WEEK 7: POPULATION GENETICS AND BAYESIAN ANALYSIS

Question 1

What are the 4 different levels of variation?

Answer 1

• Molecular level
• Cellular level
• Organism level
• Population level

Question 2

What is population and evolutionary genetics?

Answer 2

-Localised group of INTERBREEDING individuals of the SAME SPECIES

Question 3

What is the gene pool?

Answer 3

• All the alleles of a gene in the population

Question 4

What is polymorphism?

Answer 4

-Variation in a population –> multiple “morphs” or “forms” of a trait

Question 5

Are most genes polymorphic?

Answer 5

• YES

- More than one genes is present in the population

Question 6

What are the three levels of examination of variation?

Answer 6

1. MORPHOLIGICAL
2. PHYSIOLOGCIAL –> bp
3. BIOCHEMICAL -> ENZYME LEVELS

Question 7

What is an example of morphological variation?

Answer 7

• Differenes in pigmentation

Question 8

What is an example of biochemical polymorphism?

Answer 8

• ADH breaking down ethanol–> different allozymes in population (SS SF FF)

Question 9

What is a more modern form of studying variation?

Answer 9

• DNA sequence polymorphism

Question 10

Are DNA marker alleles co-dominant and if so, what can they be used to work out?

Answer 10

• YES
• Can be used to work out allele frequencies
• E.g. CCR5 gene in humans –> Receptor for HIV
• If there is a mutation with 32bp deletion can genotype with PCR

Question 11

What is the hardy weinberg principle?

Answer 11

• Describes the gene pool of a population that is NOT EVOLVING
• “If mating is random, every male gamete unites at random with every female gamete, and frequencies of pairings depend on the allele frequencies.”

Question 12

n the H-W principle, what does it mean when it states that the gene pool of a population must not be evolving?

Answer 12

• this means that the allele and genotype frequencies remain CONSTANT from generation to generation

Question 13

Can we always determine the genotype of all individuals?

Answer 13

• NO!
• Not if dominance is COMPLETE BUT we can use H-W theory to ESTIMATE the genotype frequencies –> e.g. estimating carrier frequency for recessive human disorder

Question 14

What are the 5 assumptions of the H-W equilibrium?

Answer 14

1. Population is very large
2. NO gene flow (no alleles coming in or out of the population)
3. NO natural selection
4. NO mutation
5. IS random mating

Question 15

What is MICROEVOLUTION?

Answer 15

• If any of the assumptions DO NOT apply which causes the allele and genotype frequencies to change

Question 16

Which violations are most likely to occur from the H-W assumptions?

Answer 16

-Violations in the assumptions 1-3; population is very large, NO gene flow occurs, and no natural selection

Question 17

What is genetic drift?

Answer 17

• If population size is NOT VERY LARGE (1st assumption broken), genotype and allele frequencies can change due to random sampling effects (i.e. genetic drift). e.g. loss of an allele in future generations

Question 18

What is the effect of genetic drift in smaller populations?

Answer 18

-Genetic drift acts FASTER and with GREATER consequences –> causes fixation of one allele or the other (randomly)

Question 19

Which two circumstances can INCREASE the EFFECT of genetic drift?

Answer 19

1. Bottleneck

2. Founder Effect

Question 20

What is a bottleneck and what can it be due to?

Answer 20

• Sudden dramatic DECREASE in population size

- Can be due to NATURAL DISASTERS

Question 21

What is the founder effect and what is an example?

Answer 21

• Where a LARGE population has been founded by a SMALL population
• Allele frequencies of the large pop. Depend on the alleles of the FOUNDERS –> random effect
  e. g. Amish people and Van Creval Syndrome

Question 22

What is gene flow?

Answer 22

• Migration of individuals into and out of a population can ALTER allele frequencies if genotypes migrate differentially

Question 23

Are there different effects if gene flow is unidirectional or bidirectional?

Answer 23

YES

Question 24

What is the effect if the gene flow is BIDIRECTIONAL?

Answer 24

-Reducqes the differences between populations  because it is the introduction of alleles that aren’t commonly there

Question 25

What is natural selection?

Answer 25

- If a particular genotype is better suited to an environment these individuals will produce more offspring than others and contribute to the next generation --> this changes allele frequencies - That genotype has greater “relative fitness” than others and the genotypes are selected “against”.

Question 26

What are the 3 different types of selection?

Answer 26

1. Directional selection 2. Stabilising selection 3. Balancing Selection

Question 27

What is an example of directional selection?

Answer 27

- Selective predation and pesticide resistance in insects

Question 28

What is stabilising selection and an example?

Answer 28

- Stabilising selection because it is not driving selection to one extreme or the other - E.g. Selection against low birthweights or really high birthweights

Question 29

What is balancing selection and an example? (2 types of balancing selection)

Answer 29

- Sometimes natural selection maintains two or more forms in the population - E.g. Heterozygote advantage --> Heterozygote more fit than BOTH homozygous under certain conditions - Sickle cell anaemia E.g.2. Frequency dependent selection: Selection favours the LEAST common --> left eating fish

Question 30

What is the mutation rate and what level are they normally around?

Answer 30

- µ-->Pr of mutation to a different allele PER GENE PER GENERATION -->mutation rates are generally around 10E-5 -10E-8

Question 31

Can recurrent mutation change allele frequencies?

Answer 31

- YES --> BUT mutation is EXTREMELY SLOW at changing allele frequencies and so CANNOT account for rapid genetic changes

Question 32

What is assortative mating?

Answer 32

-Between similar BUT UNRELATED individuals

Question 33

What is positive assortive mating?

Answer 33

- Bias towards choosing a similar mate - E.g. humans for skin colour and height - INCREASES THE HOMOZYGOSITY of the population

Question 34

What is NEGATIVE ASSORTATIVE MATING?

Answer 34

-Bias towards choosing a DISSIMILAR mate

Question 35

What is interbreeding?

Answer 35

- B/w RELATED individuals --> increases the number of DELETERIOUS recessive individuals (aa) in pop. + Increases homozygosity of population (reduces numbers of heterozygotes)

Question 36

What can a risk figure, or recurrent risk be calculated from?

Answer 36

- Diagnosis and mode of inheritance - Analysis of family pedigree - Results of tests-linkage studies etc.

Question 37

WHAT IS BAYES THEOREM?

Answer 37

- Method for determining the OVERALL probability of an event by considering a) All INITIAL possibilities (e.g. carrier status) --> then modifying them by incorporating b) ADDITIONAL INFORMATION (e.g. test results) - “It uses the phenotypic information in a pedigree to assess the relative probability of two or more alternative genotypic possibilities”

Question 38

1. PRIOR PROBABILITY:

Answer 38

-The INITIAL probability (based on anterior (ancestral information)

Question 39

2. CONDITIONAL PROBABILITIES

Answer 39

-Determined using MODIFYING OBSERVATIONS Based on posterior information (e.g. numbers of offspring/results of tests etc.)

Question 40

3. JOINT PROBABILITY

Answer 40

Prior Pr (1) * Conditional Pr (2)

Question 41

4. POSTERIOR/RELATIVE PROBABILITY

Answer 41

-Joint probability divided by the sum of all joint probabilities

Question 42

What is ancestral information also known as?

Answer 42

-Ancestral AKA ANTERIOR --> “prior probability”--> Pedigree information or empirical mutation frequencies

Question 43

What is modifying information also known as?

Answer 43

- Modifying AKA posterior --> “Conditional probability” --> Number of affected/unaffected children, results of tests etc.