L10 Population size and Structure

Question 1

The rate of loss of neutral variants

Answer 1

See OneNote for eqn.

Question 2

Ht

Answer 2

probability that a randomly chosen individual is heterozygous

Question 3

H0

Answer 3

freq of hets in the initial population

Question 4

t

Answer 4

generations since the initial population

Question 5

N

Answer 5

population size

Question 6

The idealized Wright-Fisher population

Answer 6

See OneNote

9 points

Question 7

The decay in heterozygosity by drift

Answer 7

See OneNote

Question 8

ibd

Answer 8

identical by descent

Identical by descent (IBD) is a term used in genetic genealogy to describe a matching segment of DNA shared by two or more people that has been inherited from a common ancestor without any intervening recombination.

Question 9

ibs

Answer 9

identical by state

Identical by state or identity by state (IBS) is a term used in genetics to describe two identical alleles or two identical segments or sequences of DNA.

Question 10

Drift reduces heterozygosity

Answer 10

In large population, hardly any loss of heterozygosity, drift is weak
Drift much stronger in small populations

Question 11

Time taken for drift to reduce heterozygosity by half

Answer 11

See OneNote for eqn.

T0.5 = 2Nln(2)

Question 12

The importance of population size

Answer 12

See OneNote

Population size does not contribute to the likelihood of a neutral mutation being fixed (fixation rate = mutation rate), hence the molecular clock BUT it does determine how long it will take for a neutral variant to fix (4N)

Question 13

Why does the proportion of adaptive aa changes (alpha) vary with species?

Answer 13

See corresponding OneNote page

Question 14

Mutation and drift

Answer 14

See OneNote for eqn and explanation

H is the probability that two alleles picked at random are different by state

Question 15

Heterozygosity in neutral sequences

Answer 15

See OneNote graph

Predicted vs observed

Expected many organisms to have extreme levels of het
BUt
Observed that correlation between population size and heterozygosity is weak

Expected and observed are so different, it was seen as a second major flaw in the neutral theory (the first being the generation time effect)

Question 16

Why is expected and observed heterozygosity so different?

Answer 16

1. Genetic hitchhiking?

2. Population size fluctuation? Population size is not always constant e.g. founders effect, bottlenecks

Question 17

Genetic hitchhiking

Answer 17

See OneNote graph

• selective sweeps
• removes variation => “genetics draft”

Question 18

Population size estimate is wrong

Answer 18

See OneNote graph

- Population size is not usually constant e.g. bottleneck events, founder effects

Question 19

Effective population size

Answer 19

• Ne may be smaller than then breeding population
• the concept of Ne allows us to accomodate the dramatic fluctuations of population sizes over time
• Ne is the size of the idealized (Wright-Fisher) population whose decay of heterozygosity equals that of the real population

Question 20

How much smaller is Ne than N?

Answer 20

See OneNote

Question 21

Hardy-Weinberg Equilibrium

Answer 21

See OneNote

Question 22

Wrights Fixation Index (F)

Answer 22

See OneNote for eqn.

F = 0 then HWE
F = 1 then no heterozygotes

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

Question 23

Wahlund Effect

Answer 23

See OneNote

• deficit in heterozygotes because of cryptic population structure
• the two combined pop is out of HWE, there is deficit in the hets BUT the two subpops are n HWE

Question 24

Using Fixation Index

Answer 24

The chi-sq tells us if its out of HWE, the F stat quantifies by how much (focusing on the hets)

Question 25

Wrights Fixation Index - population substructure

Answer 25

See OneNote

Can also help us understand the extent of population substructure - Fst, FIT

The fixation index (FST) is a measure of population differentiation due to genetic structure

FIT is not often used. It is the overall inbreeding coefficient of
an individual relative to the total population (Individual within
the Total population).

Question 26

Fst is the most commonly used

Answer 26

• just need gene frequencies from “subpopulations”
• most informative way to relate sub-population sample to total population
• “the proportion of the total het in the pop that is due to differences in the allele freq among subpopulations”

Question 27

Words for Fst numbers

Answer 27

See OneNote summary page

Question 28

Fst across Hapmap

Answer 28

See OneNote