Flashcards in Lecture 6 Deck (26)

1

##
Jukes and Cantor

(2)

###
- Corrects for multiple hits

- Assumes all nucleotides are equal

2

## Fst:

### A derivative of the Hardy Weinburg equation

3

##
Hardy-Weinberg Equilibrium:

(3)

###
- Relating gene frequencies to allele frequencies

- AA, Aa and aa, are related p2, 2pq q2

- If the gene frequency (p) of A = 80/100 the expected genotype frequencies are

(0.8 x 0.8) = 0.64 AA,

(2 x 0.8 x 0.2) = 0.32 Aa

and (0.2 x 0.2) = 0.4 aa

4

##
What is the heterozygosity of trapped mice in the East (aa) West (AA) population with cats patrolling the middle?

(3)

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- Assume we catch as many eat mice as west mice..

- Expected heterozygosity (Hexp) = 2pq = 2 x 0.5 x 0.5 = 0.5

- Observed heterozygosity -(Hexp) = 0

5

##
Wrights fixation Index (F):

(5)

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- F = (Hexp - Hobs)/Hexp

- The deviation between expected and observed normalized by expected

- F = 0, then HWE, no population structure

- F = 1, there are no heterozygotes, population structure

- The closer F is to 1 the more structure there is in the population

- Tells us how much the population is out of HWE

6

## A deficit in heterozygotes can arise due to..

### A cryptic population structure

7

## When chi-squared gives P<0.001

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- Far fewer heterozygotes than we would expect

- Deficit of heterozygotes

- Wahlund effect

8

## Wahlund effect:

###
- When a sample from a population shows that there are actually two populations

- A deficit of heterozygotes is shown

9

## Linanthus parryae the 'desert snow' helps us study..

### - The scale of population structure (regional, global), using the F indices

10

## HT=

### Total heterozygosity

11

## HS=

### Subpopulation heterozygosity

12

## HR=

### Regional heterozygosity

13

## Using the Wrights Fixation Indices (F) we can answer these questions:

###
- How much of the deviation from HWE is due to

- Sub-population structure

- Regional population structure

- Population wide deviations

- Fewer heterozygotes at the individual level

14

## FSR =

### The decrease in He among subpopulations within regions normalised by He in regions

15

## FRT =

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- The decrease in He among regions within whole populations normalised by He in whole populations

- A measure of differences of heterozygosity between geographical regions

16

## FST =

###
- The decrease in He among subpopulations within whole populations normalised be He in whole populations

- Calculating F stat based on data from sub populations, vs the total population

17

## FIT =

### The individual vs the total population, the range that these values take is -1 through 1 (because all individuals may be heterozygotes

18

##
Fst is the most commonly used because

(3)

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- We just need gene frequencies from 'subpopulations'

- It is the most informative way to relate subpopulation sample to the total population

- The proportion of the total heterozygosity in the population that is due to differences in the allele frequencies among subpopulations

19

## Fst = 0 - 0.05

### Low genetic differentiation, very low population structure

20

## Fst = 0.05 - 0.15

###
Moderate genetic differentiation, moderate population structure

21

## Fst = 0.15 - 0.25

### Great genetic differentiation, great population structure

22

## Fst = 0.25 - 1

### Very great genetic differentiation, very great population structure, lots of gene flow between them

23

## Hapmap project in humans

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- Sample from four human populations Central European Populations, Yoruba (Nigerian tribe), Chinese and Japanese

- Figure out how much population structure there is between human populations

24

## The hapmap project found:

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- Fst of over 2.8 millian SNOS is 0.11 (moderate structure), some sites have structure, others don't

- Of the total genetic variation observed between these four ethnic groups, only around 11% is due to genetic differences among groups

- ie: about 89% of the variation is common

- We observed the same variants in all populations.

25

## Why would Fst differ across the genome?

###
- In neutral sequences Fst is determined by drift and demography (spread and bottle necks) and chance

- Local positive selection increase Fst

- Balancing and negative selection decreases Fst

26