Mutation

1. Mutation • Review: DNA, RNA, Protein • Types of mutations • Mutation rates • Gene duplication • Chromosomal mutations • Analyzing genetic variation

2. DNA review

3. DNA review

4. Replication • Each strand is a template for the replication of it’s complementary strand. • Synthesis occurs 5’ to 3’,

5. Information 3 nucleotides = codon; 20 a.a. specified; 43= 64 codons; therefore redundancy. 3 stop codons U replaces T in RNA

6. Point mutations • Occur at a specific location (point) • Transitions: within group. • opportunities: 4 • Transversions: between group. • opportunities: 8 • Predicted ratio: transversions/transitions = • 2 • Observed ratio: 0.5. Why?

7. Point mutation - effects • 1) synonymous: no change in a.a.; e.g., UUU to UUC • 2) nonsynonymous, missense, replacement : a.a. change; e.g., UUU to UUA • conservative: similar a.a. • non-conservative: dissimilar a.a. • 3) nonsense: new codon is “stop” codon

8. Loss of Function Mutations DNA Template shown RNA made 5’ to 3’ • 5’-UGUUAA-3’ (stop) 5-UAC-3 5’-CUA-3’ frameshift (nonsense)

9. Loss of Function Mutations • Transposition (jumping gene)

11. Functional significance • Synonymous • Nonsynonymous • In/del: Frameshift • Stop Low High

12. Rates of mutations • 1. Estimated by loss of function mutations • Bias in “loss of function”-based estimates?

13. Rates of mutations • 1. Estimated by loss of function mutations • Bias in “loss of function”-based estimates? • Proportional to: • number of cell divisions prior to meiosis

14. Rates of mutations • 1. Estimated by loss of function mutations – observable loss of phenotype e.g., enzyme, color, etc. • Bias in “loss of function”-based estimates? • Proportional to: • genome size • As expected, mutation rates are proportional to DNA synthesis

15. Rates of mutations • 2. Estimated by sequencing • Advantage: • Silent, and functional replacement mutations detectable. • C. elegans mitochondria • 1.6 x 10-7/base/generation (Denver et al., ’00). 1000x higher than loss of function estimates. • Note: mitochondria mutation rates > nuclear. • If extrapolated to include nuclear genome, ~15 new mutations/individual/generation.

16. Are mutation rates under selection? • There is heritable variation for mutation rate. • DNA pol: T4, HIV, E. coli. • DNA repair enzymes: E. coli, Salmonella • Is that variation associated with fitness differences? • E. coli (Visser et al., ’99) • Mutation rate: High Low • Standard lab environment --------- Most fit • Novel environment Most fit ---------- • What do these results imply? • The better adapted a population, the less likely a mutation is to improve fitness.

17. The fitness effects of mutations • Mutation accumulation lines (C. elegans) • Reduced selection: low density, few progenitors (sampling error high, selection efficiency low). • Control: high density, many progenitors.

18. The fitness effects of mutations • Mutation accumulation lines (C. elegans) • Reduced selection: low density, few progenitors (sampling error high, selection efficiency low). • Control: high density, many progenitors.

19. Per mutation fitness effects • Drosophila: mean fitness reduction of heterozygous, loss of function mutation: 1-2%. • Why heterozygous? • Selection coefficient: • mean fitness of reference genotype relative to another genotype. • wbar – w1

20. Per mutation fitness effects • Random insertion of DNA sequences into E. coli or yeast. • Each point represents the fraction of the mutant lines that had selection coefficients less than/equal to that specified on the X-axis. • Most mutants reduce fitness by < 5%. • Vast majority of mutations: • Neutral (e.g., silent) – slightly deleterious (i.e., not lethal. • Rarely: beneficial