DOI: 10.5061/dryad.d51c5b0fq
title: Data from: The effects of inducible defenses on population stability in <em>Paramecium aurelia</em>

description: 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. 
description: To evaluate the POE in a protist-flatworm system, we used the
 protozoa species, *P. aurelia <em>as the</em> *prey and the
 flatworm species, *S. virginianum <em>as the predator</em>.
 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
 <em>P. aurelia</em> 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
 <em>P. aurelia</em> (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
 Arrowhead<sup>TM</sup> 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 <em>P.
 aurelia</em> 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 <em>P.
 aurelia</em>), after which Lugol’s Solution was added to the petri
 dishes for a final count of flatworms and <em>P. aurelia</em>.
 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 <em>P. aurelia</em>.
 The study design was fully replicated six times with each of the three
 clonal <em>P.aurelia</em> populations.
description: # Data from: The effects of inducible defenses on population stability in
 *Paramecium aurelia* Dataset DOI:
 [10.5061/dryad.d51c5b0fq](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