Lecture 8 Flashcards Preview

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Flashcards in Lecture 8 Deck (28):
1

Measures of nucleotide diversity
(2)

- Tally the number of segregating sites (s)
- Calculate the average pairwise divergence between alleles (pi)

2

Descriptive metrics include:
(7)

- Describe the DNA sequence in different ways
- S
- P
- MAP
- Haplotypes
- Pi
- H

3

S:
(2)

- Number of segregating sites
- Can calculate theta from S

4

p:

The frequency of a variant

5

MAP:

Minor allele frequency

6

Haplotypes:

A particular combination

7

Pi:
(2)

- Average pairwise divergence
- Under the neutral theory we expect pi = theta

8

H:

The frequency of heterozygous

9

Metrics estimated with some uncertainty include..
(2)

- Meu
- Fst

10

Meu:

Mutation rate

11

Fst:

Population structure

12

Theoretical metrics:
(3)

- Ne
- Hexp
- Theta

13

Ne:

Effective population size

14

Hexp:
(4)

- The expected number of heterozygous
- 2pq
- 4Nemeu/1+4Nemeu
- Theta/1+theta

15

Theta:
(4)

- The expected nucleotide diversity
- 4Nemeu
- Under the neutral theory we expect theta = pi
- Can also calculate theta from S

16

Tajimas D test:

- Compares theta (neutral expectation of molecular diversity) to pi (average pair wise divergence) to address frequency spectrum deviations.

17

Coalescence:
(3)

- Looking back in time the lineages of all contemporary alleles will eventually coalesce to a single ancestor
- There are n-1 coalescence per sample size of n
- On average, it will take 2Ne generations to go from a large sample down to 2 lineages

18

The effect of bottleneck on the coalescent:
(4)

- Population goes through the bottleneck and then expands again
- This will give us a coalescence tree with two arms separated by really long branch lengths.
- We will find most mutations occur in the two long arms
- Increased number of intermediate frequency, positive Tajimus D.

19

Positive Tajimus D:
(3)

- Increased number of intermediate frequency
- Bottleneck is an explanation for positive TD
- Deficit of rare variants

20

Negative Tajimus D:
(2)

- Excess of rare variants
- Coalescence with expanding population size

21

Do polymorphisms in nearby sites evolve independently?
(2)

- No! Not always
- Linkage equilibrium is a measure of this

22

Linkage Disequilibrium (LD):
(2)

- Non-random association of alleles at different loci in a population
- Correlation between different sites that can be near each other, or on different chromosomes

23

Haplotype:
(2)

- One combination of allelic states that is inherited together
- Defined by an arbitrary number of sites

24

How does linkage disequilibrium get established in the first place?
(4)

- Imagine 3 linked sites in a linkage equilibrium (of 8 haplotypes)
- A mutation occurs and increases in frequency by drift or selection
- The LD is maintained
- Recombination erodes LD over time

25

The probability that the haplotype is not broken down in G generations..
(2)

- P=(1-c) to the power of G
- Where c is the recombination rate between two polymorphisms

26

Factors affecting LD include
(6)

- Mutation
- Drift
- Limited recombination
- Admixture
- Bottlenecks
- Selective sweeps

27

Admixture:
(2)

- The mixing of two genetically differentiate populations
- LD is established between adjacent sites and different chromosomes

28

Extended LD:

Dependent on migration rate and recombination rate