Selectionist view: allele substitution and polymorphism are determined by different, selective processes. Mutation yields advantageous alleles that are driven to fixation by positive natural selection. Two or more alleles are maintained at a locus in a population by balancing selection.

Neutralist view: allele substitution and polymorphism are determined by the same evolutionary process. Mutation provides a continual supply of new alleles. Because many alleles are neutral or effectively neutral, alleles becomes fixed or lost from a population as a result of genetic drift. Polymorphism is simply a snapshot of a continuous process of mutational input and subsequent random extinction or fixation of alleles.

Gene Substitution Allele substitution/fixation: Process whereby one allele replaces an existing allele. What is the probability of fixation for new alleles? How long does the process take (fixation time)? What is the rate of allele substitution?

Fixation Probability Fixation Probability : Probability that a mutant allele (A2) will be fixed in a population Depends upon: (q) initial frequency of allele, (s) selective advantage or disadvantage, (Ne) effective population size. A1A1 A1A2 A2A2 1 1 + s 1 + 2s If assume Kimura 1962 Fixation Prob for A2 P = [1 - e-(4Ne)sq ] / 1 - e-4(Ne)s When a new allele enters a population it has a frequency of 1/2N. when s = 0: P = q = 1/2N Fixation probability for neutral allele.

2s Fixation probability for small s (positive or negative) 1 - e-4(Ne)s P = 2s Fixation probability for advantageous allele (positive s). P = What is the probability of fixation for N = 1000 vs 10,000? N = 1000 N = 10,000 s = 0.0 s = 0.01 s = - 0.001 0.0005 0.02 0.00004 0.00005 0.02 10 -20

Conditional Time to Fixation Conditional Fixation Time : mean time to fixation for mutants that will eventually be fixed in the population Conditional Time to Fixation Depends upon: (q) initial frequency of allele, (s) selective advantage or disadvantage, (Ne) effective population size. For new mutation (q = 1/2N): Neutral allele t = 4Ne generations Kimura and Ohta, 1969 Advantageous allele t = (2/s) ln (2N) generations

What is the conditional fixation time for Ne = 1000 vs 10,000 if the organism in question has a generation time of 2 years? Ne = 1000 Ne = 10,000 s = 0.0 s = 0.01 Maruyama & Kimura (1974) showed: S = -0.01 1658 yrs 1981 yrs 8000 yrs 1658 yrs 80,000 yrs 1981 yrs

Rate of Allele Substitution Depends upon: (2Nu) number of mutations arising at locus per generation, and initial frequency of new allele (1/2N) K = 2Nm x 1/2N = m rate of substitution = rate of mutation! under selection, K = 4 Nesm

Neutral Theory There are several important results from the neutral theory. The probability that a new, neutral allele eventually becomes fixed is q (its initial frequency). The average time to fixation of new, neutral alleles that are destined to be fixed is 4Ne. 3) The rate that neutral mutations are fixed = mfixation/generation). m is also the rate of mutation (e.g. substitutions/site/generation) 4) The average time between consecutive fixations = 1/m. 5) The rate of neutral evolution m depends upon neutral and effectively neutral mutations.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. Mutation is constantly generating new alleles over the course of time. Most of these mutations are eliminated immediately by purifying selection. However neutral mutations result in novel alleles.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. However neutral theory predicts that the majority of these new neutral alleles will have a short time to extinction.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. At a predictable period of time a new neutral mutation will appear that for reasons largely associated with effective population size, become established, and eventually fixed in the population. There is an extended time required for these new neutral alleles to go to fixation.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. There is an extended time, proportional to 4Ne, required for these new neutral alleles to go to fixation.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. The inverse of the rate of gene substitution is the mean time between two consecutive substitutions.

Mootoo Kimura’s concept of neutralism is illustrated in the following diagram from his original paper. If we sampled the distribution of alleles at a large number of loci at any one point in time, we would expect a large proportion of alleles to be very low in frequency, a moderate proportion to have an intermediate frequency, and a large proportion of alleles to be fixed.

~ ~ Under the neutral model an important balance is struck Rate of loss of genetic variation by genetic drift Rate of gain of genetic variation by mutation ~ ~ Although alleles come and go, the level of genetic variation remains the same. Steady state frequency of heterozygotes H = 4Nem / 4Nem + 1

Because of two important consequences of neutral evolution: (1) steady rate of allele substitution equilibrium level of heterozygosity We predict the following: There should be a positive correlation between heterozygosity at a locus and its rate of evolution.

Impact of the Neutral Theory of Molecular Evolution Led to the recognition that genetic drift can not be neglected when considering molecular evolution. Established the concept that polymorphism within populations and molecular evolution between species are two facets of the same problem. Neutral theory has become a starting point for analyses of DNA sequences…..it serves as the null model.

Each nucleotide substitution represents a unique allele fixation event that occurred in the past. species 1 allele A A T C A C T A A T G A C T ancestral allele species 2 allele A T T G A C C

A T T G A C C G A G G A T A G T G G A T A Lower rate of substitution, Gene 1 Lower rate of substitution, polymorphism G A G G A T A Gene 2 ancestral allele Gene 2 contemp. allele G T G G A T A 1 V Allele frequency Time

Causes of Variation in Substitution Rates Rate of Substitution is determined by: (1) Mutation rate Among genes Among gene regions (2) Probability of fixation Neutral, advantageous, deleterious

Interpreting Variation in DNA sequences How does natural selection modify neutral patterns?

Detecting Positive Selection Using Within # nonsyn. substitutions Species Data KA/NA > KS/NS # nonsyn. substitutions nonsyn. site # syn. substitutions syn. site > Now we consider a more complicated approach…… involving polymorphism.

Testing the Neutral Mutation Hypothesis The neutral theory predicts that polymorphism within species is correlated positively with fixed differences between species i.e. Genes that exhibit many interspecific differences will also have high levels of intraspecific polymorphism.

nonsynonymous polymorphism synonymous polymorphism McDonald-Krietman Test Assume: Only nonsynonymous mutations are adaptive Synonymous mutations are neutral Selectively adaptive (nonsynonymous) mutations more likely to be fixed. Neutral Prediction: nonsynonymous fixed synonymous fixed nonsynonymous polymorphism synonymous polymorphism = Fixed Differences Polymorphisms Nonsynonymous Synonymous 21 26 45% 2 36 5.3% % nonsynonymous G6PDH from D. melanogaster and D. simulans. Eanes et al. 1993

If most nonsynonymous substitutions are adaptive, then they will increase in frequency and be fixed more rapidly than neutral alleles. 1.0 advantageous allele Frequency neutral allele Time As a result, they spend less time in a polymorphic state, therefore contribute less to within species polymorphism.

Another example (N = 6-12 alleles per species for the coding region. Fixed Differences Polymorphisms Nonsynonymous Synonymous 7 17 29% 2 42 4.5% % nonsynonymous Adh from D. melanogaster, D. simulans, and D. Yakuba MacDonald and Kreitman 1991