Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model
Cite this dataset
Perälä, Tommi; Eloranta, Antti (2023). Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model [Dataset]. Dryad. https://doi.org/10.5061/dryad.g4f4qrfv7
Abstract
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.
README: 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
Funding
University of Jyväskylä
Natural Sciences and Engineering Research Council
European Research Council, Award: 770884
Academy of Finland, Award: 340901
Academy of Finland, Award: 317495