Lecture 10 - LD, con't & Intro to QG

Lecture 10 - LD, con't & Intro to QG - 1 Lecture 10.1 -...

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1 Lecture 10.1 - Causes and consequences of Linkage Disequilibrium, con't I. Causes of LD, con't. .. 4. Natural Selection a) "Associative" Overdominance 2 loci, "2" alleles are deleterious and completely recessive, fitness is multiplicative - If initial coupling L-D, then A1B1, A2B2 are common; A2B2 quickly removed from the population. g'type w(ij) A1B1/A1B1 1 A1B1/A2B2 1 (remember, dominance) A2B2/A2B2 (1-s) 2 - If initial repulsion L-D, then A1B2, A2B1 are common (recall question above) g'type w(ij) A1B2/A1B2 1-s A1B2/A2B1 1 A2B1/A2B1 1-s Thus, there is apparent ("associative") overdominance, which will last until recombination breaks up the L-D b) Stabilizing selection "+" alleles increase trait value, "-" alleles decrease trait value. If intermediate phenotypes are favored, ++ and -- gametes will (on average) have lower fitness than +- and -+ gametes. Thus, selection will (again) maintain repulsion L-D. Q: Under what circumstances would selection build up coupling L-D? II. Consequences of LD 1. Genetic "Hitchhiking" It is commonly observed that heterozygosity (i.e., standing genetic variation) and local (genomic) recombination rate are positively correlated. Regions of low recombination (e.g., centromeric and telomeric regions) have reduced genetic variation relative to regions of normal recombination.
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2 This pattern is observed in Drosophila , humans, Arabidopsis , Caenorhabditis , tomato, and other taxa. Obviously, heterozygosity increases with local recombination rate. One possibility: recombination is mutagenic (remember, H^ 4N e μ ) To test that possibility: Recall that from the Neutral Theory, the neutral substitution rate is equal to the mutation rate (i.e., k = μ ). So, if the substitution rate (among taxa) is higher at genes in regions of low recombination, it would imply that the mutation rate is higher in those regions. Q: On what important assumptions does this analysis depend? Since the early '90s, the dogma in evolutionary biology has been that the substitution rate is not higher in regions of low recombination. However, that dogma is changing. As more data accumulate, it is beginning to look like that the substitution rate is often lower in regions of low recombination, leading to the conclusion that recombination is mutagenic. However, it does not appear that the mutagenicity of recombination can explain the entire difference in local genetic variation. So, what about selection ? Suppose a new beneficial mutation arises and survives the vagaries of low frequency? Variation that is tightly linked to the beneficial mutation will also increase in frequency. Upon fixation of the new beneficial mutation, the only alleles present in the population at tightly linked loci will be those alleles that were initially associated with the beneficial mutation. Thus, variation at linked loci is removed from the population. This is called a "selective sweep", or "hitchhiking", as depicted in the following figure. ..
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3 The following figure depicts a population of chromosomes before a selective sweep. The red "C" at position 4 is beneficial mutation.
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This note was uploaded on 06/08/2011 for the course PCB 4674 taught by Professor Baer during the Fall '08 term at University of Florida.

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Lecture 10 - LD, con't & Intro to QG - 1 Lecture 10.1 -...

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