As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates*

Abstract

Biologists have used a wide range of organisms to study the origin of taxa and their subsequent evolutionary change in space and time. One commonly used tool is the molecular clock approach, relating substitution rates of nucleotide or amino acid sequences to divergence times. The accuracy of the molecular clock, however, has long been subject to controversy, and numerous papers have addressed problems associated with estimating divergence times. Some workers pointed out a striking imbalance between sophisticated software algorithms used for molecular clock analyses on the one hand, and the poor data on the other hand. Moreover, there is often unease among workers relative to molecular clocks because of the controversy surrounding the approach, the complex mathematical background of many molecular clock tools, the still limited number of available, user-friendly software packages, the often confusing terminology of molecular clock approaches, and the general lack of reliable calibration points and/or external clock rates. The current review therefore briefly provides an overview of analytical strategies, covering approaches based on calibration points and/or bounds, approaches based on external clock rates, and approaches that attempt to estimate relative divergence times in the absence of information that can be used for estimating substitution rates. It also deals with major problems and pitfalls associated with data and analyses, including potential errors of calibration points and bounds, the performance of the gene(s) used, estimation of confidence limits, and misinterpretation of the results of clock analyses due to problems with sampling design. A substantial part of the review addresses the question of “universal” molecular clock rates and summarizes important biological and life history variables that account for deviations from rate constancy both between lineages and at different times within lineages. The usefulness of these factors is discussed within the framework of “trait-specific” molecular clock rates. One such clock rate is introduced here for the cytochrome c oxidase subunit I (COI) gene in small dioecious, tropical and subtropical Protostomia with a generation time of approximately one year. A flow chart is provided as a “simple fool's guide” to molecular clock analyses, together with a glossary of widely used terms in molecular clock approaches. Finally, step-by-step examples are provided for calculating divergence times in the caenogastropod subfamily Pyrgulinae based on both an internal calibration point and a “trait-specific” molecular clock rate, and it is demonstrated how a relative clock approach can be used for testing evolutionary hypotheses. Our review encourages a judicious use of molecular clock analyses in evolutionary studies of invertebrates by demonstrating their great potential on the one hand and (often-manageable) problems and pitfalls on the other hand.