Population Genetics

Question 1

define Evolution

Answer 1

the change in form and/or behaviour of organisms between generations

Question 2

define Natural Selection

Answer 2

the process where some individuals produce more offspring than others, carrying forward their “better” traits that are more favourable to survival and reproduction

Question 3

Natural Selection occurs when there is…

Answer 3

Variance, Selection and Heritability of traits

Question 4

Aristotle (384-322 AD)

Answer 4

looked for evidence of “divine order”. came up with hierarchical arrangement of forms—species arranged linearly along a scale with 1=God, 2=Man, etc.

Question 5

Carolus Linnaeus (1707-1778 AD)

Answer 5

• proposed the nested system of relationships for organisms
• recognized fundamental difference b/w interbreeding within a species vs. non-interbreeding (diff species)
• believed in balance of nature (species had a specific place and would not change or go extinct)

Question 6

Comte du Buffon (1707-1788 AD)

Answer 6

• believed Linnean hierarchy of species relationships, but that there could be divergence over time due to changes in environment AND change could only happen within families

Question 7

Erasmus Darwin (1731-1802 AD)

Answer 7

• believed organisms could improve and adapt to better suit their environment (did not propose a mechanism for this)
• all life consists of “one living filament” connecting all organisms to one common ancestor

Question 8

Jean-Baptiste Lamarck (1744-1829 AD)

Answer 8

• proposed mechanism for inheritance of acquired characteristics
  1st law: use/disuse of a structure leads to its development or diminishment
  2nd law: these acquired traits are heritable
  traits better suited to the environment are favoured and rise in frequency over generations.

Question 9

Thomas Malthus (1766-1834 AD)

Answer 9

principle of overproduction - most organisms produce more offspring than can survive
- populations grow geometrically until they outstrip their food supply and resources.
- major influence on Darwin and Wallace

Question 10

Charles Lyell (1797-1875 AD)

Answer 10

proposed “Uniformitarianism”: the earth is subject to gradual, continuous change but without progress or development (remains at a steady state)

Question 11

Charles Darwin (1809-1882 AD)

Answer 11

Theory of Natural Selection:
- variability exists within species
- variant traits must be inherited
- individuals more suited to their environment will more likely survive
- said that natural selection acting on isolated populations causes them to become increasingly different from each other.

Question 12

Alfred R. Wallace (1823-1913 AD)

Answer 12

discovered Natural Selection independently of Darwin
- realized that natural selection inevitably occurs due to inferior individuals being killed off and the superior ones remaining and reproducing i.e. survival of the fittest

Question 13

Selection

Answer 13

differential (or preferential) survival and/reproduction of individuals with certain genotypes

Question 14

Fitness

Answer 14

the average contribution per parent to the next generation, including survival and reproduction

Question 15

Long term effects: WA = Wa

Answer 15

A allele freq. (p[t]) remains at its initial frequency (p[0])
“neutral”

Question 16

Long term effects: WA > Wa

Answer 16

A allele freq. (p[t]) goes to 1
“Directional Selection” favouring A

Question 17

Long term effects: WA < Wa

Answer 17

A allele freq. (p[t]) goes to 0
“Directional Selection” favouring a

Question 18

selection coefficient

Answer 18

”s” it is the proportional increase in fitness caused by replaced a with A

Question 19

What does the curve look like for the spread of beneficial allele A?

Answer 19

follows an S-shape curve, slowly at first when allele is rare AND when it is common

Question 20

how do weakly favoured alleles spread?

Answer 20

slowly, because they are not strongly favoured

Question 21

Heterozygous Advantage

Answer 21

when heterozygotes (Aa) have 5x the relative fitness compared to homozygotes

Question 22

diploid model without selection

Answer 22

Diploids allele frequencies remain at Hardy-Weinberg proportions in populations with random mating and no selection

Question 23

Polymorphism

Answer 23

when there are multiple different alleles of a single locus existing in a population.
is reached when heterozygous advantage occurs in a population

Question 24

Hardy-Weinberg Equilibrium definition & formulas

Answer 24

a principle stating that genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors (selection, mutation, drift, etc).
p^2 + 2pq + q^2 = 1

Question 25

dominance coefficient

Answer 25

"h" = measures how dominant A is with respect to fitness

Question 26

types of mutations

Answer 26

1. point mutations 2. structural mutations 3. genomic mutations

Question 27

average mutation rate in eukaryotes

Answer 27

rate = 10^(-8) ~ 10^(-10) per basepair per generation

Question 28

"u" (miu)

Answer 28

- symbol for mutation disturbing the wildtype function - "mutation load" being the reduction in fitness due to mutation

Question 29

"v" (nu)

Answer 29

- mutation restoring wildtype function - increase in fitness due to mutation

Question 30

q when h>0

Answer 30

not recessive q=u/hs

Question 31

q when h=0

Answer 31

recessive q=sqrt(u/s)

Question 32

Diploid fitness (mutation with selection)

Answer 32

WAA = 1 WAa = 1 - hs Waa = 1 - s

Question 33

if h = 0

Answer 33

mutation is recessive

Question 34

if h = 1

Answer 34

mutation is dominant

Question 35

define Genetic Drift

Answer 35

- the change in allele frequencies that results from random sampling processes that take place in populations over generations - drift is always acting on populations (so long as they are finite) - drift results in the loss or fixation of an allele, even in large populations

Question 36

is genetic drift a random process?

Answer 36

Yes, however some of its behaviours are predictable.

Question 37

does population size influence rate of genetic drift?

Answer 37

Yes in smaller populations, changes in allele frequencies from one generation to the next are greater as population size increase, allele frequencies are expected to remain polymorphic for longer i.e. larger populations are better able to retain genetic variation

Question 38

in a diploid population, what is the probability that a neutral allele fixes?

Answer 38

the probability that a neutral allele A will fix is equal to its initial frequency p

Question 39

what is the amount of time it takes for a single allele to fix?

Answer 39

2N generations with N number of haploid individuals 4N generations with N number of diploid individuals

Question 40

defin Coalescence time

Answer 40

how far you must go back in time to find the most recent common ancestor for a shared allele

Question 41

define Expected Heterozygosity

Answer 41

the probability that two alleles drawn at random are different alleles (in both haploids and diploids). H[t] = 2p[t]q[t] = 2pq

Question 42

how does H[t] (expected heterozygosity) change over time due to drift?

Answer 42

H[t] = (1-1/(2N))H[t-1]

Question 43

define Founder Effects

Answer 43

effects that occur as a result of a new population being founded by a small number of individuals from a larger population - small set of genes in the genetic pool for the population to be built on

Question 44

define Population Bottleneck

Answer 44

a severe reduction in the number of individuals in a population, resulting in a loss of genetic variation in the surviving population - can result in inbreeding, with there being few individuals the chance that two alleles recently shared a common ancestor is much higher

Question 45

what is the probability of fixing a new mutation in a large population?

Answer 45

2s in haploids 2hs in diploids - the fate of an allele in a diploid population is determined more by selection than by drift.

Question 46

define (Linkage) Disequilibrium

Answer 46

measures the genetic associations among two loci, indicating which alleles tend to be found together in an individual D = XAB*Xab - XAb*XaB *note that the loci do not need to be physically linked, they can be on different chromosomes

Question 47

if D>0

Answer 47

positive disequilibrium means its more common to see in individuals of A with B, a with b.

Question 48

if D<0

Answer 48

negative disequilibrium means its more common to see individuals of A with b, a with B

Question 49

define Recombination Rate

Answer 49

"r" = rate between two loci that determines the probability of a cross-over event between them, creating non-parental gametes also the distance between two loci (very hard to determine)

Question 50

what causes Linkage Disequilibrium?

Answer 50

several processes cause associations between loci including - Drift - Mutation - Migration - Selection

Question 51

if there's no selection, mutation, or drift can allele frequencies still change?

Answer 51

Yes, if there are genetic associations between alleles (D). Evolutionary change occurs due to mixing of alleles because of recombination. Genetic associations decay by a factor of (1-r)

Question 52

how do genetic associations decay?

Answer 52

Genetic associations decay by a factor of (1-r). They persist for longer if loci sites are closer (low r)

Question 53

how does selection effect sites that are in disequilibrium?

Answer 53

- selection on one gene site causes changes to other nearby sites linked to that gene. - if selection is stronger, the selected allele rises in frequency faster and brings its associated gene loci with it (until they're separated by recombination).

Question 54

if both sites are under selection, how does fitness change?

Answer 54

- mean fitness can decline over time due to the combined effects of selection and recombination

Question 55

what is genetic hitchhiking?

Answer 55

- when neighbouring alleles in the genome are dragged with selected alleles in increased or decreased fitness due to selection (alleles that are in linkage disequilibrium). - when there is Linkage Disequilibrium between a selected locus and neutral locus, causing the neutral allele to change in frequency.