Substitution Model - The Molecular Clock and The Units of Time

The Molecular Clock and The Units of Time

Typically, a branch length of a phylogenetic tree is expressed as the expected number of substitutions per site; if the evolutionary model indicates that each site within an ancestral sequence will typically experience x substitutions by the time it evolves to a particular descendant's sequence then the ancestor and descendant are considered to be separated by branch length x.

Sometimes a branch length is measured in terms of geological years. For example, a fossil record may make it possible to determine the number of years between an ancestral species and a descendant species. Because some species evolve at faster rates than others, these two measures of branch length are not always in direct proportion. The expected number of substitutions per site per year is often indicated with the Greek letter mu (μ).

A model is said to have a strict molecular clock if the expected number of substitutions per year μ is constant regardless of which species' evolution is being examined. An important implication of a strict molecular clock is that the number of expected substitutions between an ancestral species and any of its present-day descendants must be independent of which descendant species is examined.

Note that the assumption of a strict molecular clock is often unrealistic, especially across long periods of evolution. For example, even though rodents are genetically very similar to primates, they have undergone a much higher number of substitutions in the estimated time since divergence in some regions of the genome. This could be due to their shorter generation time, higher metabolic rate, increased population structuring, increased rate of speciation, or smaller body size. When studying ancient events like the Cambrian explosion under a molecular clock assumption, poor concurrence between cladistic and phylogenetic data is often observed. There has been some work on models allowing variable rate of evolution (see for example and ).

Models that can take into account variability of the rate of the molecular clock between different evolutionary lineages in the phylogeny are called “relaxed” in opposition to “strict”. In such models the rate can be assumed to be correlated or not between ancestors and descendants and rate variation among lineages can be drawn from many distributions but usually exponential and lognormal distributions are applied. There is a special case, called “local molecular clock” when a phylogeny is divided into at least two partitions (sets of lineages) and in each strict molecular clock is applied but with different rate.