Fast simulation of reconstructed phylogenies under global time-dependent birth–death processes

View Researcher's Other Codes

Disclaimer: The provided code links for this paper are external links. Science Nest has no responsibility for the accuracy, legality or content of these links. Also, by downloading this code(s), you agree to comply with the terms of use as set out by the author(s) of the code(s).

Authors Sebastian Höhna
Journal/Conference Name Bioinformatics
Paper Category
Paper Abstract MOTIVATION: Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth–death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit. - RESULTS: In the present article, I consider as the model a global time-dependent birth–death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth–death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).
Date of publication 2013
Code Programming Language R

Copyright Researcher 2022