Final Study GuideChapter 8: Linkage Disequilibrium & Sex1. Define linkage disequilibrium.When two loci are in a nonrandom association between a chromosomes’s genotype at one locus and its genotype at the other locus.- Chromosome freq. are NOT product of appropriate allele freq. - On a bar chart —mid lines will not align- What creates LDo Selection on multilocus genotypes Grass hoppers are green and brown- After each generation some grass hoppers have both colors (mismatched colors)- Selection kills these ones because they stand out more in the brown and green leaveso Selection in small populations (genetic drift) Population has one allele A at one locus, but two alleles, B and b, at another Mutation creates new favorable allele a, but it is on a chromosome with b allele Selection increases freq. of a, and freq. of b increases Results in LDo Admixture of populations 2 populations have different chromosome frequencies admixture of the two populations creates LD- Recombination destroys LD- If 2 loci are in LD, selection on 1 locus can cause hitchhiking by the other locusConversely, two loci are in linkage equilibrium when the genotype of a chromosome at one locus is independent of its genotype at the other locus- Chromosome freq. are product of appropriate allele freq. - On bar chart — mid lines will alignD = g(AB)g(ab) – g(Ab)g(aB)- If equals 0, then linkage equilibrium exhibited - Ranges from +0.25 to -0.25- Measures degree of linkage disequilibrium in a population2. What is genetic recombination?Genetic recombination is the creation of new combinations of alleles from sexual reproduction. - Crossing over during meiosis - Reduces LD3. Why does genetic recombination reduce linkage disequilibrium?Genetic recombination reduces LD because it tends to randomize genotypes at one locus with respect to genotypes at another.- Varies from 0 to 0.5o 0 meaning linkage is very tight Reduces LD less effectivelyo 0.5 when loci are on different chromosomes Reduces LD most effectively- Rate of decline in LD between pair of loci is proportional to rate of recombination between them4. What is the consequence of sex at the level of population genetics?It has 2 population genetic effects- Restores H-W equilibrium- Restores linkage equilibrium Without sex (asexual reproduction) females produced twice as many offspring and increased the population more each generation- Compared to with sex, which did worse, but because it only has 2 population genetic effects, it is beneficial. Sex is beneficial in host-parasite arms race- Selection repeatedly changes direction- Sex is favored because it facilitates evolutionary response to those reversals in selection5. What is Muller’s ratchet?A process by which asexual populations accumulate deleterious mutations in a irreversible manner- Sex can rescue a population from Muller’s Ratcheto In a population individuals with fewest deleterious mutations can be lost due to drifto Sex is able to bring back the lost genotypes6. Why might genetic recombination be favored in a variable environment?Because genetic recombination (sex) recreates favorable multilocus genotypes that might have been eliminated by selection.- Then the genes progress to high frequencies in the high fitness genotypes they help to create7. Why did Sewall Wright consider ‘linkage disequilibrium’ to be a ‘doubly unfortunate name’?He proved that the probability that any given allele in a population will be the one that drifts to fixation is equal to that allele’s initial frequency.Considered LD to be doubly unfortunate name because8. Linkage disequilibrium can be maintained a stable level in a population when two opposing forces are balance. What are those forces?Natural selection creates and genetic recombination destroys9. Do two loci have to be on the same chromosome to be in linkage disequilibrium?Not it does not matter if they are on the same chromosome . 10. What is the technical equivalent of ‘sex’ for a population geneticist?Reproduction involving:- Meiosis with crossing over- Mating between unrelated individualso Ex: random matingChapter 9: Quantitative GeneticsQuantitative Genetics— branch of evolutionary biology that provides tools for analyzing evolution of multilocus traits- Quantitative traits— characters with continuously distributed phenotypeso Continuous distributiono Affected by many genes Human height affected by at least 180 geneso Affected by environment o More loci = more phenotypic classes to be expectedo Many genes contribute to quantitative variationIdentifying Loci that contribute to quantitative traits- QTL — quantitative trait loci — portions of genome that influence quantitative traitso Detect presence of QTL by crossing parents from populations with fixed differences Marked loci for one parent species for one allele that was all homozygous and marked loci for other parent species for a different allele that was all homozygouso In F2 (grand offspring), look for association between phenotype and genotype at marker loci- Case of 2 monkey flowers: cardinalis and lewisiio Crossed 2 species = F1 generation Parents = homozygouso Bred pairs of individuals in F1 to produce F2 F1 = all heterozygoteso F2 you see quantitative variation in many traits F2 = heterozygotes and homozygotes- QTL Mapping— employ marker loci to scan chromosomes and identify regions containing genes that contribute to a quantitative traito Trial 1: QTL and marker physically linked (close and on same chromosome) Lewisii parent = ML QL / ML QL Cardinalis parent = MC QC / MC QC F1 all MC QC / ML QL F2 has 3 genotypes- ML QL / ML QL- MC QC / MC QC- ML QL / MC QC Homozygous for Lewisii marker = lewisii phenotype Homozygous for cardinalis marker = cardinalis phenotype Heterozygote = intermediate phenotype Marker locus and QTL are in LDo Trial 2: QTL and marker unlinked Same parents and F1 genotypes F2 has 9 genotype because unlinked- No association between genotype at the marker and phenotype influenced by QTLo Explanation: If phenotypes differ among individuals with different genotypes at particular marker (top right), then we can infer that the marker locus sits near a locus that contributes to the quantitative traitHeritability of a trait— fraction of the total variation in a trait that is due to variation in genes- Number between 0 and 1o If 0 it means that variation among individuals is due to