Lecture 4- Molecular clocks

Question 1

bootstrapping

Answer 1

random sampling of the data to create pseudoreplicates, which can then be used to help analyse genetic data

Question 2

how does bootstrapping improve tree accuracy?

Answer 2

you can look at the frequency with which a cluster appears in the new datasets, the more it occurs the stronger the evidence for its existence

Question 3

why is having a ‘molecular clock’ useful?

Answer 3

can track the timing of evolution, even where morphological changes are highly uneven or not observable

Question 4

neutralist argument on molecular evolution

Answer 4

most fixed mutations are neutral and arise by genetic drift

Question 5

selectionist argument on molecular evolution

Answer 5

most observed mutations come from balancing, fluctuating etc types of selection

Question 6

example of a fast-evolving protein which can be used to reconstruct phylogenies between closely-related organisms

Answer 6

fibrinopeptides

Question 7

substitution rate equation

Answer 7

k = N(mu)p
p= probability of fixation
mu = mutation rate per individual per gen
N = pop size (*2 for diploid)

Question 8

which types of sequence evolve fastest?

Answer 8

genes not under selection, e.g. pseudogenes

Question 9

how does N impact the chance that a negative allele will become fixed?

Answer 9

in a smaller pop, the slightly disadvantageous allele is controlled by drift, whereas when N is large, they are controlled by selection and removed. HOWEVER small N populations often have higher generation times, so can cancel out the effect

Question 10

how does generation time correlate with mutation rate?

Answer 10

longer generation time > less mutations, as there are less reproductive events for them to occur at in the same time period

Question 11

metabolic rate association with mutations

Answer 11

smaller bodied vertebrates tend to have higher mutation rates, which could be related to higher metabolisms > more oxygen free radicals > more DNA damage and mutations

Question 12

calibration methods

Answer 12

fossils, co-evolution, measurably evolving populations (using ancient DNA or frozen samples of pathogens etc), biogeography

Question 13

strict clock model

Answer 13

it is assumed that all lineages evolve at the same rate, no variation

Question 14

local clock model

Answer 14

rate varies, but is inherited- so local branches have more similar rates

Question 15

relaxed clock

Answer 15

rate varies among lineages with no restrictions