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Population Structure 2010
Population Structure 2010
Population Structure
Nonrandom Mating
Population Structure
Nonrandom Mating: Inbreeding
Population Structure
Nonrandom Mating: Population Subdivision
Population Structure
Wright’s F Statistics
Population Structure
Wright’s F Statistics
Population Structure
Genotype Frequencies for Inbred Individuals
Population Structure
Generalized Hardy-Weinberg Deviations
Genotype AA Aa aa
Frequency p 2 (1 − F ) + pF 2pq(1 − F ) q 2 (1 − F ) + qF
where q = 1 − p
The F parameter describes the deviation of the genotype
frequencies from the HWE frequencies.
When F = 0, the genotype frequencies are in HWE.
The parameters p and F are sufficient to describe genotype
frequencies at a single locus with two alleles.
Population Structure
Fst for Subpopulations
Population Structure
Fst for Subpopulations
Population Structure
Fst for Subpopulations
Population Structure
Fst for Subpopulations
Population Structure
Fst for Subpopulations
Let the relative contribution of subpopulation i be ci , where
Xr
ci = 1.
i=1
Genotype AA Aa aa
Freq. Subpopi p 2 2p q q 2
Pr i 2 Pr i i Pr i 2
Freq. Population i=1 ci pi i=1 ci 2pi qi i=1 ci qi
where qi = 1 − pi
In the population,
Prwe want to find the value Fst such that
2pq(1 − Fst ) = i=1 ci 2pi qi
Rearranging terms:
2pq − ri=1 ci 2pi qi
P
Fst =
2pq
2 2
Pr 2pq = 1 − p −Pqr and 2
Now
2
i=1 ci 2pi qi = 1 − i=1 ci (pi + qi )
Population Structure
Fst for Subpopulations
s2
A simple Fst estimate is F̂ST1 = p̂(1−p̂) , where s 2 is the
sample variance of the p̂i ’s.
Population Structure
Estimating Fst
Their estimate is
MSA − MSW
F̂ST2 =
MSA + (nc − 1)MSW
P 2
P n
i ni −
where nc = Pi i
i ni
Population Structure
GAW 14 COGA Data
Population Structure
COGA Data
mean = .011
Frequency
Population Structure
References
Population Structure