Endosymbiosis, symbiosis in which one symbiont lives inside another, is woven throughout the history of life and the story of its evolution. From the mitochondrion residing in almost every eukaryotic cell to the gut microbiome found in every human, endosymbiosis is a cornerstone of the biological processes that sustain life on Earth. While endosym-biosis is ubiquitous, many questions about its origins remain shrouded in mystery; one question in particular regards the general conditions and possible trajectories for its evolution. Modern science has hypothesized two possible pathways for the evolution of mutualistic endosymbiosis: one where an obligate antagonism is co-opted into an obligate mutualism (Co-Opted Antagonism Hypothesis), and one where a facultative mutualism evolves into an obligate mutualism (Black Queen Hypothesis). We investigated the viability of these pathways under different environmental conditions by expanding on the evolutionary agent-based system Symbulation. Specifically, we considered the impact of ectosymbiosis on de novo evolution of obligate mutualistic endosymbiosis. We found that introducing a facultative ectosymbiotic state allows endosym-biosis to evolve in a more diverse set of environmental conditions, while also decreasing the evolution of endosymbiosis in conditions where it can evolve independently.

Bacteriophages, also known as phages, are viruses that infect bacteria. They are found everywhere in nature, playing vital roles in microbiomes and bacterial evolution due to the selective pressure that they place on their hosts. As obligate endosymbionts, phages depend on bacteria for successful reproduction, and either destroy their hosts through lysis or are maintained within the host through lysogeny. Lysis involves reproduction within the host cell and ultimately results in the disruption or bursting of the cell to release phage progeny. Alternatively, lysogeny is the process by which phage DNA is incorporated into the host DNA or maintained alongside the host chromosome, and thus the phage reproduces when their host reproduces. Recent work has demonstrated that phages can exist along the parasitism-mutualism spectrum, prompting questions of how phage would evolve one reproductive strategy over the other, and in which conditions. In this work, we present an agent-based model of bacteriophage/bacterial co-evolution that enables lysogenized phage to directly impact their host’s fitness by using the software platform Sym-bulation. We demonstrate that a viral population with beneficial lysogenic phage can select against lytic strategies. This result has implications for bottom-up control of vital ecosystems.

A mutualistic symbiosis occurs when organisms of different species cooperate closely for a net benefit over time. Mutualistic relationships are important for human health, food production, and ecosystem maintenance. However, they can evolve to parasitism or breakdown all together and the conditions that maintain and influence them are not completely understood. Vertical and horizontal transmission of mutualistic endosymbionts are two factors that can influence the evolution of mutualism. Using the artificial life system, Symbulation, we studied the effects of different rates of mutation during horizontal transmission on mutualistic symbiosis at different levels of vertical transmission. We propose and provide evidence for the “Dirty Transmission Hypothesis”, which states that higher rates of mutation during horizontal transmission can select for increased mutualism to avoid deleterious mutation accumulation.

Quorum sensing is a ubiquitous strategy in which bacteria are able to sense the presence of others via the density of a secreted molecule. Vibrio harveyi is one such bacterial species that uses quorum sensing to control a public goods cooperation strategy. As with all cooperative strategies, this strategy is at risk of cheating organisms ousting cooperators. Using the platform Empirical, we first replicated the results from a wetlab experiment and then determined the effects of population structure and resource availability on the de novo evolution, short-term, and long-term stability of a quorum sensing-controlled public goods strategy. We found that environments that enabled pre-existing cooperators to remain stable were not always the same environments in which cooperation could evolve de novo. Specifically, cooperation was able to persist in the short term in semi-structured populations with low resource levels, but not be maintained over long evolutionary time scales.