Abstract
Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.
Highlights
The concept of the molecular clock has revolutionized the field of evolutionary biology by providing a foundation for evaluating the tempo of biological processes and mechanisms shaping patterns of biodiversity [1]
The most common approach for calibrating molecular clocks is to constrain the minimum age of phylogenetic relationships to dates derived from the fossil record [3] or to the timing of biogeographic events associated with lineage divergence [4]
Secondary rates estimated for the taxa of interest are ideal because these rates are more likely to be similar [7], but taxon-specific molecular clocks are unavailable for most organisms and “universal” rates for larger groups typically do not meet the assumption of rate constancy [8]
Summary
The concept of the molecular clock has revolutionized the field of evolutionary biology by providing a foundation for evaluating the tempo of biological processes and mechanisms shaping patterns of biodiversity [1]. Molecular clocks have been widely implemented to estimate divergence times, determine evolutionary rates, and to assess biogeographic hypotheses, but in practice, this powerful statistical tool requires independent information to calibrate rates and timescales into units of absolute time [2]. In cases where informative fossil and biogeographic information are unavailable, secondary or “universal” substitution rates derived from previous studies of related taxa can be used to fix evolutionary rates or inform a prior rate distribution for divergence time estimation [6]. Molecular clocks calibrated via secondary rates have been widely implemented in the absence of independent timing information [3], but because rates of genetic change can vary considerably among organisms and genes [1], rate constancy, a fundamental assumption for secondary rate calibrations, is violated [2]. Secondary rates estimated for the taxa of interest (or for closely related taxa) are ideal because these rates are more likely to be similar [7], but taxon-specific molecular clocks are unavailable for most organisms and “universal” rates for larger groups typically do not meet the assumption of rate constancy [8]
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