Population dynamics of C. elegans and C. briggsae dormancy mutants
Data files
Sep 05, 2024 version files 18.79 KB
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parameters.csv
12.96 KB
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README.md
5.83 KB
Abstract
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 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
(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.