DOI: 10.5061/dryad.tq1g3j7
title: Data from: Examining community stability in the face of mass extinction in communities of digital organisms

description: Digital evolution is a computer-based instantiation of Darwinian evolution
 in which short self-replicating computer programs compete, mutate, and
 evolve. It is an excellent platform for addressing topics in long-term
 evolution and paleobiology, such as mass extinction and recovery, with
 experimental evolutionary approaches. We evolved model communities with
 ecological interdependence among community members, which were subjected
 to two principal types of mass extinction: a pulse extinction that killed
 randomly, and a selective press extinction involving an alteration of the
 abiotic environment to which the communities had to adapt. These
 treatments were applied at two different strengths, along with unperturbed
 control experiments. We examined how stability in the digital communities
 was affected from the perspectives of division of labor, relative shift in
 rank abundance, and genealogical connectedness of the community's
 component ecotypes. Mass extinction that was due to a Strong Press
 treatment was most effective in producing reshaped communities that
 differed from the pre-treatment ones in all of the measured perspectives;
 weaker versions of the treatments did not generally produce significant
 departures from a Control treatment; and results for the Strong Pulse
 treatment generally fell between those extremes. The Strong Pulse
 treatment differed from others in that it produced a slight but detectable
 shift towards more generalized communities. Compared to Press treatments,
 Pulse treatments also showed a greater contribution from re-evolved
 ecological doppelgangers rather than new ecotypes. However, relatively few
 Control communities showed stability in any of these metrics over the
 whole course of the experiment, and most did not represent stable states
 (by some measure of stability) that were disrupted by the extinction
 treatments. Our results have interesting, broad qualitative parallels with
 findings from the paleontological record, and show the potential of
 digital evolution studies to illuminate many aspects of mass extinction
 and recovery by addressing them in a truly experimental manner.
description: MRS10_DATARaw and collated data for mean rank shiftDIT_BASE_DATARaw and collated data for basic mutual entropy/DIT analysisSTABLE_TRAJECTORY_DATAAdditional data for supplementary DIT stable trajectory analysisGSS_ALL_TREE_FILESLabeled Newick-format phylogenetic trees used for GSS calculation & analysisGSS_ALL_PHENOTYPELIST_FILESAll phenotype list files used for GSS calculation & analysisGSS_ALL_PHENOTYPELISTS.tarGSS_ALL_PICANTE_COMMTRAITFILESAll Picante-format community and trait files for GSS calculation and analysisALL_DETHISTS_NOHEADERSAll Avida detail and historic files needed to generate phylogenetic trees and for GSS analysis. Header lines stripped off for easy loading into R.MATLABSCRIPTS1MATLAB scripts for: converting population files into Newick trees (incl. Windows executable), calculating mutual entropy and phenotype lists, converting population files into Picante dataRSCRIPTS1.tarR scripts for processing and analysis of mean rank shift, mutual entropy, and GSS data. Also includes a stray MATLAB script for labeling Newick trees with phenotypic data.AVIDA_CONFIGAvida configuration files used to generate data for experimentsBCI_DATARaw and collated data for supplementary Bray-Curtis index, with MATLAB script to calculate it from Avida population filesSTRONGPRESS_POPDETAILSRecalculated Avida detail files for STRONG PRESS experimentsWEAKPRESS_POPDETAILSRecalculated Avida detail files for WEAK PRESS experimentsCONTROL_POPDETAILSRecalculated Avida detail files for CONTROL experimentsWEAKPULSE_POPDETAILSRecalculated Avida detail files for WEAK PULSE experimentsSTRONGPULSE_POPDETAILSRecalculated Avida detail files for STRONG PULSE experiments