Lecture 3: Substructure, HWE, Wahlund and inbreeding Flashcards
What is population substructure?
When expected allele frequencies are not the same for all individuals in a population.
What is population stratification?
When a clear division of “breeds” has different allele frequencies e.g. dog races.
What is the consequence of population stratification?
Increase in allele frequency estimate variance.
How to handle population stratification
Select sample populations carefully.
Collapse groups to get the wished for allele frequency.
What is population admixture?
When to ancestral populations are mixed.
What is population inbreeding?
Random mating is violated, And therefore also the probability of inheriting genes.
Is quantified using the indbreeding coefficient F:
F = P(individual inherits an allele identical by descent from both parents)
Results of inbreeding
Higher rates if homozygotes
Higher rates of recessive disorders.
Hardy weinberg equilibrium concept
a population state arising from a formula that relate allele frequency in parents to genotype frequency in offspring.
Assumptions of HWE
Random mating no inbreeding infinite population size discrete generations equal allele freq in males and females no mutation no migration no selection
What is the genotype distribution at HWE?
P(AA) = p^2 P(Aa) = 2pq P(aa) = q^2
Another interpretation of HWE
It is the same as stochastic independence of alleles.
How do you test for HWE?
You simply do a goodness of fit test, with expected values calculated from the HWE equation. Is chi-square distributed with 1 df.
What is the rule for size smallest number in table for goodness of fit?
5
HWD
Hardy Weinberg disequilibrium
What is the expected amount of alleles assuming HWE and the variance?
The inheritance of alleles in HWE is binomail on an individual level. The expectation of X is therefore n*p, two inherited chromosomes give 2p.
The variance is np(1-p). This is 2pq.
