Genetic Variation Flashcards
What are the 3 ways variation can effect fitness?
beneficial (or advantageous)
deleterious
neutral
T or F: there can be a large range of fitness effects
true, for example, deleterious mutations can be highly deleterious (lethal or sterile) to only slightly deleterious
What does it mean to call an allele advantageous/beneficial?
the allele increases fitness of an individual
What does it mean to call an allele deleterious?
the allele decreases fitness of an individual
What does it mean to call an allele neutral?
the allele has no effect on fitness
What does it mean to call an allele slightly beneficial?
the allele slightly increases fitness of the individual
What does it mean to call an allele slightly deleterious?
the allele slightly decreases fitness
Are most new mutations beneficial, deleterious, or neutral? What is the evidence / how can this be inferred?
deleterious
evidence??
Are most mutations that persist (what we see, ex. polymorphism) beneficial, deleterious, or neutral? what is the evidence / how can this be inferred?
What is the difference between new mutations and mutations that persist?
new mutations do not necessarily persist
What are the 3 influential hypotheses covered in this class about the nature of genetic variation? Who is associated with each one?
Classical hypothesis - Hermann Muller
Balance hypothesis - Theodosius Dobzhansky
Neutral theory of molecular evolution - Motoo Kimura
What was the basic idea of Muller’s classical hypothesis?
genetic variation is uncommon and mostly harmful (mostly deleterious mutations)
What was the basic idea of Dobzhansky’s balance hypothesis?
genetic variation is abundant and favoured and heterozygosity is a positive
What was the basic idea of Kimura’s neutral theory of molecular evolution?
lots of genetic variation exists, but most of it has little effect on fitness (neutral or slightly beneficial/deleterious)
Describe the results from genome sequencing the Drosophila melanogaster reference panel line
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
Which of the 3 hypotheses was correct? or more correct? what are the valuable contributions of these?
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
What does the amount of genetic variation we see depend on?
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
What are the 5 major forces in biological evolution?
- genetic drift / random sampling (chance events related to population size)
- natural selection
- mutation
- recombination (ex. differences in patterns of genomes)
- migration and gene flow
What is the Hardy-Weinberg equilibrium (HWE) principle?
demonstrates that in the absence of evolution, genetic variation stays constant
variation staying constant is a result of Mendelian inheritance
What can we use the HWE for (why is it useful)?
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
What are the 10 major assumptions of the HWE?
HWE requires:
- diploid organisms
- sexual reproduction
- non-overlapping generations
- two alleles
- the allele frequencies to be equal in males and females
- random mating occurs
- (infinite) large population size
- no migration
- no mutation
- no natural selection
What is the HWE equation based on?
the allele and genotype frequencies in zygotes of one population in one generation
What is the HWE equation?
p^2 + 2pq + q^2 = 1
What are the HWE genotype frequencies? what does the prime (‘) mean?
AA’ = p^2
Aa’ = 2pq
aa’ = q^2
ex. AA’ = AA frequency in the next generation
What is the allele frequency in zygotes? does it differ between the first generation and the next?
p’ = p
the frequency of A allele does not change between generations (ie., no evolution has occurred)
What are the symbols for allele frequencies and genotype frequencies?
allele frequencies:
A = p(hat)
a = q(hat)
genotype frequencies:
P(hat)AA
P(hat)Aa
P(hat)aa
How do you estimate the allele frequencies?
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
How do you estimate the genotype frequencies?
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
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)?
estimate from the homozygous recessive genotype (aa)
use q(hat) instead of p(hat)
What is a famous example of the complications of dominance?
the melanic moth in polluted England phenotype results from a dominant A allele
If 87% of moths in polluted England are melanic. What are the approximate allele frequencies of the dominant A allele and the heterozygote Aa?
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
What is on the x-axis of a pop G simulation?
Time in generations (number of generations)
What is on the y-axis of a pop G simulation?
P(A) - probability of A occurring = frequency of the A allele
What are the different parameters that can be altered on popG?
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
What does the blue line of no genetic drift mean in popG?
Means no genetic drift has occurred, ie., allele frequencies are not being changed my chance events
What is the raw material of evolution?
mutations
