A.? From the data given for the rs62224609 locus, what is the estimated value of Hs and Ht, and Fst for humans?? Now calculate the same using all loci and give the average values for each.? What is the best estimate of total inbreeding in the world, how do you interpret this number?
B.? Just considering GBR, FIN, and CHS, and for the rs62224609 locus, calculate Hi, Hs, Ht, Fit, Fis, and Fst,.? Now calculate same when based on all loci for those populations.
C. Based only on B, Is there subpopulation structure within GBR, FIN or CHS?? Explain
D.? Compare the Fst obtained in B with that in A.? Would you expect the value in B to be greater than, the same, or less than A?? Why?
There?d be a difference because we are only examining the subpopulation in part B.
E.? The coefficient of relationship between any two individuals in a pedigree can be found as the probability of IBD (see slide 46 of 4th set).? Without pedigrees the same value can be calculated based on the assumption that a given SNP occurred only once and is IBD with any individual who shares it.? Based on the definition of coefficient of relationship, calculate the relationship between 2 individuals in GBR (HG00096 with HG00097) and 2 individuals in CHS (HG00403 with HG00404).and the relationship between individuals of the countries GBR and CHS (HG00096 with HG00403). (hint, remember that IBD is based on 4 probabilities, the draw of the 2 alleles at that locus in the first individual and the draw of the 2 alleles at the locus in the 2nd individual. if both individuals have the same homozygous genotype, they share 2 alleles IBD and the average of the 4 probabilities is 1; if both are opposite homozygotes, they share 0 and the probability is 0; a het with a homo, they shares 1 with probability 1/2, a het with a het shares 1 with probability 1/2, see slide 48 from the 4th set of notes).
F.? From the 2nd definition of inbreeding, which is the probability that two alleles within an individual at the same locus are IBD (see Slide 29, 3rd set of notes), how much inbreeding would result if HG00096 with HG00097 mated with each other; or HG00403 with HG00404; or HG00096 with HG00403 (assuming they are opposite sex, naturallyJ.? .From this example, what general conclusion can you make about inbreeding and relationships?? If you can't figure out how to get Excel to do this across loci, just use the rs62224609 locus for partial credit
G.? Can you detect any signatures of selection between any of the super-populations?? Show calculations.
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