Testing the molecular clock using mechanistic models of 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.ISSN:0962-8452ISSN:1471-295

FossilSim:An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery

1.Key features of the fossil record that present challenges for integrating palaeontological and phylogenetic datasets include (i) non‐uniform fossil recovery, (ii) stratigraphic age uncertainty and (iii) inconsistencies in the definition of species origination and taxonomy. 2.We present an r package FossilSim that can be used to simulate and visualise fossil data for phylogenetic analysis under a range of flexible models. The package includes interval‐, environment‐ and lineage‐dependent models of fossil recovery that can be combined with models of stratigraphic age uncertainty and species evolution. 3.The package input and output can be used in combination with the wide range of existing phylogenetic and palaeontological r packages. We also provide functions for converting between FossilSim and paleotree objects. 4. Simulated datasets provide enormous potential to assess the performance of phylogenetic methods and to explore the impact of using fossil occurrence databases on parameter estimation in macroevolution.ISSN:2041-210XISSN:2041-209

Timetrees: Incorporating fossils and molecules: Editorial

ISSN:1664-802

Does time matter in phylogeny? A perspective from the fossil record

The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in phylogenetic inference of fossil taxa. Here, we apply this model in a Bayesian framework to an exemplar dataset of well-dated conodonts from the Late Devonian. We compare the results to those obtained using traditional unconstrained tree inference. We show that the combined analysis of morphology and stratigraphic data under the FBD range process reduces overall phylogenetic uncertainty, compared to unconstrained tree inference. We find that previous phylogenetic hypotheses based on parsimony and stratophenetics are closer to trees generated under the FBD range process. However, the results also highlight that irrespective of the inclusion of age data, a large amount of topological uncertainty will remain. Bayesian inference provides the most intuitive way to represent the uncertainty inherent in fossil datasets and new flexible models increase opportunities to refine hypotheses in palaeobiology

Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference

Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically not known as it may have occurred at any time during the time interval spanned by the rock layer. Bayesian phylogenetic approaches provide a coherent framework for incorporating multiple sources of evidence and uncertainty. In this study, we simulate datasets with characteristics typical of Palaeozoic marine invertebrates, in terms of character and taxon sampling. We use these datasets to examine the impact of different age handling methods on estimated topologies and divergence times obtained using the fossilized birth-death process. Our results reiterate the importance of modeling fossil age uncertainty, although we find that the relative impact of fossil age uncertainty depends on both fossil taxon sampling and character sampling. Sampling the fossil ages as part of the inference gives topology and divergence time estimates that are as good as those obtained by fixing ages to the truth, whereas fixing fossil ages to incorrect values results in higher error and lower coverage. The relative effect increases with increased fossil and character sampling. Modeling fossil age uncertainty is thus critical, as fixing incorrect fossil ages will negate the benefits of improved fossil and character sampling.ISSN:2296-701

Does time matter in phylogeny? A perspective from the fossil record

The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in phylogenetic inference of fossil taxa. Here, we apply this model in a Bayesian framework to an exemplar dataset of well-dated conodonts from the Late Devonian. We compare the results to those obtained using traditional unconstrained tree inference. We show that the combined analysis of morphology and stratigraphic data under the FBD range process reduces overall phylogenetic uncertainty, compared to unconstrained tree inference. We find that previous phylogenetic hypotheses based on parsimony and stratophenetics are closer to trees generated under the FBD range process. However, the results also highlight that irrespective of the inclusion of age data, a large amount of topological uncertainty will remain. Bayesian inference provides the most intuitive way to represent the uncertainty inherent in fossil datasets and new flexible models increase opportunities to refine hypotheses in palaeobiology