R16 patterns of genetic variation

Question 1

What are the types of genetic variation ?

Answer 1

• Single nucleotide polymorphism (SNPs)
  o Single point mutations leading to variation
  o Sickle cell anaemia is an example of this
• Insertion and deletions (INDELs)
  o Slippage of one of the strands leads to insertion or deletion
  o Slippage in the nascent or template led to insertion
  o Transposable elements
• Copy number variants (CNVs)
  o Identical repeating sequences
• Large structural variants (rearrangements)
  o Deletion, duplication, inversion, fission or fusion of chromosomes
  o Can lead to a huge change in phenotype and inheritance as one unit

Question 2

How does genetic variation arise?

Answer 2

Mutations

Question 3

How do we measure diversity using pi ?

Answer 3

pi = number of nucleotide differences between pair wise sequences / number of sequence comparisons x number of sites

Question 4

How is allele frequency calculated ?

Answer 4

frequency of a specific allele / total number of alleles

Question 5

What is the null model?

Answer 5

Hardy-Weinburg equilibrium

Question 6

What is hardy-weinberg ?

Answer 6

• In sexual, diploid, non-overlapping generations
• Where p and q represent allele frequencies of two alleles
• In randomly mating populations, expected frequencies of:
  o Hetereozygous – 2pq
  o Homozygous dominant – p^2
  o Homozygous recessive – q^2

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

Question 7

What may cause deviations from hardy-weinberg ?

Answer 7

non-random mating (assortative/disassortative mating), inbreeding, mutation, selection, drift, migration

Question 8

What is meant by mutations are random ?

Answer 8

• Different types of mutations are more common than others for example SNPs are most prevalent (CT is most common, When C is methylated (to supress transcription) destabilizes the C so undergoes deamination to form a T)
• Mutations happen more frequent in some areas, for example cytosine is usually more changed to T, than T, G and A is changed.
• Structural variants are the rarest
• Mutations are random with respect to their fitness, organisms rely on random beneficial mutations to adapt to new environments, organisms cannot make new mutations because they need them. Some bacteria can manipulate their mutation rates to change their frequency of acquiring beneficial mutations.

Question 9

If a chromosome is shorter, what type of mutation is present ?

Answer 9

Structural variant and INDELs

Question 10

Genotype Number of individuals
A1/A1 35
A1/A2 40
A2/A2 25
Total (N) 100

what is the allele frequency to A1 ?

Answer 10

p = frequency of A1 = 35+35+40/ 200 = 0.55

Question 11

What may cause an excess of homozygotes ?

Answer 11

inbreeding, assortative mating, heterozygote disadvantage, disruptive selection

Question 12

Give one possible reason (in one sentence) why you might be
seeing much lower nucleotide diversity this year compared to 5 years ago.

Answer 12

Inbreeding, bottleneck, selective sweep