Linkage Disequilibrium Practice Problems

X-linked recessive traits in humans (or in Drosophila) are observed ________.

In more males than females

The first suggestion that chromosomes may physically exchange segments came from the microscopic identification of ________.

Chiasmata

Which recombination frequency corresponds to independent assortment and the absence of linkage:

A. 0

B. 0.25

C. 0.50

D. 0.75

C. 0.50

Which recombination frequency corresponds to perfect linkage and violates the law of independent assortment:

A. 0

B. 0.25

C. 0.50

D. 0.75

A. 0

T/F: Linkage disequilibrium only occurs between alleles that are on the same chromosome.

False

Which of the following types of chromosomes are capable of recombination:

A. Homologous chromosomes

B. Autosomes

C. Sex chromosomes

D. Analogous chromosomes

A. Homologous chromosomes

T/F: D < 0 indicates that two alleles are in linkage disequilibrium.

True

Which of the following could cause LD between two loci? Select ALL that apply:

A. None of these

B. Selection

C. Inbreeding

D. Genotyping error

B. Selection

C. Inbreeding

D. Genotyping error

T/F: If two alleles are in linkage disequilibrium, then their D > 0.

False

T/F: Two loci in LD will return to linkage equilibrium after one generation of random mating.

False

T/F: If D > 0, then two alleles are in linkage disequilibrium.

True

Which of the following would be a good indication that two loci are in linkage disequilibrium?

a. dN/dS = 1

b. dN/dS =/= 1

c. D = 0

d. D =/= 0

d. D =/= 0

Aspergillus fumigatus is the leading fungal pathogen for individuals with suppressed immune systems and causes a 90% mortality rate for this population. A global analysis of A. fumigatus genetics found high levels of linkage disequilibrium among genes related to antifungal resistance, but low linkage disequilibrium among genes related to environmental tolerance. Which of the following conclusions is best supported by these observations:

A) The D value for antifungal resistance is > 0.

B) Antifungal resistance is a selective force in all environments.

C) A. fumigatus has undergone a recent bottleneck.

D) Environmental resistance genes are hitch-hiking with antifungal resistance genes.

A) The D value for antifungal resistance is > 0.

Interleukin-18 (IL-18) is a gene responsible for the production of certain inflammatory white blood cells. The most beneficial haplotype (e.g. the one that causes the least inflammation) is GTATA. What inference can be drawn from the data of IL-18 haplotype frequency in Africa?

a. Migration between North Saharan Africa and South Saharan Africa is high.

b. Carriers of the GTATA haplotype are more common in North Saharan Africa than South Saharan Africa

c. The GTATA haplotype has undergone strong positive selection

d. The GTATA haplotype is a hitch-hiker allele

b. Carriers of the GTATA haplotype are more common in North Saharan Africa than South Saharan Africa

Class II MHC proteins are responsible for antigen binding by immune cells. Although each person has numerous copies of the Class II MHC protein, each copy has high LD within it. Which of the following is a likely consequence of high LD in alleles of this protein:

A) The immune system is able to recognize the same (or very similar) antigens should they appear again because binding history is preserved.

B) The immune system is able to produce a wide variety of Class II MHC proteins.

C) Mutation rate of class II MHC proteins increases.

D) Humans are more vulnerable to drift than other species.

B) The immune system is able to produce a wide variety of Class II MHC proteins.

Schmidt-Küntzel et al (2018) inferred the time of divergence among large cats using Coalescence Methods. Is the deep divergence time of cheetahs indicative of a large population that has shrunk or a small population that has grown? Explain.

1 – Growing population

2 – Divergence appeared a long time ago, resulting in more variation than expected by chance.

Gold coral (Savalia savaglia) form many important reefs in the Mediterranean Sea. Consequently, Poliseno and colleagues (2022) sought to understand the population dynamics of this species (figure above). Based on the data, which conclusion is best supported:

a. Shallow populations have more admixture than deep populations.

b. Shallow populations have more linkage disequilibrium than deep populations.

c. Shallow populations have more adaptations than deep populations.

d. Shallow populations have more acclimation than deep populations.

b. Shallow populations have more linkage disequilibrium than deep populations.

Eastern Rock Lobster (Sagmariasus verreauxi) is an important commercial fishery in New South Wales, Australia. Consequently, Woodings and colleagues (2021) sought to understand the population dynamics of this species (figure above). Based on the data, which conclusion is best supported:

a. All three populations have D<0.

b. The SWR population has higher linkage disequilibrium than the PMC and FOR populations.

c. The SWR population is more adapted to Australian waters than the PMC or FOR populations.

d. The SWR population is more acclimated to Australian waters than the PMC or FOR populations.

b. The SWR population has higher linkage disequilibrium than the PMC and FOR populations.

Reich and colleagues (2001) measured the absolute value of linkage disequilibrium (|D’|) for populations of humans in Utah, United States and Nigeria. Which of the following conclusions is supported by their data as presented above:

a. Nigerians have randomly mated longer than Utahans.

b. Nigerians are under stronger selective pressures than Utahans.

c. Nigerians have had lower rates of migration than Utahans.

d. None of the above.

a. Nigerians have randomly mated longer than Utahans.

Myers (2021) calculated the D statistic for 4 species of snakes at once. The D value is shown as the dot with standard error bars above. Values in black were not significant while values in red were significant. Negative values indicated LD between the second and third species listed whereas positive values indicated LD between the first and third species listed. Which of the following hypotheses is supported by this data:

a. More than half of the snake species in this study showed evidence of gene flow and recent admixture.

b. Less than half of the snake species in this study showed evidence of gene flow and recent admixture.

a. More than half of the snake species in this study showed evidence of gene flow and recent admixture.

Myers (2021) wanted to know if distance affected the amount of gene flow between rattlesnakes in California. To answer this question, they calculated the D statistic for pairs of individuals (C. scutulatus and C. virdis or C. tigris and C. cerberus) and plotted this score relative to the geographic distance from which the specimens were collected. Which hypothesis was supported by the data as shown to the left?

a. In general, more distant individuals tended to have less migration.

b. In general, more distant individuals tended to have less mutation.

c. In general, more distant individuals tended to have more migration.

d. In general, more distant individuals tended to have more mutation.

a. In general, more distant individuals tended to have less migration.

Lu et al (2016) collected genomic samples of loblolly pines across the American Southeast. They were interested in studying whether populations were primarily outbreeding or inbreeding for this commercially important species. In the figures below, the graphs on the left (a and c) were based on identifying just two populations (east and west of the Mississippi River) whereas the graphs on the right (b and d) were based on identifying 7 populations (approximately one population per two states). Which of the following conclusions is supported by this data? Select ALL that apply:

a. There is substantial gene flow between east of the Mississippi and west of the Mississippi populations.

b. There is substantial gene flow within populations east of the Mississippi.

c. There is substantial gene flow within populations west of the Mississippi.

d. The Mississippi River Valley represents an important hybridization ground for east and west populations.

b. There is substantial gene flow within populations east of the Mississippi.

c. There is substantial gene flow within populations west of the Mississippi.

The figure above, by Yang et al (2014), shows the LD of nine-spined stickleback fish across five habitats (CF is short for coastal freshwater where freshwater outputs mix with marine waters). D’ is the absolute value of D so that all of the D values are positive. Which of the following inferences are supported by this data:

a. The effective population size for marine and CF habitats is larger than freshwater habitats (lake, pond, and river).

b. Selection is a stronger force in freshwater habitats than in marine and CF habitats.

c. Stickleback fish in pond habitats admix more than any other population.

d. Stickleback fish from CF habitats have the largest genomes of any population.

a. The effective population size for marine and CF habitats is larger than freshwater habitats (lake, pond, and river).

Above are LD heat maps for nine genes in a widespread species of cotton bollworm that may be related to environmental adaptation. Song et al (2015) were interested in understanding the genetic reasons for this agricultural pest becoming so common. Which of the 9 genes above would be the best target for further investigation to identify a gene under positive selection?

a. Apt

b. Cycle

c. Cyp303a1

d. Tc

e. Tpi

c. Cyp303a1

Kemper et al (2011) were searching for genetic markers of worm resistance among populations of domesticated sheep. Plotting the LD of four populations (see inset in top right corner), which of the following best explains the high LD for markers that were <0.1 distance apart:

a. There is stronger selection for alleles that are close together.

b. There is lower recombination for alleles that are close together.

c. There is greater inbreeding amongst populations with alleles that are close together.

b. There is lower recombination for alleles that are close together.