WEEK 7: POPULATION GENETICS AND BAYESIAN ANALYSIS Flashcards
What are the 4 different levels of variation?
- Molecular level
- Cellular level
- Organism level
- Population level
What is population and evolutionary genetics?
-Localised group of INTERBREEDING individuals of the SAME SPECIES
What is the gene pool?
- All the alleles of a gene in the population
What is polymorphism?
-Variation in a population –> multiple “morphs” or “forms” of a trait
Are most genes polymorphic?
- YES
- More than one genes is present in the population
What are the three levels of examination of variation?
- MORPHOLIGICAL
- PHYSIOLOGCIAL –> bp
- BIOCHEMICAL -> ENZYME LEVELS
What is an example of morphological variation?
- Differenes in pigmentation
What is an example of biochemical polymorphism?
- ADH breaking down ethanol–> different allozymes in population (SS SF FF)
What is a more modern form of studying variation?
- DNA sequence polymorphism
Are DNA marker alleles co-dominant and if so, what can they be used to work out?
- 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
What is the hardy weinberg principle?
- 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.”
n the H-W principle, what does it mean when it states that the gene pool of a population must not be evolving?
- this means that the allele and genotype frequencies remain CONSTANT from generation to generation
Can we always determine the genotype of all individuals?
- 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
What are the 5 assumptions of the H-W equilibrium?
- Population is very large
- NO gene flow (no alleles coming in or out of the population)
- NO natural selection
- NO mutation
- IS random mating
What is MICROEVOLUTION?
- If any of the assumptions DO NOT apply which causes the allele and genotype frequencies to change
Which violations are most likely to occur from the H-W assumptions?
-Violations in the assumptions 1-3; population is very large, NO gene flow occurs, and no natural selection
What is genetic drift?
- 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
What is the effect of genetic drift in smaller populations?
-Genetic drift acts FASTER and with GREATER consequences –> causes fixation of one allele or the other (randomly)
Which two circumstances can INCREASE the EFFECT of genetic drift?
- Bottleneck
2. Founder Effect
What is a bottleneck and what can it be due to?
- Sudden dramatic DECREASE in population size
- Can be due to NATURAL DISASTERS
What is the founder effect and what is an example?
- 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
What is gene flow?
- Migration of individuals into and out of a population can ALTER allele frequencies if genotypes migrate differentially
Are there different effects if gene flow is unidirectional or bidirectional?
YES
What is the effect if the gene flow is BIDIRECTIONAL?
-Reducqes the differences between populations because it is the introduction of alleles that aren’t commonly there
What is natural selection?
- 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”.
What are the 3 different types of selection?
- Directional selection
- Stabilising selection
- Balancing Selection
What is an example of directional selection?
- Selective predation and pesticide resistance in insects
What is stabilising selection and an example?
- Stabilising selection because it is not driving selection to one extreme or the other
- E.g. Selection against low birthweights or really high birthweights
What is balancing selection and an example? (2 types of balancing selection)
- 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
What is the mutation rate and what level are they normally around?
- µ–>Pr of mutation to a different allele PER GENE PER GENERATION –>mutation rates are generally around 10E-5 -10E-8
Can recurrent mutation change allele frequencies?
- YES –> BUT mutation is EXTREMELY SLOW at changing allele frequencies and so CANNOT account for rapid genetic changes
What is assortative mating?
-Between similar BUT UNRELATED individuals
What is positive assortive mating?
- Bias towards choosing a similar mate
- E.g. humans for skin colour and height
- INCREASES THE HOMOZYGOSITY of the population
What is NEGATIVE ASSORTATIVE MATING?
-Bias towards choosing a DISSIMILAR mate
What is interbreeding?
- B/w RELATED individuals –> increases the number of DELETERIOUS recessive individuals (aa) in pop. + Increases homozygosity of population (reduces numbers of heterozygotes)
What can a risk figure, or recurrent risk be calculated from?
- Diagnosis and mode of inheritance
- Analysis of family pedigree
- Results of tests-linkage studies etc.
WHAT IS BAYES THEOREM?
- 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”
- PRIOR PROBABILITY:
-The INITIAL probability (based on anterior (ancestral information)
- CONDITIONAL PROBABILITIES
-Determined using MODIFYING OBSERVATIONS Based on posterior information (e.g. numbers of offspring/results of tests etc.)
- JOINT PROBABILITY
Prior Pr (1) * Conditional Pr (2)
- POSTERIOR/RELATIVE PROBABILITY
-Joint probability divided by the sum of all joint probabilities
What is ancestral information also known as?
-Ancestral AKA ANTERIOR –> “prior probability”–> Pedigree information or empirical mutation frequencies
What is modifying information also known as?
- Modifying AKA posterior –> “Conditional probability” –> Number of affected/unaffected children, results of tests etc.
