Genetic Linkage

Question 1

what does genetic linkage mean?

Answer 1

there is a physical linkage between alleles on a chromosomes which makes the likelihood of them being inherited simultaneously very large.

Question 2

what is the type of segregation seen between loci on different chromosomes?

Answer 2

there is independent segregation- each allele from each parents has the same probability of appearing together in the gamete- the probability of AB:Ab:aB:ab is 1/4:1/4:1/4:1/4

Question 3

when does genetic linkage occur?

Answer 3

when genes are present on the same chromosome and are likely to be inherited together unless recombination occurs

Question 4

what are the expected genotype frequencies if there is no linkage between two loci in a gamete?? How does this change when there is linkage?

Answer 4

the respective p and q values multiplied- when there is linkage there is a disequilibrium between the frequencies of certain combinations- deviation is called D and is either positive or negative- there is normally an excess of the parents genotypes and defficient recombinants

Question 5

what is linkage disequilibrium?

Answer 5

the linkage disequilibrium is presented as D. the deviation in the values of observed allele frequencies and expected allele frequencies. If you consider two loci, the segregation of the alleles present at these loci into gametes will be random and independent from each other if there is no linkage. However, if there is linkage then the expected values of genotype frequency, which are based on the HW values for each allele, will deviate from the observed values. the amount that is does this by is D

Question 6

what does the value of D vary between and why?

Answer 6

-0.25 and 0.25. if no recombination has occurred at all then there will only be two genotypes which will both have the frequency of 0.5 (each taking the 0.25 from on of the other genotypes) but the more linkage that has occurred the more recombination has occurred

Question 7

what is the definition of linkage equilibrium and disequilibrium?

Answer 7

inkage disequilibrium is the non-random association of alleles at different loci i.e. the presence of statistical associations between alleles at different loci different from what would be expected if alleles were independently, randomly sampled based on their individual allele frequencies.[1] If there is no linkage disequilibrium between alleles at different loci they are said to be in linkage equilibrium.

Question 8

what is C in terms of recombination? what are its value ranges?

Answer 8

Recombination fraction (also called recombination frequency) between two loci is defined as the ratio of the number of recombined gametes to the total number of gametes produced. Recombination fraction, has a domain of 0 r 0:5, with r D 0 indicating perfect linkage and r D 0:5 meaning complete independence of the two loci.

Question 9

how do you calculate disequilbirium over time?

Answer 9

dt= do (-c) ^t

Question 10

what experimental evidence shows recombination and the achievement of linkage equilibrium over time?

Answer 10

use 2 populations of drosophila. one population has a positive association between and AB alleles meaning that they are always together and the other population has a negative association between AB meaning theses allies are never together. after 50 generations there was almost complete recombination between the loci

Question 11

what determine the strength of linkage between two loci?

Answer 11

their distance apart- the closer the loci the more likely the linkage disequilibrium value

Question 12

what are the two way in which linkage interacts with selection?

Answer 12

positive selection at one loci causes the other to “hitch hike”
the Hill-Robertson effect in which there is positive selection for one loci and negative selection for its linked loci

Question 13

explain how linkage between loci can cause ‘genetic hitchhiking”

Answer 13

it a mutation occurs at a loci that increases its S value then it will be selected for, the loci which are situated close to it will have a low recombination frequency and therefore likely to be inherited when the beneficial mutation is inherited- this is called a selective sweep

Question 14

what is a selective sweep?

Answer 14

A selective sweep is the reduction or elimination of variation among the nucleotides in neighboring DNA of a mutation as the result of recent and strong positive natural selection.

Question 15

what is background selection?

Answer 15

Background selection describes the loss of genetic diversity at a non-deleterious locus due to purifying selection against linked deleterious alleles
when deleterious mutations are selected out of the population causing drift at linked sites- drift because frequency of allele at linked loci not determined by its fitness, just its linkage

Question 16

what is the hill robertson effect?

Answer 16

at locus 1 a beneficial mutation occurs and its selected for, locus 1 is linked to locus 2. locus 1 is selected for and therefore locus 2 hitchhikes along generations. However, in an individual who does not posses the beneficial mutation a1 locus 1 and instead has a wild type locus 1, at locus 2 a beneficial mutation arises therefore this locus 2 which a wt locus 1 is selected for this means there is a clash between the two genotypes in the population: beneficial l1+wt l2 vs. wt l1 vs beneficial l2. this causes interference between fixation

Question 17

give an example of linkage between loci and selection in nature

Answer 17

human lactase persistence (adults producing lactase)
why many dont do this is because they cant digest milk as adults- missing lactase- expressed in the young and in the adults but sometimes not in the adults
number of mutations that lead to the consistent expression of these genes in aduts
a particular site -snp- that is associated with lactose persistence
different haplotypes were compared- those that have persistent allele of snp tend to share a lot of sequence left and right to each other

Question 18

what is the hill robertson effect?

Answer 18

Consider a population of individuals whose genome has only two genes, a and b. If an advantageous mutant (A) of gene a arises in a given individual, that individual’s genes will through natural selection become more frequent in the population over time. However, if a separate advantageous mutant (B) of gene b arises before A has gone to fixation, and happens to arise in an individual who does not carry A, then individuals carrying B and individuals carrying A will be in competition. If recombination is present, then individuals carrying both A and B (of genotype AB) will eventually arise. Provided there are no negative epistatic effects of carrying both, individuals of genotype AB will have a greater selective advantage than aB or Ab individuals, and AB will hence go to fixation. However, if there is no recombination, AB individuals can only occur if the latter mutation (B) happens to occur in an Ab individual. The chance of this happening depends on the frequency of new mutations, and on the size of the population

Question 19

how can you see the hill robertson effect in nature?

Answer 19

The y chromosome has a lot of inversions which case linkage between traits that cause maleness and traits that support maleness- however when deleterious mutations arise they can’t be selected out- the y chromosome is full of deleterious mutations
and in transposable elements

Question 20

how do transposable elements demonstrate the hill robertson effect?

Answer 20

in areas where there is low recombination in drosophila- Transposable elements can accumulate and not be selected out, if they are linked to beneficial alleles then they will hitch hike with them because there is interference between the positive selection of the loci and the negative of the transposable element-

Question 21

give an example of linkage in nature

Answer 21

primrose. natural populations consist of almost entirely pin and thum plants. pin phenotypes have long style and short stamens and thum have short styles and long stamens. very rarely is there long stamen and a long style. this is because the two traits are linked: pin have ga/ga and thrum have GA/ga. an intermeidate is fromed which has both through recombination: gA/ga.