Genetic Variation

Question 1

What are the 3 ways variation can effect fitness?

Answer 1

beneficial (or advantageous)
deleterious
neutral

Question 2

T or F: there can be a large range of fitness effects

Answer 2

true, for example, deleterious mutations can be highly deleterious (lethal or sterile) to only slightly deleterious

Question 3

What does it mean to call an allele advantageous/beneficial?

Answer 3

the allele increases fitness of an individual

Question 4

What does it mean to call an allele deleterious?

Answer 4

the allele decreases fitness of an individual

Question 5

What does it mean to call an allele neutral?

Answer 5

the allele has no effect on fitness

Question 6

What does it mean to call an allele slightly beneficial?

Answer 6

the allele slightly increases fitness of the individual

Question 7

What does it mean to call an allele slightly deleterious?

Answer 7

the allele slightly decreases fitness

Question 8

Are most new mutations beneficial, deleterious, or neutral? What is the evidence / how can this be inferred?

Answer 8

deleterious

evidence??

Question 9

Are most mutations that persist (what we see, ex. polymorphism) beneficial, deleterious, or neutral? what is the evidence / how can this be inferred?

Question 10

What is the difference between new mutations and mutations that persist?

Answer 10

new mutations do not necessarily persist

Question 11

What are the 3 influential hypotheses covered in this class about the nature of genetic variation? Who is associated with each one?

Answer 11

Classical hypothesis - Hermann Muller
Balance hypothesis - Theodosius Dobzhansky
Neutral theory of molecular evolution - Motoo Kimura

Question 12

What was the basic idea of Muller’s classical hypothesis?

Answer 12

genetic variation is uncommon and mostly harmful (mostly deleterious mutations)

Question 13

What was the basic idea of Dobzhansky’s balance hypothesis?

Answer 13

genetic variation is abundant and favoured and heterozygosity is a positive

Question 14

What was the basic idea of Kimura’s neutral theory of molecular evolution?

Answer 14

lots of genetic variation exists, but most of it has little effect on fitness (neutral or slightly beneficial/deleterious)

Question 15

Describe the results from genome sequencing the Drosophila melanogaster reference panel line

Answer 15

200+ Drosophila melanogaster flies from the same region of North Carolina were collected and used to create the genetic reference panel lines

later, the genomes from the panel lines were sequenced

results:
LOTS of genetic variation (SNPs and other variants) and autosomal inversions
even the length of the genomes ranged dramatically

Question 16

Which of the 3 hypotheses was correct? or more correct? what are the valuable contributions of these?

Answer 16

they were all kind of right

Muller was right in that deleterious mutations are important, but wrong because variation was more common than he predicted

Dobzhansky was kind of right in that there’s lots of variation, but he predicted more than there is

Kimura was right because neutral mutations are important and genetic drift is a force of evolution

Question 17

What does the amount of genetic variation we see depend on?

Answer 17

the species and/or population - some species or populations have more variation than others

the phenotype - does the phenotype affect fitness?
- some genes may have more variation than others

the region of the genome/chromosome
- there may be variations between Y chromosomes and X chromosomes

Question 18

What are the 5 major forces in biological evolution?

Answer 18

1. genetic drift / random sampling (chance events related to population size)
2. natural selection
3. mutation
4. recombination (ex. differences in patterns of genomes)
5. migration and gene flow

Question 19

What is the Hardy-Weinberg equilibrium (HWE) principle?

Answer 19

demonstrates that in the absence of evolution, genetic variation stays constant

variation staying constant is a result of Mendelian inheritance

Question 20

What can we use the HWE for (why is it useful)?

Answer 20

it can allow us to predict genotype and allele frequencies from each other and from one generation to the next

it can also be used as a baseline comparison (basically a null model) to show whether evolution has occurred = deviations from the HWE imply evolution

Question 21

What are the 10 major assumptions of the HWE?

Answer 21

HWE requires:

1. diploid organisms
2. sexual reproduction
3. non-overlapping generations
4. two alleles
5. the allele frequencies to be equal in males and females
6. random mating occurs
7. (infinite) large population size
8. no migration
9. no mutation
10. no natural selection

Question 22

What is the HWE equation based on?

Answer 22

the allele and genotype frequencies in zygotes of one population in one generation

Question 23

What is the HWE equation?

Answer 23

p^2 + 2pq + q^2 = 1

Question 24

What are the HWE genotype frequencies? what does the prime (‘) mean?

Answer 24

AA’ = p^2
Aa’ = 2pq
aa’ = q^2

ex. AA’ = AA frequency in the next generation

Question 25

What is the allele frequency in zygotes? does it differ between the first generation and the next?

Answer 25

p’ = p

the frequency of A allele does not change between generations (ie., no evolution has occurred)

Question 26

What are the symbols for allele frequencies and genotype frequencies?

Answer 26

allele frequencies:
A = p(hat)
a = q(hat)

genotype frequencies:
P(hat)AA
P(hat)Aa
P(hat)aa

Question 27

How do you estimate the allele frequencies?

Answer 27

use p(hat) to estimate frequency of A allele

p(hat) = (AA(2) + Aa) / n(2)

where:

AA is the # of individuals with AA genotype
Aa = # of individuals with Aa genotype

AA x 2 because there’s 2 A alleles in AA genotype
Aa x 1 because 1 A allele in Aa
n(2) because individuals are diploid so they carry 2 copies of alleles

q(hat) = 1-p(hat)

ex. 338 people, 265 CC, 66 Cc, 7 cc

p(hat) = (265(2) + 66) / 338(2) = 0.882
q(hat) = 1 - 0.882 = 0.118

Question 28

How do you estimate the genotype frequencies?

Answer 28

use allele frequencies and their probabilities and multiply by the amount of individuals in the sample

P(hat)AA = p^2 x n
P(hat)Aa = 2pq x n
P(hat)aa = q^2 x n

ex)
P(hat)CC = p^2 = (0.882)^2 = 0.778 x 338 people = 262.9

P(hat)Cc = 2pq = 2(0.882*0.118) = 0.208 x 338 people = 70.4

P(hat)cc = q^2 = (0.118)^2 = 0.014 x 338 people = 4.7

Question 29

How do you estimate allele frequencies when the homozygous and heterozygous genotypes cannot be distinguished (A is completely dominant over so AA and Aa look identical)?

Answer 29

estimate from the homozygous recessive genotype (aa)

use q(hat) instead of p(hat)

Question 30

What is a famous example of the complications of dominance?

Answer 30

the melanic moth in polluted England phenotype results from a dominant A allele

Question 31

If 87% of moths in polluted England are melanic. What are the approximate allele frequencies of the dominant A allele and the heterozygote Aa?

Answer 31

AA and Aa = 0.87
aa = 1-0.87 = 0.13

use q(hat) and allele a:

Q(hat)aa = q^2 = 0.13
sqrt (0.13) = 0.36

1 - Q(hat)aa = 1-0.36 = 0.64
P(hat)AA = p^2 = (0.64)^2 = 0.41

P(hat)Aa = 2pq = 2(0.64*0.13) = 0.46

AA frequency = 0.41
Aa frequency = 0.46
aa frequency = 0.13

Question 32

What is on the x-axis of a pop G simulation?

Answer 32

Time in generations (number of generations)

Question 33

What is on the y-axis of a pop G simulation?

Answer 33

P(A) - probability of A occurring = frequency of the A allele

Question 34

What are the different parameters that can be altered on popG?

Answer 34

population size
fitness of AA genotype
fitness of Aa genotype
fitness of aa genotype
mutation from A to a
mutation from a to A
migration rate
initial frequency of A allele
# generations
# populations
random number seed

Question 35

What does the blue line of no genetic drift mean in popG?

Answer 35

Means no genetic drift has occurred, ie., allele frequencies are not being changed my chance events

Question 36

What is the raw material of evolution?

Answer 36

mutations