Relaxed phylogenetics and dating

Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times.Strict and relaxed clock models are used in Bayesian estimation of divergence times.We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times.Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation.It is sometimes called a gene clock or an evolutionary clock.The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages (based on the molecular clock hypothesis (MCH)).The genetic equidistance phenomenon was first noted in 1963 by Emanuel Margoliash, who wrote: "It appears that the number of residue differences between cytochrome c of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged.

All of the analyses described here are implemented in the open access software package BEAST 1.5.4 (In 1967, Allan Wilson and his then doctoral student Vincent Sarich described an "evolutionary clock" for albumin proteins and exploited the clock to date the common ancestor of humans and chimpanzees to five million years ago [].

The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny.

Each branch in a phylogeny (subtending a clade) is a possible location for a change of rate from one local clock to a new one.

Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors.

The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0.

Relaxed phylogenetics and dating