Total-Evidence Dating under the Fossilized Birth-Death Process.

Chi Zhang,Seraina Klopfstein,Tanja Stadler,Tracy A Heath,Fredrik Ronquist

doi:10.1093/sysbio/syv080

Abstract

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth–death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.

Highlights

Assigned to individual fossils based on the dating of the strata in which they are found
These data, together with molecular sequences sampled from extant taxa, are analyzed in an integrative framework to directly inform the inference of divergence times, while accounting for uncertainty in the placement of the fossils in the phylogeny
The expected proportion of ancestral fossils is consistently close to zero in the induced priors except for two cases involving the same type of fossilized birth–death” (FBD) model (Table 4, pcFBD_Rnd)

Summary

Introduction

Assigned to individual fossils based on the dating of the strata in which they are found. One of the essential strengths of the total-evidence dating approach is that it allows the probabilistic model to be expanded to include additional sources of information that could be important in dating but have not been modeled explicitly before We exploit this to address the fossilization process and the sampling procedure, both of which potentially have a major impact on divergence time estimates. Höhna et al (2011) showed that incorrect modeling of the sampling process can cause major problems in inferring speciation and extinction rates under standard birth– death models, especially in cases where investigators tried to maximize the taxonomic diversity in the sample Such diversified sampling is arguably more common than random sampling in species-level data sets, and is even explicit in all studies at higher taxonomic levels. We assess the influence of assumptions about the fossilization and sampling processes on the inferred divergence times, especially focusing on random and diversified sampling strategies

Results

Discussion

Conclusion