1. Selection upon codons BIOS E-127 11.09.28

2. *Aside: shallow trees are strange… And ignore question 7. of assignment…

3. Degenerate Code

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

5. Codons correspond to anticodons on tRNAs

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

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

8. Different GC content alters codon usage Mutational Bias 232 Bacterial genomes - Guchte 2006

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

10. 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

11. 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

12. Why is there selection on codons?

13. (Agashe et al., in prep)

14. Wednesday, 10/5 Evolution of digital organisms (AVIDA) Midterm exam… Phylogenetics assignment due by midnight, Sunday (10/2)