Simulating the Evolutionary Effects of Environmental and Genetic Variation on Life History in Caenorhabditis

Background Information

Caenorhabditis elegans is a millimeter long roundworm (or nematode) found worldwide in soil and rotting plant matter. It commonly serves as an ideal model organism for various types of genetic and evolutionary experimental studies due to its fast life cycle, ease of maintenance, and simple neurological structure. Click here to watch a brief informational C. elegans video.

C. elegans Life History Model

I recently completed a Master of Science in Biology (Evolution/Behavior/Ecology Department), conducting research in a lab led by Dr. Scott Rifkin. I studied the evolution of a particular phase of the worm life cycle called dauer. This stage of development is an intermediate larval stage during which the worm can “choose” to go into a stasis-like state given difficult environmental conditions (e.g. overcrowding or lack of food) [Hu, 2007]. As part of my research, I developed a population ecology/evolution model in Python to simulate the development of a group of individuals and/or their offspring, their interactions with each other, and their responses to specific environmental conditions. The model takes many realistic factors into account (e.g. genetics and the role of “randomness” in decision-making) [Avery, 2014] when determining if a particular worm will go into the dauer phase of development. I also conducted studies in the laboratory to improve particular aspects of the model and, in the future, more experiments can be performed to test the accuracy of its predictions.

Abstract of the Thesis

Nematodes such as Caenorhabditis elegans, C. briggsae, C. remanei, and C. nigoni are model organisms that primarily reside in rotting fruit and plant matter, feeding on the bacteria that inhabit these degrading vegetation [Frézal & Félix, 2015]. When conditions are poor, worms must decide whether to go into a larval stage called dauer [Avery, 2014]. Entering dauer would allow the worms to survive for months; however, the risk of dying in dauer is high and this results in a tradeoff. I created an extensive model in Python to simulate the population dynamics and decision-making strategies of worms and their responses to various environmental conditions. This model includes genes related to both dauer and travel direction decision making strategies. Experiments showed significant evolution of both genes when there is stronger selection against worms in dauer, both genes when there is higher frequency of food availability, the dauer gene only when the dauer genotype to phenotype mapping is altered, and neither gene when seasonality in terms of environmental productivity is introduced. Stronger selection against worms in dauer led them to evolve a lower likelihood of dauer and a preference for traveling away from neighbors. A higher frequency of food availability also led them to evolve a lower likelihood of dauer but a preference for traveling towards food. A higher genotype to phenotype mapping value led them to evolve a lower likelihood of dauer as well. However, there may be some underlying patterns present in many of these experiments that require further study.

Files

• The file called "vectorized_RG.py" contains the model as well as various different functions for graphing the resulting data.
• The file called "modified_RG.py" also contains the model, but this script is prepared to run in the terminal. It requires user input to run.
• The file called "Worms_Life_Model.ipynb" is used to graph the results of each simulation. Just change the location and it will create many figures.
• The file called "muller_code.R" creates a couple of muller plots, but is used in conjunction with one of the functions in Python and the data from the simulation.

References

1. Avery, L. (2014). A model of the effect of uncertainty on the C elegans L2/L2d decision. PLoS ONE, 9(7).
2. Frézal, L., & Félix, M.-A. (2015). The Natural History of Model Organisms: C. elegans outside the Petri dish. eLife, 4. https://doi.org/10.7554/eLife.05849.001
3. Hu, P.J. Dauer (August 08, 2007), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.144.1, http://www.wormbook.org.