Flashcards in Lecture 8 Deck (28):

1

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Measures of nucleotide diversity

(2)

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- Tally the number of segregating sites (s)

- Calculate the average pairwise divergence between alleles (pi)

2

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Descriptive metrics include:

(7)

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- Describe the DNA sequence in different ways

- S

- P

- MAP

- Haplotypes

- Pi

- H

3

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S:

(2)

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- 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

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Pi:

(2)

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- Average pairwise divergence

- Under the neutral theory we expect pi = theta

8

## H:

### The frequency of heterozygous

9

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Metrics estimated with some uncertainty include..

(2)

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- Meu

- Fst

10

## Meu:

### Mutation rate

11

## Fst:

### Population structure

12

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Theoretical metrics:

(3)

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- Ne

- Hexp

- Theta

13

## Ne:

### Effective population size

14

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Hexp:

(4)

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- The expected number of heterozygous

- 2pq

- 4Nemeu/1+4Nemeu

- Theta/1+theta

15

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Theta:

(4)

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- The expected nucleotide diversity

- 4Nemeu

- Under the neutral theory we expect theta = pi

- Can also calculate theta from S

16

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Tajimas D test:

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

17

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Coalescence:

(3)

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- 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

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The effect of bottleneck on the coalescent:

(4)

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- 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

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Positive Tajimus D:

(3)

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- Increased number of intermediate frequency

- Bottleneck is an explanation for positive TD

- Deficit of rare variants

20

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Negative Tajimus D:

(2)

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- Excess of rare variants

- Coalescence with expanding population size

21

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Do polymorphisms in nearby sites evolve independently?

(2)

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- No! Not always

- Linkage equilibrium is a measure of this

22

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Linkage Disequilibrium (LD):

(2)

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- 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

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Haplotype:

(2)

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- One combination of allelic states that is inherited together

- Defined by an arbitrary number of sites

24

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How does linkage disequilibrium get established in the first place?

(4)

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- 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

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

(2)

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- P=(1-c) to the power of G

- Where c is the recombination rate between two polymorphisms

26

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Factors affecting LD include

(6)

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- Mutation

- Drift

- Limited recombination

- Admixture

- Bottlenecks

- Selective sweeps

27

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Admixture:

(2)

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- The mixing of two genetically differentiate populations

- LD is established between adjacent sites and different chromosomes

28