One way to test these theories is to look at th number of silent vs.

1. Neutral or Selectionist? One way to test these theories is to look at th number of silent vs. non-synonymous substitutions over a given region of DNA are silent point mutations in DNA (no effect on phenotype) more common or less common than non-synonymous changes? Negative selection: amino acid substitutions are less common than silent DNA substitutions (change is bad) Positive selection: non-synonymous amino acid substitutions are more common than silent substitutions

2. Polymorphic sites 1: DNA changes Some positions are polymorphic (different nucleotides are found) between some of the species - a single nucleotide is fixed within each species Other positions are polymorphic within one species, but are otherwise fixed among species

3. Polymorphic sites 2: amino acid changes S or T V or F different amino acids can occur at a site within one species different amino acids can be fixed between species

4. Normally, most substitutions that survive to be detected are silent 1. DNA – 17 polymorphic sites 2. amino acid – 4 polymorphic sites (= non-synonymous changes) When non-synonymous changes pile up faster than silent changes (given that codons differ in whether one mutation can change the amino acid), it indicates positive selectionis acting to quickly fix mutations before they get lost to drift

5. Neutral or Selectionist? Evidence for positive selection suggests selection is driving the rate at which mutations are fixed as proteins evolve Smith & Ayre-Walker (2002) compared ratio of non-synonymous (dN) to synonymous (dS) substitutions within 2 Drosophila species, and between the two species, over the whole genome - found many sites where there were more non-synonymous changes between the species than within either species - indicates that selection favored differences between species - they estimated 45% of amino acid differences between the 2 species had been fixed by positive selection

6. Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rateacross Drosophilasimulans genome Different regions of the genome can differ in how often crossing over occurs – some places have more, others less Some genes are more polymorphic than others (have more alleles) Neutral theory predicts no relationship between amount of genetic polymorphism (# of alleles) and how often crossing over happens  Why does selectionist theory predict a correlation?...

7. Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... ...it will also tend to favor “B” and “D” alleles, if they happen to be linked to “C” on a chromosome A B C D E F a b c d e f

8. Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... A B C D E F ...all these alleles will be lost, unless they can get onto the “winning team”  i.e., any chromosome with a C allele a b c d e f

9. Neutral or Selectionist? in regions of high recombination, linked loci can escape the effects of selection on nearby genes  crossing over “breaks up the team” Even if selection strongly favors C allele... alleles of other genes can cross over onto C chromosomes A B C D E F ab C d e f a b c d e f In regions of high recombination, many alleles at linked loci can “hitchhike” onto chromosomes with favorable alleles, and thus survive selection  greater overall polymorphism

10. Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rate across Drosophilasimulans genome in regions of low recombination, linked locican’t escape the effects of selection on nearby genes if selection strongly favors “big C” allele of the C gene... A B C D E F a b c d e f ...all these alleles get lost  The correlation is strong evidence that selection acts on alleles all the time, across the whole genome  Supports selectionist theory, not neutral theory

11. Non-random mating: Inbreeding Violates one of the assumptions of Hardy-Weinberg Can affect genotype frequencies without affecting allele frequencies Selfing (not the same as cloning) - many plants and some animals can self-fertilize - homozygotes always give rise to homozygotes - heterozygotes produce 1/2 homozygotes and 1/2 heterozygotes Aa AA Aa aa 1 : 2 : 1

12. Non-random mating: Inbreeding Result: in every generation of selfing, the # of heterozygotes is halved - however, the allele frequencies are unchanged thus, inbreeding also causes loss of heterozygosity, and has a strong evolutionary impact -

13. Inbreeding and loss of heterozygosity Case study: malaria parasite - most people in New Guinea are infected by only one mosquito - most reproduction occurs between brother and sister offspring when another mosquito bites an infected person (inbreeding) prediction: there should be an excess of homozygotes at loci that are polymorphic - in other words, even when there are a lot of alleles out there, selfing should result in few heterozygotes

14. Inbreeding and loss of heterozygosity very polymorphic loci

15. Coefficient of inbreeding Inbreeding among more distant relatives has the same effect, but less drastic Degree of relatedness is reflected in a measure called the coefficient of inbreeding, F Fis the probability that the two alleles in an individual are related by descent from a common ancestor F = 0.5 for selfing: there’s a 50/50 chance selfing will produce an offspring with both alleles derived from the same parental allele

16. Coefficient of inbreeding Fis the probability that the two alleles in an individual are related by decent from a common ancestor

17. Coefficient of inbreeding Ordinary genotype frequencies predicted by Hardy-Weinberg: AA Aa aa p2 2pq q2 In an inbred population, genotype frequencies are given by: AA Aa aa p2(1-F) + pF 2pq(1-F) q2(1-F) + qF -- why? odds of getting a homozygote = sum of 2 possible ways way #1 - p x (odds of an unrelated p), which is p x p(1-F) way #2 - p x (odds of a related p), which is pF

18. Coefficient of inbreeding In an inbred population, genotype frequencies are given by: AA Aa aa p2(1-F) + pF 2pq(1-F) q2(1-F) + qF test: insert the value F = 0 - this is true for unrelated gametes - gives you the Hardy-Weinberg genotype odds

19. Inbreeding depression Although inbreeding doesn’t change allele frequencies, it creates an excess of homozygotes This exposes loss-of-function alleles, which are normally masked in heterozygotes - creates lower fitness among offspring of relatives

20. Inbreeding depression Keller et al. (1994) followed a population of sparrows (small birds) on a Canadian island for 15 years Two population crashes, in 1980 (27 survivors) and 1989 (11 survivors) Inbreeding coefficient of survivors (those still alive in the crash year) was much lower than the average value in the year before the crash ones who survived the terrible winters were the least inbred; inbreeding lowers survival chances when environment goes bad inbreeding coefficient population size