Molecular Evolution in a Systematic Context

1. Historical and process-oriented perspectives
2. Changes in nucleotide sequence
   1. Point mutation rate
      1. Synonymous
      2. Nonsynonymous
   2. Mutator mutations
   3. Rate of nucleotide substitution
      1. Relative rate test
   4. Transition vs Transversion rate
   5. Molecular clocks
3. The neutral theory
4. Relationship between nucleotide sequence and amino acid sequence
   1. Genetic codes
   2. Codon usage
      1. Quite variable among organisms, rather consistent within organisms
   3. Patterns of selection
      1. Probability of accepted mutation
5. Gene structure
   1. Introns
   2. Insertion, deletion, and rearrangements
   3. Exon shuffling
6. Genome structure
   1. Genome size
      1. Converson factors (from Li, 1997)
         • 1pg ~ 0.98x109bp = 980Mb
         • 1 dalton ~1.62x10-3bp
   2. Gene duplication
   3. Multigene families
   4. Concerted evolution
   5. Isochores
   6. Analysis of entire genomes
      1. Error-prone elements in pathogenic bacteria
7. Genome rearrangements
8. Transfer of genetic material among organisms
   1. Sex
   2. Conjugation
      1. Plasmids
   3. Transposable elements
   4. Horizontal gene transfer