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100
Linkage disequilibrium VS Linkage equilibrium
Disequilibrium = nonrandom association between alleles at two or more loci

Expected frequencies differ from observed frequencies


Equilibrium = random association between alleles at two or more loci

expected frequencies = observed frequencies

100
How to estimate the haplotype frequencies at linkage equilibrium:
multiply the frequencies of the alleles
100
What is linkage disequilibrium important?

A.K.A what are the potential maladaptive results of linkage disequilibrium?

1. "associative overdominance" 

2. "background selection"

3. Genetic hitchhiking

4. selective sweep

100
What reduces linkage disequilibrium?
Recombination mixes alleles among haplotypes (linkage declines with time)
100
What is 'broad sense heritability'?
proportion of phenotypic variation that is due to individual genetic variation:


Hb = Vg/Vp

200
Stuff that causes linkage disequilibrium in random-mating population:
1. selection on multilocus genotype


2. genetic drift

3. population admixture


200
What assumptions are under the H-W theorem?
frequencies stay the same!


NO:

selection

mutation

migration

infinite population size

random mating


^^ chromosome frequencies only stay the same under linkage equilibrium (if in disequilibrium, chromosome frequencies go closer to equilibrium during each generation)

200
Describe associative overdominance.

- apparent heterozygote advantage due to negative selection at linked loci (if having Ab/aB is selected for, even though individually a and b are deleterious, it's hard to eliminate deleterious alleles)

200
What is quantitative genetics?
study of the evolutionary properties of traits under polygenic inheritance (continuous, meristic or threshold)
200
Vg = Va + Vd + Vl describe the variables
Va = variation due to effects of alleles independent of effects of other alleles 


Vd = variation due to dominance effects at a locus

Vi = variation due to interactions among loci

Vd + Vi => deviations from correlation btwn parent + offspring

300
Conditions if in equilibrium:
1. B on A = B on a

2. frequency of an haplotype (AB) = A X B (frequencies of alleles)

3. D (coefficient of disequilibrium) = 0 (since D = Frequencies of AB X ab - frequencies of aB X Ab)


300
how many haplotypes when:

2 alleles at 2 loci


and how many geno from the # of haplo?

4 haplo


10 geno

300
Describe background selection
When a highly fit allele declines because it is linked to a deleterious allele
300
Why is quantitative genetics important?
includes most traits related to evolution, ecology, agriculture, hunting and fishing regulation, medicine, conservation, follow Mendel's laws and H-W
400
Can populations have identical allele frequencies but different chromosome frequencies in 2-loci H-W?
YEP!
400
Allele frequencies + haplotype frequencies (when calculating D (linkage disequilibrium coefficient) MUST =
equal to 1


Looking at 

if D = 0 -> loci are completely unlinked (equilibrium)

if D = + or - -> loci are completely linked (equilibrium)

400
Describe genetic hitchhiking
when a deleterious allele can become fixed if on the same chromosome as a beneficial one
400
Response of quantitative traits to selection depends on:
- how many polymorphic loci for the trait

- distribution of effects (many loci = small effect, OR few loci = big effect)

500
Define Haplotype
multilocus genotype of a chromosome or gamete
500
What causes linkage disequilibrium?
1. Physical linkage

    - loci are close together on a chromosome


2. selection on multi-locus genotypes

    - if predation targets people w/ less capital lettered alleles, B will pair with a and A will pair with b

3. genetic drift

   - random change of frequency of alleles in finite populations

4. population admixture

    - combining two populations with different allele and chromosome frequencies resulting in disequilibrium (excess or reduced number of certain haplotypes)


500
Describe selective sweep
reduction or elimination of variation due to strong selection
500
Ways we can determine genetic basis of quantitative traits?
1. quantitative trait mapping (2 phenos, linkage map, cross pollinate...etc. flowers!)


2. candidate genes (genes w/ functions known in other organisms)

3. heritability (common garden experiments)