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Flashcards in G24 Deck (24):
1

What kind of nt change occurs more frequencty?

transition mutation

2

what is a transition mutation

purine to purine A G
pyrimidine to pyrimidine T ->C

3

what is a transversion mutation

Purine to pyrmidine vv
A - T
A - C
G - T
G -C

4

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

5

What do we need to correct for when measuring sequence divergence

changes we dont see

6

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

7

what is the acctual no. of substitutions when sequence diveregence is low

is very close to the observed no.

8

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

9

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.

10

how does the Kimura 2 model differ from the Jukes Cantor model

it takes into accounts transversions as well as transitions

11

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

12

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.

13

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.

14

what kind of effect do silent substitutions show

generation time effect

15

what are motherless genss

geness that appear out of non coding DNA but then have high mutation rates

16

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

17

give an example of a greatly constrained gene

carboxyl peptidase, any AA sub will kill the organism

18

what does it mean if dN/dS =1

neutral so no selection at all - pesudo gene,
de novo motherless are close to 1

19

what does it mean if dN/dS >1

evolutionary arms race, not whole gene bits of gene typically large.

20

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
transposition
replication slippage
unequal crossing over - relatively infrequent

21

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

22

when is the molecular clock linear

over absolute time irrespective of the number of generations that have passed

23

why do globin genes show absolute time effect

because they have a specific purpose they are functionally constrained

24

what show a linear trend over generation time?

silent mutation
not selected