Microbial evolution in changing environments

Abstract

{\it Chapter 1.} Compensatory mutations play a critical role in the evolution of drug resistance in microorganisms. Most directly, they serve to alleviate the fitness cost commonly associated with initial drug resistance mutations. Here we use experimental evolution to examine adaptation to the cost of rifampicin resistance in an antibiotic-free environment, and ask whether compensatory mutations that restore fitness back to ancestral levels could also be further increasing the level of drug tolerance in these resistant isolates. We suggest that the identity of the initial resistance conferring mutations may influence the relative frequency at which drug tolerance increases during compensatory evolution through epistatic interactions. {\it Chapter 2.} The evolutionary transition to multicellularity likely began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. In this chapter, we focus on how the transition to multicellularity may be stabilized against evolutionary reversion when environmental conditions change and tip the balance of selection back in favor of unicellularity. Using mathematical modeling, we show how multicellular adaptations can act as evolutionary "ratchets", limiting the potential for reversion to unicellularity. {\it Chapter 3.} Evolutionary transitions in individuality (ETIs) occur when formerly autonomous organisms evolve to become parts of a new, ‘higher-level’ organism. Here we explore the key role that simple multicellular life cycles in facilitating this transition. Specifically, we use mathematical models to compute how canonical early life cycles vary in their ability to fix beneficial mutations via mathematical modeling. Building on our prevous work (Chapter 2), we show how life cycles that lack a persistent single-cell stage and develop clonally are far more likely to fix ‘ratcheting’ mutations that limit evolutionary reversion to the pre-ETI state. {\it Chapter 4.} Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changes in the environment. Theory suggests that the adaptive value of plasticity depends on the degree of environmental heterogeneity and the existence of environmental cues that provide reliable information about selective conditions. We tested this prediction using experimental evolution. We find that temporally varying selection can favor the evolution of phenotypic plasticity in experimental populations of yeast when selection is predictable but that plasticity is lost when selection in unpredictable. {\it Chapter 5.} Fitness trade-offs, while central to all of life history theory, are thought to take on a particularly important role during major evolutionary transitions such as the evolution of multicellularity. Specifically, trade-offs between survival and reproduction may drive increases in complexity and cellular differentiation. Here we used computer simulations of digital mulitcellular organisms to explore how trade-offs could promote the evolution of multicellular complexity. {\it Chapter 6.} In this chapter, we review how game theory can be a useful first step in modeling and understanding interactions among bacteria that produce and resist antibiotics. We introduce the basic features of evolutionary game theory and explore model microbial systems that correspond to some classical games. Each game discussed defines a different category of social interaction with different resulting population dynamics (exclusion, coexistence, bistability, cycling). We then explore how the framework can be extended to incorporate some of the complexity of natural microbial communities.