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1

Question

Answer

2

Lecture 1

Population Genetics.

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What is a population?

Group of interbreeding individuals in the same space at the same time.

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What is genotype frequency?

Percentage of individuals with a particular allelic combination within the population.

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What is allele frequency?

Percentage of copies of a particular variant of a gene.

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What is heterozygosity?

Percentage of heterozygous genotype bearers within the population.

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What is heterozigosity used for?

Measurement of variability of a gene/polymorphism.

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What are the two equations derived from the Hardy-Weinberg model?

p+q=1; p^2+2pq+q^2=1

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What are the assumptions made by the Hardy-Weinberg model?

Panmitic populations; No selection; No mutation; No migration; Infinite/very large population size; Allele frequencies identical in males and females.

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How does migration reduce homozygosity?

By breaking the Wahlund Effect which increases homozygosity.

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How is change in homozygosity calculated?

?H = ((p(1)^2+p(2)^2)/2) - p(ext)^2.

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What is the Wahlund Effect?

Reduction of heterozygosity caused by structurisation of a population.

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What effect does population size have on drift?

An individual with 10 offspring has a greater impact on allelic frequencies than an individual with 2 offspring. The effect difference decreases with increasing population size. Small populations more likely to drift quicker.

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How can genetic drift be modeled?

Pick an allele at random. Copy and reintroduce into the population. Repeat 2N times.

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What is the effect of habitat loss on genetics of a population?

Reduced size - Increased drift, Variation lost quicker.

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How can the loss of variation be measured?

By measuring the change in heterozygosity: ?H = (1/2N) x H

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What is the effect of quick size recovery after habitat loss? Explain.

Maintains low heterozygosity. Heterozygosity is increased by introducing mutations. Mutations take a long time to settle within the population.

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What is mutation?

Spontaneous generation of a new variation (allele).

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What is the mutation rate of humans?

? = 2.5x10^-8 per nucleotide per generation; U = ? x number of nucleotides (per genome per generation).

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How can heterozygosity be calculated using ??

?H = 2?(1-H)

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What is mutation-drift balance?

Rate of new mutation = Rate of loss of variation due to fixation/extinction.

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How can mutation-drift balance be used to calculate heterozygosity of a population?

?H = 2?(1-H); ?H = (1/2N)H; 2?(1-H)=(1/2N)H => H = 4N?/(1+4N?)

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How can amount of variation be estimated using only ? and N?

if 1/?>>N - Little/no variation; If 1/?<

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What is the difference in variation between SNPs and Microsatellites?

SNP: ?=2.5x10^8; Microsatellites: ?=0.004. N ~10,000; SNPs have little variation. Microsatellites show lots of variation.

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What is neutral variation?

Variation in mutation-drift balance. No effect on phenotype - not affected by selection. Often in introns or synonymous mutation.

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When can presence of selection be confirmed?

When allele frequencies (variation) departs from H-W and M-D.

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Lecture 2

Selection.

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What is selection?

Change in allele frequencies in populations associated with changes in relative fitness of the allele phenotypes.

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What are the 3 qualitative types of selection?

Artificial, Natural, Sexual.

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Describe artificial selection.

Human domestication of animals which are selectively interbred to show the desired phenotype in offspring.

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Describe natural selection.

Variation in fitness provided by different alleles allows the most adaptive variants to survive. Main driving force of evolution.

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Describe sexual selection.

Driven by preference of opposite sex. Explains sexually appealing traits and their continuous existence (Peacock's tail). Appleal usually reflects health/fitness of the individual. Natural selection with a twist.

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What are the 3 quantitative types of selection?

Purifying, Positive, Balancing.

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Describe purifying selection.

Rejection of injurious variations - C.Darwin. Removal of deleterious mutations.

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What are the effects of purifying selection?

Reduces diversity created by mutations. Maintains conserved DNA sequences.

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Give an example of a DNA sequence conserved by purifying selection.

21/30 amino acids of Cytochrome C conserved between animals and plants.

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Some deleterious mutations are harder to eradicate than others. What are they?

Non-lethal mutations. Late-onset mutations (Huntington's).

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What causes Tay-Sach's Disease?

Mutation of HEXA gene - involved in proper CNS function.

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Why is the mutation causing TS, not a dominant mutation?

Completely lethal by reproductive age therefore no chance of inheritance - No fixation.

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Give a H-W model for relative fitness of the three genotypes of HEXA.

p^2 = 1; 2pq = 1; q^2 = (1-s)q^2.

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What is 's' used for in H-W models?

Selection coefficient. Shows the relative impact of selection on fitness of the genotype.

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Describe positive selection.

Alleles that are advantageous to the individual in their environment, are selected for.

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What are the effects of positive selection?

Reduction in diversity. Increase in homozygosity until fixation.

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Give an example of purifying selection. Explain.

Insecticide resistance in mosquitoes. Even though heterozygotes are resistant, their frequency decreases because of extinction of susceptible individuals.

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When may insecticide resistance become deleterious?

Insecticide no longer used. Unnecessary fitness expended on resistance.

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Describe balancing selection.

Selection for the heterozygous phenotype. Having both alleles is advantageous (Overdominance) or disadvantageous (Underdominance).

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What is the effect of balancing selection?

Increase in variation.

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Give an example of Overdominance.

Sickle cell anaemia. Cells not sickle enough to cause problems. Too sickle for plasmodia to reproduce. Geographical distribution of Haemoglobin S allele closely follows distribution of malaria.

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Give an example of Underdominance.

Speciation.

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How can the significance of selection on a population be determined?

Using the chi squared test on genotype frequencies and seeing whether the departure from H-W is significant or not.

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How is relative fitness assigned?

Relative to most fit homozygote (that will have fitness of 1).

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With respect to H-W, what is 'h' and how is it calculated?

h is the heterozygote effect. Calculated by using the formula "Relative fitness = 1-hs".

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What can be deduced from h values?

If 0 - Allele is recessive; If 1 - allele is dominant; 1>h>0 - Incomplete dominance; h1 - Underdominance.

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Why is selection analysis using H-W not always accurate?

Departure will occur without selection if one of the assumptions is broken (false positive). Only tests departure from H-W. Only detects significant departure. Selection may act on a population without H-W departure.

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How else can selection be tested for? Describe possible outcomes.

Mutation-Drift balance: H = 4Nu/(1+4Nu). H > Expected - Balancing selection; H < Expected - Positive or Purifying selection.

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What are the limitations of using M-D to test for selection?

N is unknown for many species. U is difficult to measure.

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What genetic technique can be used to test for selection?

Measuring heterozgosity of multiple SNPs. Polymorphisms with heterozygosity significantly lower than that of others show positive or purifying selection.

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What are the assumptions made by using SNP polymorphism?

N will be the same for all SNPs (accurate). U will be the same for all SNPs - not always accurate.

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Give an example of reduction of Heterozygosity of a gene because of selection.

IGF1 gene - Insulin-like Growth Factor Gene 1. Determines skeleton size in dogs. Lots of variation in large dogs; Reduced H in small dogs (+ve/purifying selection).

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In summary, what are the 3 main selection tests used?

Test for H-W equilibrium. Using heterozygosity values of SNPs. Using a multispecies approach.

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Lecture 3

Quantitative Genetics.

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What are quantitative traits?

Continuous polymorphic traits. Described by frequency distribution curves.

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How can the number of phenotypes of a quantitative gene be derived from number of alleles?

Phenotypes = genes responsible x alleles per gene + 1

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What is phenotypic variance? How is it denoted?

Variance due to genes + Variance due to environment. s^2(P) or V(P).

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What is broad-sense heritability?

Measure of the degree to which phenotypic variance is due to genes.

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What is the formula or broad-sense heritability?

H^2 = s^2g/s^2p = s^2g/(s^2g+s^2e).

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What does a H^2 value of 1 represent?

All variation being genetic.

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What does a H^2 value of 0 represent?

All variation being environmental.

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What is a common misconception regarding H^2?

H^2 describes how much of the trait is genetic. It doesn't, it describes how much of the varitio is genetic.

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What is narrow-sense heritability?

Measure of the degree to which s^2p os due to additive genetic factors.

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Give an example of a quantitative trait.

Skeleton size in dogs.

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How are the genes responsible for skeleton size in dogs found?

Highly variable genetic markers used. Markers which show linkage (co-inherit) with the trait are likely incorporated in the gene sequence of the responsible gene.

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What are QTLs?

Variable markers associated with gene responsible for quantitative trait.

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What were the findings in dogs regarding skeleton size QTLs?

44QTLs on 22 chromosomes.

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What are the requirements for QTL mapping by linkage?

Homozygous strains and crosses. Model organisms. Large pedigree. In humans only useful with traits that have a major genetic component.

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What is allelic association?

Linkage disequilibrium.