Genetic Distance

Question 1

Genetic Distance

Answer 1

Given a pair of aligned sequence, how many generations passed between the 2 having a common ancestor
Representative of the specie doesnt matter because we are too similar, less than 0.1% difference. Some species have more variety between each other

Question 2

SNP

Answer 2

Single Nucleotide Polymorphism
Point Mutation, copying error: 1 nucleotide change
Position in a sequence: allele

Question 3

Variation

Answer 3

Sexual reproduction: diploid genome, half mum, half dad. Crossover
Point mutations, copying errors
Mitochondrial DNA: only mom and no cross over !! thus only point mutations -> track maternal line

Question 4

Mutations

Answer 4

Mutation in one individual can become the norm: it is fixed
Substitution rate: rate the mutations become fixed. higher for beneficial mutations
Mutation rate: rate of new mutation

new mutation: 1/2N (N size of population

Equal probabilities of each base mutating is too simple
Transition more probable than transversion because less harmful. Transition A to G, C to T

Question 5

Proportional Genetic Distance

Answer 5

Compute Genetic distance by looking at the proportion of bases that are different between the sequence
simple but increasingly innacurate as time pass : saturation

Question 6

Saturation

Answer 6

On average 1 mutation per site
2 random sequence of same length will match 1/4 of the site => genetic distance 1/4
As time pass more and more mutations => saturation

Question 7

Estimation genetic distance

Answer 7

true genetic distance >= observed differences
There are back mutations !!

transition matrix probability alpha/3 to go to another nucleotide and 1-alpha to stay
put matrix to the power k when k generations have passed

too simple because assume equal probas

alpha for transition and beta for transversion

Question 8

Jukes cantor formula

Answer 8

This is a correction, lowers the effect of saturation
find actual genetic distance K from observed distance d
if d small then will more or less equal
if d>3/4 then there is saturation, it is as if random sequence and K is undetermined

Question 9

Kimura model

Answer 9

this is a correction for saturation
Determines the fraction of transitions P ( A to G, C to T) and transversion Q (A to T, C to G, A to C, T to G: do Square to see them )
P+Q is equal to the observed distance d used in the Jukes cantor correction
More realistic than Jukes Cantor because take into consideration the 2 types of mutations: transition more probable because less harmful !!!