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Evolutionary and Population Genetics > Genetic variation, HW equilibrium, Inbreeding, and Effective Population Size > Flashcards

Genetic variation, HW equilibrium, Inbreeding, and Effective Population Size Flashcards

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1
Q

What does population genes answer?

A

Questions that can’t be answered by molecular genetics

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2
Q

When is a single base change called an SNV?

A

If only present in one individual, or if rare

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3
Q

When is a single base change called a mutation?

A

If rare and observed in disease context

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4
Q

When is a single base change called a SNP?

A

If common in the population

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5
Q

Non-synonymous mutation

A

AA change occurs

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6
Q

Frameshift mutation

A

Insertion or deletion of nucleotide bases in numbers that are not divisible by 3. Changes the subsequent AAs and can cause premature stop codon

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7
Q

Name 4 methods for detecting genetic variation in DNA

A
  1. PCR + electrophoresis
  2. Sanger sequencing
  3. Whole-genome SNP genotyping
  4. Next-generation sequencing
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8
Q

Steps of PCR

A
  1. Denaturation - heat DNA strand to 95C to break the hydrogen bonds
  2. Primer annealing - After first step with end up with 2 separate strands. Cool back down to 50-65C and primers anneal to the template strand by forming H bonds at the exact position they compliment the DNA
  3. Extension - Heat to 72C which is optimal temp for thermal Taq polymerase enzyme to synthesis new strands of DNA in 5’ to 3’ direction

repeat about 25 times

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9
Q

After how many rounds is the first target length strand found?

A

2

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10
Q

Why does DNA migrate slowly to positive charge in a gel electrophoresis

A

Phosphates carry a slight negative charge

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11
Q

Why does DNA migrate slowly to positive charge in a gel electrophoresis

A

Phosphates carry a slight negative charge

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12
Q

Steps in Sanger sequencing

A
  1. Amplify region by PCR
  2. Dye-terminator PCR - DNa polymerase is added with chain terminators ddNTPS in a ratio of 100:1 respectively. PCR extension finishes when ddNTP bonded with template strand. Each ddNTP iis fluorescently labelled with a colour corresponding to the base
  3. Capillary electrophoresis - To read the sequence we measure the mass of each DNA fragment at single basepair resolution and detect the fluorescence signals
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13
Q

Whole-genome sequencing

A
  1. Genomic DNA is fragmented into regions of 200bps
  2. SNP probes complementary to the sequence upstream of SNP added
  3. We get base pairing between fragmented DNA and complementary probe
  4. Like Sanger sequencing there are chain terminator ddNTPs
  5. SNP chips read sequence
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14
Q

What do the colours of an SNP chip mean?

A

Green = homozygous A/A
Red = homozygous B/B
Yellow = heterozygous A/B

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15
Q

Next generation sequencing

A
  1. Genomic DNA is fragmented into pieces of 400/500bps
  2. Ligases add sequence adapters - extra pieces of DNA on either side of template DNA
  3. On a flow cell there are oligonucleotides complimentary to adapter 1 and adapter 2
    ddNTP chain terminators are reversible
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16
Q

Hardy-Weinberg definition and equation

A

genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors

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

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17
Q

What are the 5 principles of Hardy-Weinberg equilibrium?

A
  1. No mutation
  2. Random mating
  3. No gene flow (migration)
  4. Infinite population size
  5. No selection
18
Q

What is the inbreeding coefficient (F) for the offspring of half-sibilings?

A

0.125

19
Q

What is the F for full siblings?

A

1/4

20
Q

What is the F for half siblings?

A

1/8

21
Q

What is the F for first cousins and double first cousins?

A

1/16 and 1/8 respectively

22
Q

What is the F for Uncle-niece

A

1/8

23
Q

What is the probability of being homozygous at a locus for unrelated individuals?

A

p^2 + q^2

24
Q

What is the probability of being homozygous at a locus for related individuals?

A

p^2 + q^2 + 2pqF

25
Q

What does assortative mating lead to?

A

Increase homozygosity

26
Q

What does negative assortative mating (disassortative mating) lead to?

A

Increase in heterozygosity

27
Q

What is another name for inbreeding?

A

Endogamy

28
Q

What is an effective population size (Ne)

A

Size of idealised population required to see same genetic variation

29
Q

Estimating Ne via inbreeding

A

Inbreeding reduces heterozygosity

30
Q

Panmixia

A

Random mating

31
Q

Panmictic index

A

Pt = 1 - Ft (where Ft is the inbreeding coefficient at generation t)

32
Q

What is the modern method of estimating Ne?

A

Identity-by-descent (IBD) in SNP-chip data

Length distribution between all paris of individuals in a cohort can be used to estimate Ne of previous generations

33
Q

Estimating Ne further back in time

A

Pairwise sequential Monte Carlo (PSMC) method

34
Q

8 Factors affecting Ne

A
  1. Division into two sexes
  2. Variation in offspring numbers
  3. Inbreeding
  4. Mode of inheritance
  5. Age and stage structure
  6. Changes in population size
  7. Spatial structure
  8. Genetic structure
35
Q

How does division into two sexes affect Ne?

A

A small number of individuals of one sex can greatly reduce effective population size below the total number of breeding individuals

36
Q

How does variation in offspring number effect Ne?

A

A larger variance in offspring number than expected with random variation reduce Ne below N

37
Q

How does inbreeding affect Ne?

A

The correlation between the maternal and paternal alleles of an individual caused by inbreeding reduces Ne

38
Q

How does mode of inheritance affect Ne?

A

The Ne experienced by a locus depends on its mode of transmission

39
Q

How does age and stage structure affect Ne?

A

Ne is much lower than N

40
Q

How does changes in population size affect Ne?

A

Episodes of low population size have a disproportionate effect on the overall value of Ne

41
Q

How does spatial structure affect Ne?

A

Limited migration between populations greatly increase Ne for the whole population, whereas high levels of local extinction greatly decrease Ne

42
Q

How does genetic structure affect Ne?

A

Balancing selection increases Ne
Directional selection reduces Ne

Evolutionary and Population Genetics (7 decks)

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