DOI: 10.5061/dryad.67506q4
title: Data from: Alteration of (frequency-dependent) fitness in time-shift experiments reveals cryptic co-evolution and uncoordinated stasis in a virtual Jurassic Park

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 experimental platform for addressing topics in
 both short-term and long-term evolution, such as whether co-evolving
 multispecies communities are dominated more by biotic or abiotic factors,
 and whether evolutionary stasis affects performance as well as ecological
 profile. 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 (Strong and Weak), along with unperturbed Control
 experiments. We performed several kinds of competition experiments using
 simplified versions of these communities to see whether long-term
 stability that was implied previously by ecological and phylogenetic
 metrics was also reflected in terms of performance, i.e. whether fitness
 was static over long periods of time. Results from Control and Weak
 treatment communities revealed almost completely transitive evolution,
 while Strong treatment communities showed higher incidences of
 intransitivity, with pre-treatment ecotypes often able to displace some of
 their post-recovery successors. However, pre-treatment carryovers more
 often had lower fitness in mixed communities than in their own fully
 native conditions. Replacement and invasion experiments pitting single
 ecotypes against pre-treatment reference communities showed that many of
 the invading ecotypes could measurably alter the fitnesses of one or more
 residents, usually with depressive effects, and that the strength of these
 effects increased over time even in the most stable communities. However,
 invaders taken from Strong treatment communities often had little to no
 effect on resident performance. While we detected periods of time when the
 fitness of a particular evolving ecotype remained static, this stasis was
 not permanent and was uncoordinated, never affecting an entire community
 at once. Our results lend support to the fitness-deterioration
 interpretation of the Red Queen hypothesis, and highlight community
 context-dependence in determining fitness, the shaping of communities by
 both biotic factors and abiotic forcing, and the illusory nature of
 evolutionary stasis. Our results also demonstrate the potential of digital
 evolution studies to illuminate many aspects of evolution in interacting
 multispecies communities.
description: FULL_COMM_COMP_CONFIG_PT1 Avida configuration files for full community competitions, part 1 (RAR archive)   REPINV_CONFIG_PT1 Avida configuration files for replacement and invasion experiments, part 1. (RAR archive)   FULL_COMM_COMP_CONFIG_PT2 Avida config files for full community competitions, part 2 (RAR archive)   REPINV_CONFIG_PT2 Avida config files for replacement and invasion experiments, part 2 (RAR archive)   PLOTS Base plots of fitness assays and community competitions (RAR format)   CC_IBR_PT1 Processed cumulative count and instantaneous birth rate files, pt. 1 (RAR archive)   CC_IBR_PT2 Processed cumulative count and instantaneous birth rate files, pt. 2 (RAR archive)   EXCEL_SPREADSHEETS Excel spreadsheets (.XLS and .XLSX formats) containing processed data and analysis for fitness assays, ecotype identification, summaries for full-community and invasion trials, and selection coefficient comparisons (RAR format)   SEQUENTIAL_FULL_COMM_COMP Data for sequential full-community competitions in Supplement B. (RAR format)   SELCOEFF_TEXTFILES Text files for plotting histograms of replacement and invasion trial selection coefficients (RAR format)   STABLE_COMM Stable communities for generating Avida config files to run fitness assays and competition experiments (RAR format)   SCRIPTS MATLAB and R scripts for processing, analyzing, and plotting data from fitness assays and competition experiments. (RAR format)   SEQ_COMM_COMPS_LINEAGE_COUNT_FILES Raw labeled-lineage count files for sequential community competitions in Supplement B (RAR archive)   LLTEST_REPLACEMENT_3000 Raw Avida data for detailed replacement experiments, rep. 3000 (RAR archive)   LLTEST_REPLACEMENT_3300 Raw Avida data for detailed replacement experiments, rep. 3300 (RAR archive)   LLTEST_REPLACEMENT_4100 Raw Avida data for detailed replacement experiments, rep. 4100 (RAR archive)   LLTEST_REPLACEMENT_4200 Raw Avida data for detailed replacement experiments, rep. 4200 (RAR archive)   LLTEST_REPLACEMENT_7900 Raw data for detailed replacement experiment, rep. 7900 (RAR archive)   LLTEST_REPLACEMENT_9600 Raw data for detailed replacement experiment, rep. 9600 (RAR archive)   LLTEST_REPLACEMENT_10600 Raw data for detailed replacement experiment, rep. 10600 (RAR archive)