura 1981

10. Species differ in codon usage bias Without considering selection, why might different species have different codon usage patterns? Massey 2003 6 Leucine Codons

11. Different GC content alters codon usage Mutational Bias 232 Eubacterial genomes - Guchte 2006

12. Is there selection on codon bias? Four levels of evidence: 1.Genome level 2.Species level 3.Tissue level 4.Gene level Evidence: Non-random patterns of codon usage that are difficult to explain without selection

13. Selection on codons 1.Throughout genomes Same organism, so not explained by differences in tRNA abundance or mutational bias 2. Between species Why does the pattern decrease from E. coli to Human? Drummond and Wilke 2008 expression optimal codons High Expression level genes have high codon bias

14. Selection on codons 3. Within tissues Plotkin et al 2004 Red = selectively expressed in human testes Blue – selectively expressed In human ovaries

15. Selection on codons 4. Within genes Conserved sites more likely to use preferred codons Likely to find Preferred codon Likely to find Unpreferred codon Species in alignemnt: Os = Oryza sativa, Pp = Physcomitrella patens, Dd = Dictyostelium discoideum, Hs = Homo sapiens, Dr = Danio reiro, Dm = Drosophila melanogaster, Sc = Saccharomyces cerevisiae, Sp = Schizosaccharomyces pombe, Pf = Plasmodium falciparumGene = ubiquitin/SUMO-1 like protein Wang et. al. 2001

16. Why is there selection on codons? Many hypotheses relate to speed and accuracy of translation Translation Speed: Use of rare, unpreferred codons means the ribosome has to wait until a rare tRNA passes by. Translation Accuracy: While waiting, the liklihood that the wrong tRNA inserts the wrong amino acid may increase.

17. Codon Bias and Translation Speed Faster translation could allow more protein to be made: Might explain why highly expressed genes have more preferred codons *Does not explain within gene codon bias Slow translation may be desirable when translating certain parts of the protein: Translation speed may correlate with folding Some parts fold quickly, but some fold slowly Means sometimes unpreferred codons are advantageous Selection results from the cost of improper folding How could translation speed pose a selective cost or advantage? Hypotheses

18. Costs of improper protein folding

19. Codon Bias and Translation Accuracy Errors in translation affect folding of protein product: Loss of function Wasted resources Harmful misfolded byproducts Errors in translation affect function directly: Protein folds but cannot do it’s job How do these address correlation between highly expressed genes and codon bias? How could translation accuracy pose a selective cost or advantage? Hypotheses

20. Weak selection Is population size dependent – WHY? Smaller populations are more stochastic: 7 heads and 3 tails in 10 coin flips - possible vs. 70,000 heads and 30,000 tails in 100,000 coin flips – rare!

21. Weak selection Is population size dependent Other possible types of weak selection: Do humans and mammals have selection on codons? Much stronger in microbes! Allow us to study these patterns -ascertain mechanistic basis for selection -determine average effect of mutation Genome size Number of introns Urrutia & Hurst 2003

22. 1.Could effect dN/dS (or other measures of selection)...but, It’s very weak selection that doesn’t effect all genes 1.Useful to detect HGT 2.Helpful to consider when building genetically modified organisms 4.Medical applications – Coleman et al. 2008 Implications of selection on synonymous sites Pride et al 2006