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Software, HWE, Fst. Infile s. Infiles. ….converts infiles for more than 60 pop gen programs. http://bcrc.bio.umass.edu/pedigreesoftware/node/2. Software (during the week). Pop gen GenAlEx – Allele frequencies, Fst , Amova , PCA, mm (convert infiles )

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Infiles
Infiles

….converts infiles for more than 60 pop gen programs.

http://bcrc.bio.umass.edu/pedigreesoftware/node/2


Software during the week
Software (during the week)

Pop gen

GenAlEx – Allele frequencies, Fst, Amova, PCA, mm (convert infiles)

Structure and Structure harvester

Genepop (web, HWE, Fst)

SMOGD (web, Dest)

PCAgen

*Arlequin – Fst, Amova, Outlier

Spatial

Tuesday: Geneland

Wednesday: Circuitscape

Thursday: GIS, Geste

Friday: Fdist2, Bayescan, Adegenet, Scythesam



Software hwe fst

Locus 3

Locus 1

Locus 2

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Hardy-Weinberg theorem

Random mating?

HS: 0.5 0.49 0.49

HO: 0.5 0.42 0.58

FIS: 0 + -

No sign deviation from HWE


Software hwe fst

Locus 1

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Hardy-Weinberg theorem

HS: 0.5 0.5 0.5

HO: 0.17 0.25 0.08

FIS: +++ +++ +++

Deviation from HWE – strong inbreeding, selfing?


Software hwe fst

Locus 1

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Hardy-Weinberg theorem

HS: 0.5 0.5 0.49

HO: 0.5 0.5 0.17

FIS: 0 0 +++

1 locus deviates from HWE – null allele? selection?



Software hwe fst

Hobs = 0.17

Hs = 0.3

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Hobs = 0.5

Hs = 0.49

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Hobs = 0

Hs = 0

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Ht = 0.5

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Mean Hs = 0.26


Software hwe fst

Two island populations

(one locus; two alleles R and B)

Fst = 0


Software hwe fst

Two island populations

(one locus; two alleles R and B)

Fst = 1


Software hwe fst

Two island populations

(one locus; two alleles R and B)

Fst = 0-1


Software hwe fst

Two island populations

(one locus; two alleles R and B)

Global:

pA= 75%

pB = 25%

Fst = ?

pA= 100%

pA= 50%, pB = 50%

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Problem with fst when highly variable loci are used
Problem with Fst when highly variable loci are used

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Hs = 0.5

Ht = 1 – (Expected Homozygosity) = 1-(4*0.25^2) = 0.75

Fst = (0.75-0.5)/075 = 0.25/0.75 = 0.33

Fst = is the degree of Fixation in the Subpopulation relative to the Total population


Problem with fst when highly variable loci are used1
Problem with Fst when highly variable loci are used

Dest = [(Ht-Hs)/(1-Hs)] * [n/(n-1)], where n is the number of populations

Jost (2008) Molecular Ecology 17, 4015–4026

doi: 10.1111/j.1365-294X.2008.03887.x