Data from: Parasite-mediated changes in host traits alter food web dynamics
Data files
Jan 10, 2024 version files 126.26 MB
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figure2_data.csv
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figure3_data.csv
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figure4_data.csv
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figureS1_data.csv
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figureS2_data.csv
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figureS3_data.csv
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figureS4_data.csv
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LakeConstance_colors.txt
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LakeConstance_labels.txt
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LakeConstance_links.txt
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LakeConstance_TP.txt
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README.md
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Results.mat
Abstract
Parasites commonly alter the phenotype of their host, thereby influencing competitive and consumer-resource interactions. This could trigger a cascade effect on the dynamics of biological communities, but the role of parasites in ecosystem processes is poorly understood. In this study, we investigate how parasite-induced trait modifications shape the dynamics of a complex lake food web using an allometric trophic network model (ATN). We simulated infections of stage-structured fish host populations via increased maintenance costs and predation risk. Our results show that host trait modifications can significantly impact host demography, with stage-specific biomass declines up to 60%. However, less severely affected host stages buffered these effects and sustained the population. Importantly, host biomass decline altered the dynamics of species interactions and these effects cascaded through the entire community, with biomass changes observed at all trophic levels. Our findings emphasize the importance of incorporating both indirect parasite effects and host life history in ecological network studies for more realistic simulations of community dynamics.
README: Data from: Parasite-mediated changes in host traits alter food web dynamics
Authors and correspondence:
Tommi Perälä, tommi.a.perala@jyu.fi, https://orcid.org/0000-0002-4995-5997
Ines Klemme, ines.klemme@jyu.fi, https://orcid.org/0000-0001-9757-7356
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
"figure2_data.csv" - Simulation output data for producing Figure 2 in the manuscript as a comma-separated list. First is the title row followed by the data. The figure illustrates changes in the biomass of 30 functional guilds (guild labels are represented in the column 'guild') in a lake food web. These changes are induced by increased host maintenance costs due to parasitic infections, with the maximum increase set to 10%, 25%, and 50% (column 'parameters'). Percentage changes in biomass, relative to the absence of parasitism, are produced for three scenarios based on the susceptible host or hosts: perch (column 'P'), whitefish ('W'), and both species ('WP').
"figure3_data.csv" - Simulation output data for producing Figure 3 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by a reduced refuge-searching rate due to parasitic infections, with the maximum reduction set to 50%, 90%, and 99%.
"figure4_data.csv" - Simulation output data for producing Figure 4 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by parasites simultaenously increasing host maintenance costs and reducing host refuge-searching rate, with the following combinations of maximum increase/reduction: 10%/50%, 25%/90%, and 50%/99.
"figureS1_data.csv" - Simulation output data for producing Figure S1 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by an increased capture rate due to parasitic infections, with the maximum increase set to 100%, 250%, and 500%.
"figureS2_data.csv" - Simulation output data for producing Figure S2 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by parasites simultaenously increasing host maintenance costs and reducing host refuge-searching rate, with the following combinations of maximum increase/reduction: 10%/50%, 10%/90%, and 10%/99.
"figureS3_data.csv" - Simulation output data for producing Figure S3 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by parasites simultaenously increasing host maintenance costs and reducing host refuge-searching rate, with the following combinations of maximum increase/reduction: 25%/50%, 25%/90%, and 25%/99.
"figureS4_data.csv" - Simulation output data for producing Figure S4 in the manuscript as a comma-separated list. The figure and data structure are similar to Figure 2, but here changes in biomass are induced by parasites simultaenously increasing host maintenance costs and reducing host refuge-searching rate, with the following combinations of maximum increase/reduction: 50%/50%, 50%/90%, and 50%/99.
"LakeConstance_colors.txt" - List of food web node colors. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi
"LakeConstance_labels.txt" - List of food web node labels. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi
"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
"LakeConstance_TP.txt" - List of prey-averaged trophic positions 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 80618 struct
DefaultOptions 1x1 2792 struct
OPTIONS 1x55 82694 cell
RESULTS 1x55 175055136 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]
"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)
"vb" - von Bertalanffy parameters L0 [cm], Linf [cm] and k [1/year] for fish species
"species" - Fish species identifier
"phi" - The fraction of parasite infected biomass in a fish guild
"mu" - The average number of parasites per infected individual in a fish guild
"Phi" - Hypothetical distribution of the number parasites in a fish guild
"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
"Parasitism" - Parasitism submodels
"Maintenance" - Increased maintenance cost model
"Version" - Model version (for [whitefish perch])
"mu_max" - Number of parasites required for the maximal effect
"PreyRefuge" - Decreased prey refuge search rate model
"Version" - Model version (for [whitefish perch])
"mu_max" - Number of parasites required for the maximal effect
"IncreasedPredationRisk" - Increased capture rate model
"Version" - Model version (for [whitefish perch])
"mu_max" - Number of parasites required for the maximal effect
"Simulation" - Simulation options
"nGrowthDays" - Number of days in a growth season [day]
"periodL" - Length of the actual simulation [year]
"burninL" - Length of the burn in period [year]
"nYears" - Total number of years in the simulation [year]
"OPTIONS" is a 1×55 cell array containing the name of the scenario and the scenario-specific options in structure arrays for each of the 55 different scenarios, such as the used versions of the different parasitism submodels and their parameter values (see "DefaultOptions" above).
"RESULTS" is a 1x55 struct array containing the simulation outputs for each of the 55 different scenarios specified in the OPTIONS cell array of structure arrays.
RESULTS =
1×55 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]
Code/Software
This section consists of the zip-file called Klemme_et_al_2023_Oikos.zip containing the simulator software. The contents of the zip-file are:
"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)
"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.R" - Generate Figure 2 of the manuscript in R
"figure3.R" - Generate Figure 3 of the manuscript in R
"figure4.R" - Generate Figure 4 of the manuscript in R
"figureS1.R" - Generate Figure S1 of the manuscript in R
"figureS2.R" - Generate Figure S2 of the manuscript in R
"figureS3.R" - Generate Figure S3 of the manuscript in R
"figureS4.R" - Generate Figure S4 of the manuscript in R
"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)
"LakeConstance.mat" - MATLAB formatted binary file containing the simulation input variable "Data" as described above
"parseOptions.m" - Overwrites defaultOptions with scenario specific options
"printFigureDataToCSV.m" - Extract the figure data from results and save as csv-files
"reproductionAndAging.m" - Age class transfer and reproduction of fish species
"setScenarioOptions.m" - Specifies scenario-specific options
"TableS4.m" - Print data for TableS4 of the manuscript
"TP_PreyAveraged.m" - Calculates prey-averaged trophic positions of the nodes in the food web.
"trophicPositionsToFile.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