Data from: The effects of inducible defenses on population stability in Paramecium aurelia
Data files
Oct 15, 2025 version files 168.87 KB
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DataforMcClure_et_al_2025.xlsx
163.16 KB
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README.md
5.71 KB
Abstract
What stabilizes predator-prey dynamics is often debated and not well understood. One proposed stabilizing mechanism is that the inducible defenses of prey decrease predation risk by creating a portion of the prey population that is invulnerable to predation, leading to a reduction in trophic interaction strength. We investigated the potential stabilizing effects of inducible morphological defenses in the protozoan, Paramecium aurelia, across a range of nutrient concentrations to better understand a potential stabilizing mechanism of systems under nutrient enrichment (Paradox of Enrichment).Using P. aurelia clones that differ in their ability to induce defenses, we found that the most susceptible clone that does not express any known inducible defense showed reduced survival along a gradient of increasing nutrient concentrations. Clones expressing either inducible or permanent morphological defenses (increasing body width in response to predation threat) were not significantly affected by increasing nutrients demonstrating a potential benefit of these defenses. However, when evaluating population stability (coefficient of variation) rather than survival, we found a stabilizing effect of increasing nutrients on all P.aurelia populations. Our results demonstrate varied effects of increasing nutrients on population stability depending on the level of defense expression and stability metric used. Our results reinforce that choice of stability metric can alter conclusions about population stability and persistence, highlighting the need to adopt multiple metrics and approaches.
Dataset DOI: 10.5061/dryad.d51c5b0fq
Description of the data and file structure
This dataset includes the population patterns of the protozoan, Paramecium aurelia, under an increasing nutrient concentration gradient and for a predator present/absent treatment over the course of 40 days (~40-80 generations). These data also include the time to extinction for each predator-prey treatment combination.
Brief Methods Description: To evaluate the POE in a protist-flatworm system, we used the protozoa species, P. aurelia, as the prey and the flatworm species, S. virginianum as the predator. Paramecium aurelia was used as the prey species due to the ability to rapidly raise large populations and easily quantify inducible defenses. In a petri dish, 30mL of media at a pre-determined nutrient concentration was added along with 100 protists and 10 flatworms. Every third day, both a sample of the protists as well as the total population of flatworms were counted. A 3 mL sample of each population was collected, preserved, and stained using 5% Lugol’s Solution, and then counted using a Bogorov counting chamber. If no P.aurelia were observed in the sample, the whole petri dish was then scanned to ascertain if there were still P. aurelia present in the whole population. If a population (either predator or prey) was recorded as zero in two consecutive sampling events, the population was deemed extinct, and the petri dish was removed from the experiment. At each sampling event, 3 mL of the appropriate media was then added to each petri dish to account for the removed sample and to maintain a base level of fresh nutrients. Additionally, Arrowhead Mountain Spring Mineral Water (USA) was added to each population every other week to account for any potential evaporation throughout the experiment. The experiment ran for 40 days (~ 40-80 generations of P. aurelia), after which Lugol’s Solution was added to the petri dishes for a final count of flatworms and P. aurelia.
Clonal Populations: Clonal populations included a range of inducible defense strategies. One clone (“FD4”) is “permanently induced” (i.e., expresses increased width with or without predators present), one clone (“EV2”) that does not induce (i.e., no significant increase in width with predators present), and one clone (“AUR”) shows induced changes in width in the presence of predators.
Files and variables
File: DataforMcClure_et_al_2025.xlsx
Description: This dataset includes the population patterns of the protozoan, Paramecium aurelia, under an increasing nutrient concentration gradient and for a predator present/absent treatment over the course of 40 days (~40-80 generations). These data are found in the DATA tab.
These data also include the time to extinction for each predator-prey experiment. These data include the treatment combinations for that population experiment, how many days it took until a population (either predator or prey) went extinct, and whether it was the predator or prey population that went extinct first. These data are found in the TIME TO EXTINCTION tab.
Variables
In the DATA tab:
- Sample Num: Sample number (for keeping track of number of populations and experiments)
- Nutrient: The nutrient concentration of that treatment (i.e., 0.03, 0.07, 0.15, 0.30, 0.60, and 0.80 g.L-1)
- Clone: Protist clonal population (i.e., FD4, AUR, or EV2)
- Pred: Whether predators were present or absent (coded as P for present and A for absent)
- Rep: Replicate number
- Protist Num: Starting population of protists
- Predator Num: Starting population of predators
- Date: Start date of the experiment
- Protist Count: 3ml sub-sample protist population size
- Predator Count: Predator population size
- Person Counting: Researcher measuring population size for that sampling event
- Notes: Notes include both notable events or observations, as well as when populations were not observed within that observation period and whether those populations recovered. Other important notes include when a 1mL subsample was taken instead of a 3 mL (due to high population counts) and if there was a suspected rotifer invasion within that sample.
- Total Count: Total protist population size based on subsample measured in the Protist Count column and the total volume of the petri dish (30mL). For example the population measured in a 3mL subsample was multiplied by 10 to get an estimate of the full population within the petri dish. NOTE: some populations were measured at 1mL given the large population size and the total count was adjusted in these columns for these specific instances.
In the TIME TO EXTINCTION TAB:
- Clone: Protist clonal population (i.e., FD4, AUR, or EV2)
- Nutrient: The nutrient concentration of that treatment (i.e., 0.03, 0.07, 0.15, 0.30, 0.60, and 0.80 g.L-1)
- Pred: Whether predators were present or absent (coded as P for present and A for absent)
- Rep: Replicate number
- Extinction Date: Date when one of the two populations went extinct (either predator or prey)
- Extinction Days: Number of days from the start of the experiment until one of the two populations (either predator or prey) went extinct
- Predator or Prey: Which population went extinct first -- Predator (coded as W), Prey (coded as P), both at the same time (coded as Both), or neither if both populations reached the end of the experiment (coded as N/A).
- Notes: Any notable events or observations
Code/software
Microsoft Excel
To evaluate the POE in a protist-flatworm system, we used the protozoa species, *P. aurelia as the *prey and the flatworm species, *S. virginianum as the predator. Paramecium aurelia *was used as the prey species due to the ability to rapidly raise large populations and easily quantify inducible defenses. For use in the experiment, three clonal populations of P. aurelia were chosen to represent three different levels of an inducible defense. One clone (“FD4”) isolated from First Dam in the Logan River (41°44'31.7"N, 111°47'24.5"W) is “permanently induced” (i.e., expresses increased width with or without predators present), one clone (“EV2”) that does not induce (i.e., no significant increase in width with predators present), and one clone (“AUR”) shows induced changes in width in the presence of predators. *Stenostomum virginianim *populations, a known predator of P. aurelia (Hammill et al., 2010, 2015; Kratina et al., 2007), were grown from a single individual collected in the Logan River (41°44'31.7"N, 111°47'24.5"W).
All experimental populations were maintained in new petri dishes that had been soaked in DI water for at least 24 hours before the start of the experiment. In each dish 30mL of media at a pre-determined nutrient concentration was added along with 100 protists and 10 flatworms. These initial populations of predator and prey were determined based on preliminary analyses that demonstrated that these populations are below the carrying capacity of both species but are high enough to minimize stochastic extinction events early in the experiment. Protozoa pellets (© Carolina Biological supply) dissolved in ArrowheadTM mineral water and filtered through Melitta Super Premium Unbleached brown filters (Melitta Group, Germany; were used to generate a gradient of six different nutrient levels (0.03, 0.07, 0.15, 0.30, 0.60, and 0.80 g.). Every third day, both a sample of the protists as well as the total population of flatworms were counted. A 3 mL sample of each population was collected, preserved, and stained using 5% Lugol’s Solution, and then counted using a Bogorov counting chamber. If no *P.aurelia *were observed in the sample, the whole petri dish was then scanned to ascertain if there were still P. aurelia present in the whole population. If a population (either predator or prey) was recorded as zero in two consecutive sampling events, the population was deemed extinct, and the petri dish was removed from the experiment. At each sampling event, 3 mL of the appropriate media was then added to each petri dish to account for the removed sample and to maintain a base level of fresh nutrients. Additionally, Arrowhead Mountain Spring Mineral Water (USA) was added to each population every other week to account for any potential evaporation throughout the experiment. The experiment ran for 40 days (~ 40-80 generations of P. aurelia), after which Lugol’s Solution was added to the petri dishes for a final count of flatworms and P. aurelia. In addition to the design above, trials were run under the same nutrient levels but without predators present to better understand the underlying growth rate and population patterns of P. aurelia. The study design was fully replicated six times with each of the three clonal P.aurelia populations.