Topic 11: Genetic distance Flashcards
What is genetic distance?
Measures of genetic differentiation based on different models of mutation.
What is the difference between genetic differentiation methods (X2 and F-stats) and genetic distance measures of differentiation?
Genetic differentiation methods are relative differences, as they are dependent on within population diversity (hard to compare across loci and species)
Genetic distance is another method of genetic differentiation based on models of mutations and are better at comparing across loci and species
What are three properties of genetic distance?
The genetic distance from a population to itself is 0
The genetic distance between two populations is greater than or equal to 0
A good genetic distance measure will have a linear relationship between the time since two populations have separated (they separate and allele frequencies change in a predictable rate)
What is the infinite allele model?
Assumes that each mutation creates a unique allele in the population, therefore an allele arises only once
Number of possible mutations: N=3^900
If all mutations are equally probable it is unlikely that a mutation will occur at the same position.
What is the infinite site model?
Assumes that each mutation is at a new unique site (nucleotide), therefore a mutation at a nucleotide arises once and only once creating a new unique allele (can count how many)
What is the difference between the infinite allele model and the infinite site model?
In the infinite site model the number of sites (nucleotide) differences can be counted.
What is the stepwise mutations model? What separates it from the IAM and the ISM?
Alleles form a ladder and mutations of an allele are either one step above or one step below the position of the allele on the ladder.
Most mutations of microsat alleles are either one repeat unit larger or smaller.
This counts reversions in the total count of alleles, which are not seen by the infinite allele model because it it not technically new, and the same reasoning goes for the infinite site model.
You cannot compare heterozygosities across both models because they make different assumptions
Hex is higher for IAM and ISM and lower for SMM because it takes reversions into account
What is Nei’s minimal distance? What is the issue with this measure?
This is the variable Dm, and it is based on the infinite allele model.
The problem with this is that the minimal distance reaches an asymptote after some amount of time, even though more differences accumulate. Ideally a genetic distance remains linear over time
What is Nei’s standard distance?
This is Ds and it modifies the minimal distance (Dm), and account for multiple mutations at a locus.
Dm has a maximum of one, but Ds can be greater than one and remains linear over longer periods of time than Dm
What is the genetic distance Dn?
This is a modification of Nei’s minimal distance based on the INFINITE SITE MODEL of mutation.
Dij is the new term in this population and it is the number of nucleotide differences between the ith allele Ai and the jth allele Aj
If dij=1 for all alleles then Dn=Dm
What are the meanings of the letters in the equations?
d: differences
X and Y are the different subpopulations
i and j indicate different alleles
What does the stepwise mutation model indicate about allele sizes?
If microsats evolve in a stepwise fashion, with each mutation causing +1 or -1 repeat unit, then the differences between allele sizes should be correlated to the time since they shared a common ancestor (closer alleles
What is a method that derives a distance more closely related to the time since two populations shared a common ancestor?
Allele size information
What is Shrivers stepwise distance?
It is a modification of Nei’s minimal distance for microsatellites that is based on the stepwise mutation model.
delta ij is the number of repeat units between the first and last allele and then x and y are the different population and i and j are the different alleles.
