DOI: 10.5061/dryad.9zw3r22p7
title: Data from: Exploring the macroevolutionary impact of ecosystem engineers using an individual-based eco-evolutionary simulation

description: Ecosystem engineers can radically reshape ecosystems by modulating the
 availability of resources to other organisms through modifying either
 physical or biological aspects of the environment. The introduction or
 removal of ecosystem engineers from otherwise stable ecosystems can impact
 the diversity of co-occurring species, such as driving local extinctions
 of native taxa. While these impacts are well established over ecological
 timescales for a wealth of taxa, the macroevolutionary implications of the
 onset of ecosystem engineering behaviours are less clear. Despite this
 uncertainty, ecosystem engineering has been implicated in several major
 transitions in Earth's history including the appearance of extensive
 bioturbation during the Cambrian substrate revolution and associated
 Ediacaran-Cambrian turnover and the Great Oxygenation Event. Whether
 ecosystem engineers are frequently associated with turnover and extinction
 in deep time is not known. Here we investigate this with an
 eco-evolutionary simulation framework in which we assign lineages the
 ability to impact the fitness of co-occurring taxa through
 phenotype-environment feedback. We explore numerous conditions, including
 how frequently these feedbacks occur, and whether ecosystem engineers
 modify or create niches. We show that there is no general expected outcome
 from the introduction of ecosystem engineers. In a minority of runs,
 ecosystem engineering lineages completely dominate, rendering all others
 extinct, but in others, they persist (but do not dominate), or die out. We
 suggest that ecosystem engineers have complex impacts but possess the
 capacity to profoundly shape diversity, and it is appropriate to consider
 them alongside other exogenous extinction drivers in deep time. 
description: # Data from: Exploring the macroevolutionary impact of ecosystem engineers
 using an individual-based eco-evolutionary simulation
 [https://doi.org/10.5061/dryad.9zw3r22p7](https://doi.org/10.5061/dryad.9zw3r22p7) This folder contains the supplementary information for the paper *Exploring the macroevolutionary impact of ecosystem engineers using an individual-based eco-evolutionary simulation* In the root directory, there is a bash script called Run_pipeline.sh - running this will extract the data to your machine, and then run the required R analyses before outputting the figures for you in the root directory. It may be necessary to provide these execute permissions (i.e. run chmod +x ./Run_pipeline.sh in the root directory). ## Subfolder "Simulation\_data" Inside the subfolder "Simulation_data", there are five compressed folders: (1) Baseline_runs.zip, (2) EE_once_add_mask.zip, (3) EE_once_overwrite_mask.zip, (4) EE_persistent_add_mask.zip, and (5) EE_persistent_overwrite_mask.zip These folders contain the raw data generated by TREvoSim 3.0.0 (1) in the absence of ecosystem engineering, (2) when a mask is added at the halfway point but otherwise left unaltered, (3) when a mask is added at the halfway point and overwritten every 500 generations, (4) when a mask is overwritten at the halfway point, and (5) when a mask is overwritten at the halfway point and overwritten every 500 generations respectively. If being run manually (i.e. not using the shell script), these should be extracted to identically named folders within Simulation_data ## Subfolder "Analytical\_pipeline" Inside subfolder "Analytical_pipeline", there three R scripts. If the analysis is manual (i.e. not using the shell script), these should be run in the following order: (1) data_processing_and_analysis.R, (2) plotting_figure_3.R, and (3) rate_calculation_and_plotting.R data_processing_and_analysis.R generates lineage through time data from the raw TREvoSim outputs for all EEs and a randomly selected non-EE, calculates the proportion of replicates in which these lineages survive and dominate for each simulation, and collates the final species richness of each replicate. plotting_figure_3.R plots the proportion of replicates in which randomly selected non-EE and EE lineages survive until the end of the simulation, dominate the simulation, and go extinct. rate_calculation_and_plotting.R calculates the per-iteration, per-lineage extinction and speciation rates for each simulation and plots them.