EB11 (part 2)

Question 1

what is the rate of divergence comparitively in the three degenerative degrees in humans and rodents
what does this indicate

Answer 1

1. zero fold lowest rate of change divergence - indicate purifying selecction
2. 4 fold: fasterest rate of change
3. 2 fold = average rate of change

Question 2

what kind of divergence do introns show in humans and rodents

Answer 2

similar to 4 fold - fast divergence

** however sometimes introns express control sites so may have lower mutation rate

Question 3

what kind of divergence do 3’ flanking sites show in humans and rodents

Answer 3

similar to 4-fold = fast divergence

Question 4

what kind of divergence do 5’ flanking sites show in humans and rodents

Answer 4

similar to 3 fold divergence

as often contain regions important for expression of genes

Question 5

what kind of divergence do psuedogenes show in humans and rodents

Answer 5

similar to 4 fold - nearly neutral so mutate quickly

Question 6

what is an abalone

Answer 6

large marine mollusc releasing sperm into the sea

Question 7

how do abalone sperm and egg differ in selection preferences

Answer 7

male: many sperm competing for access to egg, selects fastest sperm to fuse
female: one egg to accept the best sperm and avoid polyspermy, which is fatal to the embryo= selects for changes in egg receptor to achieve ‘poor fit’ to sperm surface and slow down fusion.

Question 8

what is lysin

Answer 8

a membrane bound protein that binds to the eggs envelope and unravels it thus allowing fertilisation
* regulates species specific interaction between sperm and egg

Question 9

why in lysin interesting in abalones

Answer 9

as it shows divergence across the 25 abalone species

Question 10

what is the neutral expectation for dN/dS

Answer 10

1

expect to evolve at equal rates if evolvign neutrally

Question 11

what is the dN/dS for abalone lysin in different parts

Answer 11

~ 3 at the periphery of the molecule which interacts with the egg membrane - shows fast divergence, positive selection - coevo chase between male and female gamete receptors
~ 0.09 at part forming the core of the molecule (more constrained to maintain overall structure) showing slow divergence. = purifying selection

Question 12

what is VDE

Answer 12

an intein selfish element with homing endonuclease inside the host VMA gene in yeast

Question 13

what does intein mean

Answer 13

it resides and is hosted by hosts genes: if reside inside an important gene it reduces the risk of losing its home to selection, especially if HEG is deleterious

Question 14

how does HEG enzyme work

Answer 14

HEG enzyme recognises site in homologue allele cuts (ds break); cell uses homologue containing HEG to repair break, copying HEG into non-HEG homologue, thus doubling the no. of HEG copies in the genome

Question 15

what is HEG an example of

Answer 15

super mendalian inheritance

converts +/- to +/+ homozygote

Question 16

how were VDE sites in yeast analysed

Answer 16

alignment of VDE sequences from 14 species of Saccharomyces

sites tested by site directed mutagenesis to identify sites important for function.

Question 17

what did analysis of VDE sites show

Answer 17

sites critical for splicing function are 100% invariant - self splicing intron
non- critical sites show much higher degrees of variability. e.g. sites critical for endonuclease lack of conservation, indicates various state of degneration of endonuclease formation

Question 18

what sites tend to be highly conserved

Answer 18

functionally important sites

Question 19

what can conserved sites in an alignment be used to deduce

Answer 19

functionality of sites, e.g. find control sites in non-coding regions etc.

Question 20

what is the neutral expectation for dN/dS and pN/pS

Answer 20

that dN/dS = pN/pS = 1