Welcome to TREvoSim’s User Manual

The [Tr]ee [Evo]lutionary [Sim]ulator program.

TREvoSim is an individual-based evolutionary model, focussing on the simulation of evolutionary trees and associated character data through a first-principles approach. It shares a number of elements in common its sister package REvoSim (see Garwood et al. 2019, Furness et al. 2023 in relevant references), but it differs in species concept, and eschews both space and sexual reproduction.

The Palaeoware logo

TREvoSim has been released with the intention that it can be used as a multi-purpose platform for the study of many evolutionary phenomena, but in particular, it acts as one of a limited number of methods for simulating character data and tree topology at the same time, and is one of very few individual-based simulations capable of doing so. As with REvoSim, this package is complementary to the many other approaches of studying evolution on a range of different timescales, and will be continually developed by the core team to expand its capabilities.

Note

A sensible place to start learning more is the Introduction, and further details are included in the papers listed below.

e: palaeoware@gmail.com

w: https://github.com/palaeoware

Relevant references

Garwood, R.J., Spencer A.R.T. and Sutton, M.D. 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology 62(3),339-355. DOI: 10.1111/pala.12420 (describes the initial release of REvoSim, including fitness algorithm).

Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G. and Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology 69(5):897-912. DOI: 10.1093/sysbio/syaa012 (describes, and utilises, TREvoSim v1.0.0)

Mongiardino Koch, N., Garwood, R.J. and Parry, L.A. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B 288(1950):20210044. DOI: 10.1098/rspb.2021.0044 (describes, and utilises, TREvoSim v2.0.0)

Mongiardino Koch, N., Garwood, R.J. and Parry, L.A. 2023. Inaccurate fossil placement does not compromise tip-dated divergence times. Palaeontology 66 (6): e12680. DOI: 10.1111/pala.12680 (utilises TREvoSim v2.0.0)

Garwood, R.J., Spencer, A.R.T., Bates, C.T.M., Callender-Crowe, L.M., Dunn, F.S., Halliday, T.J.D., Keating, J.N., Mongiardino Koch, N., Parry, L.A., Sansom, R.S., Smith, T.J., Sutton, M.D., and Vanteghem, T. 2024. TREvoSim v3: An individual based simulation tool for generating trees and morphological data. Journal Of Open Source Software (describes v3.0.0)

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