24 Genome evolution and change in sequences over time Flashcards
(35 cards)
Cause of change in nucleotide sequence
mutations
causes of change in genome size 5
polyploidy chromosomal duplication/fusion transposition replication slippage unequal crossing over
mutation rates in melanogaster is higher or lower than lamda bacteriophage per base pair replication
melanogaster 8.4 x 10 -11 (lower)
lamda bacteriphage 2.4 X 10 -8
purines
a g
pyrimidines
t c
what does the bovid CO2 gene divergence over time show wrt transition and transversions ?
transition become saturated due to back mutations
no longer accurate and base pair differences no longer increasing as may switch back
transversions occur less
which sequence divergence is observable?
SINGLE SUBSTITUTION
MULTIPLE SUBSTITUTION
COINCIDENTAL SUBSTITUTION
which sequence divergences are noty observable?
parallel
convergent
back
what are the sequence divergent types (6)
single multiple coincidental parallel convergent back
what models can be used to estimate sequence divergence>
Jukes- cantor
Kimura 2 parameter
what is jukes cantor
model
d= 3/4 ln ( 1 - 4/3 P )
d=distance
p=proportion of nucleotide differences
maximum likelihood estmate
doesnt take into account more transitions
assumes equal mutation of ATGC
what model takes into account transitions ae more frquent
Kimura 2
what is molecular clock ? how does it work
some protei ncoding genes act in clock manner
rate of evo same across species
for example globins
molecular clock failure
in HIV and HIV2 divergence. clock says 50 years.later evidence said 200,000 years.did this by taking isolate then a year later see change
what is absolute time effect
rate of evo independent of generation time
Globins detail
absolute time effect
envolve at same rate in humans sharks and carp
are silent substitution undergoing generatin time effcet
yes.
in elephants- can look at sequence of past but in mice after 200,00 years sequence will be obsolete.
becaue they are neutral
neutral vs deleterious in
a) fuctionally constrained
b) less functionally constrained
c) non coding DNA
a) mostly deleterious
b) neutral/deleterious
c) mostly neutral
functional constrain
stronger the constrain the
range of alternative nucleotides that is acceptable at a site without affecting negatively the function or structure of the gene or the gene product. The stronger the functional constraints , the slower its rate of substitution will be.
are silent mutations under slection?
low level
codon bias
if ratio =1
if ratio is less than 1
1=neutral so no selection ie pseudo gene / de novo
less than 1= MHC being selected for so arms race
what ratio do you look at for rate variation among genes ?
look at rate variation by seeing
dN/dS non synonymous:synonymous ratio
do constrants just apply to single gene?
no operate in different regions of a single gene ie 5' flanking region 5'UTR Introns 3'UTR
chnage in genome size 5
polyploidy chromosomal duplication/fusion transposition replication slippage unequal crossing over
