Population Genetics Flashcards
What is a VNTR? Diseases associated with VNTRs?
A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. Fragile X-Syndrome.
4 differences to measure genetic diversity:
Nucleotide state difference (sequencing) Length difference (microsatellites) Functional difference (ABO blood group) Electrophoretic difference (allozyme)
Hardy–Weinberg Equilibrium
p + q =1
p² + q² + 2pq = 1
Calculate frequency of an allele?
AA Aa aa Calculate frequency of A
5 50 45
((5x2)+50)/200
=(10+60)/200
=70/200
=0.35
General form of F statistics equation and what are F statistics?
F = 1 - (Ho/He)
Where Ho = Observed heterozygosity
and He = Expected heterozygosity
F statistics describe the statistically expected level of heterozygosity in a population.
Fis
Departure from HW within a deme .
Used as a measure of inbreeding. 0 is no inbreeding.
Fis = 1 - (Ho/He)
Fst
Departure from HW between demes.
Measures population structure, where 0 is unstructured and panmitic (randomly mating) and 1 is complete isolation and structure.
Fst = 1 - (Hs/Ht)
Fst = 1 - (seperated groups/ one group (i.e. panmitic))
% of selfing equation
S= (2*Fis)/(1+Fis) = % of offspring arisen from selfing
Inbreeding
Causes reduced fitness
Increased homozygosity and reduced heterozygosity
Can determine inbreeding by taking the shortest path (N) from one parent of an individual to the second.
F = (1/2)^N x (1+Fca) , where Fca is the inbreeding coefficient of the common ancestor. Fca is 0 if no inbreeding for common ancestor.
Autozygous
Identical by descent
Allozygous
Identical by state (i.e. not directly related, but same genetic info)
Demes
Group of individuals that belong to the same taxonomic group
Measuring gene flow:
- Calculation of Nm from Fst
- Nm is the average number of migrants per generations
- Lower Fst (less structure) means higher gene flow - Private alleles
- Alleles that only occur in one population
- More private alleles = less gene flow - Direct estimates
- Directly observing migrants moving between populations via marking after birth or the spread of rare alleles etc.
General effects of gene flow:
Causes a reduction in genetic differences between populations.
Causes an increase of genetic variation within population.
Know how to genotype a gel!
I.e. if bands appear in both A and a regions then heterozygote, if only in A or a then homozygote of the respective allele.
Purging
Natural removing “unfit” individuals and deleterious alleles from a population e.g. in mice.
Leads to a reduction in inbreeding depressions in small populations.
Heterosis
Heterozygote advantage, commonly used in plant breeding
Calculate relative fitness:
Selective advantage = Fittest (W) /2nd Fittest (W)
Obs Exp Obs:Exp W(Relative Fitness) Sel. Adv.
AA 29 185 0.1567 0.15/1.15 = 0.13
AB 2993 2601 1.15 1.15/1.15 = 1 1.14
BB 9365 9525 0.983 0.98/1.15 = 0.85
Muller’s Ratchet
A process in which absence of recombination, especially in an asexual population, results in accumulation of deleterious mutations, irreversibly.
These alleles are compensated for by beneficial ones.
Populations have a balance between mutation and BLANK and mutation and BLANK
Balance between mutation and drift (production of alleles vs loss of alleles)
Balance between mutation and selection (production of alleles vs purging of alleles)
Note, positive mutations are rare, a small amount is sufficient to sustain a population.
Lethal Equivalent
A combination of selective effects that on average have the same impact on the composition of the gene pool as one death; for example, two carriers at 50% risk of dying would be the lethal equivalent of one carrier at 100% risk;
Mutation-Selection Equilibrium Equations
Δqmut = μp :Rate of p mutating to q μ = mutation rate, p = 1-q, q = freq. of deleterious allele a Δqsel = (-spq²) / (1-sq²) : rate of change due to selection S = selection coefficient
3 Types of selection
- Directional
- Stabilsing
- Diversifying/Disruptive
Equation when rate of mutation is equal to rate of selection:
q = √(μ/s)
Gives the mutation rate that offsets loss of alleles to keep it in equilibrium