Comparative methods without phylogeny: Estimation of macroevolutionary rates from the fossil record

Daniele Silvestro

University of Lausanne, Switzerland silvestro.daniele@gmail.com

(in English)

ATTENTION: En raison des mesures de restriction d’accès au Campus Triolet, les personnes extérieures à l’Université de Montpellier doivent venir munies de: AFFICHE IMPRIMÉE + UNE PIECE D'IDENTITÉ.

Phylogenetic comparative methods have progressed very rapidly in recent years and substantially improved our understanding of macroevolutionary processes, such as the tempo and mode of speciation, extinction, migration, and phenotypic diversification. These methods rely on dated phylogenies, which are mostly restricted to extant species. Since present biodiversity only represents a small fraction of the organisms that have ever lived, inferring evolutionary dynamics exclusively from extant taxa may have limited power. Here, I present PyRate, a suite of quantitative methods to analyze fossil data and infer macroevolutionary processes, in the absence of an explicit phylogenetic hypothesis. Paleontological data, despite their inevitable incompleteness, can be analyzed in this framework to reliably infer speciation and extinction rates and their temporal trends. Using case studies from plant and animal clades I demonstrate the power of the method to detect trait-based diversification, selectivity in mass extinction events, and clade competition through diversity dependence. Building upon this framework, a new dispersal-extinction-sampling model is developed to tackle other key aspects in macroevolution, namely the spatial dynamics and historical biogeography of taxa. Analyses of simulated and empirical data show that fossil-based estimates outperform those obtained from phylogenies of extant taxa. Thus, quantitative analyses of fossil data can provide important insights into macroevolutionary processes.

Recent publications:

Silvestro D., Antonelli A., Salamin N. & Quental T.B. (2015) The role of competition in evolutionary replacements of North American canids. Proceedings of the National Academy of Sciences USA 112: 8684–8689.

Silvestro D., Cascales-Miñana B., Bacon C.D. & Antonelli A. (2015) Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. New Phytologist 207: 425–436.

Silvestro D., Schnitzler J., Liow L.H., Antonelli A. & Salamin N. (2014) Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology 63: 349–367.