Selective Sampling of Species and Fossils Influences Age Estimates Under the Fossilized Birth-Death Model.

Michael Matschiner

doi:10.3389/fgene.2019.01064

Abstract

The fossilized birth–death (FBD) model allows the estimation of species divergence times from molecular and fossil information in a coherent framework of diversification and fossil sampling. Some assumptions of the FBD model, however, are difficult to meet in phylogenetic analyses of highly diverse groups. Here, I use simulations to assess the impact of extreme model violations, including diversified sampling of species and the exclusive use of the oldest fossils per clade, on divergence times estimated with the FBD model. My results demonstrate that selective sampling of fossils can produce dramatically overestimated divergence times when the FBD model is used for inference, due to an interplay of underestimates for the model parameters net diversification rate, turnover, and fossil-sampling proportion. In contrast, divergence times estimated with CladeAge, a method that uses information about the oldest fossils per clade together with estimates of sampling and diversification rates, are accurate under these conditions. Practitioners of Bayesian divergence-time estimation should therefore ensure that the dataset conforms to the expectations of the FBD model, or estimates of sampling and diversification rates should be obtained a priori so that CladeAge can be used for the inference.

Highlights

With increases in the sizes of molecular datasets and improvements to inference methodology, our understanding of the timeline of evolution has grown tremendously over the past two decades
The dependence on a known topology has been relaxed in subsequent implementations of the model in BEAST 2 (Gavryushkina et al, 2014; Gavryushkina et al, 2017; Bouckaert et al, 2019), MrBayes (Ronquist et al, 2012; Zhang et al, 2016), and RevBayes (Höhna et al, 2016) all of which allow the inference of fossil positions based on morphological information instead of requiring the user to know their positions a priori
My analyses of simulated data show that the fossilized birth–death (FBD) model can produce highly inflated age estimates when sampling of species and fossils is not complete or random but selective

Summary

Introduction

With increases in the sizes of molecular datasets and improvements to inference methodology, our understanding of the timeline of evolution has grown tremendously over the past two decades. One of the most significant methodological developments for the estimation of divergence times has been the fossilized birth–death (FBD) model (Stadler, 2010; Heath et al, 2014), a phylogenetic framework that combines the two processes of species diversification and fossil sampling. The FBD model was first available for inference in the program DPPDIV (Heath et al, 2014), allowing the estimation of divergence times from a molecular dataset and a user-provided tree with a fixed topology. The FBD model has further matured with the integration of stratigraphic-range information and different speciation modes (Silvestro et al, 2018; Stadler et al, 2018), time-variable diversification and sampling (Gavryushkina et al, 2014), coalescent processes (Ogilvie et al, 2018), and the estimation of divergence times without assuming molecular or morphological clocks (Didier and Laurin, 2018)

Methods

Results

Conclusion