EHJ352H1 Lecture Notes - Lecture 5: Selective Sweep, Linkage Disequilibrium, Slc24A5
12 Oct 2016
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Testing for adaptive evolution: ka/ks > 1 - would be hard to observe, ka/ks > pa/ps - could suggest significant positive selection, a = amino acid, non-synonymous. Both methods (cid:396)e(cid:395)ui(cid:396)e (cid:396)e(cid:272)u(cid:396)(cid:396)e(cid:374)t adapti(cid:448)e e(cid:448)olutio(cid:374) o(cid:396) you (cid:449)ould(cid:374)"t (cid:396)eally get a (cid:374)u(cid:373)(cid:271)e(cid:396) that would show that genes are fixating faster than you would expect under neutrality. Pick up genes subject to recurrent adaptation (ex. Immunity and reproductive genes: get multiple repeated cases of adaptive changes occurring. What about unique events of adaptive evolution: can be lots of key adaptations that occurred due to a single gene. Effects of positive selection on neutral polymorphism: reduced diversity due to selective sweeps, causes an increase in linkage disequilibrium, shift in snp frequencies - end up with an excess of rare variants. Get much higher between population variation because there is a lot of fixation (local adaptation) Distinguishing natural selection vs demographic history: genome-wide patterns of diversity.
