Building an adaptive trait simulator package to infer parametric diffusion model along phylogenetic tree

Abstract

The development of an adaptive trait simulator package for inferring trait evolution along a phylogenetic tree is shown. Stochastic processes of the continuous type are broadly applied to modeling trait evolution when the evolutionary relationship among species and traits of study interest are present. By including several popular stochastic processes, evolutionary information embedded in a dataset can be revealed. The highlights of the method include: 1.The implementation of the popular Cox-Ingersol-Ross process for modeling rate evolution within the package to prevent rates from becoming negative and thus is potentially a useful extension to study adaptive trait evolution in randomly evolved environment.2.The established trait simulator approach along with approximate Bayesian computation procedure provides a feasible statistical inference without model likelihood.3.The procedure proposed for trait simulator along phylogenetic tree can be applied to all established models of trait evolution in literature, thus providing users an alternative option to analyze their data.

Keywords: Brownian motion; Cox-ingersoll-ross process; Ornstein-uhlenbeck process; Phylogenetic comparative method; Statistical modeling; Trait evolution.