Evidence of Selection on Genomic GC Content in Bacteria

1. Evidence of Selection on Genomic GC Content in Bacteria Falk Hildebrand Adam Eyre-Walker

2. Genomic G+C content

3. Genomic GC content

4. Codons Non-synonymous 2-fold : TTT TTC 4-fold : CCT CCC CCA CCG ATA CCC CTA CCT GCT 123 Synonymous

5. Genomic GC content

6. Variation

7. Correlations

8. Explanations • Mutation bias • Suoeka (1961) & Freese (1962) • Intrinsic and/or extrinsic • Selection • Many authors • Biased gene conversion • Anonymous referees

9. Correlates • Genome size • positive correlation • Lifestyle • higher GC in free living • Aerobiosis • higher GC in aerobic • Nitrogen utilization • higher amongst N fixers • Temperature • higher amongst thermophiles?

10. Evidence of selection I • Escherichia coli • Mutation pattern • 273 GCAT versus 131 ATGC • Predicted GC content = 0.32 • Observed GC content = 0.50 • Observed GC at neutral sites = 0.58 Lynch (2007) Origins of genome architecture

11. Evidence of selection II • Phylogenetic analyses • Mycobacterium leprae(Lynch 2007) • Escherichia coli (Balbi et al. 2009) • 5 pathogenic bacteria (Hershberg and Petrov 2010)

12. Phylogenetic analysis G A A G G G

13. Evidence of selection II • Phylogenetic analyses • Mycobacterium leprae(Lynch 2007) • Escherichia coli (Balbi et al. 2009) • 5 pathogenic bacteria (Hershberg and Petrov 2010) • Excess of GC  AT

14. Test of mutation bias • If GC content is • Due to mutation bias alone • Stationary • And the infinite sites assumption holds • Then • # GCAT mutations = # ATGC mutations

15. Why? • If GC stationary • #GCAT subs = #ATGC subs • All neutral mutations have same chance of fixation • #GCAT muts = #ATGC muts

16. Identifying mutations Strain 1 ACT GCT TTG GCT TTA TGG Strain 2 ACT GCT TTG GCT TTA TGA Strain 3 ACT GCT TTG GCT TTA TGG Strain 4 ACT GCT TTCGCT TTA TGA Strain 5 ACC GCT TTC GCT TTA TGG Strain 6 ACT GCT TTG GCT TTA TGG TC CG GA

17. Orienting mutations Outgroup ACT GCT TTC GCT TTA TGG Strain 1 ACT GCT TTG GCT TTA TGG Strain 2 ACT GCT TTG GCT TTA TGA Strain 3 ACT GCT TTG GCT TTA TGG Strain 4 ACT GCT TTCGCT TTA TGA Strain 5 ACC GCT TTC GCT TTA TGG Strain 6 ACT GCT TTG GCT TTA TGG TC CG GA GCAT = 1 ATGC = 1

18. Orienting mutations Strain 1 ACT GCT TTG GCT TTA TGG Strain 2 ACT GCT TTG GCT TTA TGA Strain 3 ACT GCT TTG GCT TTA TGG Strain 4 ACT GCT TTCGCT TTA TGA Strain 5 ACC GCT TTC GCT TTA TGG Strain 6 ACT GCT TTG GCT TTA TGG TC GC GA GCAT = 1 ATGC = 1

19. Test of mutation bias • If GC content is • Due to mutation bias alone • Stationary • And the infinite sites assumption holds • Then • # GCAT = # ATGC

20. Four-fold synonymous sites

21. Codons Non-synonymous 2-fold : TTT TTC 4-fold : CCT CCC CCA CCG ATA CCC CTA CCT GCT 123 Synonymous

22. Data • Popset • Keyword “bacteria” • 8 or more sequences from same species • 149 bacterial species • 8 phyla, 15 classes and 77 genera • 1 or more genes • 10 or more synonymous polymorphisms • 4-fold diversity < 0.1

23. Overall result P<0.0001

24. Bias versus GC4 GCAT Z = GCAT

25. Phylogenetic distribution

26. Potential problems • Infinite sites assumption • Sequencing error

27. Infinite sites assumption • Each mutation occurs at a site which is not polymorphic

28. Infinite sites assumption • If GC content stationary • #GCAT subs = #ATGC subs • All neutral mutations have same chance of fixation • #GCAT muts = #ATGC muts

29. Finite sites assumption • If GC content stationary • #GCAT subs = #ATGC subs • All neutral mutations have same chance of fixation • #GCAT muts = #ATGC muts • But some mutations not evident as poly

30. Finite sites • GC rich sequence • Implies • rate of ATGC > rate of GCAT • Mutation rate low • #ATGC poly = # GCAT poly • Mutation rate high • #ATGC poly < # GCAT poly

31. Finite sites theory uμ GC AT vμ Assume : stationary popn stationary GC

32. Finite sites theory

33. Finite sites theory 0.95 0.9 0.8 0.7 0.6

34. Predicting Z • Assume • finite sites • neutrality • Use GC4 to get f • Use observed diversity to estimate μ • Predict Z

35. Zpred

36. Z-Zpred

37. Mutation rate variation

38. Z-Zpred (exponential rates)

39. Sequencing error

40. Explanations • Non-stationary base composition • Selection for translational efficiency • Biased gene conversion • Selection upon base composition

41. Explanations • Non-stationary base composition • Selection for translational efficiency • Biased gene conversion • Selection upon base composition

42. Non-stationary GC content

43. Non-stationary base composition

44. Explanations • Non-stationary base composition • Selection for translational efficiency • Biased gene conversion • Selection upon base composition

45. Selection on codon usage

46. Translational efficiency

47. Explanations • Non-stationary base composition • Selection for translational efficiency • Biased gene conversion • Selection upon base composition

48. Biased gene conversion A T A G C G C G C T C G

49. Four gamete test G A G T C A C T G A G T C A No recombination Recombination

50. Biased gene conversion