Class05-ClassSlides-Spring 2011-03292011

# Class05-ClassSlides-Spring 2011-03292011 - Genetic Analysis...

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1 Genetic Analysis II (385) – Population Genetics Lecture 05 Date: 03/29/11 Instructor: Professor Derek Gordon Office: Life Sciences Building, Room 128 Phone: 445-3386 Phone: 445 3386 E-mail: [email protected] Office Hours: Tues, Thurs: 12:00pm – 1:15pm, and by appt. Review - How do we compute the two- locus gamete frequencies over time using formula(generations) in presence of linkage? 3/29/2011 PopGen 5 - 2011 2

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2 Genetic linkage and recombination 3/29/2011 PopGen 5 - 2011 3 HWE and Linkage When considering two (or more) loci, one must also account for the presence of linkage disequilibrium . account for the presence of . This is very much like HWE disequilibrium (i.e., where the markers are unlinked) but approach to final equilibrium is much slower. Under random mating, gametes combine at random . Hence, if the frequency of (say) an AB gamete is 0.4 and an ab gamete is 0.1, then 3/29/2011 4 freq(AB/AB) = 0.4 2 , freq(ab/ab) = 0.1 2 , freq(AB/ab) = 2 * 0.4 * 0.1. PopGen 5 - 2011
3 HWE and Linkage However, the frequencies of gametes in a population can change by recombination from generation to generation change by recombination from generation to generation unless they are in linkage equilibrium (which is also called gametic-phase equilibrium ). Factor in a recombination rate “c ”. “c” may vary between .5 (complete recombination) and 0 (no recombination). 3/29/2011 5 PopGen 5 - 2011 Computing gamete frequencies over time using formula The essential formula to compute these frequencies is frequencies is: Freq(AB gamete at generation t) = D AB (t) + f(A)f(B). 3/29/2011 PopGen 5 - 2011 6 Here, D AB (t) = the disequilibrium value of the AB gamete at generation t.

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4 3/29/2011 PopGen 5 - 2011 7 Cart before horse? 3/29/2011 PopGen 5 - 2011 8
5 I wanted to give you these neat-o formulas for computing gamete frequencies over time using a frequencies over time using a formula. Perhaps it’s better to first understand how we’d compute the gamete frequencies over one generation! 3/29/2011 PopGen 5 - 2011 9 Class Exercise: Generation 0 AB =.40, c = recombination = .05. Ab =.20, aB =.20, ab =.20. 3/29/2011 PopGen 5 - 2011 10 What are gamete frequencies after one generation?

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6 Probability of Gamete Frequency in next generation Gntype Type Freq AB Ab aB ab AB Ab aB ab AB/AB 1 0.16 1 0 0 0 0.16 0 0 0 AB/Ab 2 0.08 0.5 0.5 0 0 0.04 0.04 0 0 AB/aB 3 0.08 0.5 0 0.5 0 0.04 0 0.04 0 AB/ab 4 0.08 0.475 0.025 0.025 0.475 0.038 0.002 0.002 0.038 Ab/AB 2 0.08 0.5 0.5 0 0 0.04 0.04 0 0 Ab/Ab 5 0.04 0 1 0 0 0 0.04 0 0 Ab/aB 6 0.04 0.025 0.475 0.475 0.025 0.001 0.019 0.019 0.001 Ab/ab 7 0.04 0 0.5 0 0.5 0 0.02 0 0.02 aB/AB 3 0.08 0.5 0 0.5 0 0.04 0 0.04 0 aB/Ab 6 0.04 0.025 0.475 0.475 0.025 0.001 0.019 0.019 0.001 aB/aB 8 0.04 0 0 1 0 0 0 0.04 0 aB/ab 9 0.04 0 0 0.5 0.5 0 0 0.02 0.02 ab/AB 4 0.08 0.475 0.025 0.025 0.475 0.038 0.002 0.002 0.038 ab/Ab 7 0.04 0 0.5 0 0.5 0 0.02 0 0.02 ab/aB 9 0.04 0 0 0.5 0.5 0 0 0.02 0.02 ab/ab 10 0.04 0 0 0 1 0 0 0 0.04 Total 0.398 0.202 0.202 0.198 3/29/2011 11 PopGen 5 - 2011 Some facts about this table 1. Frequency of a genotype computed just the way you expect it is, as the product of the individual gamete frequencies.
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## This note was uploaded on 04/04/2011 for the course GENETICS 385 taught by Professor Brennemanandgordon during the Spring '11 term at Rutgers.

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Class05-ClassSlides-Spring 2011-03292011 - Genetic Analysis...

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