EB12

Question 1

what do the three types of selection do

Answer 1

purifying selection removes deleterious alleles
positive selection fixes advantageous alleles
balancing selection retains variability

Question 2

What was the study on HIV evolution

Answer 2

RNA from 19 viruses collected from patients over 20 years

Question 3

what did the study on HIV evolution show

Answer 3

over 60 years showed a 20% genetic distance from root of the tree
* an independent test of predictions, indicating a regular clock like rate of change in HIV-1.
frozen 1959 HIV isolate fit close to the predicted line for divergence given age

Question 4

what is the DRBI allele

Answer 4

one of ~100 genes that make up the human leukocyte antigen (HLA) complex; a 4mp long region of DNA on chromosome 6

Question 5

what is HLA homologous to

Answer 5

MHC of mammals and other vertebrates

Question 6

what does HLA play a role in

Answer 6

tissue compatibility (self/non self-recognition) and defence against pathogens and parasites

Question 7

what does humans DRBI genes show

Answer 7

high polymorphism

Question 8

what is the relationship between DRBI genes in apes and monkeys

Answer 8

gene lineages coalesce into a CA long before the divergence of apes from old world monkeys, so alleles between species are often more closely related than alleles within species

Question 9

what does high polymorphism of DRBI indicate

Answer 9

balancing selection
for maintaining polymorphisms over long evolutionary time, due to heterozygote advantage and or frequency dependent selection.

Question 10

how does pi differ between synonymous and non synonymous loci

Answer 10

106 gene samples
non synonymous had a smaller pi (sequence) than synonymous
*non synonymous pi was 1/3 size of synonymous
** shows less mutations in non synonymous to maintain AA

Question 11

what is G6PD

Answer 11

glucose 6 phosphate dehydrogenase

3 alleles in humans B, A- and A+

Question 12

how do G6PD allele B and A- differ

Answer 12

7 differences between sequnecea

Question 13

how do G6PD allele B and A+ differ

Answer 13

4 differences between sequences

Question 14

how do G6PD A- and A+ differ

Answer 14

3 differences between sequences

Question 15

what is pi

Answer 15

the probability that a random pair of sequences from a population differ at a given nt.
can average all sites of a locus to get the average pairwise divergence of all sequences in a sample

Question 16

how long is the G6PD gene

Answer 16

5022 bp

Question 17

what is the average pairwise divergence of all G6PD sequences

Answer 17

(7+4+3) /(3*5022)
sum of differences/ no. of sequences compared X length of sequence

= 0.00093

Question 18

what is wattersons theta (thetaw)

Answer 18

the no. of polymorphic sites in the alignment of sequneces per bp corrected for sample size of sequences

Question 19

Why is it important to correct for sample size as in thetaw

Answer 19

because the larger the sample size the more polymorphic sites will be found

Question 20

how does thetaw correct for sample size

Answer 20

instead of timsing by no. of sequences compared (k)
x by (1 + 1/(k-1)
where k is the no. of sequences compared

Question 21

what does thetaw give

Answer 21

another estimate of polymorphism

Question 22

how else does thetaw differ from pi (other than sample size)

Answer 22

asks how many sights are variable all togehter in the alignment (aka how many sites are there all together with polymorphism) (how many sites can change = biggest no. of changes observed in a sequence).

Question 23

how would thetaw be calculated for G6PD

Answer 23

7/(5022*(1+1/2)

= 0.00093 = SAME

Question 24

how can theta be estimated (two ways)

Answer 24

from pi or by directly counting the no. of polymorphic sites

Question 25

how would thetaw and pi differ if another sequence was added to the G6PD analysis

Answer 25

it would add more polymorphic sites, so theta w would increase however it would not contribute much to the average no. of differenes.
therefore thetaw > pi

Question 26

what does a thetaw greater than pi indicate

Answer 26

an excess of sites with low frequency rare differences

Question 27

what does pi greater than thetaw indicate

Answer 27

most differences are concentrated in a few sites maintaining polymorphism at high frequencies.

Question 28

what should ideal population estimates values of theta w and pi be

Answer 28

the same theoretical value

as measuring diversity in different ways