DOI: 10.5061/dryad.m62ms
title: Data from: Interactive effects of predator and prey harvest on ecological resilience of rocky reefs

description: A major goal of ecosystem-based fisheries management is to prevent
 fishery-induced shifts in community states. This requires an understanding
 of ecological resilience: the ability of an ecosystem to return to the
 same state following a perturbation, which can strongly depend on species
 interactions across trophic levels. We use a structured model of a
 temperate rocky reef to explore how multi-trophic level fisheries impact
 ecological resilience. Increasing fishing mortality of prey (urchins) has
 a minor effect on equilibrium biomass of kelp, urchins, and spiny lobster
 predators, but increases resilience by reducing the range of predator
 harvest rates at which alternative stable states are possible.
 Size-structured predation on urchins acts as the feedback maintaining each
 state. Our results demonstrate that the resilience of ecosystems strongly
 depends on the interactive effects of predator and prey harvest in
 multi-trophic level fisheries, which are common in marine ecosystems but
 are unaccounted for by traditional management.
description: Rocky reef multi-trophic
 level fisheries model: baselineR script to run the
 baseline model.Baseline.RRocky reef multi-trophic level fisheries model: equilibria FL x FUR script to run simulations across values of both lobster and urchin fishing ratesEquilibria_FL_FU.RRocky reef multi-trophic level fisheries model: equilibria FL x sigmaR script to run simulations across values of lobster fishing and urchin recruitment facilitation strengthEquilibria_FL_Sigma.RRocky reef multi-trophic level fisheries model: equilibria FU x sigmaR script to run simulations across values of urchin fishing and urchin recruitment facilitation strengthEquilibria_FU_Sigma.RRocky reef multi-trophic level fisheries model: Hysteresis FL x FUR script to run simulations testing for hysteresis across values of lobster and urchin fishingHysteresis_FL_FU.RRocky reef multi-trophic level fisheries model: Hysteresis FL x sigmaR script to run simulations testing for hysteresis across values of lobster fishing and urchin recruitment facilitationHysteresis_FL_Sigma.RRocky reef multi-trophic level fisheries model: Hysteresis FU x FLR script to run simulations testing for hysteresis across values of urchin fishing and lobster fishingHysteresis_FU_FL.RRocky reef multi-trophic level fisheries model: Hysteresis FL x FU- No Size StructureR script to run simulations testing for hysteresis across levels of lobster and urchin fishing, attack rates of predators on urchins are all equal (ie, no size-structured predation)Hysteresis_FL_FU_NoSizeStructure.RRocky reef multi-trophic level fisheries model: Hysteresis FL x FU- Extra Size StructureR script to run simulations testing for hysteresis across values of lobster and urchin fishing with predator attack rates on urchins more disparate across sizes (ie, enhanced size-structured predation)Hysteresis_FL_FU_XtraSizeStructure.RRocky reef multi-trophic level fisheries model: BistabilityR script to run simulations examining the full range of parameter space (FL x FU) at sigma= 0, 0.5, and 0.95. Attack rates are set at the baseline level. This provides regions of kelp forest, urchin barren, and bistability.Stability_FL_FU.RRocky reef multi-trophic level fisheries model: Bistability No Size StructureR script to run simulations examining the full range of parameter space (FL x FU) at sigma= 0, 0.5, and 0.95. Attack rates are set to be equal across urchin sizes. This provides regions of kelp forest, urchin barren, and bistability.Stability_FL_FU_NoSizeStruct.RRocky reef multi-trophic level fisheries model: Bistability Extra Size StructureR script to run simulations examining the full range of parameter space (FL x FU) at sigma= 0, 0.5, and 0.95. Attack rates are set for enhanced size-structured predation. This provides regions of kelp forest, urchin barren, and bistability.Stability_FL_FU_XtraSizeStruct.RRocky reef multi-trophic level fisheries model: Global sensitivity analysisR script to run a global sensitivity analysis (GSA) of all 24 parameters in the rocky reef multi-trophic level fisheries model. This GSA uses random forest to quantify parameter importance to the modeled outcome (mean trophic level at equilibrium). It then uses classification and regression trees to determine specific breakpoints in parameter space which drive modeled outcome. We use a uniform distribution for each parameter to set up 4,000 parameter sets which we then simulate the model using. Other distributions can also be used (Gaussian provided very similar results).GSA_Uniform.RRocky reef multi-trophic level fisheries model: baseline & hysteresis with external recruitmentR script to run simulations of the rocky reef multi-trophic level fisheries model now including a constant level of external recruitment into the small urchin compartment. We simulate the baseline time series as well as tests of hysteresis for: FL x FU, FL x sigma, and FU x sigma.Baseline_Hysteresis_ExtraRecment.RRocky reef multi-trophic level fisheries model: SheepheadR script to run simulations testing the effect of changing predator attack rates and handling times to reflect predation by the fish, California sheephead.Sheephead.RRocky reef multi-trophic level fisheries model: baseline + harvestR script to run simulations calculating lobster and urchin fishery harvest at each time step. We use these to estimate the fishery harvest level at maximum sustainable yield (F_msy) for lobsters at three levels of urchin harvest.3stage_WithHarvest.R