4 - population genetics Flashcards
what is assumed in the theory of allele frequency?
1) random mating
2) no evolutionary forces (natural selection, genetic drift, )
3) no mutation
how do you test if Hardy-Weinberg equilibrium explains the difference between the expected vs observed allelic frequencies?
use χ-squared test
χ-squared = sum of [(observed - expected)^2 / observed]
if p<0.001, deviations are not by chance and population is not in HW equilibrium
name 5 reasons why populations deviate from HW equilibrium
1) mutation
• HW assumes there is no mutation
2) non-random mating
• leads to excess of homozygotes
• inbreeding → homozygosity across whole genome
• assortive mating (i.e. between alike individuals) → homozygosity within certain genes, ↑ linkage disequilibrium
3) natural selection
• elimination of individuals with deleterious phenotypes
4) population subdivision
• populations separate and become different
5) migration
• introduction of new genotypes via migration alters allele frequencies
• usually a deficit in heterozygotes
genetic drift has a strong affect in what type of population?
small
what is the function for frequency of heterozygotes in a population?
H’ = (1 - 1/2N)H
how does random genetic drift impact heterozygosity?
in one generation, random genetic drift causes heterozygosity to decline by 1/2N, where N = population size
list and briefly describe three types of dynamic equilibrium
1) mutation-drift balance
- mutation replenishes the variability that is lost due to drift (neutral alleles)
- [𝛾 = 1/(2N)]
- when 2u(1-H) = (1/2N)H, heterozygote is in equilibrium and will not change
2) selection-mutation balance
- rate of mutation of deleterious recessive allele same as rate of elimination by selection
- decrease in recessive homozygotes
- [u = sp^2]
3) polymorphism balance
- heterozygote superiority
- a = a
how is dynamic equilibrium different in small and large populations?
drift dominates dynamic of small populations
mutation dominates dynamic of large populations
what type of selection occurs when there is overdominance?
balancing selection / balanced polymorphism
homozygotes are lost but heterozygotes are preserved
what is linkage equilibrium and when does it occur?
linkage disequilibrium = imbalance in recombinant and parental gametes
linkage equilibrium occurs when the fraction of parental gametes equals the fraction of recombinant gametes
what is the relationship between the distance b/w two chromosomes and the linkage disequilibrium
LD decays with distance along the chromosome
close linked loci produce few recombinants
far apart loci produce many recombinants
how is molecular evolution influenced by function?
a molecule with fewer functional constraints will evolve faster
substitutions will be neutral, not deleterious
what does Tajima’s D measure and what do the values mean?
Tajima’s D is a statistic that measures the number of polymorphic mutations (π) compared to the number of segregating mutations (θ)
D = 0: π = θ (neutral expectation)
D < 0:
excess of low frequency polymorphisms
purifying selection, population expansion, or hitchhiking
D > 0:
excess of high frequency polymorphisms
balancing selection
what does the dN/dS ratio measure and what do the values mean?
dN = rate of non-synonymous mutations per non-synonymous site dS = rate of synonymous mutations per synonymous site
dN/dS > 1: replacements are beneficial
sN/dS = 0: replacements are neutral
dN/dS < 1: replacements are deleterious
what is the McDonald-Kreitman Test and what do the values mean
measures what proportion of mutations are due to positive selection
silent sites are always neutral and therefore fixate slowly. these largely contribute to polymorphism
replacement sites are mainly deleterious. if neutral, act as a silent site. if beneficial, fixate quickly and do not contribute to polymorphism
use chi-squared test to determine significance
