Genome evolution and adaptation in a long-term experiment with Escherichia coli [1]

1. Genome evolution and adaptation in a long-term experiment with Escherichia coli [1] Richard Wolfe

2. Introduction • Adaptation – a change that improves an organisms chances of survival and reproduction • Mutations are not necessarily beneficial. • In order to examine the tempo and mode of genomic evolution, 40,000 generations of E.coli were sequenced. • The genomes were sequenced at 2K, 5K, 10K, 15K, 20K and 40K generations. • These genomes were compared to the ancestral stain. • Almost 20 year long experiment. • Glucose was limiting nutrient. • 12 populations

3. Introduction • Deletion – nucleotide removed • Insertion – nucleotide added • IS insertion – insertion sequence – entire sequence added • Inversion – section removed, inverted, reinstalled • 45 mutations in 20K generation • Include 29 single-nucleotide polymorphisms SNPs inserted • Include 16 deletions, insertions and other polymorphisms DIPs

4. Mutations Found

5. Rates of Genomic and Fitness Improvement

6. Discussion • Genomic evolution is near-linear. • Normally this would suggest neutral evolution, mutations do not matter. • Fitness is not linear and the rate of improvement slows down over time. • Indicates that the rate beneficial mutations are occuring is declining and/or their their average benefit is becoming smaller. • These effects should cause the rate of genomic evolution to decelerate but, it remains the same.

7. Discussion • Hypothesis: only a small fraction of all substitutions are beneficial and most are neutral. The beneficial substitutions occur in early generations and adapt to the conditions of the experiment. The neutral mutations occur later and the rate of fitness improvement slows down. • Evidence to reject hypothesis: • 1. You would expect to find mutations that did not change the protein sequence but, all 26 point mutations found in coding regions (22 in 20K) changed the protein sequence. • 2. You would not expect to see mutations in the same genes in the other 11 populations if due to random drift but if by selection then same genes would be mutated because they evolved in same environments.

8. Discussion • 3 cases where all 11 populations have substitutions in same gene • 9 genes have mutations in other lines • Only 2 cases where no mutation has occured

9. Discussion • 3. You would expect many mutations would not become fixed but, almost all mutations that occur early are present in the rest of the generations. • 4. Strains with neutral mutations would have no fitness advantage but, isogenic strains with ancestral and derived alleles show a significant advantage.

10. 40K Genome Analysis • After 26K generations a greatly elevated rate of genomic evolution occured. • 40K genome contained 627 SNP and 26 DIP mutations • 40K genome 1.2% smaller than ancestor. • Unlike the mutations before 20K, only a small number of these later mutations are beneficial

11. References 1. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF; Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. October 2009, 461:1243-1247.