Population Genetics Flashcards

1
Q

What is a VNTR? Diseases associated with VNTRs?

A

A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. Fragile X-Syndrome.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

4 differences to measure genetic diversity:

A
Nucleotide state difference (sequencing)
Length difference (microsatellites)
Functional difference (ABO blood group)
Electrophoretic difference (allozyme)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Hardy–Weinberg Equilibrium

A

p + q =1

p² + q² + 2pq = 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Calculate frequency of an allele?

A

AA Aa aa Calculate frequency of A
5 50 45

((5x2)+50)/200
=(10+60)/200
=70/200
=0.35

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

General form of F statistics equation and what are F statistics?

A

F = 1 - (Ho/He)
Where Ho = Observed heterozygosity
and He = Expected heterozygosity
F statistics describe the statistically expected level of heterozygosity in a population.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Fis

A

Departure from HW within a deme .
Used as a measure of inbreeding. 0 is no inbreeding.
Fis = 1 - (Ho/He)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Fst

A

Departure from HW between demes.
Measures population structure, where 0 is unstructured and panmitic (randomly mating) and 1 is complete isolation and structure.
Fst = 1 - (Hs/Ht)
Fst = 1 - (seperated groups/ one group (i.e. panmitic))

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

% of selfing equation

A

S= (2*Fis)/(1+Fis) = % of offspring arisen from selfing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Inbreeding

A

Causes reduced fitness
Increased homozygosity and reduced heterozygosity
Can determine inbreeding by taking the shortest path (N) from one parent of an individual to the second.
F = (1/2)^N x (1+Fca) , where Fca is the inbreeding coefficient of the common ancestor. Fca is 0 if no inbreeding for common ancestor.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Autozygous

A

Identical by descent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Allozygous

A

Identical by state (i.e. not directly related, but same genetic info)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Demes

A

Group of individuals that belong to the same taxonomic group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Measuring gene flow:

A
  1. Calculation of Nm from Fst
    - Nm is the average number of migrants per generations
    - Lower Fst (less structure) means higher gene flow
  2. Private alleles
    - Alleles that only occur in one population
    - More private alleles = less gene flow
  3. Direct estimates
    - Directly observing migrants moving between populations via marking after birth or the spread of rare alleles etc.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

General effects of gene flow:

A

Causes a reduction in genetic differences between populations.
Causes an increase of genetic variation within population.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Know how to genotype a gel!

A

I.e. if bands appear in both A and a regions then heterozygote, if only in A or a then homozygote of the respective allele.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Purging

A

Natural removing “unfit” individuals and deleterious alleles from a population e.g. in mice.
Leads to a reduction in inbreeding depressions in small populations.

17
Q

Heterosis

A

Heterozygote advantage, commonly used in plant breeding

18
Q

Calculate relative fitness:

A

Selective advantage = Fittest (W) /2nd Fittest (W)
Obs Exp Obs:Exp W(Relative Fitness) Sel. Adv.
AA 29 185 0.1567 0.15/1.15 = 0.13
AB 2993 2601 1.15 1.15/1.15 = 1 1.14
BB 9365 9525 0.983 0.98/1.15 = 0.85

19
Q

Muller’s Ratchet

A

A process in which absence of recombination, especially in an asexual population, results in accumulation of deleterious mutations, irreversibly.
These alleles are compensated for by beneficial ones.

20
Q

Populations have a balance between mutation and BLANK and mutation and BLANK

A

Balance between mutation and drift (production of alleles vs loss of alleles)
Balance between mutation and selection (production of alleles vs purging of alleles)
Note, positive mutations are rare, a small amount is sufficient to sustain a population.

21
Q

Lethal Equivalent

A

A combination of selective effects that on average have the same impact on the composition of the gene pool as one death; for example, two carriers at 50% risk of dying would be the lethal equivalent of one carrier at 100% risk;

22
Q

Mutation-Selection Equilibrium Equations

A
Δqmut = μp :Rate of p mutating to q
μ = mutation rate, p = 1-q, q = freq. of deleterious allele a
Δqsel = (-spq²) / (1-sq²) : rate of change due to selection
S = selection coefficient
23
Q

3 Types of selection

A
  1. Directional
  2. Stabilsing
  3. Diversifying/Disruptive
24
Q

Equation when rate of mutation is equal to rate of selection:

A

q = √(μ/s)

Gives the mutation rate that offsets loss of alleles to keep it in equilibrium

25
Q

Linkage disequilibrium

A

The non-random association of alleles at two or more loci in a general population.
e.g. Disequilibrium = A only paired with B and a only paired with b
D = Pab - Pa*Pb
Pab = Observed haplotype frequency ( Haplotype: set of genetic determinants located on a single chromosome that are usually inherited together.)
With time, linkage disequilibrium (D) decays towards linkage equilibrium (0)
Pa and Pb = Observed allele frequency

26
Q

Absolute Fitness

A

The change in a single genotype in abundance over one generation.
n(t+1) = Wn(t)
n = abundance of a genotype and time “t” and “t+1”
W = Absolute fitness

27
Q

Examples of genetic markers:

A

SNP’s, allozymes, Microsatellites, DNA sequencing

Genetic markers used to track inheritance.

28
Q

Homoplasy

A

A trait/sequence shared by a set of species that is not present in their common ancestor. I.e. obtained from different paths.

29
Q

4 effects of genetic drift on small populations

A
  1. Allele frequency’s fluctuate at random, some disappear, some fluctuate
  2. Reduces genetic variation of the population
  3. Frequency of harmful alleles can increase
  4. Differences between populations can increase
30
Q

Expected loss of heterozygosity after “t” generations

A

ft = 1 - (1-(1/2N)^t
Note:
Initial frequency of a new mutant = 1/2N
Loss of mutant = 1 - (1/2N)

31
Q

Effective Population size

A

Ne =(4𝑁𝑓*𝑁𝑚)/(𝑁𝑚+𝑁𝑓)

32
Q

Neutral Evolution and the Molecular Clock

A
t = d/2k 
d = neutral substitutions
k = rate of accumulation of d
t = generation time

Molecular clock = use of mutation rate to determine the time when two or more life forms diverged.

𝑘=2𝑁𝜇 x 1/2𝑁=𝜇

33
Q

Examples of Directional Selection

A
  1. Size of black bears in Europe
    - Size decreased in interglacial periods
    - Size increased in glacial periods
  2. Beak size of finches
    - Wet years -> More smaller seeds, rarely eat larger seeds
    - Dry years -> Less smaller seeds, eat more larger seeds
    - Beaks specialised to eat specific seed types
  3. Sockeye salmon migration
    - To reproduce salmon migrate to the rivers in which they were born
    - Directional selection is causing salmon to arrive earlier (i.e have an earlier migration timing)
34
Q

Examples of Stabilising Selection

A
  1. Plant height
    - Plant too small -> out-competed for sunlight
    - Plant too tall -> susceptible to wind damage
    - Stabilises plant size at a medium height
  2. Bird clutch size
    - Lay too many eggs -> not enough resources -> death
    - Too little eggs -> minimal offspring production and survival
    - So the birds produce a moderate number of eggs to maximise offspring production and survival.
35
Q

Examples of Diversifying/Disruptive Selection

A
  1. Rabbit fur
    - BB = Black fur, Bb = Grey fur, bb = white fur, incomplete dominance
    - Grey rabbits not camouflaged by either white or black environments and so are more susceptible to predation. This is an example of heterozygote disadvantage.
  2. Peppered moths in London
    - BB = Black moth , Bb = Grey moth, bb = white moth incomplete dominance
    - Black moth camouflaged in industrial buildings
    - White moths camouflaged outside
    - Grey moths are seen in both environments
    - Heterozygote disadvantage