DOI: 10.5061/dryad.vx0k6djx7
title: Data from: Parasite-mediated changes in host traits alter food web dynamics

description: 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.
description: # Data from: Parasite-mediated changes in host traits alter food web
 dynamics --- Authors and correspondence: Tommi Perälä,
 ,
 Ines Klemme,
 , 
 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
 
 "LakeConstance_labels.txt" - List of food web node labels. Used
 for producing Figure 1 of the manuscript using
 
 "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
 
 "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 
 "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
 (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
 (see Data section)
 "guildLabelsToFile.m" - Utility function for generating data for
 producing Figure 1 of the manuscript using
 (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 (see
 Data section) "updateGuildInfo.m" - Utility function for
 indexing and size information of matrices "webDriver.m" - Main
 simulation script