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The biological world is complex. Communities contain a multitude of interacting species, while populations contain extensive genetic variation. How much complexity must one consider to understand patterns and processes of interest? When are species interactions and community properties shaped by evolution? Conversely, when is evolution altered by community context? I test these questions in a series of experiments with simple microbial communities. The first data chapter investigates the impact of competition on the evolution of phage resistance in bacteria. This work demonstrates that community context can dramatically alter the evolution of resistance to phage. Next I tested the impact of evolution on assembly of a three species community. I demonstrate that evolution can influence the content of a microbial community by altering the process of assembly. Finally, I investigated the evolutionary origin and maintenance of cross-feeding mutualisms. This work suggests that species interactions can enable novel evolutionary pathways, and that evolution can significantly increase the productivity of cross-feeding communities. Jointly these experiments suggest that consideration of the interplay between ecological and evolutionary forces can provide insight into the complexity of the natural world. / text

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Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 106-113). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of Texas at Austin, 2009. / Title from PDF title page (University of Texas Digital Repository, viewed on Sept. 16, 2009). Vita. Includes bibliographical references.

The standard representation of evolutionary relationships is a bifurcating tree. However, many types of genetic exchange, collectively referred to as reticulate evolution, involve processes that cannot be modeled as trees. Increasing genomic data has pointed to the prevalence of reticulate processes, particularly in microorganisms, and underscored the need for new approaches to capture and represent the scale and frequency of these events. This thesis contains results from applying new techniques from applied and computational topology, under the heading topological data analysis, to the problem of characterizing reticulate evolution in molecular sequence data. First, we develop approaches for analyzing sequence data using topology. We propose new topological constructions specific to molecular sequence data that generalize standard constructions such as Vietoris-Rips. We draw on previous work in phylogenetic networks and use homology to provide a quantitative measure of reticulate events. We develop methods for performing statistical inference using topological summary statistics. Next, we apply our approach to several types of molecular sequence data. First, we examine the mosaic genome structure in phages. We recover inconsistencies in existing morphology-based taxonomies, use a network approach to construct a genome-based representation of phage relationships, and identify conserved gene families within phage populations. Second, we study influenza, a common human pathogen. We capture widespread patterns of reassortment, including nonrandom cosegregation of segments and barriers to subtype mixing. In contrast to traditional influenza studies, which focus on the phylogenetic branching patterns of only the two surface-marker proteins, we use whole-genome data to represent influenza molecular relationships. Using this representation, we identify unexpected relationships between divergent influenza subtypes. Finally, we examine a set of pathogenic bacteria. We use two sources of data to measure rates of reticulation in both the core genome and the mobile genome across a range of species. Network approaches are used to represent the population of S. aureus and analyze the spread of antibiotic resistance genes. The presence of antibiotic resistance genes in the human microbiome is investigated.

Genome plasticity in soil bacteria is predicted to be evolutionarily advantageous, allowing bacteria to sample genetic variation for adaptation to local soil ecology. In the field population of mesorhizobia where the symbiosis island (ICEMlSym[R7A]; an I̲ntegrative C̲onjugative E̲lement) was first identified, individual members were found to have significant chromosomal variation downstream of the phe-tRNA gene or phe-tRNA integrated ICEMlSym[R7A]. However, the nature of this genetic variation and whether it contributed to the adaptation of the indigenous mesorhizobia to their field environment were unknown. This work focused on a nodule isolate, Mesorhizobium sp. strain R88B, a member of the indigenous mesorhizobial population that received ICEMlSym[R7A] from strain R7A. The region downstream of ICEMlSym[R7A] was sequenced, revealing three distinct regions of non-conserved DNA, totalling 34.5 kb. Integrated directly downstream of ICEMlSym[R7A] was IMEMlAdh[R88B], a 24.3-kb novel I̲ntegrative M̲obilisable E̲lement. Using a PCR-based assay, it was shown that the IMEMlAdh[R88B] integrase could excise not only IMEMlAdh[R88B], but also a dual-IMEMlAdh[R88B]/ICEMlSym[R7A] hybrid, indicating the potential mobility of IMEMlAdh[R88B], and a likely evolutionary intermediate of a novel ICE. However, a functional role for MadA, (a putative adhesin and the sole adaptive trait encoded on IMEMlAdh[R88B]) was not discovered. Southern hybridisations with the mesorhizobial population provided evidence for the existence of a novel family of IMEs in the mesorhizobia, which, by diversifying their internal sequences, provide allele-specific variation to the population. The two other regions downstream of IMEMlAdh[R88B] possessed no obvious mobile genetic element structures, and only the region adjacent to the core-chromosome encoded ORFs with putative functions. Mutation of two of these ORFs, fhuD1 and fhuB1, identified their function as two of the four components of a ferrichrome ABC-uptake (Fhu) system. Using genetic screens, the remaining components of this transporter were mapped to two separate loci. Thus, the functional transporter in R88B was a composite of at least two independently-acquired Fhu systems. The genetic screens also revealed that ferrichrome utilisation was dependent on a TonB energy-transduction system encoded downstream of the Fhu ATPase gene, fhuC. Expression studies on the three fhu loci demonstrated that, despite their separate acquisition, their expression was coordinately up-regulated in response to low-iron conditions. Bioinformatics on the predicted promoter regions of the fhu genes identified the binding site of the rhizobial Fur analogue, RirA, which is likely to be responsible for this expression profile. Southern hybridisations of DNA isolated from members of the mesorhizobial population revealed the three fhu loci were not conserved in the mesorhizobial population. The presence of FhuA was the best predictive marker for the trait. It is proposed that multiple rounds of acquisitions and recombinations, both illegitimate and legitimate, formed this transporter, with the constant need for iron offset by the negative selection pressure of FhuA being a target for phage. None of the Fhu-specific genes was present in the sequenced M. loti strain MAFF303099 though flanking sequences were, further emphasizing the role of genome microevolution in forming the Fhu phenotype.