DOI: 10.5061/dryad.g4f4qrfv7
title: Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model

description: Current ecological research and ecosystem management call for improved
 understanding of the abiotic drivers of community dynamics, including
 temperature effects on species interactions and biomass accumulation.
 Allometric trophic network (ATN) models, which simulate material (carbon)
 transfer in trophic networks from producers to consumers based on
 mass-specific metabolic rates, provide an attractive framework to study
 consumer-resource interactions from organisms to ecosystems. However, the
 developed ATN models rarely consider temporal changes in some key abiotic
 drivers that affect e.g. consumer metabolism and producer growth. Here, we
 evaluate how temporal changes in carrying capacity and light-dependent
 growth rate of producers and in temperature-dependent mass-specific
 metabolic rate of consumers affect ATN model dynamics, namely seasonal
 biomass accumulation, productivity and standing stock biomass of different
 trophic guilds, including age-structured fish communities. Our simulations
 of the pelagic Lake Constance (LC) food web indicated marked effects of
 temporally changing abiotic parameters on seasonal biomass accumulation of
 different guild groups, particularly among the lowest trophic levels
 (primary producers and invertebrates). While the adjustment of average
 irradiance had a minor effect, increasing metabolic rate associated with
 1–2˚C temperature increase led to a marked decline of larval (0-year age)
 fish biomass, but to a substantial biomass increase of 2- and 3-year-old
 fish that were not predated by ≥4-year-old top predator fish, European
 perch. However, when averaged across the 100 simulation years, the
 inclusion of seasonality in abiotic drivers caused only minor changes in
 standing stock biomasses and productivity of different trophic guilds. Our
 results demonstrate the potential of introducing seasonality in and
 adjusting the average values of abiotic ATN model parameters to simulate
 temporal fluctuations in food-web dynamics, which is an important step in
 ATN model development aiming to e.g. assess potential future
 community-level responses to ongoing environmental changes.
description: # Eloranta et al. (2023) Effects of temporal abiotic drivers on the
 dynamics of an allometric trophic network model - software codes and
 simulation outputs *** Author and correspondence: Tommi Perl,
 tommi.a.perala@jyu.fi, https://orcid.org/0000-0002-4995-5997 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
 "1\_LakeConstance\_colors.txt" - List of food web node colors.
 Used for producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi
 "1\_LakeConstance\_labels.txt" - List of food web node labels.
 Used for producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi
 "1\_LakeConstance\_links.txt" - Adjacency matrix describing the
 trophic interactions in the food web as a comma-separated list. Used for
 producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi
 "1\_LakeConstance\_TL.txt" - List of prey-averaged trophic
 levels of the nodes in the food web. Used for producing Figure 1 of the
 manuscript using https://network-visualization.bio.jyu.fi
 "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 82590 structDefaultOptions 1x1 4352 structOPTIONS 1x15
 96396 cellRESULTS 1x15 210824120 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" - 1x32 Structure array containing guild
 specific information with fields: ``` "label" - Guild label
 "name" - Guild name "type" - Guild type
 (Detritus/Producer/Consumer/Fish) "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]
 "hatchery" - The amount of fish stocked each year [mugC/m3]
 "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 and Consumer 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" - Abiotic driver submodel
 options ``` "CarryingCapacity" - Producer time-dependent
 carrying capacity model "Version" - Model version "Kc"
 - Original constant carrying capacity [mugC/m3] "z" - Decay
 component [1/day] "tmax" - Time of the average carrying capacity
 [day] "GrowthRate" - Producer light dependent intrinsic growth
 rate model "Version" - Model version "Iadj" -
 Adjustment to the mean irradiance level [W/m2] "h" - Epilimnion
 depth [m] "lambda" - Bulk attenuation coefficient [1/m]
 "I0" - Half-saturation irradiance [W/m2] "cL0" -
 Scaling coefficient "MetabolicRate" - Consumer temperature
 dependent metabolic rate model "Version" - Model version
 "T0" - Standard temperature [degreeC] "Q10" -
 Temperature-dependency coefficient "cT0" - Scaling factor
 "Temperature" - Time-dependent temperature model
 "Version" - Model version "Tadj" - Adjustment to the
 mean temperature [degreeC] "dTadj" - Yearly temperature rise
 increment [degreeC/year] ``` "Simulation" - Simulation options
 ``` "nGrowthDays" - Number of days in a growth season [day]
 "nYears" - Number of years in the simulation [year] ```
 "OPTIONS" is a 115 cell array containing the name of the
 scenario and the scenario-specific options in structure arrays for each of
 the 15 different scenarios, such as the used versions of the different
 abiotic driver submodels and their parameter values (see
 "DefaultOptions" above). "RESULTS" is a 1x15 struct
 array containing the simulation outputs for each of the 15 different
 scenarios specified in the OPTIONS cell array of structure arrays. RESULTS
 = 115 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] "G" -
 Consumption gains for each simulation year for each consumer-resource pair
 [mugC/m3] "P" - Productivity of primary producers for each
 simulation year [mugC/m3] ## Code/Software This section consists of the
 zip-file called Eloranta\_et\_al\_2023\_EcolEvo.zip containing the
 simulator software. The contents of the zip-file are:
 "1\_LakeConstance.mat" - MATLAB formatted binary file containing
 the simulation input variable "Data" as described above
 "addIndices.m" - Utility function for indexing different
 components in the ODE solution "adjacencyMatrixToFile.m" -
 Utility function for generating data for producing Figure 1 of the
 manuscript using https://network-visualization.bio.jyu.fi (see Data
 section) "atn\_ode.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
 "Figure6.m" - Generate Figure 6 of the manuscript
 "Figure7.m" - Generate Figure 7 of the manuscript
 "FigureS1.m" - Generate Figure S1 of the manuscript
 "FigureS2.m" - Generate Figure S2 of the manuscript
 "guildColorsToFile.m" - Utility function for generating data for
 producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi (see Data section)
 "guildLabelsToFile.m" - Utility function for generating data for
 producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi (see Data section)
 "main.m" - Run simulations and generate all figures
 "parseOptions.m" - Overwrites defaultOptions with
 scenario-specific options "reproductionAndAging.m" - Age class
 transfer and reproduction of fish species "setScenarioOptions.m"
 - Specifies scenario-specific options "TP\_PreyAveraged.m" -
 Calculates prey-averaged trophic positions of the nodes in the food web.
 "trophicLevelsToFile.m" - Utility function for generating data
 for producing Figure 1 of the manuscript using
 https://network-visualization.bio.jyu.fi (see Data section)
 "updateGuildInfo.m" - Utility function for indexing and size
 information of matrices "webdriver.m" - Main simulation script