Much of biology, especially evolutionary theory, makes assumptions about the individuality of living things. A population, for example, is made up of individuals. Those individuals sometimes reproduce, creating new individuals. The very use of these concepts requires that living individuals can be distinguished both synchronically and diachronically. There are many examples in nature, however, in which a living system is present, but it is not clear how to understand that system's individuality. Plants, fungi, colonial marine invertebrates, insect colonies, and symbiosis are all classic cases that have puzzled biologists interested in understanding their population structure and evolution. Scientific exploration of these issues has connections with traditional philosophical terrain, particularly the ontology of persistence and the nature of individuality broadly construed. A biologically informed philosophical literature has arisen in recent years, aimed at understanding the nature of biological individuality and its role in biological theorizing. My dissertation makes two kinds of contributions to this current literature. One contribution is theoretical, reframing our thinking about biological individuality. I distinguish between two categories of individuality and argue that they play different roles in theorizing about nature. One important kind of individual is that of the organism, understood as an entity that persists through space and time, takes in and processes resources from the environment, and maintains physiological autonomy. Another important kind of individual is that of the evolutionary individual, understood as an entity that has the capacity to participate in processes of natural selection. Distinguishing between these two types of individuality has theoretical utility, keeping clear the distinctive kinds of biological processes that individuals engage in. The other contribution of my dissertation involves detailed natural historical analysis of three kinds of problem cases. Using the framework articulated earlier in the dissertation, I assess the individuality of symbioses between larger organisms and their microbial associates, mushroom-producing fungi, and the classic case of ant colonies. The combined result of the assessments is a hierarchical pluralism about biological individuality. / Philosophy

Nematodes in the genus Steinernema (Nematoda: Steinernematidae) and their associated bacteria Xenorhabdus spp. (Gamma-Proteobacteria) are an emergent model of terrestrial animal-microbe symbiosis. Although interest in this association initially arose out of their potential as biocontrol agents against insect pests (Tanada and Kaya, 1993), this mutualistic partnership is currently viewed more broadly under the umbrella of basic sciences to inform ecology, evolution, biochemistry, molecular, among other disciplines (Burnell and Stock, 2000; Forst and Clarke, 2002).Despite advances in the discovery and field application of this nematode-bacterium partnership, and the growing popularity of this model system, relatively little has been published to uncover the evolutionary facets of their association. This study adds to the body of knowledge regarding nematode-bacteria symbiosis by 1) producing novel, multi-gene phylogenies for Steinernema and Xenorhabdus; 2) proposing a possible scenario for historical association in the form of a cophylogenetic hypothesis; 3) describing a newly discovered Steinernema species from France.

Symbiotic associations between animals and microbes are widespread in nature, yet the factors controlling the abundance and distributions of particular symbionts are mostly unknown. Vertically transmitted (VT) symbionts can invade host populations by providing net benefits to hosts. While most beneficial symbiotic interactions that have been characterized are nutritional, other major pathways likely exist that facilitate symbiont transmission within host populations. Natural enemies, for example, are important selective forces in shaping the life history of many invertebrates and hosts may benefit from collaborations with microbes to aid in their defense.In this dissertation I have addressed the role of VT, facultative (= secondary) symbionts (SS) of Acyrthosiphon pisum in mediating interactions with an important natural enemy, the parasitic wasp, Aphidius ervi. I found that, in a common genetic background, two A. pisum SS (R- and T-type SS) confer resistance to A. ervi, by causing mortality to developing wasp larvae. Defensive mutualisms with microbes provide a mechanism for the spread and persistence of VT symbionts.A. pisum superinfected with both R- and T-type SS were found to be more resistant to parasitism that those singly infected with either SS. Despite this added benefit to resistance, R + T-type superinfections were rare in a survey of A. pisum symbionts, likely attributable to severe fecundity costs. R-type densities increased dramatically in superinfected hosts and over-proliferation of SS may result in poor aphid performance. Thus, interactions among the symbionts themselves also likely play a critical role in determining the distributions of symbionts in nature.I also found that four T-type isolates from A. pisum, and one from another aphid species, all conferred resistance to parasitism in the same A. pisum host background. The levels of resistance varied greatly among isolates, including one that conferred nearly complete resistance. A single T-type isolate was also found to confer similar levels of resistance in five A. pisum backgrounds. These results indicate that SS-mediated resistance is a general phenomenon in A. pisum and that the SS isolate is more important in determining the level of resistance than is the aphid genotype or interaction between isolate and aphid genotype.

Subspace clustering identifies the attribute support for each cluster as well as identifying the location and number of clusters. In the most general case, attributes associated with each cluster could be unique. A multi-objective evolutionary method is proposed to identify the unique attribute support of each cluster while detecting its data instances. The proposed algorithm, Symbiotic Evolutionary Subspace Clustering (S-ESC) borrows from symbiosis in the sense that each clustering solution is defined in terms of a host, which is formed by a number of co-evolved cluster centroids (or symbionts). Symbionts define clusters and therefore attribute subspaces, whereas hosts define sets of clusters to constitute a non-degenerate clustering solution. The symbiotic representation of S-ESC is the key to making it scalable to high-dimensional datasets, while a subsampling process makes it scalable to large-scale datasets. Performance of the S-ESC algorithm was found to be robust across a common parameterization utilized throughout.

Several fungal endophytes (C. protuberata, F. culmorum, and C. magna) confer stress tolerance to plants in the presence of certain pressures. This relationship is known as habitat-adapted symbiosis; its mechanism is currently unknown. Here, sFTIR, FTIR coupled to an FPA detector, and Raman spectromicroscopy are used to examine whether any biochemical differences exist between different isolates of the same species: one that can confer stress tolerance to plants and the other that cannot. No major differences have been observed in spectra that can differentiate between those endophytes that confer stress tolerance and those that do not. However, some hy-phae from both isolates of C. protuberata have been found to contain mannitol; its pres-ence may be more common in geothermal rather than non-geothermal isolates. Mannitol is a compound involved in providing stress tolerance to fungi. Any role that it may have in the mechanism of habitat-adapted symbiosis will need further investigation.

Recently, one of the more significant measures on the part of the Cuban government to enhance resiliency of the existing economy was the announcement of a series of economic and social policy proposals referred to as lineamientos. These emphasize the importance of achieving long-term solutions for sustainable development, including, among other things, a need to improve food and energy self-sufficiency for the country. This research explores the possibility that an eco-industrial development approach could support these goals with a focus in the agricultural and agro-industrial sectors. Two concepts were applied to this intended new paradigm; namely integrated food and energy systems (IFES) and industrial symbiosis (IS). Three municipalities of the eastern province of Santiago de Cuba provided the regional basis for the research and were explored using an asset mapping approach to identify key facilities, material inputs, outputs and flows, infrastructure, and skills sets. Consultations with various stakeholder groups were conducted to gain insight in the current relationships and existing operational conditions that could inform the types of barriers and opportunities related to undertaking exchange and collaborative activities. The findings show that residues and by-products flows from various agricultural and agro-industrial operations can provide the basis for symbiotic networks that enable the generation of energy and added -value products of use to the region. The symbiotic linkages among agricultural and agro-industrial actors can give rise to an integrated food and energy production network (IFEPN) in the region where existing agricultural cooperatives, along with other emerging forms of social enterprise can support the development of this network. Considered a vital approach to solve problems in Cuba, collaboration is their most valuable asset for the successful development of the network.

Several fungal endophytes (C. protuberata, F. culmorum, and C. magna) confer stress tolerance to plants in the presence of certain pressures. This relationship is known as habitat-adapted symbiosis; its mechanism is currently unknown. Here, sFTIR, FTIR coupled to an FPA detector, and Raman spectromicroscopy are used to examine whether any biochemical differences exist between different isolates of the same species: one that can confer stress tolerance to plants and the other that cannot. No major differences have been observed in spectra that can differentiate between those endophytes that confer stress tolerance and those that do not. However, some hy-phae from both isolates of C. protuberata have been found to contain mannitol; its pres-ence may be more common in geothermal rather than non-geothermal isolates. Mannitol is a compound involved in providing stress tolerance to fungi. Any role that it may have in the mechanism of habitat-adapted symbiosis will need further investigation.

Typescript. / Bibliography: leaves [161]-173. / xii, 173 l illus., tables

Typescript. / Bibliography: leaves 369-373. / xv, 373 l illus., tables

Thesis (Ph. D.)--University of Auckland, 1990. / Includes bibliographical references.