Testing the molecular clock using mechanistic models of both fossil preservation and molecular evolution

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions

Closing the gap between palaeontological and neontological speciation and extinction rate estimates.

Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the "birth-death chronospecies" model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes

Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny

Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic

Bayesian molecular clock dating of species divergences in the genomics era

It has been five decades since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics, to studying the macroevolutionary process of speciation and extinction, to estimating a timescale for Life on Earth

Exploring uncertainty in the calibration of the molecular clock

Calibration is a critical step in every molecular clock analysis but it has been the least considered. Bayesian approaches to divergence time estimation make it possible to incorporate the uncertainty in the degree to which fossil evidence approximates the true time of divergence. We explored the impact of different approaches in expressing this relationship, using arthropod phylogeny as an example for which we established novel calibrations. We demonstrate that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes. We illustrate a procedure for deriving calibration densities in Bayesian divergence dating through the use of soft maximum constraints

Seven rules for simulations in paleobiology

Simulations are playing an increasingly important role in paleobiology. When designing a simulation study, many decisions have to be made and common challenges will be encountered along the way. Here, we outline seven rules for executing a good simulation study. We cover topics including the choice of study question, the empirical data used as a basis for the study, statistical and methodological concerns, how to validate the study, and how to ensure it can be reproduced and extended by others. We hope that these rules and the accompanying examples will guide paleobiologists when using simulation tools to address fundamental questions about the evolution of life

Bayesian Molecular Clock Dating Using Genome-Scale Datasets.

Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation in the branches of a phylogenetic tree and the use of flexible fossil calibration densities to describe the uncertainty in node ages. The advent of next-generation sequencing technologies has led to a flood of genome-scale datasets for organisms belonging to all domains in the tree of life. Thus, a new era has begun where dating the tree of life using genome-scale data is now within reach. In this protocol, we explain how to use the computer program MCMCTree to perform Bayesian inference of divergence times using genome-scale datasets. We use a ten-species primate phylogeny, with a molecular alignment of over three million base pairs, as an exemplar on how to carry out the analysis. We pay particular attention to how to set up the analysis and the priors and how to diagnose the MCMC algorithm used to obtain the posterior estimates of divergence times and evolutionary rates