Molecular Clock: Testing

Abstract

The molecular clock hypothesis originally rested on the assumption of rate constancy across lineages of a phylogeny, which would produce an approximately steady rate of accumulation of deoxyribonucleic acid or amino acid changes through time. This assumption has been questioned on the basis of increasingly large data sets, which have shown significant variability of evolutionary rates in lineages. To address this issue, tests have been developed to examine whether rates of molecular evolution vary significantly among taxonomic groups or phylogenetic lineages. Two major types of tests exist: those based on comparisons of genetic distances and those based on likelihood ratios. The first ones compare genetic distances between two species (or groups of species) relative to an outgroup; the latter ones compare maximum likelihood values for the same phylogeny calculated with and without the constant rate assumption. In those cases where the rate constancy assumption is violated, modern molecular clocks (relaxed clocks) are now being applied to implement rate heterogeneity in the time estimation process. Key Concepts Evolutionary rates among lineages can be constant or variable. The first molecular clock methods developed (strict, or global, clocks) assumed constant rates. Many datasets have been shown to violate the rate constancy assumption. Testing for rate constancy is a key step before estimating times. Parametric and nonparametric rate tests are available. Variable rates may follow different distributions (autocorrelated or uncorrelated). While autocorrelation seems more common, it is advisable to test for the best fitting distribution.