Molecular Clock Hypothesis

Measurably evolving pathogens

• evolutionary rate: the estimated rate at which the nucleotide changes (per sit per genome) are observed within a population sampled over a particular timescale

• Substitution rate: the rate at which these nucleotide changes become fixed at the population level (# substitutions/unit time)

  • We don’t always have a good idea of whether a nucleotide is fixed or not across the entire population

• Mutation rate: the rate at which novel mutations arise (per site or per genome) when genomes replicate, most of which are subsequently removed by purifying selection.

  • This rate represents the upper biological limit for the amount of genetic change per unit of time

Differences in evolutionary rates

• Evolutionary rates are faster in smaller genomes

• Bacteria evolve more slowly than viruses

• DNA viruses evolve more slowly than RNA viruses

Virus evolutionary rates

• Replicating DNA: proofreading by exonuclease

• Replicating RNA: RNA-dependent RNA polymerase (or RNA-dependent DNA polymerase in case of retroviruses), there is no such proofreading activity

• 10^-3 mutations/site/replication = 1 mutation per 1000 bases every time RNA virus replicates

RNA Viruses Evolutionary Rates

• High mutation rate → RNA-dependent RNA polymerase and RNA-dependent DNA polymerase have no proofreading activity

• High replication rate → viruses replicate very fast

Mutation Rates

• difficult to measure real mutation rate (s/n/c not true mutation rate)

• Mutation rates correlated with evolutionary rates

• Definitions

  • s/n/c = substitutions per nucleotide site per cell infection

  • s/n/y = substitutions per nucleotide site per year in the population

Measuring evolving populations

Phylogenetic clock models

• constrain the distance from each tip to the root of the tree

• Branch lengths become proportional to sampling day

• Rescales genealogies into natural units of time

• Calculate time points of internal nodes and when MRCA lived

• For epidemics, can infer what time in the past an outbreak started

Measurably evolving populations

• plot evolutionary divergence (root to tip) versus sampling date

• Check for “temporal signal” in sequences (but not a real statistic regression analysis)—-

• If temporal signal, build phylogenetic trees scaled by time

  • Constrain tips to end at their sampling date

  • Infer the dates of internal nodes of the tree using a model

  • Calibrate phylogenetic tree and evolutionary rate by tips

Principles of the Molecular Clock

• assumption: evolutionary rates are like a clock ticking at a particular rate or pace

  • Allows for deducing the timing of past divergences by extrapolating evolutionary rates (for fast-evolving microbes)

  • Does not work for slow-evolving organisms, because not enough molecular evolution has passed in observable time to use tip sampling dates as calibration (can use fossils or known/assumed substitution rates)

• Reality: clock does not tick at exactly the same rate over time

  • Changes in population size, natural selection, etc.

  • Molecular evolutionary models can account for interlineage variation but uncertainty increases when estimating older divergence times (deep internal nodes)