EB12 Flashcards
(28 cards)
what do the three types of selection do
purifying selection removes deleterious alleles
positive selection fixes advantageous alleles
balancing selection retains variability
What was the study on HIV evolution
RNA from 19 viruses collected from patients over 20 years
what did the study on HIV evolution show
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
what is the DRBI allele
one of ~100 genes that make up the human leukocyte antigen (HLA) complex; a 4mp long region of DNA on chromosome 6
what is HLA homologous to
MHC of mammals and other vertebrates
what does HLA play a role in
tissue compatibility (self/non self-recognition) and defence against pathogens and parasites
what does humans DRBI genes show
high polymorphism
what is the relationship between DRBI genes in apes and monkeys
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
what does high polymorphism of DRBI indicate
balancing selection
for maintaining polymorphisms over long evolutionary time, due to heterozygote advantage and or frequency dependent selection.
how does pi differ between synonymous and non synonymous loci
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
what is G6PD
glucose 6 phosphate dehydrogenase
3 alleles in humans B, A- and A+
how do G6PD allele B and A- differ
7 differences between sequnecea
how do G6PD allele B and A+ differ
4 differences between sequences
how do G6PD A- and A+ differ
3 differences between sequences
what is pi
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
how long is the G6PD gene
5022 bp
what is the average pairwise divergence of all G6PD sequences
(7+4+3) /(3*5022)
sum of differences/ no. of sequences compared X length of sequence
= 0.00093
what is wattersons theta (thetaw)
the no. of polymorphic sites in the alignment of sequneces per bp corrected for sample size of sequences
Why is it important to correct for sample size as in thetaw
because the larger the sample size the more polymorphic sites will be found
how does thetaw correct for sample size
instead of timsing by no. of sequences compared (k)
x by (1 + 1/(k-1)
where k is the no. of sequences compared
what does thetaw give
another estimate of polymorphism
how else does thetaw differ from pi (other than sample size)
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).
how would thetaw be calculated for G6PD
7/(5022*(1+1/2)
= 0.00093 = SAME
how can theta be estimated (two ways)
from pi or by directly counting the no. of polymorphic sites
