Lecture 8- Detecting selection in molecular sequences

Question 1

example of how selective and demographic processes can become confused

Answer 1

generate similar trees- e.g. population growth and a selective sweep will look similar, and population subdivision and balancing selection also will

Question 2

dn/ds model

Answer 2

looks at the ratio of synonymous and non-synonymous mutations, can be used to compare forces of selection and drift

Question 3

what s values represent what

Answer 3

if s is around 0, this is drift
if s is above 0, positive selection
if s is below 0, negative selection

Question 4

when should dN/dS > 1

Answer 4

if some replacement mutations are beneficial- this usually doesn’t appear for whole genes, this technique works best when applied to parts of genes or single codons

Question 5

what points of a gene should have higher dN/dS

Answer 5

parts which form the active sites of genes, e.g. antigen recognition sites or parts of pathogens associated with immune responses

Question 6

why might a silent change not be neutral

Answer 6

overlapping genes, alternate reading frames etc can mask impact of a gene, especially common in viruses
regulatory elements can also have silent mutations being under selection

Question 7

mcdonald-kreitman test

Answer 7

looks at the levels of polymorphism and divergence at neutral and functional sites to determine what was driven to fixation by positive selection, usually in a species and a closely related outlier group

Question 8

hard vs soft sweep

Answer 8

soft sweeps involve multiple haplotypes sweeping at the same time, whereas a hard sweep involves a singular haplotype with an advantageous allele rising in frequency

Question 9

link between linkage disequilibrium and selective sweeps

Answer 9

in a faster sweep, there is less time for linkage disequilibrium to break up alleles, so the impact of it is seen much further away, whereas the impact of a slower sweep is more localised as there is time for recombination