Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3551. Adviser: Evan DeLucia. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3556. Adviser: Evan DeLucia. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0790. Adviser: James W. Dalling. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Methylmercury (MeHg), the organic form of mercury (Hg), is a neurotoxin that bioaccumulates and magnifies through trophic transfer up the aquatic food chain, moving from the primary producers to the top predators and causing health problems in humans. The purpose of this study was to identify biogeochemical features of the watershed that lead to elevated levels of methyl mercury concentrations in the water in 10 stream sub-catchments. The % wetland, proximity of wetland to the stream and the slope of the sub-catchment, dissolved organic carbon, watercolor, conductivity, pH, sulfate and iron were shown to influence methyl mercury concentrations. Duplicate water samples (1L) were taken on a weekly basis between March 2005 and May 2007 and analyzed for MeHg using the GC-AFS for species detection. Many of these variables are covariables, where the slope of the river drainage basin is of critical importance. Shallow slopes are characterized by wetlands and waterlogged soils that result in watersheds with high DOC concentration, low pH and high iron concentration. In these soils, oxygen is low and iron is reduced to the more soluble form and binds to DOC, giving rise to color. MeHg production in these regions is also favored and MeHg binds to DOC and, thus, export from the watershed into the stream, especially during precipitation events.

Habitat loss is widely acknowledged as the leading cause of extinctions and is occurring at an alarming rate and affecting biodiversity globally. I measured the rate of habitat loss using satellite-based land cover change data. First, I modelled the potential suitable habitat of the Marbled Murrelet on Vancouver Island using two techniques and compared those results to in-situ field measurements. Both modelling techniques predicted declines in suitable habitat between the years, although one technique was better at predicting suitable habitat. I also compared rates of habitat loss in areas of high species endangerment to those with lower endangerment over a 15-year period in three Canadian ecozones. In two ecozones, rates of habitat loss were higher in sites of high species at risk richness than those with low richness. These results underscore the importance of using remote sensing data as a monitoring tool critical habitat for species at risk in Canada.

Animals associate with microbes in complex interactions with profound fitness consequences. These interactions play an enormous role in the evolution of both partners, and recent advances in sequencing technology have allowed for unprecedented insight into the diversity and distribution of these associations. However, our understanding of the processes generating those patterns remains in its infancy. Here, I explore variation in microbiomes across two animal lineages—ants and mammals—to tease apart the role of these process in the evolution of gut microbiota. First, I explore patterns of phylogenetic correlation in gut microbiota of herbivorous Cephalotes ants and hominid apes. By examining the sensitivity of phylogenetic correlation to analytical parameters, I show that these outwardly similar patterns are likely to be the result of very different processes in each host lineage. Next, I examine in more depth the interacting effects of diet and phylogeny on the structure of baleen whale microbiomes. Whales consume a diet that differs dramatically from that of their closest extant relatives, the herbivorous artiodactyls. I use a combination of marker gene and shotgun metagenomic sequencing to show that a phylogentically conserved host trait, the multichambered gut, leads to functional and taxonomic similarities of whale gut microbiomes to those of their herbivorous ancestors via the fermentation of animal polysaccharides in the exoskeletons of their prey. Finally, I return to ants to examine how major shifts in the nature of gut microbial association correspond to host ecology. Using measures of absolute bacterial abundance, rather than diversity, I test the hypothesis that evolution of symbiosis with microbes has facilitated ants’ dominance of tropical rainforest canopies. Surprisingly, I find differences in the abundance of gut bacteria in different ant lineages that span many orders of magnitude, suggesting that evolutionary transitions in the functional role of symbiosis in this animal lineage correspond not only to changes in the diversity of these associations, but to changes in kind. The results of these studies help to clarify the roles of history and selection in structuring animal gut microbiota, hinting that the interaction of these factors may fundamentally differ between animal lineages. / Biology, Organismic and Evolutionary

In this thesis I investigate how the individual components of biological systems interact, and how the form of these interactions determines overall system behavior. The interactions I study occur at widely different scales: from whole ecosystems to individual genes. Despite these differences, the approaches I use share similarities: in both realms I apply systematic experimental perturbations, then utilize mathematical and computational tools to identify novel properties of these interactions and to interpret their importance. In the first study, I examine how 3-way species interactions affect ecosystems dynamics. Ecological models typically assume that interactions occur among pairs of species. While higher-order interactions among greater numbers of species are thought to occur in natural ecosystems, the strength and overall importance of these interactions for ecosystem behavior has been unclear. My study focuses on species interactions mediated by antibiotic toxins, which either inhibit or kill antibiotic sensitive species. Here I develop a quantitative 3-way interaction assay to measure how the inhibition of a sensitive species by an antibiotic producer is affected by the presence of a third “modulator” species. Systematically testing combinations of species and antibiotics, I find that antibiotic degradation by the modulator species frequently attenuates the inhibition of the sensitive species. I then use simulations and mathematical models to show that such 3-way interactions can dramatically alter ecosystem dynamics. Ecosystems of antibiotic producing, sensitive and resistant species are thought to coexist only when they are spatially separated in the environment, but these conclusions are based on models that assume pairwise species interactions. Surprisingly, I find that the 3-way interactions created by the counteraction of antibiotic production and degradation enable coexistence even in well-mixed environments. These findings are robust to choices of parameters and modeling assumptions, and shed light on the role of antibiotic production and degradation in maintaining the diversity of natural microbial communities. In the second study, I shift to the molecular scale and develop strategies for deciphering multiple protein and mRNA selective pressures that affect gene function. Recent technological advances in “Mutagenomics”, i.e. large-scale mutagenesis and phenotyping, have enabled the systematic mapping of fitness landscapes. Current challenges include the difficulty of applying such methods to essential genes, which control many core biological processes, and also the problem of interpreting high-dimensional fitness landscapes in terms of sensible biochemical properties. Here I present advances on both fronts: first by developing MAGE-seq, a high-throughput method that combines genome engineering with a DNA sequencing-based assay to enable rapid measurement of fitness landscapes anywhere on the Escherichia coli genome. Second, I describe methods of analysis to identify key properties that determine gene fitness through a case study of infA, an essential translation initiation factor (IF1). At the protein level, I find that selection is determined primarily by amino acid properties like hydrophobicity, flexibility, size and charge, and I relate these properties to protein folding and function; at the mRNA level, I show that selection is strongest in the early regions of the gene, where codon preferences are determined by the formation of RNA hairpins containing the start codon and by the avoidance of deleterious motifs such as out-of-frame start codons. Disruption of this optimal RNA structure determines codon preferences in later regions of the gene, suggesting that gene evolution is constrained by both mRNA and protein properties. Together these experimental and analytical methods make it possible to systematically identify and engineer the key properties of biological function genome-wide. / Systems Biology

The Andean mountain chains of South America are home to exceptionally high levels of biodiversity, including one-sixth of all plant species. Among them, the 550 species in the Neotropical bellflower clade (Campanulaceae: Lobelioideae) represent one of the single largest endemic radiations. In this dissertation, I perform a series of studies, ranging from alpha taxonomy to phylogenetic comparative biology, to understand this group’s evolution. In Chapter 1, I resolve phylogenetic relationships of the Neotropical bellflowers from five plastid DNA regions using maximum likelihood and Bayesian inference. This phylogeny greatly improves the resolution within this group and highlights the need for taxonomic revisions. My results demonstrate that the majority of species of Centropogon, Burmeistera, and Siphocampylus together form a primarily mainland Neotropical clade, collectively termed the centropogonids. Within the centropogonids, I identify high support for the monophyly of Burmeistera and the polyphyly of Centropogon and mainland Siphocampylus. Caribbean Siphocampylus, however, group with other Caribbean lobelioid species. Ancestral character state reconstruction identifies a dynamic pattern of fruit evolution within the centropogonids, which underscores the difficulty of diagnosing broad taxonomic groups on the basis of fruit type. Finally, we identify that the centropogonids form a Pan-Andean radiation with broad habitat diversity, which sets the stage for a subsequent chapter in my thesis (Chapter 4). In Chapters 2 and 3, I describe four species of centropogonids as new to science. In Chapter 2, two species of Burmeistera from the Cordillera de Talamanca are described: B. serratifolia Lagom. & D. Santam., endemic to Panama, and B. monroi D. Santam. & Lagom., from both Panama and Costa Rica. These species are included in a dichotomous key to all Central American species of Burmeistera. In Chapter 3, I describe two species of Siphocampylus from the Central Andes of Peru and Bolivia: S. antonellii Lagom. & D. Santam., endemic to high elevation grasslands of Calca, Peru, and S. siberiensis Lagom. & D. Santam., endemic to cloud forests of Cochabamba, Bolivia. Both species are robust shrubs that produce tubular pink flowers that are likely pollinated by hummingbirds. In Chapter 4, I use the Neotropical bellflowers as a model system to understand the triggers of rapid diversification in the Andes. I explore the interaction of abiotic and biotic factors by applying a series of diversification models that incorporate orogeny, climate, and biological trait evolution to a time-calibrated phylogeny of the group. Here, I demonstrate that speciation rates rose with increasing Andean elevation, while extinction decreased during global cooling. Of these, climate appears to have played the more important role, which I attribute to preadaptation to cool climates. Biotic traits that facilitate plant-animal mutualisms, specifically fruit type and pollination syndrome, additionally enhanced diversification rates. These results suggest that, while the Andes acted as a species pump for this lineage, a synergistic interaction of abiotic and biotic factors underlies its rapid diversification, which culminated in one of the fastest plant radiations documented to date: the centropogonids. This study underscores the complex interplay of ecological and historical determinants in generating the world’s biodiversity. Finally, in Chapter 5, I use comparative methods to explore shifts between vertebrate pollination syndromes in the centropogonid clade. Such shifts, which are often associated with convergent floral phenotypes, are invoked as key factors underlying floral diversification in angiosperms. Using phylogenetic principal components analyses, I show that, despite morphological similarities between these pollination syndromes, centropogonid flowers adapted to pollination by bats and by hummingbirds fall into separate regions of morphospace. I further document the repeated evolution of pollination syndromes: the clade is ancestrally hummingbird pollinated, and bat pollination has evolved independently fourteen times, with nine reversions to hummingbird pollination. An obligate relationship with sicklebill hummingbirds, characterized by extremely curved bills, evolved only once. While the evolution of floral morphology has been dynamic in this clade, there is no difference in diversification rate in hummingbird and bat pollinated linages. These results suggest that specialized pollination syndromes are not evolutionary dead-ends. Instead, shifts between vertebrate pollinators may have greatly facilitated the maintenance of an ancestrally high diversification rate among centropogonid species. / Biology, Organismic and Evolutionary

Ant-plants provide ants with rewards such as housing and food in exchange for protection from herbivores. These protection mutualisms are complex webs of both direct interactions, such as ants feeding on host plant extrafloral nectar, and indirect interactions mediated by 'third party' species, such as ants consuming exudates from hemipterans feeding on the host plant. While some indirect interactions are well understood, in many cases our understanding is hindered by an incomplete picture of the relevant third-party species. In this dissertation, I explore third-party interactions of three obligately phytoecious ant species on the African ant-plant Vachellia drepanolobium (formerly Acacia drepanolobium) - Crematogaster mimosae, C. nigriceps and Tetraponera penzigi. First, I examine relationships between ants and fungi. I show behavioral differences towards fungi among the three ant species, and then use multiplexed amplicon sequencing to characterize their associated fungal communities. Each ant species harbors its own distinctive fungal community, and these communities are similar for each species even at two field sites separated by 200 kilometers. The ants may vector fungi when they colonize new host trees. T. penzigi most likely uses fungi as a food source, and fungi may also have nutritional or other growth implications for the host plant. Second, I investigate relationships between ants and 'myrmecophiles' - i.e. 'ant loving' arthropods that live alongside ants in the domatia. I show that myrmecophile communities differ among the three ant species, but are also highly context dependent, differing strongly between locations and sampling periods. Surprisingly, several species of myrmecophilous Lepidoptera are herbivorous, but are more commonly associated with the 'better' ant mutualists, C. mimosae, whose workers defend more effectively against browsing mammalian herbivores. My results show that plant ants shape both fungal communities and myrmecophile communities in domatia of their V. drepanolobium host plants. These third-party species may be viewed as 'extended phenotypes' of the ants, and are essential elements whose effects need to be incorporated into our understanding of the ant-plant protection mutualism. / Biology, Organismic and Evolutionary

In this thesis, we study collective phenomena that arise from microscopic fluctuations at the individual level of two different living populations. First, we study evolutionary dynamics of two-species competitions in a well-mixed environment subject to population size fluctuations. We demonstrate a mechanism for neutral evolution such that population size fluctuations favor a fixation of one species over the other. An effective evolutionary dynamics for fluctuation-induced selection is derived. We then investigate strong mutualism, in a limit where a varying population size can strongly influence the evolutionary dynamics. We determine fixation probabilities as well as mean fixation times taking into account the population size degree of freedom. The results elucidate the interplay between population size fluctuations and evolutionary dynamics in well-mixed systems. Second, we investigate  single species marine population  subject to a constant flow field and quenched random spatially fluctuating growth rates.  We show that the non-equilibrium steady-state population density of a generalized Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation develops a flow-driven striation pattern.  The striations are highly asymmetric with a longitudinal correlation length that diverges linearly with the flow speed and a transverse correlation length that approaches a finite velocity-independent value. The findings suggest that, although the growth disorder can be spatially uncorrelated, correlated population structures with striations emerge naturally at sufficiently strong advection. / Physics