The genome as an evolutionary timepiece

Abstract

Themolecular clock is a valuableandwidelyused tool for estimatingevolutionary rates andtimescales in biological research. There has been considerableprogress in the theory and practice ofmolecular clocksover the past five decades.Althoughthe idea of a molecular clock was originally put forward in the context of protein evolution and advanced using various biochemical techniques, it is now primarily applied to analyses of DNA sequences. An interesting but very underappreciated aspect ofmolecular clocks is that they can be based on genetic data other than DNA or protein sequences. For example, evolutionary timescales can be estimated using microsatellites, protein folds, and even the extent of recombination. These genome features hold great potential for molecular dating, particularly in cases where nucleotide sequences might be uninformative or unreliable. Here we present an outline of the differentgenetic data types thathavebeen used formolecular dating, andwedescribe the features thatgoodmolecular clocks should possess.We hope that our article inspires further work on the genome as an evolutionary timepiece.