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1 Roadmap Optimal mutation rate Dominance and its implications Why is an allele dominant or recessive? Overdominance (heterozygote advantage) Underdominance (heterozygote inferiority)

2 One minute responses Q: How could a higher mutation rate benefit an individual? Comment: More pictures less text! (I ll try.)

3 One more look at degrees of freedom Fictional data for sickle-cell hemoglobin (alleles A and S) in African- American adults Normal AA 400 Carrier AS 90 Affected SS 10 Thinking about df: Suppose I told you: How many people I sampled How many of each allele I found How many AS carriers I found Are there any possible surprises left in the data? (AA? SS?) This is why there is only 1 df

4 How could a higher mutation rate benefit an individual? Need high-diversity offspring Need rapid change away from current phenotype

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7 Genomic deterioration Practice problem pa = ν ν + µ Assume HIV-1 virus has a mutation rate of per base per generation Assume 100 critical bp in the env gene As before, a reverse mutation has to hit the same base and restore its original state What is pa (frequency of healthy allele) after 1 generation? What would happen to this gene if it were not under selection?

8 Practice problem pa = ν ν + µ Assume HIV-1 virus has a mutation rate of per base per generation Assume 100 critical bp in the env gene What is pa (frequency of healthy allele) after 1 generation? Very hard to figure out all the mutant viruses, but we can just count the non-mutant ones chance of no mutation at one site (0.999) 100 chance of no mutation at 100 sites = 0.904

9 Genomic deterioration Practice problem pa = ν ν + µ µ = = 0.1 ν = 0.001/3 = After 1 generation we lose 10% of our copies At equilibrium, pa = ν ν+µ = = Without natural selection, mutation would rapidly destroy the HIV genome

10 McClintock s genome shock hypothesis Barbara McClintock showed that transposition in maize increases when the plant is stressed drought salt insects Her genome shock theory is that mutation gives the plant a chance to produce offspring that can survive in a crisis Alternative is that a sick plant simply loses control of its transposons

11 Do organisms try to minimize mutation rate? Deinococcus radiodurans shows that mutation rate can go very low Why don t all organisms do that? Alternative theories: It s expensive and not worthwhile Moderate mutation rate is an advantage quicker adaptation Large increases in mutation rate are very bad for humans: BRCA1, BRCA2 These mutations allow single cells to evolve faster, which a multi-cellular organism doesn t want...

12 Outline Dominance and its implications 1. What makes one allele dominant over another? 2. Codominance and incomplete dominance 3. Dominance is not superiority! 4. Overdominance 5. Underdominance

13 Some useful terms Genotype the alleles present in an organism Phenotype the traits shown by an organism Homozygote two copies of the same allele Heterozygote copies of two different alleles

14 Definitions Dominant phenotype is seen in the heterozygote Recessive phenotype is NOT seen in the heterozygote Incompletely dominant heterozygote is intermediate (pink vs. red/white) Co-dominant heterozygote expresses both alleles fully (AB blood type)

15 What makes one allele dominant over another? Usually recessive: Deletion or null allele Allele that makes non-functional or poorly functional product Allele that underproduces product Control mutation that disables an ON switch Examples: dysfunctional CF alleles temperature-sensitive color of Siamese cats O allele of ABO system

16 General rule for LOF mutations Half the amount of wild type gene product is sufficient to give a wild type phenotype Example : Tyrosinase [enzyme activity] threshold wild type phenotype albino phenotype wild type allele = C mutant = c Genotype: CC Cc cc 1 wild type copy enzyme activity above threshold needed for normal pigmentation, so carriers unaffected (mutant allele recessive)

17 What makes one allele dominant over another? Usually dominant or incompletely dominant: Allele that overproduces product Control mutation that disables an OFF switch Examples: Adult lactase production Achondroplastic dwarfism

18 What makes one allele dominant over another? Often dominant or co-dominant: Allele that produces a novel product Control mutation that introduces a new switch Examples: Sickle-cell trait (disease is recessive but heterozygote has definite phenotype) A and B alleles of ABO

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20 Allelic series Each allele is recessive to the one before it Each allele is dominant to the one after it Example: tyrosinase locus in cats Wild-type tyrosinase used to make melanin (brown-black pigment)

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22 Different ways to the same phenotype Alleles, not phenotypes, have dominance White color in cats can come from a dominant mutation which kills melanin-producing cells White can also come from a recessive mutation which prevents melanin synthesis

23 Codominance and incomplete dominance Codominant: shows the full phenotype of both alleles. Both alleles produce functional, but different, products Example: A and B in the ABO blood group system Incompletely dominant: shows intermediate phenotype. Often a dosage effect Examples: Pink color in heterozygous flowers White spotting in cats (homozygote has more white than heterozygote)

24 Incomplete dominance of white-spotting gene Homozygous wild type Heterozygous Homozygous mutant This mutation reduces spreading of pigment cells during development.

25 Discussion question Sickle cell hemoglobin forms into long, stiff chains; normal hemoglobin doesn t Sickle cell homozygotes have severe disease due to chain formation which damages ( sickles ) red blood cells Heterozygotes show some sickling but not severe disease Is this codominance or incomplete dominance?

26 One gene can have multiple effects Dominant-mutation white cats generally deaf White-spotting gene also affects eye color

27 Dominance is not superiority! Examples: Huntington s disease dominant is worse than recessive Cystic fibrosis dominant is better than recessive Tongue rolling probably neutral Dominant alleles can be common ( wild type ) or rare. In the absence of selection, dominant alleles have no particular tendency to increase over recessive ones.

28 Overdominance Watch out! This term sounds as though it s the same kind of thing as dominance, but it refers to an advantage or disadvantage, not just to which allele is expressed. Overdominant alleles are alleles with codominance or incomplete dominance in which the heterozygote is fitter than either homozygote. Sometimes called hybrid vigor Examples: Many commercially sold grains and vegetables Sickle-cell anemia (in presence of malaria)

29 Underdominance Again, watch out! dominance. Underdominance is not the same kind of thing as Underdominant alleles are alleles with codominance or incomplete dominance in which the heterozygote is less fit than either homozygote. Examples: Heterozygote of HLA-DR3 and HLA-DR4 has higher diabetes risk than either homozygote Mimicry in butterflies

30 Underdominance In the African butterfly Pseudacraea eurytus the orange and blue homozygotes each resemble a local inedible species, but the heterozygote resembles nothing in particular and is vulnerable to predators.

31 One-minute responses Tear off a half-sheet of paper Write one line about the lecture: Was anything unclear? Did anything work particularly well? What could be better? Leave at the back on your way out

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