lecture 4 Flashcards
molecular clock
the hypothesis that genes evolve at constant rates through time and across species.
divergence dating
the practice of using genetic data to estimate when species diverged.
phylogenies with branch lengths proportional to time provide
more information about evolutionary history than trees with branch lengths in units of substitution/site.
divergence time estimation
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.
global molecular clock
assume that the rate of change is constant over time across the tree branch lengths = % of sequence divergence.
molecular clock other info:
- 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.
are the substitutions observed between species more often the result of natural selection or neutral evolution?
key point: silent mutations (synonymous) vs replacement (non-synonymous) substitutions.
neutral theory of molecular evolution
- 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.
molecular clock steps:
- 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.
molecular clock advantages:
- the simplest model.
- assume the rate of change is the same on every branch.
- we explain long/short branches due to differences in time.
factors that skew a molecular clock:
- 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.
degree of selective constraint dictates
rate of molecular evolution.
selective constraint
the ability of a protein to tolerate random mutations.
highly constrained molecules
most mutations are deleterious, and few are neutral.
weakly constrained molecules
more mutations are neutral and few are deleterious.
alternative to molecular clocks: local clocks
- 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.
divergence dating
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.
sequence data provide information on
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.
point estimation of divergence time
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).
Bayesian methods
prior distributions for rate and time. assume a reasonable range that covers the extremes.
- problems: defining “reasonable” can be difficult.
fossil calibration
fossil and geological data can be used to estimate the absolute ages of ancient diversification.
