Can manipulative parasites modify host-mediated trophic effects? Experimental evidence from Schistocephalus solidus and three-spined sticklebacks
Data files
Mar 24, 2026 version files 79.45 KB
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DrakulaCode.zip
69.66 KB
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README.md
9.80 KB
Abstract
Parasites can alter host traits, thereby reshaping host interactions and modifying density- and trait-mediated effects in trophic cascades. But despite increasing research in parasite ecology, the cascading effects of parasitism from individual hosts to population and community levels remain underexplored. Here, we aim to fill this gap by conducting a large-scale mesocosm experiment replicating key phases of the parasite’s development to test our hypothesis that the trophically transmitted tapeworm Schistocephalus solidus weakens stickleback-driven trophic cascades by altering host performance and feeding behaviour. We quantified parasite effects on three-spined sticklebacks (Gasterosteus aculeatus) and their prey communities. Schistocephalus solidus infection reduces stickleback body condition and shifts zooplankton biomass, transiently dampening the likelihood and strength of stickleback-driven trophic cascades at specific time points of infection. Using structural equation models, we show that parasite-driven trait-mediated indirect effects (TMIEs) are equivalent to density-mediated indirect effects (DMIEs) on trophic cascades. Strikingly, our results suggest that infection increases per capita zooplankton consumption of fish and amplifies parasite-driven TMIEs, counterbalancing the effects of DMIEs due to fish mortality.Overall, our findings highlight the complexity of host-parasite interactions and their community and ecosystem-level consequences.
Associated Research Paper
Title: Can manipulative parasites modify host-mediated trophic effects? Experimental evidence from Schistocephalus solidus and three-spined sticklebacks
Repository Description
This repository contains the code, data, and models for analyzing ecological data related to fish diets, zooplankton biomass, and trophic cascades. The project is organized into several directories for reproducible research and efficient data analysis.
Repository Structure
Contains raw data files used in the analyses:
-data/FishDiet.csv: Data on fish status and diet composition (metadata)
| Column Name | Description |
|---|---|
| Tank | Identifier for the experimental tank. |
| Fish_ID | Unique identifier for each fish. |
| Full_mass_g | Total mass of the fish (g). |
| Block | Block identifier for experimental design (e.g., randomized block design). |
| Treatment | Experimental treatment applied to the tank (e.g., control (No fish), fish no parasite (P-), and Fish and Parasite (P+). |
| Family_P | Family of the parasite infecting the fish (if applicable). |
| Parasite | Boolean vale if fish was infected (if applicable). |
| Infected | Binary indicator of infection status (1 = infected, 0 = not infected). |
| Lean_mass_g | Lean mass of the fish (g), excluding parasite mass. |
| End_Size_mm | Final size of the fish (mm) at the end of the experiment. Calculated based of photos. |
| Parasite_load_N | Number of parasites infecting the fish. |
| P_load | Short name for Parasite_load_N. |
| P_mass_gr_sum | Total mass of all parasites in the fish (g). |
| P_mass_gr_mean | Mean mass of individual parasites in the fish (g). |
| P_mass_gr_std | Standard deviation of parasite mass in the fish (g). |
| scaled_mass_index | Body condition measured as Scaled mass index. |
| Cladocera | mg of Cladocera (a type of zooplankton). |
| Benthic_Macro | mg of benthic macroinvertebrates. |
| Chydoridae | mg of Chydoridae (a family of cladocerans). |
| Benthic_Micro | mg of benthic microorganisms. |
| Copepods | mg of copepods (a type of zooplankton). |
| Rotifera | mg of rotifers. |
| Surface | mg of surface-dwelling organisms. |
| S_Full_weight_mg | Full weight of the stomach contents (mg). |
| S_Empty_weight_mg | Empty weight of the stomach (mg). |
| Food_weight_mg | Weight of the food in the stomach (mg), including unidentify food. |
| PS_by_block | Diet similarity (Pianka's index) calculated within experimental blocks. |
| PS_by_tank | Diet similarity (Pianka's index) calculated within tanks. |
| PS_all | Diet similarity (Pianka's index) calculated across all samples. |
| Comments | Additional notes or comments about the sample or data. |
Missing values in FishDiet.csv:
Empty cells in this file represent missing or not applicable data. R reads these empty cells as NA automatically, which is required by the analysis scripts. The specific cases are:
- Family_P: Empty for fish in the P- (parasite-free) treatment. These fish were not exposed to any parasite family, so the field is not applicable.
- End_Size_mm: Empty for two fish (A191 and A192) whose photographs were not available, making photo-based size measurement impossible (data not available).
- scaled_mass_index: Empty for the same two fish (A191 and A192) because the scaled mass index depends on
End_Size_mm, which could not be calculated without a size measurement (data not available). - P_mass_gr_std: Empty for fish infected by a single parasite (parasite load = 1). The standard deviation of parasite mass is mathematically undefined when only one parasite is present (not applicable).
- Comments: Empty when there are no additional notes for the observation (not applicable).
-data/ZooplanktonBiomass.csv: Data on zooplankton biomass (metadata)
| Column Name | Description |
|---|---|
| Tank | Identifier for the experimental tank. |
| Block | Block identifier for experimental design (e.g., randomized block design). |
| Treatment | Experimental treatment applied to the tank (e.g., control, predator). |
| Sampling | Sampling event identifier (e.g., time point or replicate). |
| Week | Week of the experiment when the data was collected. |
| Calanoida | Biomass (mg/L) Calanoida (a type of zooplankton). |
| Daphniidae | Biomass (mg/L) Daphniidae (a family of water fleas). |
| Polyphemidae | Biomass (mg/L) Polyphemidae (a family of zooplankton). |
| Bosminidae | Biomass (mg/L) Bosminidae (a family of small crustaceans). |
| Chydoridae | Biomass (mg/L) Chydoridae (a family of cladocerans). |
| Cyclopoida | Biomass (mg/L) Cyclopoida (a type of copepod). |
| Nauplius | Biomass (mg/L) nauplius larvae (early stage of crustaceans). |
| Chaoborus | Biomass (mg/L) Chaoborus (a genus of phantom midges). |
| Leptodora | Biomass (mg/L) Leptodora (a genus of predatory water fleas). |
| Ploima | Biomass (mg/L) Ploima (a type of rotifer). |
| Acari | Biomass (mg/L) Acari (mites). |
| Sididae | Biomass (mg/L) Sididae (a family of cladocerans). |
| Keratella | Biomass (mg/L) Keratella (a genus of rotifers). |
| Ostracoda | Biomass (mg/L) Ostracoda (seed shrimp). |
| Scapholebris | Biomass (mg/L) Scapholebris (a genus of cladocerans). |
| Trichocera | Biomass (mg/L) Trichocera (a genus of midges). |
| phytoplankton | Biomass (ug/L) phytoplankton (microscopic algae). |
| N_infected | Number of infected fish in the tank. |
| N_fish | Total number of fish in the tank. |
| Prevalence | Proportion of infected fish (N_infected / N_fish). |
| ZooBM | Total zooplankton biomass in the tank. |
Figures/
Directory for storing generated figures from the analyses.
Models/
Contains model outputs and related files.
R/
Contains R scripts for data analysis and visualization:
00-MasterScript.R: Main script to run all analyses in sequence. Sets up environment, loads data, and sources all analysis scripts.01-Survival.R: Analysis of fish survival across treatment groups. Creates Figure 1A showing survival rates with Bayesian credible intervals.02-Parasite.R: Analysis of parasite prevalence and load. Creates panels for Figure 2 showing parasite infection patterns.03-StomachFullness.R: Analysis of stomach fullness index and its relationship with body condition. Creates thedatandataset used by subsequent analyses.04-BodyCondition.R: Analysis of the effects of parasite exposure and infection on fish body condition (scaled mass index). Creates Figure 2 panels.05-DietComposition.R: Analysis of taxonomic diet composition using multivariate Beta regression. Tests whether treatment affects prey proportions. Creates Figure 3.06-ZooplanktonAnalyses.R: Analysis of zooplankton community composition, diversity, and biomass across treatments and time. Creates Figure 4 showing temporal dynamics.07-TrophicCascade.R: Structural equation models (SEM) to quantify density- and trait-mediated indirect effects (DMIE/TMIE). Creates Figure 5 showing relative contributions of mechanisms. SourcesTC_scenario1.RandTC_scenario2.R.TC_scenario1.R: SEM analysis under Scenario 1 (early mortality assumption). Fits four SEM versions, selects the best model via LOO-CV, and calculates DMIE/TMIE contributions with weekly temporal variation.TC_scenario2.R: SEM analysis under Scenario 2 (late mortality assumption). Same structure as Scenario 1 but assumes all fish survived until the final sampling week.functions.R: Custom functions used across scripts (e.g.,detect_project_root(),safe_print(),fullness(),LOS(),TC_LOS(),Perct_change_post(), etc.).
Usage
1. Set Up Your Environment
Ensure you have R installed on your system. You can download it from CRAN.
If you use RStudio, make sure to set up the working directory to the DrakulaCode folder. In VScode, you can open the DrakulaCode folder and the working environment will be automatically set up.
2. Install Required R Packages
The script uses several R packages. Run the following command in your R console to install any missing packages:
Run the following command in your R console to install the required packages:
install.packages(c("tidyverse", "brms", "smatr", "tidybayes", "broom", "broom.mixed","ggplot2", "HDInterval", "patchwork", "ggpubr", "extrafont", "rstan", "vegan", "MASS", "corrplot"))
3. Run the master script:
Open R/00-MasterScript.R in RStudio or your preferred IDE and execute it to run all analyses.
Outputs
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Figures generated from the analyses will be saved in the
Figures/directory. -
Models can also be save as RDS files in the
Models\folder.