Lecture 18

Question 1

what is positive selection?

Answer 1

increases the allele frequency in a poopulation. positive selection occurs when an allele is beneficial and has a high average fitness (similar to directional selection)

Question 2

what is negative selection/purifying selection?

Answer 2

decreases the frequency of an allele in a population. negative selection cocurs when an allele is deleterious or harmful and has low average fitness

Question 3

How do genes that are under purifying selection typically evolve?

Answer 3

genes that are under purifying selection typically evolve very slowly and are conserved for long periods of time

Question 4

do genes under purifying selection have long or short coalescnce time?

Answer 4

very long

Question 5

Is neutral variation under selection?

Answer 5

neutral variation is not under selection, but it is subject to drift

Question 6

why might selection be weaker when it comes to molecular evolution, rather than trait based evolution? state 4 reasons.

Answer 6

• lots of regions of dna do not code for proteins
• notall dna variation results in protein variation (synonymous mutations)
• not all protein variation results in phenotypic variation
• not all phenotype variation results in changes in fitness

Question 7

how does fixation of neutral mutations occur?

Answer 7

through genetic drift, not selection

Question 8

what is the neutral theory?

Answer 8

neutral mutations will yield nucleotide substitutions at a rate equivalent to the rate of mutation

therefore, if we know the mutation rate, we can use the number of base pair substitutions to estimate the time since two groups shared an ancesto

Question 9

what is the molecular clock?

Answer 9

• how we date/estimate things, based on what we know about population size and mutation rate
• we can use the number of base pair substitutions to estimate the time since two groups shared an ancestor

Question 10

how can the molecular clock be used to look at related species?

Answer 10

we can use the molecular clock to look at the relationship between related species, as long as we are sequencing the same gene. so we can look across different groups and see how divergent they are (between and within species)q

Question 11

what is dN/dS?

Answer 11

increased substitution rates that alter gene function within a species compared to neutral expectation

Question 12

what is Fst outliers?

Answer 12

an increase in differentiation between populations in genomic regions under selection

Question 13

what is selective sweep?

Answer 13

extended linkage disequilibrium around the beneficial allele, and a decrease in genetic variation around the selected site

Question 14

what is a synonymous mutation?

Answer 14

does not chance the amino acid sequence of the protein, should evolve at a neutral rate

Question 15

what are non synonymous mutations?

Answer 15

• alters the amino acid sequence of the protein
• faster evolution than synonymous sites indicate positive selection
• slower evolution than synonymous sites indicates purifying selection
• same rate evolution indicates neutral

Question 16

why is comparing the ratio between synonymous and non synonymous mutations useful? dN/dS

Answer 16

it is useful because it is generally not affected by differences in the mutation rate or drift, which affect both synonynmous and non synonymous sites equally. therefore it is good to be used to detect selection on dna sequences

Question 17

mutations in the third position are…?

Answer 17

synonymous

Question 18

mutatios in the first and second position are …?

Answer 18

non synonymous

Question 19

how do you scale dN/dS to make them comparable?

Answer 19

(# non synonymous subs)/(# non synonymous sites)

and

(# synonymous subs)/(# synonymous sites)

Question 20

what is neutral evolution in terms of dN and dS?

Answer 20

• dN=dS or dN/dS=1
• wen substitutions are neutral

Question 21

what is positive selection in terms of dN and dS?

Answer 21

• dN>dS (ratio larger than 1)
• when substitutions are advantageous
• this would mean more non synonymous mutations, and they were beneficial, so selection kept them around

Question 22

what is purifying selection in terms of dN and dS?

Answer 22

• dN<dS (less than one)
• when subsitutions are deleterious
• if more synonymous, means that if a mutation were to pop up in non synonymous area, it was removed since it was harmful

Question 23

how does Fst measure gene flow?

Answer 23

Fst measured gene flow between populations by looking at differences in allele frequencies

Question 24

what happens if the frequency of an allele differs between populations more than other alleles?

Answer 24

when the frequency of an allele differs between populations more than oher alleles (more than the baseline) then it suggests that another process is producing the extreme outliers

Question 25

what does the Fst outlier method detect?

Answer 25

the Fst outlier method detects loci with allele frequencies that are more different than expected between populations. these loci are likely to be in regions of the genome experiencing strong selection