L10 Population size and Structure Flashcards
The rate of loss of neutral variants
See OneNote for eqn.
Ht
probability that a randomly chosen individual is heterozygous
H0
freq of hets in the initial population
t
generations since the initial population
N
population size
The idealized Wright-Fisher population
See OneNote
9 points
The decay in heterozygosity by drift
See OneNote
ibd
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.
ibs
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.
Drift reduces heterozygosity
In large population, hardly any loss of heterozygosity, drift is weak
Drift much stronger in small populations
Time taken for drift to reduce heterozygosity by half
See OneNote for eqn.
T0.5 = 2Nln(2)
The importance of population size
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)
Why does the proportion of adaptive aa changes (alpha) vary with species?
See corresponding OneNote page
Mutation and drift
See OneNote for eqn and explanation
H is the probability that two alleles picked at random are different by state
Heterozygosity in neutral sequences
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)
Why is expected and observed heterozygosity so different?
- Genetic hitchhiking?
2. Population size fluctuation? Population size is not always constant e.g. founders effect, bottlenecks
Genetic hitchhiking
See OneNote graph
- selective sweeps
- removes variation => “genetics draft”
Population size estimate is wrong
See OneNote graph
- Population size is not usually constant e.g. bottleneck events, founder effects
Effective population size
- 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
How much smaller is Ne than N?
See OneNote
Hardy-Weinberg Equilibrium
See OneNote
Wrights Fixation Index (F)
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
Wahlund Effect
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
Using Fixation Index
The chi-sq tells us if its out of HWE, the F stat quantifies by how much (focusing on the hets)
Wrights Fixation Index - population substructure
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).
Fst is the most commonly used
- 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”
Words for Fst numbers
See OneNote summary page
Fst across Hapmap
See OneNote
