DOI: 10.5061/dryad.dv41ns23c
title: Non-trophic interactions amplify kelp harvest-induced biomass oscillations and biomass changes in a kelp forest ecological network model

description: Kelp forests are important marine ecosystems providing habitat for
 numerous species. Despite over 50 years of mechanical harvesting in the
 Northeast Atlantic, the indirect impacts of kelp harvesting and associated
 habitat loss on faunal species within kelp forests remain poorly
 understood. We investigated the consequences of kelp harvesting by
 developing an allometric trophic network model for a subtidal Northeast
 Atlantic kelp forest (dominated by Laminaria hyperborea). Additionally, we
 designed a novel mechanistic model to explore the non-trophic interactions
 between kelp and age class 0 Atlantic cod (Gadus morhua) and kelp and
 European lobster (Homarus gammarus), specifically focusing on the
 increased survival benefits provided by the kelp habitat. Simulations were
 conducted over a 50-year period, incorporating harvesting cycles of 2, 5,
 and 9 years, as well as low and high harvesting intensities. Our findings
 reveal the complex dynamics resulting from kelp harvesting. The recovery
 of kelp biomass was observed with 5- and 9-year harvesting cycles, whereas
 a decline was observed with a 2-year cycle. Furthermore, the non-trophic
 interaction facilitated a higher pre-harvest biomass for both the European
 lobster and the Atlantic cod compared to scenarios without this
 interaction. These results highlight the multitrophic effects of kelp
 harvesting and emphasize that the recovery of kelp-associated species may
 not necessarily align with kelp recovery, depending on harvesting
 intensity and recovery periods. Importantly, our study contributes to a
 better understanding of the ecological consequences of kelp harvesting and
 underscores the need for sustainable management practices to mitigate
 habitat loss in kelp ecosystems.
description: # Perälä et al. (2023) Non-trophic interactions amplify kelp
 harvest-induced biomass oscillations and biomass changes in a kelp forest
 food web model *** Authors and correspondence: Tommi Perälä,
 tommi.a.perala@jyu.fi, https://orcid.org/0000-0002-4995-5997 Susanna
 Pesari, susannapesari@hotmail.com Contents: Data: Simulation outputs
 Software: Simulator software and codes for running the simulations and
 producing the figures in the manuscript. ## Data This section consists of
 the following files and directories "README.md" - This readme
 file "Results.mat" - MATLAB formatted binary file containing
 simulation outputs and input variables In MATLAB, Results.mat can be
 loaded using the load command. In R, loading of a mat-file is done using
 the readMat function from the R.matlab package. The Results.mat file
 contains the following variables: Name Size Bytes Class Data 1x1 385678
 struct DefaultOptions 1x1 5280 struct OPTIONS 1x8 9008 struct RESULTS 1x8
 712764288 struct Data is a structure array containing the necessary input
 information about the species and their interactions in the food web.
 "Data" "B0" - Half-saturation density parameters of
 the functional response [mugC/m3] "d" - Intraspecific consumer
 interference parameters of the functional response [m3/mugC] "y"
 - Maximum consumption rate scaling factor parameters "q" -
 Hill's exponent parameters of the functional response "e" -
 Assimilation efficiency parameters "Guilds" - 1x123 Structure
 array containing guild specific information with fields: "label"
 - Guild label "name" - Guild name "type" - Guild type
 (Detritus/Producer/Consumer/Fish/Kelp) "igr" - Intrisict growth
 rate [1/day] (Producers only) "mbr" - Mass-specific metabolic
 rate [1/day] (Consumers and Fish only) "binit" - Initial biomass
 [mugC/m3] "age" - Age of fish age class "f_m" -
 Maintenance respiration coefficient "c" - Intraspecific producer
 competition coefficient "s" - Fraction of exudation (Producers
 only) "diss_rate" - Dissolution rate of POC to DOC [1/day]
 "f_a" - Activity respiration coefficient (Consumers and Fish
 only) "invest" - Strength of reproductive investment (Fish only)
 "Pmat" - Proportion of mature biomass (Fish only)
 "bodymass" - Individual body mass [mugC/individual] (Producer,
 Fish, Consumer and Kelp) "lambda" - Kelp utilization multiplier
 (Kelp habitat users only) "adjacencyMatrix" - Food web link
 structure "DefaultOptions" structure array contains the default
 options for the simulation that are overwritten by the scenario-specific
 options when needed. Contains the following nested structure
 "DefaultOptions" "Model" - Submodel options
 "Kelp" - Kelp habitat effect and harvest model options
 "alpha" - Kelp habitat user transfer rate to kelp habitat
 "Harvest" - Kelp harvest model options "cycle" -
 Length of the kelp harvest cycle [year] "rate" - Kelp harvest
 rate [1/year] "Simulation" - Simulation options
 "nGrowthDays" - Number of days in a growth season [day]
 "periodHarvestingL" - Length of the harvesting period [year]
 "periodRecoveryL" - Length of the recovery period after
 harvesting [year] "burninL" - Length of the burn in period
 [year] "startHarvest" - The start year of harvesting
 "endHarvest" - The end year of harvesting "nYears" -
 Total number of years in the simulation [year] "OPTIONS" is a 18
 cell array containing the name of the scenario and the scenario-specific
 options in structure arrays for each of the 8 different scenarios (see
 "DefaultOptions" above). "RESULTS" is a 1x8 struct
 array containing the simulation outputs for each of the 8 different
 scenarios specified in the OPTIONS cell array of structure arrays. RESULTS
 = 18 struct array with fields: "B" - Biomasses at the end of
 each simulation year [mugC/m3] "allbiomasses" - Biomasses at the
 end of each simulation day [mugC/m3] "GF" - Reproductive output
 of each fish guild for each simulation year [mugC/m3] ## Code/Software
 This section consists of the zip-file called
 Perala\_et\_al\_2023\_MarEcolProgSer.zip containing the simulator
 software. The contents of the zip-file are: "atnODE.m" -
 Gradient function of the model describing the dynamics during the growth
 season "compileOdeData.m" - Utility function for optimizing the
 model for the ODE solver "Figure2.m" - Generate Figure 2 of the
 manuscript "Figure3.m" - Generate Figure 3 of the manuscript
 "Figure4.m" - Generate Figure 4 of the manuscript
 "Figure5.m" - Generate Figure 5 of the manuscript
 "KelpForest.mat" - MATLAB formatted binary file containing the
 simulation input variable "Data" as described above
 "main.m" - Runs simulations, plots figures and creates tables
 "parseOptions.m" - Overwrites defaultOptions with scenario
 specific options "reproductionAndAging.m" - Age class transfer
 and reproduction of fish species "setScenarioOptions.m" -
 Specifies scenario-specific options "Table2.m" - Generates Table
 2 of the manuscript "updateGuildInfo.m" - Utility function for
 indexing and size information of matrices "webDriver.m" - Main
 simulation script