1. The neutral theory of molecular evolution
Motoo Kimura (1968)
High levels of polymorphism (variation) in protein and DNA sequences among individuals and species are difficult to reconcile with mutation-selection equilibrium (Ch 5.4)
Most mutations affecting fitness are deleterious, hence quickly eliminated by selection
Ergo: Essentially all new mutations eventually fixed are neutral, and evolve only by genetic drift
Do evolutionary biologists ever tire of debating whether selection or drift dominates the evolutionary process?

2. Why use DNA and protein molecules to study evolution?
In principle, character homology and independence can be assured
Very large number of characters can be studied
Only 4 precisely-defined character states in DNA; 20 in protein
DNA sequencing is easy, fast, and cheap; genome projects
Many (perhaps the majority) of living species lack distinctive morphological features
Neutral mutations accumulate in a clocklike manner

3. Drawbacks to molecular methods
In practice, orthology and paralogy can be difficult to distinguish in gene families
Not generally applicable to fossil taxa
Gene phylogenies vs. species phylogenies
Not all mutations are neutral

4. What makes the molecular clock tick?
Probability of fixation of a neutral allele = p (the current allele frequency)
What is the fixation probability for a new neutral mutation in a diploid population?
1/(2N)
New mutations arise at a rate of m (# mutations per DNA base pair per generation; typically ~10-8)
What is the frequency of new mutations in a diploid population?
(2N)m * L (length of genome in base pairs; typically in eukaryotes)
Rate of fixation of new neutral mutations =
1/(2N) * (2N)m * L = mL
Since genome length (L) is a constant within a species, neutral mutations go to fixation at a rate equal to the mutation rate – m is the “ticking speed” of the clock.

5. Which type of mutation should “tick” faster?

6. Why do some clocks tick faster than others?

7. Empirical evidence for the molecular clock; from Hartl and Clark Principles of Population Genetics, Fig. 12 p. 361

8. Evolutionary rates for different regions of genes; from Hartl and Clark Principles of Population Genetics, Fig. 17 p. 373

9. Variation in substitution rates
Nonsynonymous (‘replacement’) substitution rates are variable and relatively low. Why?
Promoter (5’ upstream) flanking regions of genes have intermediate rates of substitution even though they are noncoding. Why?
Synonymous (‘silent’) substitution rates are high.
Intron substitution rates are high.
Pseudogene substitution rates are highest. Why?

10. dN/dS When will dN/dS < 1 ? When will dN/dS = 1 ?

11. Genes with dN/dS >> 1
Major histocompatibility complex (MHC)
Immunoglobulins
Self-incompatibility loci in plants
Sperm-egg recognition proteins in abalone