Welcome to REvoSim’s User Manual

The [R]apid [Evo]lutionary [Sim]ulator program.

REvoSim is an individual-based evolutionary model, using a simplified first-principles evolutionary model to facilitate high computational efficiency, allowing the simulation of large populations incorporating space, over geological time, using modest computer hardware. It can simulate populations of 10⁵ –10⁷ digital organisms over geological timescales, and incorporates spatial and temporal environmental variation, recombinant or asexual reproduction, mutation and dispersal. Speeds attainable depend on the computer hardware in use, the size of the populations simulated, and details of the experimental setup (most notably on whether species tracking and fitness recalculation are activated). With a typical 2018 desktop computer, speeds of between 500,000 and 1,000,000 iterations per hour can be achieved for populations of around 250,000.

REvoSim has been in development since 2008, and has been released with the intention that it can be used as a multipurpose platform for the study of many evolutionary phenomena. While it was designed with macroevolutionary studies in mind, it is also applicable to microevolutionary problems. As such it is complementary to the many other approaches of studying evolution on a range of different timescales. It is continually developed by the core team to expand its capabilities.

t:@palaeoware

e:palaeoware@gmail.com

w:https://github.com/palaeoware

Relevant references

Software 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. https://doi.org/10.1111/pala.12420

Furness, E.N., Garwood, R.J. and Sutton, M.D., 2023. REvoSim v3.0.0: A fast evolutionary simulation tool with ecological processes. JOSS. Submitted.

Other references:

Furness, E.N., Garwood, R.J., Mannion, P.D. and Sutton, M.D., 2021. Evolutionary simulations clarify and reconcile biodiversity-disturbance models. Proceedings of the Royal Society B, 288(1949), p.20210240. https://doi.org/10.1098/rspb.2021.0240

Furness, E.N., Garwood, R.J., Mannion, P. D. & Sutton, M.D. 2021. Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations. Ecology and Evolution 11(13): 8923-8940. https://doi.org/10.1002/ece3.7730

Table of Contents

• 1. Introduction
  • 1.1. Overview
  • 1.2. Simulation setup
  • 1.3. Output setup
  • 1.4. Quick start
• 2. Compiling, Installation, and Requirements
  • 2.1. Installation
  • 2.2. System requirements
  • 2.3. Compiling from Source
• 3. Concepts and Example Usage
  • 3.1. Concepts
  • 3.2. Example Usage
• 4. Window Layout
  • 4.1. Main Menu
    • 4.1.1. Commands
    • 4.1.2. Tools
    • 4.1.3. Help
  • 4.2. Main Toolbar
  • 4.3. Population Scene
    • 4.3.1. Population Count
    • 4.3.2. Mean Fitness
    • 4.3.3. Visualisation system 1
    • 4.3.4. Visualisation system 2
    • 4.3.5. Settles
    • 4.3.6. Breed/Settle Fails (R=Breed; G=Settle)
    • 4.3.7. Species
    • 4.3.8. Interactions
    • 4.3.9. Breed list
    • 4.3.10. Pathogens word 1
    • 4.3.11. Pathogens word 2
    • 4.3.12. Stolen energy
  • 4.4. Environment Scene
  • 4.5. Information Bar
• 5. Configuring your Organisms
  • 5.1. Organism settings
  • 5.2. Breed settings
  • 5.3. Settle settings
  • 5.4. Genome Words and Systems
• 6. Setting up the Simulation
  • 6.1. Environment settings
  • 6.2. Simulation size
  • 6.3. Simulation settings
  • 6.4. Phylogeny settings
  • 6.5. Linkages
    • 6.5.1. Create new linkage
    • 6.5.2. Edit linkage
• 7. Configuring Interactions
  • 7.1. Interaction settings
  • 7.2. Pathogen settings
• 8. Configuring Outputs and Run End Log
  • 8.1. Output options
  • 8.2. Run end log
  • 8.3. Run end log options
  • 8.4. Other options
  • 8.5. Custom logs
• 9. Running Log
  • 9.1. Buttons
  • 9.2. Header text
  • 9.3. Iteration text
  • 9.4. Species text
  • 9.5. v3.0.0 log options
    • 9.5.1. Iteration keywords
    • 9.5.2. Species keywords
  • 9.6. v2.0.0 log
• 10. Genome comparison dock
• 11. Advanced Options
  • 11.1. Count peaks
  • 11.2. Custom Random Numbers
• 12. Command Line Options
  • 12.1. Running via SSH
  • 12.2. Single-letter switches
  • 12.3. Long option only switches
• 13. Tests
  • 13.1. REvoSim test log
    • 13.1.1. Test zero - Annotated output
  • 13.2. Failed Tests