W3 L3 MCK test v2 Flashcards
What is alpha
Alpha is the number of changes in aa that is adaptive
Alpha calculation
A= 1-DsxPn/DnxPs
If alpha is close to 1= selectionist model
If alpha is closer to 0 = neutral model
Prerequisite in alpha calculation
- No adaptive variants are observed in our sample of polymorphism
- None of the synonymous variants (in divergence or polymorphism data are adaptive)
- No deleterious mutations fixed in the population
The idealized wright fisher population
- Diploids
- Each allele is equally likely to be sampled in the next generation (no selection)
- Allele chosen without considering the other alleles chosen for that generation (random mating)
- No spatial population structure (no migration from other pops)
- Sampling with ‘replacement’ ie. self fertilization (hermaphroditism) is possible!
- Generations are distinct and non overlapping
- Population size constant
- No family size differences
- No environmentally induced variation
The decay in heterozygosity by drift formula
H1=H0(1-1/2N)^t
H: the frequency of heterozygosity in a population
G; the frequency of homozygousity in the population
H=1-G
The time taken for drift to reduce heterozygosity by half is:
T0.5=2 N ln(2)
Predicted heterozygousity in neutral sequences
H=4Nu/(1+4Nu)
Why is the observed and expected heterozygousity is different
- unable to have a constant population size
-there will be selection
Effective population size (Ne)
-Ne may be smaller than the breeding population
-the concept of Ne allows us to accommodate the dramatic fluctuations of population sizes over time
* Ne is the size of the idealized (Wright-Fisher) population whose decay of heterozygosity equals that of the real population.
Genetic hitchhiking
A favorable mutation removes variations (selective sweep) which lead to removal of heterozygousity
