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Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a "contextual organismality" framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.

Background: Steinernematid nematodes form obligate symbioses with bacteria from the genus Xenorhabdus. Together Steinernema nematodes and their bacterial symbionts successfully infect, kill, utilize, and exit their insect hosts. During this process the nematodes and bacteria disassociate requiring them to re-associate before emerging from the host. This interaction can be complicated when two different nematodes co-infect an insect host. Results: Non-cognate nematode-bacteria pairings result in reductions for multiple measures of success, including total progeny production and virulence. Additionally, nematode infective juveniles carry fewer bacterial cells when colonized by a non-cognate symbiont. Finally, we show that Steinernema nematodes can distinguish heterospecific and some conspecific non-cognate symbionts in behavioral choice assays. Conclusions: Steinernema-Xenorhabdus symbioses are tightly governed by partner recognition and fidelity. Association with non-cognates resulted in decreased fitness, virulence, and bacterial carriage of the nematode-bacterial pairings. Entomopathogenic nematodes and their bacterial symbionts are a useful, tractable, and reliable model for testing hypotheses regarding the evolution, maintenance, persistence, and fate of mutualisms.

Myrmecophytic plant species form associations where the ant colony inhabits structures in the plant and offers protection against herbivory in exchange for food and shelter. Widely distributed across the tropics, myrmecophytic mutualisms are particularly diverse in the Neotropics, a region characterized by the rapid and recent uplift of the Andean mountain range. It has been suggested that the abrupt change in terrain triggered the emergence of new niches, new barriers to gene ow and speciation. Studying ant-plant associations in the Neotropics not only provides insight into how associations evolve in time but also the impact that external factors, such as geographic changes, have in the evolution of mutualisms. Because of its wide distribution on both sides of the Andes, The Tococa guianensis- Azteca system is useful to explore the effects the Andean uplift had on the evolution of mutualisms. This thesis aims to 1. Identify the ants associating with T. guianensis and the lineages of ants and plants involved in the mutualisms in different populations on both sides of the Andes, 2. generate genomic data for both ants and plants to increase sampling of loci, and 3. estimate and calibrate the species trees to compare patterns of phylogenetics and temporal congruence between ants, plants and the Andean uplift. Most ant-plant studies focus on only one partner or study both partners by using already collected data for one of them. This project is the first study inferring the evolutionary history of both partners associated at that point in time and across a large area. This thesis identifies two main Azteca lineages associated with T. guianensis, each one distributed on different sides of the Andes. It addresses the monophyly of T. guianensis (and related species) and why such monophyly cannot be confirmed. Results show how both plants and ants were geographically structured congruent with timing of a split of populations coinciding with the Andean uplift. Moreover, four plants and fifteen ant genomes were assembled and used to estimate gene and species trees. For Tococa, candidate markers were selected for future resolution of the plant's phylogeny. Different histories but similar divergence times between ants and plants suggest that the mutualism has evolved in response to geographic changes rather than through codiversication, but that the mutualism persists thanks to the availability of the host. The information generated during this study provides the basis to understand the evolution of mutualisms, the genomic features of ants and plants and opens the possibility for Tococa and Azteca to become a model system.

The mutualism between the dioecious Ficus tinctoria and its pollinators was studied at Hsitzewan, Kaohsiung. I investigated the phenology of F. tinctoria from December 2004 to May 2006. Wasps trapped in sticky boards were recorded from April 2005 to May 2006. The average diameter of receptive figs (B phase) of female F. tinctoria was significantly different from that of functional male trees (P < 0.01), but both with similar coloration. The durations of pre-receptive figs (A phase) through wasp- releasing figs (D phase) or mature figs (E phase) in F. tinctoria were slight longer in winter and spring (8.3-8.8 weeks) than in summer and autumn (6.8-7.0 weeks). The receptive figs were asynchronous both within-tree and among-trees. The receptive figs occurred in every month of 2005 and without seasonality. There were considerable overlaps (82.6%) in the receptive figs between functional male and female trees. The frequency of tender leaf phase of F. tinctoria was positively correlated with local rainfall and temperature, but the frequency of leaf falling phase was negatively correlated with them. The frequency of receptive figs of female trees was only positively correlated with rainfall, and the frequency of their interforal figs (C phase) were both negatively correlated with rainfall and temperature. Fig production of functional male F. tinctoria was not correlated with rainfall and temperature. There are five species of fig wasps, including one species of pollinator (Liporrh opalumgibbosae), one species of Sycoscapter, two species of Philotrypesis, and one species of Neosycophila. No significant difference was found in the average number of 4 species of fig wasps from D phase figs (6.3 pollinators, 8.8 Philotrypesis sp.1, 5.7 P. sp.2, and 5.7 Sycoscapter sp.1 per fig). In addition, one species of Sycophila (Eurytomidae) was also found inside figs of F. tinctoria. The coordination between D phase figs of male F. tinctoria to its B phase was iii 26.2%, which was similar to the coordination of it to B phase of female trees (29.5%). However, more pollinators arrived on male trees than that on female trees. The coordination between pollinators and B phase figs of male trees (43.0%) was higher than that of female trees (14.6%). Fig-pollinator mutualism in F. tinctoria is probably maintained by its asynchronous phenology, and aseasonal changes of the receptive figs. Seed production at female trees can be maintained by a small size of pollinator populations.

Species exist in complex biotic environments, engaging in a variety of antagonistic and cooperative interactions. While these interactions are generally recognized to be context-dependent, varying in outcome in the presence of other interactions, studies tend to focus on each interaction in isolation. One of the main classes of species interaction is mutualism, in which partner species gain a net benefit from their interaction. However, mutualisms are beset by a variety of species that can reduce or even eliminate the benefits of mutualism through exploitation of and competition for the resources and services offered by mutualists. These exploiter species potentially threaten the ecological stability of mutualisms and may alter selection on mutualistic traits. Thus, understanding the ecology and evolution of mutualisms requires consideration of interactions with exploiter species. In this dissertation, I investigated the effects of exploiter species on mutualisms between plants and pollinators using a combination of eco-evolutionary modeling, optimization theory, and behavioral studies. Using two adaptive dynamics models of coevolution in exploited pollinating seed parasite mutualisms, I found that exploiters reduce mutualist densities and select for more parasitic mutualists. Nevertheless, the models demonstrate that intraspecific competition for host resources and host defense of those resources restrict the ecological conditions that lead to extinction of the mutualism, as well as the chances of evolution to extinction. Thus, exploiters are unlikely to be the threat to mutualisms that has been assumed previously. On the other hand, in another type of exploitation, exploitative predators may pose a greater threat to investment in mutualism than has been presumed. Through both optimal foraging theory and behavioral experiments on bumble bees, I found that the risk from ambush predators can change pollinator floral preferences when predators preferentially use high-quality flowers to locate their prey. This research suggests that predators of mutualists may have important top-down effects and that further research is needed to investigate the effects of exploitative predators on selection on mutualist traits.

Thesis--Auburn University, 2007. / Abstract. Vita. Includes bibliographic references (p.57-63).

Thesis (Ph. D.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 159-179). Also available on the World Wide Web.

Thesis (Ph. D.)--Florida State University, 2006. / Advisor: Walter R. Tschinkel, Florida State University, College of Arts and Sciences, Dept. of Biological Science. Title and description from dissertation home page (viewed Sept. 22, 2006). Document formatted into pages; contains vii, 89 pages. Includes bibliographical references.

Polymicrobial communities often show complex patterns of metabolic and ecological interactions, yet our understanding of how the properties of communities emerge from the metabolic rules of species interactions is still limited. A central feature of metabolic interactions within microbial communities is ‘cross-feeding’, where one species or lineage consumes the metabolic by-products of another. Cross-feeding bacteria excrete and consume a wide range of metabolites and this sets the stage for diverse intra- and inter-specific metabolic interactions. In this thesis, I use ecological and evolutionary theory to address a number of critical questions posed by cross-feeding bacteria, with a particular focus on the role played by microbial metabolism in driving the emergence and dynamics of microbial interactions. First, I explore the conditions that favour the emergence and maintenance of cooperative cross-feeding and show that the evolutionary outcome depends strongly on the shape of the trade-off curves between the costs and benefits of cooperation. Second, I investigate the origins of cross-feeding interactions via single lineage diversification and derive new predictions on the physiological mechanisms that may explain the stable coexistence of a cross-feeding polymorphism that evolved from a single clone. Third, I investigate what are the ecological consequences of cross-feeding metabolic interactions and demonstrate theoretically that a simple mechanism of trade can generate a diverse array of ecological relationships. Furthermore, I show the importance of the metabolic by-product properties in determining the ecological outcome. Fourth, I investigate how metabolic constraints of individual species shape the emergent functional and structural relationships among species. I show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Furthermore, I show that these emergent community properties are driven by demographic feedbacks. In general, these findings support the idea that bridging microbial ecology and metabolism is a critical step toward a better understanding of the factors governing the emergence and dynamics of polymicrobial interactions.