Bayesian total evidence dating reveals the recent crown radiation of penguins
The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).
Code (0)
등록된 구현이 없습니다.
Tasks
MORPHSimilar Papers 제목 키워드 기반
Molecular Clock Dating using MrBayes
This paper provides an overview and a tutorial of molecular clock dating using MrBayes, which is a software for Bayesian inference of phylogeny. Two modern approaches, total-evidence dating and node dating, are demonstra…
Bayesian InferenceUnfolding AlphaFold's Bayesian Roots in Probability Kinematics
We present a novel theoretical interpretation of AlphaFold1. The seminal breakthrough of AlphaFold1 in protein structure prediction by deep learning relied on a learned potential energy function, in contrast to the later…
Probabilistic Deep LearningProtein Structure PredictionUnforeseen Evidence
I propose a normative updating rule, extended Bayesianism, for the incorporation of probabilistic information arising from the process of becoming more aware. Extended Bayesianism generalizes standard Bayesian updating t…
Reliable Uncertain Evidence Modeling in Bayesian Networks by Credal Networks
A reliable modeling of uncertain evidence in Bayesian networks based on a set-valued quantification is proposed. Both soft and virtual evidences are considered. We show that evidence propagation in this setup can be redu…
Generalised Bayesian distance-based phylogenetics for the genomics era
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic metho…
Bayesian Inference