EB12 part 2 Flashcards
(29 cards)
What does Tajimas D(ifferences) do
tests for imbalances in polymorphism frequencies in the data set
what does pi equal under the standard neutral model
pi = thetaw = 4Neu
what do significant differences between pi and thetaw indicate
deviation from SNM due to
demography: i.e. population not in equilibrium or subdivided (not panmitic or not neutral)
what is tajimas D
(pi-thetaw)/sd
sd = standard deviation
what is tajimas d simialr to and why
simialr to t test as differences greater than sd are unlikely under the null hypothesis
what contributes more to pi common or rare variants.
common variants contribute more than rare variants to measures of pairwise differences like pi
how do rare variants contribute to thetaw compared to pi
thetaw is based on counting the no. of polymorphic sites, regardless frequency of alelles, so an excess of rare alleles will greatly inflate thetaq while contributing little to pi
thetaw > pi
what does it mean if Tajimas D is negative
there is an excess of rare variants indicating purifying selection against them, probably due to purifying selection
what does it mean if tajimas D is positive
theres an excess of common variants, i.e. excess of sites with high frequencies of alleles indicating balancing selection, maintaining diversity.
what is TLR4
toll like receptor gene involved in immune response
what doe tajimas d for TLR4 show
TD: significantly negative for NS sites in TLR4: suggests purifying selection, keeping varaints at these sites at low frequencies suggesting could be deleterious
TD: non significant for non coding sites.
what were sites with purifying selection in TLR4 later shown to be associated with
meningococcal ingections with mutations in these sights leading to an increased susceptibility to infection
what is a selective sweep
strong selection at one site will result in loss of variation in neighbouring sites despite neutrality as neighbours carried by linkage
what might lack of variation (heterozygosity) in a long stretch of DNA indicate
positive selection for an advantageous allele within that region
or purifying selection against deleterious alleles
Give an example of a selective sweep in drosophila
two regions of D. melanogaster X chromosome show less variability in non-African compared to African populations.
this indicates fixation of adaptive mutations as D. melanogaster spread out of africa
give an example of a selective sweep in humans
lactase persistance
part of chromosome containing lactase tolerance gene is highly homozygous over a large area.
what can homozygosity tracks associated with lactase persistance tell us
length of this area can be used to infer when the selective sweep occured
the more recent the less time recombination has had to dissociate from the selected locus, so younger the change.
how does distribution of lactase persistance vary
decreases from north to souther europe - from high cattle areas to lower
what does recombination do
removes or reduces effects due to linkage, therefore prevents loss of genetic diversity
under neutral model what should rate of divergence and rare of polymorphism be
under neutral polymorphisms (both silent and non silent) are fixed at equal rates and therefore the ratio of divergences should be equal to the ratio of polymorphisms
dN/dS = pN/pS
(dN/dS)/(pN/pS )= 1
what does (dN/dS)/(pN/pS) < 1 show
slower fixation of AA changing alleles indicating purifying selection
what does (dN/dS)/(pN/pS) > 1 show
faster fixation of AA changing alleles compared to expectation indicating postiive selection
what is the Mcdonald Kreitman test
a simple test for deviations from neutrality
what are the varaibles in the mcdonald kreitman test
X: fixed non synonymous
Y: fixed synonymous
Z: polymorphic (p) non synonymous
U: polymorphic (u) non synonymous
