1. Software, HWE, Fst

4. Infiles

5. Infiles ….converts infiles for more than 60 pop gen programs. http://bcrc.bio.umass.edu/pedigreesoftware/node/2

7. 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

8. HWE

9. Locus 3 Locus 1 Locus 2 BB BB BB AB AA AA AB AB AB AA AB AB BB BB BB AA AA AA AB AB AB AB AB AB AA AA AA AB AB AB BB BB BB AB AB AB 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

10. Locus 1 Locus 2 Locus 2 BB AB BB AA AA AA AA AA AA BB BB BB BB BB BB AA AA AA AB AB AA AB AB AB AA AA AA BB BB BB BB BB BB AA AA AA Hardy-Weinberg theorem HS: 0.5 0.5 0.5 HO: 0.17 0.25 0.08 FIS: +++ +++ +++ Deviation from HWE – strong inbreeding, selfing?

11. Locus 1 Locus 2 Locus 3 BB BB BB AA AA AA AB AB BB AB AB AB BB BB BB AA AA AA AB AB AA AB AB AA AA AA AA AB AB AB BB BB BB AB AB AA 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?

12. Fst

13. Hobs = 0.17 Hs = 0.3 AB AB AA BB AA AA AB AA AB AB BB AB AA AB AA AA AA AA AA BB BB AB AA Hobs = 0.5 Hs = 0.49 AA AA Hobs = 0 Hs = 0 BB BB BB BB BB BB BB BB BB Ht = 0.5 BB BB Mean Hs = 0.26

14. Two island populations (one locus; two alleles R and B) Fst = 0

15. Two island populations (one locus; two alleles R and B) Fst = 1

16. Two island populations (one locus; two alleles R and B) Fst = 0-1

17. Two island populations (one locus; two alleles R and B) Global: pA= 75% pB = 25% Fst = ? pA= 100% pA= 50%, pB = 50% AA AA AA AB AA AA AB BB AA AA AA AA AA AA AB AA AB AA AB AA AB AA BB BB

18. Problem with Fst when highly variable loci are used CC DD AB BB CC AA CD CD BB AB DD BB AB DD CD AB AB CD CC AA AB AA CD CD 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

19. 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

20. Computer exercises