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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)

- 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)

- 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

- 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 =

- 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)

- 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

- 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:

- 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

Which variants showed us the most variation across human genomes?

- The lactase gene (Lct)
- For many people the ability to digest lactase disappears in childhood (ages 3 - 4)
- Lactase persistence is in high frequencies among populations with histories of cattle/dairy farming
- This is due to natural selection favouring the lactase persistance allele