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?

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

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

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 108-1010 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.

Which type of mutation should “tick” faster?

Why do some clocks tick faster than others?

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

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

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?

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

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