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Syst Biol. 2018 Mar 1;67(2):304-319. doi: 10.1093/sysbio/syx075.

A General Model for Estimating Macroevolutionary Landscapes.

Author information

Department of Systematic and Evolutionary Botany (ISEB), University of Zurich, Zurich, Switzerland.
Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa.
Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, France.
Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA.
Department of Fish Ecology and Evolution, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Center for Ecology, Evolution, and Biogeochemistry, 6047 Kastanienbaum, Switzerland.


The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks. This model is based on a general partial differential equation widely used in statistical mechanics: the Fokker-Planck equation, also known in population genetics as the Kolmogorov forward equation. We thus call the model FPK, for Fokker-Planck-Kolmogorov. We first explain how this model can be used to describe macroevolutionary landscapes over which quantitative traits evolve and, more importantly, we detail how it can be fitted to empirical data. Using simulations, we show that the model has good behavior both in terms of discrimination from alternative models and in terms of parameter inference. We provide R code to fit the model to empirical data using either maximum-likelihood or Bayesian estimation, and illustrate the use of this code with two empirical examples of body mass evolution in mammals. FPK should greatly expand the set of macroevolutionary scenarios that can be studied since it opens the way to estimating macroevolutionary landscapes of any conceivable shape. [Adaptation; bounds; diffusion; FPK model; macroevolution; maximum-likelihood estimation; MCMC methods; phylogenetic comparative data; selection.].

[Indexed for MEDLINE]

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