DOI: 10.5061/dryad.9p8cz8wk3
title: Population dynamics of C. elegans and C. briggsae dormancy mutants

description: Dormancy allows organisms to survive hostile conditions and is
 hypothesized to enable species to coexist in fluctuating environments.
 Although determining how species avoid extinction is critical to
 understanding the dynamics of natural populations, experimental work
 exploring if and when dormancy rescues populations from extinction remains
 rare. We conducted an experiment, where we grew two species of nematode at
 three temperatures. Strains of Caenorhabditis elegans had mutations
 altering their propensity to enter a dormant stage and Caenorhabditis
 briggsae was a single strain with a wildtype background. We used those
 empirical results to parameterize a model and simulate competitive
 outcomes in fluctuating environments between the two species. We show that
 upregulating the dormancy pathway rescues populations that would otherwise
 go extinct, thereby increasing coexistence between competing species. By
 leveraging the genetic tools available from a model system, this study
 provides experimental confirmation that dormancy specifically facilitates
 species coexistence and thereby promotes diversity. This study system
 could be used more expansively to explore the role of dormancy in species
 interactions.
description: # Dormancy promotes coexistence in fluctuating environments **Description
 of the data and file structure** This R project
 “Worm_Coexistence_Oikos.R.proj” contains the data and and bespoke
 functions written.  ## **Files list (files found within
 Worm\_Coexistence\_Oikos.zip)** CoexistenceSimulation_v6.0_Functions1.R
 CoexistenceSimulation_v6.0_Functions2.R analysisUtilityFunctions_v6.0.R
 master_data.csv parameters.csv monocultureCoexistResults.tsv ##
 **Description** CoexistenceSimulation_v6.0_Functions1.R – Functions
 required to run simulation CoexistenceSimulation_v6.0_Functions2.R –
 Functions required to run simulation analysisUtilityFunctions_v6.0.R–
 Utility functions for analysing the simulation data
 Figure_1_Experimental_Results.R– This file generates Figure 1
 Figure_3_Population_Dynamics_Plots– This file generates Figure 3
 Figure_4_StackedBar&Euler– This file generates Figure 4  
 Figure_S3_Comparing_ConspvsHeterosp_Params– This file generates
 Supplementary Figure S3. parameters.csv– A .csv file containing parameters
 used in the simulation. Column description are as follows: * species– The
 species for which the measurement was made. “brig” = *Caenorhabditis
 briggsae*. “elegans” =   *Caenorhabditis elegans* (categorical)
 * Straindes– A categorical variable stating the level of
 dauer for the strain (categorical) * Strainlab–  A categorical variable
 describing the strain (categorical) * straincode– The mutant code
 (categorical) * temp_change_levels– The first number is the temperature
 during the experiment the second number is the temperature during dauer
 worm recovery part of the experiment (categorical) * new.temp– The
 temperature (degrees Celsius) during dauer worm recovery part of the
 experiment (categorical). ”NA” indicates when the treatment was in the
 first part of the experiment and thus there was no new temp. * Temp– The
 temperature (degrees Celsius) during the experiment (categorical) *
 mumax.mean–  The average maximum growth rate
 ![](file:///C:/Users/s2995092/AppData/Local/Temp/msohtmlclip1/01/clip_image002.png) (continuous) * value.max.mean– The average maximum population size (discrete) * total_dauer_worms– The total number of dauer worms produced (discrete) * dorm_invest– The dormancy parameter (*h*). The ratio of dauer worms: maximum population size (value.max.mean) (continuous) * Code– An identifier for each of the 9 treatments (categorical) * Competition– The nature of the competitive environment (categorical) * temp_change– A variable indicating whether the temperature (degrees Celsius) changed between the first part of the experiment (Temp) and the second part, when dauer worms were reactivated (new.temp) master_data.csv – A .csv file containing population size for each replicate for each day of the experiment for all treatments. Column description are as follows: * Day– The day (after start of experiment) on which the measurement was made (discrete) * new.temp–  The temperature (degrees Celsius) during dauer worm recovery part of the experiment (categorical).”NA” indicates when the treatment was in the first part of the experiment and thus there was no new temp. * res–  Whether the data is from the recovery part of the experiment (categorical) * Temperature– The temperature (degrees Celsius) during the experiment (categorical) * Code– The mutant code (categorical) * Replicate– The replicate number (categorical) * Species.1–  The species for which the measurement was made. “brig” = *Caenorhabditis briggsae*. “elegans” =   *Caenorhabditis elegans* (categorical) * Strain.1–  The mutant code (categorical) * Species.2–  The second species for which the measurement was made. “brig” = *Caenorhabditis briggsae*. “elegans” =   *Caenorhabditis elegans* (categorical) * Strain.2–  The mutant code (categorical) for the second species * Competition–  The nature of the competitive environment (categorical) * starve_day_merge– The calendar day that we categorised the replicate as having consumed all resources. Includes whether the replicate was contaminated or not. (mixed, ordinal). “NA” indicates there is no calendar day or contamination recorded. * nFluorWormsL4Adult.sum– The number of *C. briggsae* adult worms counted (numeric).“NA” indicates that there were no individuals of the stain/species present in this treatment. * nNonFluorWormsL4Adult.sum– The number of *C. elegans* adult worms counted(numeric).“NA” indicates that there were no individuals of the stain/species present in this treatment. * nFluorWormsDauer.sum– The number of *C. briggsae* dauer adult worms counted (numeric).“NA” indicates that there were no individuals of the stain/species present in this treatment. * nNonFluorWormsDauer.sum– The number of *C. elegans *dauer adult worms counted (numeric).“NA” indicates that there were no individuals of the stain/species present in this treatment. monocultureCoexistResults.tsv– A .tsv file containing the number of simulations that we documented coexistence. We use this data to generate Figure 4. Column description are as follows: * strain– The *C. elegans* strain. (WT=Wiltype, ip=Insensitive to pheromone, id=Increased  dauer)   * pulse– The pulse where coexistence was assessed (ranging from 1-15)(continuous) * cat– The strains that had coexistence in the same temperature conditions (categorical). * n– The number of simulations where coexistence occurred at the end of the simulation (discrete) * totn– The total number of simulations (discrete) **Code/Software** We used the statistical software R for this project (R version 4.3.2). The packages required are loaded within each script. It is set up as an R project.