<p> <b>Chapter 1.</b> We propose a method for predicting the ecological function of host-associated microbes using neural networks trained on a feature space of labeled ecological interactions from the literature. The feature space is constructed over the Laplacian spectral density distributions of the networks formed by linking the phylogenies of the host and microbial clades through their ecological associations. A classifier trained on 51 interactions with known ecology and 100 simulated controls was used predict the ecological function in the microbimes of 14 species of wild-caught cichlid fish from the Lake Tanganyika adaptive radiation observed using 16S rRNA sequencing. </p><p> <b>Chapter 2.</b> Genomic patterns of divergence are examined using whole-genome resequencing of three sympatric cichlid species pairs with similar functional and ecological differentiation but different ages, revealing a signature of genomic divergence. Regions of elevated relative differentiation exhibit increased absolute differentiation. We detect a signature of convergent evolution across all three species pairs. Our results suggest that functional phenotypic differentiation is associated with a signature of genomic divergence. </p><p> <b>Chapter 3.</b> We show that evolutionary innovations can result in competitive inferiority and extinction. The modified pharyngeal jaws of cichlid fishes and several marine fish, a classic example of evolutionary innovation, are not universally beneficial. Analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to predator niches. This competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal, previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion. </p><p> <b>Chapter 4.</b> We map protein sequences from the Global Ocean Survey to protein families and use non-negative matrix factorization (NMF) to approximate linear combinations of ecological components with characteristic functional and site profiles. We identify functional signatures, estimate functional distance between sites, and find that an NMF-filtered measure is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We find that functional distance is more strongly correlated with environmental distance than geographic distance in agreement with prior studies. </p><p> <b>Chapter 5.</b> We describe the unique technical, logistical, organizational, and ethical issues from the 2013 Indigo V Indian Ocean Expedition research cruise from Cape Town, South Africa, to Phuket, Thailand aboard the S/Y <i>Indigo V.</i> An inventory the surface water population of bacterioplankton was collected and basic measurements of ocean physics and chemistry were tabulated. </p><p> <b>Chapter 6.</b> We report on the microbial diversity across the Indian Ocean and a lagoon in the Chagos Archipelago. The community within the lagoon differed from adjacent community despite constant water exchange, driven by photosynthetic cyanobacterium Synechococcus. Enrichment of photosynthesis-related transcripts and nutrient cycling indicate influence of primary production on community structure. A five-fold diurnal increase in viral transcripts within the lagoon suggests concomitant bacteriophage influence. </p><p> <b>Chapter 7.</b> We present a novel ChIP-seq workflow for archaea using <i>Halobacterium salinarum</i> sp. NRC-1 and map binding sites of natively expressed transcription factors. Relative to ChIP-Chip and qPCR, it improves spatial resolution and reduces cost. </p><p> <b>Chapter 8.</b> Pique is a user-friendly, freely licensed ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. Output is provided in standardized file formats for manual curation and data exploration. </p><p> <b>Chapter 9.</b> With appropriate handling, 3D printers produce sterile components from non-sterile thermoplastic feedstock without post-fabrication treatment. </p><p> <b>Chapter 10.</b> We present a method for fabricating single-use microtiter plates with volumes calibrated for each sample, allowing the use of multichannel pipettes for general liquid handling operations. Many custom plates can be 3D printed simultaneously, resulting in substantial savings in cost and time. </p><p> <b>Chapter 11.</b> The growth kinetics of 48 strains of building-associated bacteria were measured aboard the International Space Station. One strain, <i> Bacillus safensis</i> JPL-MERTA-8-2, grew 60% better in microgravity. </p><p>

<p> Plants and the insects that feed on them dominate diversity in terrestrial ecosystems: half of all named species are contained within these two groups. Herbivorous insects (herbivores) are abundant and diverse, yet paradoxically, two thirds of insect orders contain no major lineages of herbivores, implying barriers to the evolution of this trophic interaction. How herbivory evolves and why herbivores are so diverse are questions that are key to understanding the processes that have shaped global biodiversity. Yet, most lineages of herbivores are ancient with sister groups either absent or too divergent for a comparative genomic analysis to yield a mechanistic understanding of both their origin and diversification. Many of the exceptions to this pattern are among the Diptera, where lineages such as the leaf-mining drosophilids in the genus <i>Scaptomyza</i> have emerged within the last 10 million years. <i>Scaptomyza</i> is particularly well-suited for identifying the adaptations associated with the evolution of herbivory because it is embedded within the paraphyletic genus <i>Drosophila</i>, which contains species with 25 sequenced genomes, and is closely related to <i>D. melanogaster </i>, the genetic model, and a taxon with one of the most well-studied nervous systems. </p><p> Behavior is thought to be one of the earliest adaptations during the evolution of herbivory and niche shifts in general. Insects undergoing a niche shift likely lose their preferences for their ancestral diet, and also evolve an attraction to novel cues indicative of their new oviposition substrate. Once females lay eggs in a new environment, herbivores must consume the new diet, despite the fact that it may contain aversive chemicals and a different balance of macronutrients compared to the ancestral diet. Using the herbivorous <i> Scaptomyza flava</i> as a model system, the primary aim of my dissertation was to use methods in comparative genomics, chemical ecology, ethology, and neural imaging to characterize the mechanistic basis of behavioral changes associated with the evolution of herbivory in insects. </p><p> Using a comparative genomics approach, I found that targeted gain- and loss-of-function mutations were associated with the evolution of herbivory in the genus <i>Scaptomyza</i>. First, four Odorant (Olfactory) Receptor (OR) genes were lost in herbivorous species of <i>Scaptomyza </i>, which are deeply conserved among microbe-feeding drosophilids. The OR genes lost code for receptors that detect yeast-volatiles and are known to stimulate oviposition, feeding and attraction behaviors in <i>Drosophila </i> species. Consistent with these losses was also a loss of detection sensitivity to ligands of these ORs, specifically short-chain aliphatic esters such as ethyl and propyl acetate, major yeast-produced odorants. <i> S. flava</i> female flies were also unresponsive to volatiles produced by active yeast cultures, in contrast to <i>D. melanogaster</i> flies. </p><p> In contrast to some other specialized lineages of <i>Drosophila </i>, I found no evidence of increased or mass chemosensory gene loss, with one interesting and novel exception. The majority of the genes encoding the Plus-C subfamily of Odorant Binding-like proteins (OBPs) are deleted or pseudogenized in <i>Scaptomyza</i>. Additional conserved cysteine residues that form disulfide bonds that stabilize the tertiary structure characterize this subfamily. Interestingly the extra disulfide bonds in Plus-C OBPs are known to be vulnerable to attack by toxic breakdown products of glucosinolates, isothiocyanates, chemicals that are characteristic of <i>S. flava</i>'s host plants in the mustard family. Other than the loss of OBPs, I found <i> S. flava</i> to have multiple duplications of genes encoding ORs, OBPs, gustatory receptors (GRs) and ionotropic receptors (IRs), some of which showed evidence for positive selection (<i>Or67b, Obp49a, Gr33a, Ir67a</i> and <i>Ir76a</i>). Among receptors expressed in the gustatory system, losses, duplications and genes with selection regime changes were more often orthologs of genes expressed in bitter gustatory neurons in <i>D. melanogaster </i>, especially gustatory sensory neurons with a broad expression of gustatory receptor genes. Changes, such as deletions, duplications and increased amino acid substitution rates, were also found among genes encoding receptors implicated in reproductive behavior including the loss of an anti-aphrodisiac receptor, <i>Gr68a</i>, which could be associated with a switch from males chemically guarding mated females with anti-aphrodisiacs to physical guarding behavior where males remain on the backs of females post-mating. (Abstract shortened by ProQuest.)</p><p>

<p> Nutrient cycling plays a critical role in maintaining biodiversity and ecosystem services in agricultural, urban, and natural lands. However, across landscapes there is substantial unexplained heterogeneity in nutrient cycling. Classic thinking holds that abiotic factors are the source of this spatial heterogeneity with a secondary role of plant biomass. However, recent work suggests that higher trophic levels or variation in traits at the level of plant genotype may also play an important role in structuring nutrient environments. For instance, herbivores may indirectly create heterogeneity in cycling through the induction of chemical and structural changes in plants traits. Phenotypic plasticity due to anti-herbivore defense may then alter nutrient cycling rates by changing the microbial breakdown of plant litter inputs. Alternatively, variation among plant genotypes in the expression of these same traits may overwhelm the influence of phenotypic plasticity on soil processes. Both genetic and environmentally based changes in plant traits have separately been demonstrated to alter soil processes, but their interaction and the relative importance of these sources of variation across local landscapes is unknown.</p><p> I address this question by developing a plant trait-mediated, conceptual framework of nutrient cycling. I then evaluate this framework within an old-field ecosystem by focusing on the dominant plant species, <i>Solidago altissima </i>, and its dominant grasshopper herbivore, <i>Melanoplus femurrubrum </i>, using a combination of lab assays, a greenhouse pot experiment, a field mesocosm experiment, and field surveys. First, I demonstrate that goldenrod individuals exhibit both genotypic variation and phenotypic plasticity in plant defensive trait responses across a nutrient and herbivory gradient in the greenhouse. At low nutrient supply, genotypes tolerate herbivory (inducing plant physiological changes that decrease the negative impact on fitness) while at high nutrient supply, the same genotypes induce a resistance response detectable through lower herbivore growth rates. These environmentally mediated changes in plant trait expression then altered the ability of a common microbial community to decompose senesced litter harvested from the same plants. Induced resistance in the population of genotypes grown at high nutrient levels led to decreased litter decomposition of herbivore legacy litter. In contrast, at low nutrient supply, herbivore legacy litter decomposed more efficiently compared to control litter. This suggests that the interaction between herbivory and nutrient supply could cause context-dependent acceleration or deceleration of nutrient cycling. As a result, trait plasticity may mediate effects of multiple environmental conditions on ecosystem processes in this system.</p><p> I tested this hypothesis using a three-year, raised bed, field experiment examining the effect of plasticity and locally relevant genetic variation on ecosystem processes in a naturalistic setting. Genotype clone clusters were planted in homogenized soil in enclosed cages with varying nutrient supply and grasshopper herbivory. Again, I documented strong genetically and environmentally-based trait variation in plant allocation, growth, and leaf traits. I next explicitly linked these genetic and plastic functional trait changes to concurrent changes in a variety of soil processes (microbially available carbon, plant available nitrogen, nitrogen mineralization potential, and microbial biomass) and litter decomposition rates. Importantly, partitioning functional trait variation into genetic and environmental components improved explanatory power. I also documented potential differences in herbivore effects on "slow" vs. "fast" cycling in soil microbially available C pools. Within both experiments the magnitude of trait variation measured was similar to the variation expressed by individuals across a focal field.</p><p> Taken together, this dissertation demonstrates that plant genotype, herbivores, and nutrients can all modify litter decomposition and other soil processes within ecosystems through differential expression of plant functional traits. Due to the spatially clumped, clonal, and dominant nature of goldenrod, the genetic and herbivory-driven changes documented here could lead to a predictable mosaic of soil process rates across a single old field landscape. This work also highlights the complex interplay between genetically and environmentally-based trait variation in determining population and ecosystem processes within landscapes and improves our understanding of the often-overlooked indirect effects of plant/herbivore interactions on nutrient cycling It suggests that herbivores may shape not only the evolution of plant populations, but also the soil nutrient environment and microbial community in which plants live. This sets up the potential for eco-evolutionary feedbacks between plant defense expression and soil nutrient availability. More broadly, it suggests that biotic factors, in addition to abiotic ones, play a key role in determining local-scale soil nutrient availability patterns and should potentially be accounted for within ecosystem models. These results are particularly salient in a world where anthropogenic nitrogen inputs continue to rise and climate change is predicted to increase herbivory and thus plant defensive trait induction on landscapes. </p>

Inferring ancestral gene orders in a phylgenomic tree is an important topic in comparative genomics. In this thesis, three different approaches have been used to infer ancestors, first, using common intervals in a model-free approach and extending it to using common clusters and neighbourhood parameter; second, using double cut and join operation (DCJ); third, using breakpoint distance. A statistically fair comparison between the performance of DCJ and breakpoint criteria ends the thesis. Away from any assumptions or considerations, probabilistic or combinatorial, about specific processes involved in rearranging genomes, we present a new phylogenetic reconstruction method based solely on common intervals. The objective function to be optimized is simply the sum over the tree branches of the symmetric difference between the two sets of intervals associated with the genomes at the two ends of the branch. To achieve this goal, we use dynamic programming optimization to determine the presence of common intervals at the ancestral nodes of the phylogeny. Noticing the drawback that the concept of common intervals suffers from, we introduce the concept of generalized adjacency to find common clusters using a neighborhood parameter that turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. Again, we use dynamic programming optimization to determine the presence of individual edges at the ancestral nodes of the phylogeny. The DCJ (double cut and join) operation introduced by Yancopoulos et al. in 2005 is the most inclusive operation to date as it can generate all the movement rearrangements. One year later, Bergeron et al. restated the DCJ model and produced a simplified (linear) algorithm, which is now the most general existing algorithm to transform one genome into another using genome rearrangements events. Motivated by both, the most inclusive operation, DCJ, and its most general algorithm, we study the small phylogeny problem in the space of multichromosomal genomes under the DCJ metric. This is similar to the existing MGR (multiple genome rearrangements) approach, but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Thanks to Tannier et al., the first polynomial solution to the median problem has been found in only one context, namely the case of breakpoint distance on multichromosomal genoms where chromosomes are unconstrained as to linearity or circularity. This motivated us to study the small phylogeny problem using breakpoint median as a third approach, that is different both biologically and computationally from the common intervals and DCJ approaches, and then to compare statistically the performance of both criteria, breakpoint and DCJ. Keywords: phylogenetic tree, genome rearrangment, inversion, reciprocal translocation, transposition, block interchange, common intervals, generalized adjacency, neighborhood parameter, graph bandwidth, multiple genome rearrangement (MGR), double cut and join (DCJ), breakpoint (BP), excess explanatory rate.

The divergence of the two superfamilies belonging to the Infraorder Catarrhini – Cercopithecoidea (Old World monkeys) and Hominoidea (apes, including humans) – is generally assumed to have occurred during the Oligocene, between 38 and 20 million years ago. Genetic studies indicate that this time period was one of active genetic evolution under strong purifying selection for catarrhine primates. This includes selective pressures on the glycoprotein galactosyltransferase 1 (GGTA1) gene and subsequent inactivation "clocked" at approximately 28 ma, possibly prior to the Cercopithecoidea/Hominoidea split. The GGTA1 gene codes for an α1,3 galactosyltransferase (GT) enzyme that synthesizes a terminal disaccharide, αgalactosyl (αGal), found on glycoproteins and glycolipids on the surface of cells in the tissues of most mammals. Currently, catarrhines are the only mammals studied for the terminal αGal residue that do not express this sugar on their cell surfaces. The proposed selective advantage of this mutation for catarrhines is the ability to produce anti-Gal antibodies, which may be an effective immune component in neutralizing αGal-expressing pathogens, as certain helminthes, many bacteria, including those found in primate guts, and some viruses derived from GGTA1 positive species express αGal on their surfaces. However, many viruses are known to utilize host cell carbohydrates in various ways such as binding receptors or attachment proteins, making these moieties "hot spots" for selective evolution. Cell surface αGal may have predisposed ancestral catarrhines to pathogens and toxins that could utilize the terminal sugar moieties on host cells as binding sites or in other capacities during infection. I found that, in fact, the presence or absence of cell surface αGal affects the course of certain viral infections. Infections of paired cell lines with differential expression of GT showed that Sindbis viruses (SINV) preferentially replicate in αGal-positive cells, whereas herpes simplex viruses type 1 and type 2 (HSV-1 and HSV-2) preferentially grow in cells lacking αGal. In both cases, differences in infection levels resulted from the ability of the virus to successfully initiate infection. This points to a role for αGal in the early stages of viral infections. I also showed that GT knockout mice infected with HSV-2 had higher viral load and greater pathology compared to WT B6 mice that naturally express αGal. The increased susceptibility of KO mice to HSV-2 was not due to an immune component as differences in viral load and pathology were even more evident in immunocompromised mice. This clearly indicates that αGal expression in cells or animal hosts can affect the course of viral infections. I was not able to further confirm differences in susceptibility to HSV 1 and 2 using mouse backcrosses (KO x WT). Unknown genetic factors, that are independent of αGal expression, may be introduced during the crosses that need to be further investigated. Infections of KO and WT mice with other herpes viruses did not yield definitive data and require further studies with suitable reagents. The mechanism by which GT-dependent differential susceptibility to viruses operates still remains to be deciphered. However, it is clear that susceptibility to certain viral infections is tied to the presence or absence of αGal on the surface of host cells. Overall, these results have implications for the evolution of resistance to viral infections in catarrhines. Pathogens exert great selective pressure on their hosts, and it is possible that a pathogen, able to exploit αGal, could have helped shape primate lineage evolution during the Oligocene.

The migration of the cranial neural crest is an essential part of cranio-facial development in every vertebrate embryo. The cranial neural crest (CNC) is a transient population of cells that forms the lateral border of the anterior neural plate. In the tailbud stage Xenopus embryo, the neural crest cells delaminate from the neural tube, and undergo a large-scale migration from the dorsal to ventral region of the embryo. The CNC travels along distinct pathways, and populates specific regions of the embryos face. Once the CNC ceases migrating, it differentiates into a variety of tissues that are essential for cranio-facial structure and function. Some of these tissues include bones, muscle, cartilage, and ganglia. The CNC receives a concert of signals from neighboring tissues during and after CNC migration as well as signals transmitted among CNC cells, which act together to determine the fate of each CNC cell. Therefore, the proper migration of the CNC is an essential part of cranio-facial development. What molecules are important for the process of CNC migration? As one might imagine, a milieu of different molecules and interactions are essential for this complicated embryological process to occur. The work presented in this dissertation will focus on the role of a cell adhesion molecule that is important for Xenopus CNC migration. Typically, the amount of cell adhesion decreases within tissues undergoing migration. This behavior is essential to allow fluidity within the tissue as it moves. However, cell adhesions are fundamental for cell migration to occur because the moving cells need a platform on which to mechanically propel themselves. These interactions can occur between the migrating cell and extracellular matrix molecules (ECM), or can happen between cells. The cranial neural crest utilizes both cell-ECM and cell-cell interactions during the process of migration. The amount of cell adhesion mediated by either of these mechanisms will depend on where the cell is located within the CNC. Cells located at the periphery of the CNC tissue, which is surrounded by a matrix of ECM, will have more cell-ECM interactions. Cells located deeper in the CNC tissue, where there is little ECM, will rely more on cell-cell interactions. The work presented in this thesis focuses on a cell-cell adhesion molecule that is part of the cadherin superfamily of molecules. With this in mind, these studies should be descriptive of the environment within the CNC, and to a less degree the environment between the CNC and the surrounding tissues. The work presented in this dissertation will focus on cadherin-11, which is a classical cadherin that is specifically expressed in the cranial neural crest during its migration. How does cadherin-11 function in the CNC during this process? The work presented here suggests that the main role of cadherin-11 in the CNC is to perform as a cell adhesion molecule. However, too much cell adhesion is inhibitory to migration. In this respect, many of the studies described in this work indicate that cadherin-11 mediated cell adhesion is tightly regulated during CNC migration. Here I show that cadherin-11 is extracellularly processed by ADAM metalloproteases, ADAM9 and ADAM13, which removes the adhesive domain of cadherin-11. This extracellular cleavage event occurs throughout CNC migration, and is likely the main mechanism that regulates cadherin-11 mediated cell adhesion. Cleavage of cadherin-11 by ADAMs does not seem to affect its ability to interact with cytoplasmic binding partners, β-catenin and p120-catenin. This observation supports the idea that the “purpose” of cadherin-11 cleavage is to regulate cell adhesion, and not to induce (cell autonomous) signaling events. Additionally, the secreted extracellular domain of cadherin-11 (EC1-3) retains biological activity. This fragment can bind to a number of cell surface molecules in tissue culture including full-length cadherin-11 and specific members of the ADAM family. This observation suggests that EC1-3 may interact with full-length cadherin-11 molecules in vivo, and inhibit cadherin-11 mediated cell adhesion during CNC migration. EC1-3 can rescue CNC migration in embryos that overexpress cadherin-11, further supporting this hypothesis. Many of the above observations have been published in my first-author paper entitled “Extracellular processing of cadherin-11 by ADAM metalloproteases is essential for Xenopus cranial neural crest migration” published in the journal Molecular Biology of the Cell in 2009. Some of the unpublished work in this dissertation further focuses on how EC1-3 effects CNC migration in an ex vivo environment. During these studies, the observation was made that overexpression of EC1-3 in a cranial neural crest explant produces abnormal directional movement. In these experiments, it appeared as though certain regions of the CNC explant were “attracting” other regions of the explant. The preliminary studies described in chapter IV are aimed at answering the question; does EC1-3 attract migrating CNC cells? Here, we generated a Matlab program in order to effectively quantify the amount of directional movement of CNC explants presented with a source of EC1-3. In addition to quantifying cell directionality, this program can also decipher between cells moving with random or directed motion, and measure the velocity of cell migration within certain coordinates. Therefore, this program should be useful other ex vivo studies that require the observation of these features. To conclude, the work presented in this dissertation suggests that the role of cadherin-11 during cranial neural crest migration is predominately based on the adhesive function. In order for CNC migration to proceed, the amount of cadherin-11 mediated cell-cell adhesion is tightly regulated throughout this process. These cell-cell interactions are likely important for “sheet” and “branch” migration where CNC cells maintain a lot of cell-cell cohesion.

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