Modelling trait-dependent speciation with approximate Bayesian computation


Type
Article
Change log
Authors
Bartoszek, K 
Liò, P 
Abstract

Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is hampered by the lack of robust software to estimate the numerous parameters of the speciation process. In this work we present an R package, pcmabc, based on Approximate Bayesian Computations, that implements three novel phylogenetic algorithms for trait-dependent speciation modelling. Our phylogenetic comparative methodology takes into account both the simulated traits and phylogeny, attempting to estimate the parameters of the processes generating the phenotype and the trait. The user is not restricted to a predefined set of models and can specify a variety of evolutionary and branching models. We illustrate the software with a simulation-reestimation study focused around the branching Ornstein-Uhlenbeck process, where the branching rate depends non-linearly on the value of the driving Ornstein-Uhlenbeck process. Included in this work is a tutorial on how to use the software.

Description
Keywords
q-bio.PE, q-bio.PE, cs.LG, stat.AP, stat.ML, 65C05, 62F15, 62P10, 92-08, 92B10
Journal Title
Acta Physica Polonica B, Proceedings Supplement
Conference Name
Journal ISSN
1899-2358
2082-7865
Volume Title
12
Publisher
Jagiellonian University