Flashcards in G24 Deck (24):
What kind of nt change occurs more frequencty?
what is a transition mutation
purine to purine A G
pyrimidine to pyrimidine T ->C
what is a transversion mutation
Purine to pyrmidine vv
A - T
A - C
G - T
what is genetic saturation waht can this be seen in
Genetic saturation is the reduced appearance, which occurs over time, of sequence divergence rate that results from reverse mutations, homoplasmies and other multiple changes occurring at single sites along two genetic lineages.
can be seen in transition mutations but not transversion
What do we need to correct for when measuring sequence divergence
changes we dont see
What kind of changes can be seen and what changes cannot be seen
seen: single substituion, multiple substitution, coincidental subsitution
not seen: parrallel, convergent or back
what is the acctual no. of substitutions when sequence diveregence is low
is very close to the observed no.
what is the equation for the jukes cantor model
what is it
d(distance) = -3/4ln(1-4/3p)
where p = proportion of nt differences
multiple hit correction equation produces maximum liklihood estimate of the no. of nt subs between two species
what are the assumptions for the jukes cantor model?
rate of nt sub is the same for all pairs of the 4 nts,
equality of substitution rates among sites, equal nt frequences
doesnt correct for higher rate of transitional substitutions as compared to transversional substitutions.
how does the Kimura 2 model differ from the Jukes Cantor model
it takes into accounts transversions as well as transitions
give an example of the failings of the molecualr clock in virology
HIV-1 and HIV-2
rather than take fossil, isolate A and then later take B from same patient, use this to show changer per year.
this showed dthat HIV 1 and 2 are about 50% divergent
wanted to discover when they diverged from each other, figure was 50 years or so using molecular clock
however later evidence showed them to be 200,000 years diverged, although more likekly to be millions of fyears
what do comparisons of paralogous globin genes in different species show?
that different globin species seem to be evolving at the same rate as envisioned by amount of change between them,
despite differences in breeding geernation time etc, between shark humans and carp beta globins
- shown that globins seem to be on absolute time, independent of generation time.
What effect does the generation time effect have on evoltuion
The shorter the generation time, the more generations can be seen in a fixed period of time. Since mutations occur at gamete formation and fertilisation, this would mean that the rate of evolution is faster.
what kind of effect do silent substitutions show
generation time effect
what are motherless genss
geness that appear out of non coding DNA but then have high mutation rates
How can you measure how fast a gene will evolve
using dN/dS ratios
N = non synonmous substitutions
dN = proportion of non synonmous (change in aa protein)
dS = synonmous - doesnt change AA = assumed to be neutral as doesnt change AA so sam sub rate across sequence
give an example of a greatly constrained gene
carboxyl peptidase, any AA sub will kill the organism
what does it mean if dN/dS =1
neutral so no selection at all - pesudo gene,
de novo motherless are close to 1
what does it mean if dN/dS >1
evolutionary arms race, not whole gene bits of gene typically large.
How can genome size change
polyploidy - gene dosage stops effects
aneuploidy - non disjunction gives abnormal chromosome no.
chromsomal duplication/fussion - fusion more frequent than duplication
unequal crossing over - relatively infrequent
give an example of codon usage bias
despite the fact that CUG and CUA both code for leucine and change is considered silent, evidence shows mutations are under low level of selection to mainatian codon bias. - perhaps for house keeping genes
when is the molecular clock linear
over absolute time irrespective of the number of generations that have passed
why do globin genes show absolute time effect
because they have a specific purpose they are functionally constrained