F13 lecture 19 v3

Contribute to ld looked at phenotypic and gene0c

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Unformatted text preview: 5, pa=0.75, pB=0.25, pb=0.75 allele frequency A 0.75 a 0.25 B 0.25 b 0.75 haploid genotype AB Ab aB ab expected pA*pB pA*pb pa*pB pa*pb frequency 0.1875 0.5625 0.0625 0.1875 If genotype frequencies significantly differ from these expecta0ons, then there is significant linkage disequilibrium (LD) between the A and B loci quan0fying LD •  D = (observed genotype frequency – expected genotype frequency) haploid genotype observed expected frequency frequency for D = 0.05 AB pA*pB 0.1875 pA*pB+D 0.2375 Ab pA*pb 0.5625 pA*pb-D 0.5125 aB pa*pB 0.0625 pa*pB-D 0.0125 ab pa*pb 0.1875 pa*pb+D 0.2375 recombina0on •  c (or some0mes r) is used as a variable for recombina0on rate •  loci on different chromosomes c=0.5 (maximum recomb, rate) => “unlinked” •  because of independent assortment •  loci far away from each other on same chromosome c=0.5 => “unlinked” •  loci closer together c<0.5 –  loci are “linked” popula0ons take 0me to arrive at linkage equilibrium causes of linkage disequilibrium •  close gene0c linkage –  in the absence of other factors, D will decrease exponen0ally (see previous slide) •  “epista0c selec0on” •  e.g. heterostyly in English primrose (Primula...
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