1 / 22

Comprehensive Population Genetics Software for HWE and Fst Analysis

Discover robust software solutions for population genetics analysis, capable of converting input files for over 60 programs. Our toolkit includes functionalities for GenAlEx, Structure, Genepop, SMOGD, Arlequin, Geneland, Circuitscape, and more, providing features like allele frequency calculation, Fst estimates, AMOVA, PCA, and outlier detection. Enhance your research with user-friendly tools for Hardy-Weinberg Equilibrium (HWE), genetic diversity assessment, and spatial analysis of populations. Visit us for resources and tutorials to streamline your data analysis.

jackson-rowe
Download Presentation

Comprehensive Population Genetics Software for HWE and Fst Analysis

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Software, HWE, Fst

  2. Infiles

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

  4. 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

  5. HWE

  6. 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

  7. 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?

  8. 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?

  9. Fst

  10. 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

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

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

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

  14. 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

  15. 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

  16. 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

  17. Computer exercises

More Related