lecture 4

Question 1

molecular clock

Answer 1

the hypothesis that genes evolve at constant rates through time and across species.

Question 2

divergence dating

Answer 2

the practice of using genetic data to estimate when species diverged.

Question 3

phylogenies with branch lengths proportional to time provide

Answer 3

more information about evolutionary history than trees with branch lengths in units of substitution/site.

Question 4

divergence time estimation

Answer 4

the goal is to estimate the ages of interior nodes of the phylogeny to understand timing and rates of evolutionary processes.

• model how rates are distributed across the tree
• describe the distribution of speciation events over time.
• external calibration information for estimates of absolute node times.

Question 5

global molecular clock

Answer 5

assume that the rate of change is constant over time across the tree branch lengths = % of sequence divergence.

Question 6

molecular clock other info:

Answer 6

• Zuckerkandi and Pauling in 1962 - noticed uniformity in the rate at which amino acid substitutions accumulated among species.
• One amino acid substitution occurs for every eleven to eight million years.

Question 7

are the substitutions observed between species more often the result of natural selection or neutral evolution?

Answer 7

key point: silent mutations (synonymous) vs replacement (non-synonymous) substitutions.

Question 8

neutral theory of molecular evolution

Answer 8

• observation: silent substitutions (synonymous) outnumber replacement (non-synonymous) substitutions by a factor of 5 or 10.
• conclusion: the majority of molecular evolution involves neutral mutations and random genetic drift.
• open question: what is the relative importance of random genetic drift vs natural selection?
• genetic drift and fixation of new mutations.

Question 9

molecular clock steps:

Answer 9

• step 1: measure the amount of divergence between species - compare amino acid (or DNA) sequences.
• step 2: apply substitution rate (ex. one change per 15 million years).
• step 3: calculate the divergence time between species.

Question 10

molecular clock advantages:

Answer 10

• the simplest model.
• assume the rate of change is the same on every branch.
• we explain long/short branches due to differences in time.

Question 11

factors that skew a molecular clock:

Answer 11

• mutation rates vary across species (metabolism, ecology).
• rates vary across genes (selection).
• differences in generation times - mutations occur in generations, not years.
• population size - genetic drift is stronger in smaller populations.
• difference in DNA repair mechanisms.

Question 12

degree of selective constraint dictates

Answer 12

rate of molecular evolution.

Question 13

selective constraint

Answer 13

the ability of a protein to tolerate random mutations.

Question 14

highly constrained molecules

Answer 14

most mutations are deleterious, and few are neutral.

Question 15

weakly constrained molecules

Answer 15

more mutations are neutral and few are deleterious.

Question 16

alternative to molecular clocks: local clocks

Answer 16

• different parts of the phylogeny have different rates.
• allow for infrequent rate changes on the tree.
• advantages: rate shifts occur infrequently and close relatives have the same rate.

Question 17

divergence dating

Answer 17

sequence data are only informative on relative divergences. we need external information (like fossils or rates) to calibrate (scale) the tree to absolute time. branch lengths = rate * time.

• rate and time are confounded.
• infinite amounts of data cannot separate rate and time.
• methods for dating species divergence estimate the substitution rate and time separately.

Question 18

sequence data provide information on

Answer 18

branch length. for any possible rate, there is a time that fits the branch length perfectly. need to make assumption about rate or time to calibrate the tree.

Question 19

point estimation of divergence time

Answer 19

assume a fixed conversion between rate and time.
- problems: does not include any uncertainty and false precision (inadvertently suggest that humans diverged from Chimpanzees on a Monday).

Question 20

Bayesian methods

Answer 20

prior distributions for rate and time. assume a reasonable range that covers the extremes.
- problems: defining “reasonable” can be difficult.

Question 21

fossil calibration

Answer 21

fossil and geological data can be used to estimate the absolute ages of ancient diversification.