L8 Molecular Population Genetics 1 Flashcards
Measure of nucleotide diversity
See OneNote
- count number of polymorphic site
- frequency spectrum for minor alleles
- haplotypes
Frequency spectrum
See OneNote
minor allele count for each of the segregating sites
Pairwise comparison
see OneNote
Pi
average pairwise divergence/nucleotide diversity
- used to describe variation in your data
Descriptive metrics
S = # of segregating sites p = freq. of a variaant MAF = minor allele frequency Haplotypes = a particular combination pi = average pairwise divergence Hobs = freq. of heterozygotes
Metrics “estimated” with some uncertainty
mu = mutation rate Fst = population structure
Theoretical metrics
Ne = effective population size Hexp = expected number of heterozygotes theta = expected nucleotide diversity = 4Nemu
Under the neutral theory we expect theta = pi
We can calculate theta from S
Under the neutral model - S
S gives an expectation for nucleotide diversity
Tajimas D test
compares theta (netrual expectation) to pi (observed) to address frequency spectrum deviations
- If there is no deviation between pi and theta, neutrality supported, tajimas D = 0
- If -ve, many more rare sites
- If +ve, less rare sites, more intermediate sits
Why would the spectrum differ from expectation?
- selection?
- adaptation?
- demographic event?
Ancestral derived allele count
Could include an outgroup and determine what the ancestral state is
Gives us a longer frequency spectrum
Various more powerful frequency spectrum tests use outgroup sequences to polarise changes and “unfold” the spectrum
Coalescence
See OneNote
The alleles coalesce to a particular point, to one ancestral allele
On average, it will take 2Ne generations to go from a large sample down to two lineaes
On average, it will take 2Ne for the last two lineage to coalesce (but 96% CI goes form 0.05Ne to 7.4Ne)
The effect of a bottle neck on a coalescent
Positive Tajimas D => less rare sites, more intermediate sites
Coalescing with expanding population size
Negative Tajimas D => excess of rare sites
Linkage Disequilibrium (LD)
- the non-random association of alleles at the different loci in a population
- recombination erodes LD over time
