Midterm 1

Question 1

Population Genetics

Answer 1

The study of genetic composition of a population and processes that shape the composition.

Question 2

What is the common goal of population genetics research?

Answer 2

To deduce process from composition.

Question 3

What is a population?

Answer 3

A group of individuals of the same species that occupy an area.

Question 4

What is genetic composition?

Answer 4

Genotype counts, genotype frequencies, nucleotide frequencies, haplotype freq., others.

Question 5

Genotype Counts

Answer 5

Number of genotypes in the population.

Question 6

What are the processes that effect genetic compisition?

Answer 6

• Selection, mutation, random genetic drift, dispersal/migration
• Recombination, horizontal gene transfer, insertions/deletions

Question 7

MIC

Answer 7

Minimum inhibitory concentration
- Lowest of the antibiotic yielding no
visible growth

Question 8

MSC

Answer 8

Minimum selective concentration
- [ ] of antibiotic that resistant and
susceptible genotypes have equal
fitness - where the lines cross

Question 9

Traditional Selective Window

Answer 9

Range of antibiotic concentrations
considered high enough, such that
resistant genotype outcompetes susceptible

Question 10

Sub-MIC Selective Window

Answer 10

Additional range of antibiotic concentrations when resistant genotype outcompetes susceptible.

Question 11

Absolute Fitness

Answer 11

A parameter that predicts (or predicts in part) the growth in numbers of a generatio.

Question 12

What is the difference between growth rate (r), and absolute fitness (λ)

Answer 12

Growth Rate (r) - Continuous
Absolute Fitness (λ) - Finite rate of increase, discrete time.

Question 13

Relative Fitness (ω)

Answer 13

Absolute fitness of a genotype divided by the absolute fitness of a standard (reference) genotype.

Question 14

Selection coefficient (s)

Answer 14

Proportional increase (s>0) or decrease (s<0) in relative fitness of a genotype relative to the reference.

Question 15

MSC occurs when s = ?
resistant and susceptible genotypes have ____ fitness

Answer 15

s = 0
resistant and susceptible genotypes have EQUAL fitness

Question 16

Where would you observe MSC on a graph?

Answer 16

Where the line crosses line on graph or where the two lines transect

Question 17

Population Structure

Answer 17

The nonrandom distribution of genotypes geographically due to limited dispersal or local adaptation.

Question 18

Geographic variation in frequency is an indicator of ____ because…

Answer 18

Population structure because it shows limited dispersal.

Question 19

What is segregating site (S)

Answer 19

A nucleotide site in a sample that is variable

Question 20

Balancing Selection

Answer 20

Two or more genotypes selectively maintained in a population.
- Build up of mutations along deep branches increases π = lots of pairwise differences
- negative frequency dependent selection

Question 21

Selective Sweep

Answer 21

Recent beneficial genotype arises and rapidly increases.
- short time scale
- unique mutations
- few pairwise differences (nucleotide differences are small)

Question 22

π - S/a > 0

Answer 22

Balancing Selection
- a = the summation of 1/k

Question 23

π - S/a < 0

Answer 23

Selective Sweep
- a = the summation of 1/k

Question 24

π - S/a = 0

Answer 24

No selection

Question 25

In an ancestral recombination graph upstream goes...

Answer 25

Left

Question 26

In an ancestral recombination graph downstream goes...

Answer 26

Right

Question 27

Recombination can result in _____ coalescent histories for _____ regions of the genome

Answer 27

different

Question 28

Describe Model-based gene tree estimation and it's goal

Answer 28

Model-Based - ML - Bayesian Goal: Estimate history if common descent Share ancestor w each-other before sharing ancestor w other lineages.

Question 29

Distance-based gene tree estimation

Answer 29

Distance-based - UPGMA - Neighbour-joining Goal: Cluster sequences based on genetic similarity Genetically more similar to each other compared to other lineages

Question 30

What is more probable: a transition or a transversion?

Answer 30

Transition is more probable than transversion.

Question 31

T or F: for teo lineages to coalesce they must be in the same deme?

Answer 31

True

Question 32

Do we expect genotypes sampled in the same deme to coalesce with each other first, before coalescing with genotypes sampled in a different deme when: N<

Answer 32

Yes

Question 33

Do we expect genotypes sampled in the same deme to coalesce with each other first, before coalescing with genotypes sampled in a different deme when: N > T, m = 0

Answer 33

No

Question 34

Do we expect genotypes sampled in the same deme to coalesce with each other first, before coalescing with genotypes sampled in a different deme when: N < T, m = 0.1

Answer 34

No

Question 35

Random Genetic Drift

Answer 35

Changes in genotypes frequencies due to random sampling in finite populations.

Question 36

Explain the birth death process

Answer 36

1. Random individual gives birth 2. Random individual dies

Question 37

Explain how gene trees can be used to detect recombination across the genome of a population of viruses

Answer 37

If different regions of a genime have different coalescent histories, then this is evidence for recombination between regions

Question 38

can individuals coalesce while they are in different demes?

Answer 38

No

Question 39

Explain why we expect drift to be greater in small versus large populations

Answer 39

There is a greater change in genotype frequency in when you add or remove one genotype in small populations which is consistent with drift being greater.

Question 40

Why do we expect selection to be more efficient in a large versus a small population?

Answer 40

In smaller populations a decrease by 1 copy lowers the frequency of the genotype to a greater extent than the larger population which is going against the direction of selection.

Question 41

Why is it the extremes of genotype frequencies produce similar probabilities of not changing during a birth death event?

Answer 41

Because when a genotype is at high frequency, it is likely to be picked both to reproduce and die during a birth death event, so genotype frequencies are not expected to change too much

Question 42

Why are intermediate frequencies a lower probability of unchanging during a birth death event?

Answer 42

This is because when a genotype is an intermediate fequency, it is more likely that a different genotype is chosen to reproduce versus die, so genotype frequencies are more likely to change.