Evol Ecol Res 18: 41-59 (2017)     Full PDF if your library subscribes.

Bayesian estimation of multiple clade competition from fossil data

Daniele Silvestro1,2,3, Mathias M. Pires4, Tiago B. Quental4 and Nicolas Salamin2,3

1Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden,  2Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland,   3Swiss Institute of Bioinformatics, Lausanne, Switzerland and  4Department of Ecology, University of São Paulo, São Paulo, SP, Brazil 

Correspondence: D. Silvestro, Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden. email: daniele.silvestro@bioenv.gu.se


Background: The diversification dynamics of clades is governed by speciation and extinction processes and is likely affected by multiple biotic, abiotic, and stochastic factors. Using quantitative methods to analyse fossil occurrence data, one may infer rates of speciation and extinction in a Bayesian framework. Moreover, Silvestro et al. (2015a) recently developed a Multiple Clade Diversity Dependence birth–death model (MCDD) to determine whether diversification dynamics can be explained by positive or negative effects of interactions within or between co-existing clades. However, the power and accuracy of this model and its general applicability have yet to be thoroughly investigated.

Aims: Explore the properties of the existing MCDD implementation, which is based on Bayesian variable selection. Introduce an alternative parameterization based on the Horseshoe prior and show the properties of this approach for Bayesian shrinkage in complex models. Test the ability of the model to correctly identify within and between diversification interference under a suite of different diversification scenarios.

Methods: Use simulations to assess and compare the power and accuracy of the two algorithms.

Results: Diversity dependence within and between clades can be inferred with confidence in a wide range of scenarios using the MCDD model. The two implementations provide comparable results, but the new Horseshoe prior estimator appears to be more reliable, albeit slightly more conservative. The MCDD model is a powerful framework to analyse the putative effects of ecological interactions on macroevolutionary dynamics using fossil data and provides a sound statistical basis for future method developments.

Keywords: Bayesian shrinkage, diversity dependence, fossils, macroevolution.

IF you are connected using the IP of a subscribing institution (library, laboratory, etc.)
or through its VPN.


        © 2017 Daniele Silvestro. All EER articles are copyrighted by their authors. All authors endorse, permit and license Evolutionary Ecology Ltd. to grant its subscribing institutions/libraries the copying privileges specified below without additional consideration or payment to them or to Evolutionary Ecology, Ltd. These endorsements, in writing, are on file in the office of Evolutionary Ecology, Ltd. Consult authors for permission to use any portion of their work in derivative works, compilations or to distribute their work in any commercial manner.

       Subscribing institutions/libraries may grant individuals the privilege of making a single copy of an EER article for non-commercial educational or non-commercial research purposes. Subscribing institutions/libraries may also use articles for non-commercial educational purposes by making any number of copies for course packs or course reserve collections. Subscribing institutions/libraries may also loan single copies of articles to non-commercial libraries for educational purposes.

       All copies of abstracts and articles must preserve their copyright notice without modification.