Aerobic carbon monoxide (CO) oxidation is used by phylogenetically and physiologically diverse microorganisms inhabiting a variety of terrestrial and aquatic ecosystems. Activity assays, culture-based studies, and molecular-based approaches targeting the coxL gene, encoding the large subunit of CO dehydrogenase, were used to investigate the role of temperature in structuring CO-oxidizing communities at Kilauea Volcano, Hawaii. CO uptake activity was assessed for unvegetated and vegetated temperate volcanic deposits that experience different temperature regimes due to plant development during ecosystem succession. Both CO-oxidizing communities had similar short-term responses to temperature; however, results from extended incubations (30 d) at elevated temperature (55 °C) indicate that succession expanded the capacity of the vegetated community to adapt to high temperature. Aerobic CO uptake was also examined for geothermal sites including two soils and two microbial biofilms at the Puhimau geothermal area and Kilauea Iki crater. CO oxidation occurred at elevated temperatures for all sites assessed; however, cardinal temperatures for CO activity were not strongly correlated to in situ temperatures. These results also extended the known upper temperature limit (80 °C) for aerobic CO oxidation. Culture-based methods targeting thermophiles at these sites yielded 31 newly isolated thermophilic CO-oxidizing strains in 8 genera. Two strains were formally described as novel species. The isolation of multiple Thermogemmatispora strains (Class: Ktedonobacteria) led to exploration of CO oxidation in this group; CO oxidation was found to be a common trait among Ktedonobacteria. Additionally, geothermally-heated biofilms at Puhimau were dominated by Ktedonobacteria as determined from coxL clone libraries, 16S rRNA gene pyrosequencing, and analysis of coxL fragments from a biofilm metagenome. Thermophiles are known to exist in temperate environments, but their maintenance and activity remain unclear. We examined the activity of thermophilic CO-oxidizing bacteria under different temperature regimes including 25 °C, 55 °C, and an oscillating temperature regime (20 55 °C). Three hours per day above 45 °C was sufficient for growth and CO oxidation activity. CO oxidation at moderate temperatures could contribute to maintenance metabolism and survival of thermophiles under suboptimal conditions. Collectively these studies show that thermophilic CO oxidizers are active and abundant in thermal systems on Kilauea Volcano.

The greenhouse gas methane mainly regulated by microbial processes. Methanogenic archaea, a major biological source of methane, are a diverse group of organisms that produce methane as a metabolic byproduct. The generation of methane takes place in diverse anoxic environments using CO2 and other reduced substrates. The release of methane into oxic environments often is regulated by methanotrophic Proteobacteria and Archaea, specialized groups of bacteria that use methane as sole sources of carbon and energy. These organisms can play major roles in the regulation of methane transport into the atmosphere and make up one part of the methane cycle. Pools of are methane thought to be sequestered from interacting with the global methane cycle may exist beneath the worlds glaciers and ice sheets. These environments are cold, dark, and anoxic. Thereby these environments would be suitable for the growth and metabolism of methanogenic bacteria. Subglacial environments harbor active microbial ecosystems that potentially impact biogeochemical cycling and contribute significantly to global iron, sulfur, and carbon cycles. Recent molecular and biogeochemical evidence has suggested that subglacial environments are sources of the greenhouse gas methane. Here we present molecular and geochemical evidence of microbially derived subglacial methane being released at sites of subglacial discharge from a glacial terminus near Kangerlussuaq, Greenland. Dissolved methane in subglacial discharge was measured in samples collected during the summer of 2012 and ranged from 0.97 to 85 µM; δ13CH4 values for the methane indicated a biological origin. Duplicate samples that were not killed at time of collection showed depleted methane concentrations and heavy enrichment in δ13CH4 after four months of 4°C incubation. Molecular evidence, in the form of reverse transcribed pmoA mRNA and 16S rRNA, for active methanotrophs and recently active methanogens was found in these samples. Furthermore, a return visit to the subglacial site the following year provided additional evidence of an active methanotrophic community based on time series incubations (methane oxidation rates of 0.31 μM day-1). These data provide the first evidence suggesting that active microbial oxidation of subglacial methane is occurring at the western margin of the Greenland Ice Sheet.

This dissertation investigated the cellular and molecular basis of osmoregulation in developing and adult Gulf killifish, Fundulus grandis, acclimated to salinities ranging from fresh water to sea water. In chapter 2, F. grandis embryos were reared in 0.1, 5, and 32 ppt water from 2 days (d) post fertilization until late embryogenesis. There were no discernable differences among salinities in the morphology of osmoregulatory organs, including the pharyngeal arches, digestive tract, or kidney. The localization and abundance of Na+/K+ ATPase (NKA), Na+/K+/2Cl- cotransporter (NKCC), and the chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) on the external surfaces of these tissues support a role in osmoregulatory as early as prior to hatch. In addition, F. grandis larvae were exposed from hatch to 0.1, 5, and 32 ppt water until 6 weeks post hatch (wph). Differential localization of NKCC and CFTR during osmotic challenges indicated putative altered functions of the intestine and gills, but not of the kidney in larval F. grandis. In Chapter 3, adult F. grandis were acutely transferred from 5 ppt water to 0.1, 1, and 5 ppt water for 7 d, or were acclimated to 0.1 ppt water then acutely transferred to 0.1 and 32 ppt water for 7 d. The mRNA and protein levels of NKA, NKCC, and CFTR in the intestine were differentially affected by the hypo- or hyperosmotic challenges. Localization of transport proteins suggested differences in intestine function associated with salinity acclimation. The anterior and posterior intestine may function in HCO3- or Cl- secretion during exposure to 0.1 ppt water; the anterior intestine from 32 ppt acclimated fish may facilitate both Cl- and water absorption; and the posterior intestine during exposure to 32 ppt water may facilitate HCO3- or Cl- secretion. In chapter 4, the roles of these proteins in the anterior intestine of F. grandis were assessed using an electrophysiological approach coupled with pharmacological inhibition of transporters. A high apical CFTR activity in the anterior intestine during acclimation in fresh water was observed. In conclusion, salinity acclimation affected the possible functions of osmoregulatory tissues of larval F. grandis, as well as the putative functions in ion/water regulation in the intestine of adult F. grandis.

The effects of DNA damage signaling on the DNA replication of the polyomavirus SV40 are examined in this dissertation. Infection of monkey cells with SV40 results in large amounts of cellular DNA damage signaling through the cellular kinases ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR). Literature pertaining to DNA replication, DNA repair, DNA damage signaling, and polyomaviral replication is first discussed. This is followed by a number of experiments testing the molecular mechanisms that necessitate DNA damage signaling by ATM and ATR during SV40 infection. Furthermore, the contribution of ATM and ATR to SV40-induced cell cycle arrest and repair protein recruitment to viral DNA replication centers is explored. After an examination of how my experiments fit in with relevant manuscripts, I discuss the possible consequences of the aberrant products found upon inhibition of DNA damage signaling during SV40 DNA replication and how my current studies can be advanced. Additionally, the connection between DNA damage signaling and DNA repair and the implications of my dissertation to cellular DNA replication are discussed.

This research utilizes aphids to address some of the emerging themes in social evolution. To begin to address these themes, I identified traits to measure sociality in aphids. I found that for the ecological and behavioural traits tested, housekeeping and defense, there were quantifiable differences between social and nonsocial species. However, there was no clear threshold that differentiated social from nonsocial species, meaning that definitions of sociality in aphids depend in part on the traits that are measured. Next, I explored a major theme of social evolution, the ability of groups to protect the nest from predators, by characterizing adaptations for defense. I found that aphid soldier elicit an overexpression of the melanization immune response in victims causing toxicity which leads to death, and successful defense of the nest. Finally, cooperation is inherently vulnerable to exploitation by cheaters. Aphids present a rare opportunity to study the effect of cheaters on groups due to multiple unique life history traits. I characterized the consequences of cheaters for weakly and nonsocial species and, contrary to our expectations, the presence of cheaters has the strongest negative effect on the nonsocial species, compared to the social or weakly social species. The results suggest that there is a more complex relationship between competition and relatedness than previously realized. Taken together, these results offers a new perspective on the role of defense, social immunity and kin selection in the evolution of sociality in this disparate group.

Small noncoding RNAs including miRNAs and siRNAs play significant roles in gene regulation via the mechanism of RNA interference (RNAi) and have been exploited to conduct loss-of-function studies. The discovery that these small RNAs can regulate genes at the post-transcriptional level by interacting with mRNA targets has enabled researchers to understand their importance in normal cellular processes as well as disease processes. Although extensive findings have been illuminated at the post- transcriptional level, there are still some questions regarding roles of small RNAs at the level of transcription (DNA) using higher vertebrate models. Using zebrafish, we explored a novel transcriptional gene silencing method and found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable silencing in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Silencing was mediated by the RNAi enzyme, Dicer and ChIP analyses detected an enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.

Though among the most controversial topics in systematic and evolutionary biology, species are a fundamental unit in biology, and are utilized by and critical to a wide variety of studies in the life sciences. Despite this importance, little work has focused on developing and examining objective methods for species delimitation until recently. Further, New Guinea and the surrounding regions are among the most diverse and geologically complex regions globally, yet the region remains poorly explored biologically, and little work has examined the evolutionary history of the fauna in the region. To investigate the influence of factors such as sampling intensity, species richness, and phylogenetic structure on discovery methods for species delimitation, I combine simulated and empirical data. In Chapter 1, I use simulated data to examine the accuracy of three discovery methods for species delimitation under a variety of different sampling strategies. I find that genetic clustering algorithms, such as Structurama, can be highly accurate in identifying even recent divergences with limited sampling of individuals and of loci, and that Gaussian clustering can be similarly accurate, though somewhat less sensitive to detecting recent divergences. However, my results show that nonparametric delimitation is highly sensitive to errors in gene genealogy estimation, and generally fails to delimit species accurately when true coalescent gene genealogies are unknown, as in empirical applications. In Chapters 3 and 4, I apply these methods empirically to examine the species boundaries, as well as the phylogeny and other aspects of the evolutionary history of, scincid lizards of the C. bicarinata and C. fusca groups, respectively. My results in Chapter 3 indicate that species delimitation analyses may be prone to underestimating the number of species by identifying only higher levels of clustering in systems with deep phylogenetic structure. I additionally find evidence for several cryptic species in the group, including deep, species-level divergence among the populations of C. storri from Australia, the Aru Islands, and New Guinea, despite their recent connectivity via Sahul Shelf emergence during Pleistocene glaciations. Through also examining niche evolution in the group, I find evidence for niche conservatism among most species in the group, but two species, C. bicarinata and C. sp. Amau from eastern Papua New Guinea, show evidence for environmental niche divergence. Analyses of the C. fusca group in Chapter 4 provide further evidence for a tendency of discovery methods for species delimitation to under-detect species in groups with high diversity or deep phylogenetic structure. Genetic clustering algorithms based on the complete dataset only identify a small number of clusters that correspond largely to deep phylogenetic clades, but when restricted to within these clades, this method identifies clusters that correspond well to finer, putative species-level structure. I also find evidence for extensive cryptic diversity in this group, identifying 28 distinct species among my sampling of 16 currently recognized species, as well as other incongruence with current taxonomy, including synonymous species and mis-assigned populations, supporting previous evidence of the need for extensive taxonomic revision in the C. fusca group. My biogeographic analyses also providence evidence that the C. fusca group likely evolved in Australia or Australia and New Guinea before diversifying in New Guinea, dispersing at least twice across Lydekkers line into Wallacea, and possibly also recolonizing Australia. Finally, in Chapter 5, I take a more comprehensive approach, and combine genomic and morphological data to test the validity of and examine the demographic history of two putative species of Tribolonotus from the islands of Buka and Bougainville in the northwestern Solomon Archipelogo. I use next-generation sequencing to collect a genomic dataset of several thousand loci, and apply species discovery (genetic clustering algorithms) and species validation (Bayes factor delimitations) to test for speciation between these populations. My results support this speciation event, despite the recent connectivity between these islands. I also collect a suite of morphological characters for this group and provide evidence for morphological divergence and diagnosibility. Demographic analyses applied using approximate Bayesian computation and diffusion analysis further provide evidence for a complex demographic scenario in which migration between these populations continued for some time following their initial divergence, but subsequently decreased in rate or ceased entirely. Combined, these results yield extensive insight into the utility of several methods for species delimitation, the taxonomy and systematics of Carlia and Tribolonotus in New Guinea and the surrounding regions, and the complex processes responsible for driving the generation and maintenance of the phenomenal diversity in the Sahul shelf region.

Species interactions play a prominent role in the establishment and spread of many invasive species. However, rarely are invasions studied in more than a direct pairwise species context, or with consideration to how species interactions can vary biogeographically. Using field surveys combined with common garden and greenhouse experiments, I investigated how multitrophic above and belowground interactions influence plant invasions at large spatial scales. I focused on comparisons between sympatric native and invasive lineages of Phragmites australis, a wetland grass distributed throughout North America. I conducted a field survey to examine support for the enemy release hypothesis in a tritrophic framework. In North America, the invasive lineage of P. australis escaped from introduced Lipara gall-flies, attributed to greater vertebrate predation on Lipara infesting the invasive than the native lineage. A complementary common garden experiment revealed that enemy release of the invasive P. australis lineage from Lipara was driven by local environmental conditions rather than genetic differences between the two lineages. Importantly, local enemy release was strongest at northern latitudes, generated by genetically based non-parallel latitudinal gradients in Lipara herbivory for the native and invasive lineages. This phenomenon could translate to biogeographic variation in invasion success and is worthy of investigation across a range of invaded systems and species interactions. I also conducted a greenhouse experiment to examine the interactive effects of rhizosphere soil biota, interspecific competition, and nutrient availability on performance of P. australis and native smooth cordgrass, Spartina alterniflora. All lineages of P. australis suffered negative impacts from soil biota, suggesting this interaction does not directly facilitate the success of invasive P. australis. However, the most interesting result from this experiment was that soil biota from the invasive P. australis lineage negatively impacted S. alterniflora, whereas soil biota from the native lineage had a positive impact. This indirect spillover of pathogens and mutualists interaction may have important implications for invasion success and restoration. In summary, my dissertation highlights the importance of examining biological invasions in a biogeographic and multitrophic context and has broad implications for the understanding and management of biological invasions.

The relationship of the macrocyclic rust fungus PUccinia poarum with its pycnial-aecial host, Tussilago fapfaPa, and its uredial-telial host, Poa ppatensis, has been investigated, using light microscopy, electron microscopy and micro-autoradiography. Aspects of the morp- hology and ontogeny of spores and sari, which were previously disputed, have been clarified. Monokaryotic hyphae grow more densely in the intercellular spaces of Tussilago leaves than the dikaryotic intercellular hyphae on Poa. Although ultrastructurally sbnilar, monokaryotic hyphae differ from dikaryotic hyphae in their interaction with host cell walls, often growing embedded in wall material which may project into the host cells. The frequency of penetration of Poa mesophyll cells by haustoria of the dikaryon is greater than that of Tussilago cells by the relatively undifferentiated intracellular hyphae of the monokaryon. Intracellular hyphae differ from haustoria in their irregular growth, septation, lack of a neck-band or markedly constricted neck, the deposition of host wall-like material in the external matrix bounded by the invaginated host plasmalemma and in the association of callose reactions \vith intracellular hyphae and adjacent parts of host walls. Monokaryotic and dikaryotic infections differ also in the changes induced in the organization and ultrastructure of their respective host cells. Intracellular hyphae in bundle sheath, xylem parenchyma, transfer cells of phloem parenchyma and companion cells, give the monokaryon of P. poaPUm direct access to nutrients translocated in vascular tissue of Tussilago. Bundle sheath cells of Poa contain unusually long haustoria but· there is no penetration of the endodermis and vascular tissue by the dikaryon. After uptake of tritiated glycerol by infected tissue, microautoradiographic investigation shows radioactivity to be concentrated in sporulation structures, haustoria and, in the case of Poa, in host nuclei. Cells of uninfected tissues differ from those of infected tissue in accumulation of label in chloroplasts. These studies contribute to an understanding of the physiological interaction of P. poaPUm with its alternate hosts.

The sedge family, Cyperaceae, is a large group with approximately 5,000 species distributed among ca. 100 genera. Sedges are economically and ethnobotanically important. They are conspicuous members of many floras around the world and provide vital food and cover for wildlife. The focus of this dissertation is on the genus Cyperus, which includes about 900 species. Due to its large size, advancements in knowledge of Cyperus are made in small bites. The molecular phylogenetics component of this research focused on New World Cyperus. Chapter 2 presents a phylogentic analysis employing sequences from the nuclear ITS region. Chapter 3 presents a more robust analysis using five genic loci, including sequences from nuclear ITS plus four plastid loci. This research was the first to estimate the phylogenetic position of the monotypic genus Karinia. Karina has been included in Cyperus in the past, and is here resolved as a member of the Ficinia clade which is consistently estimated as sister to the Cyperus clade in molecular studies. Karinia was embedded in a clade with Sciproides. Its morphology, including perennial habit, dense head-like inflorscences, and spirally-arranged floral scales, are consistent with that of Scirpoides. Another important result of this work is the resolution of the predominantly Central American Cyperus andinus and C. seslerioides as belonging to section Leucocephali. This study strongly supports section Leucocephali, whose members utilize C3 photosynthesis, as sister to C4 Cyperus. Members of section Leucocephali are adapted to open seasonally dry grasslands, which may be the ecological intermediary to the evolution of C4 photosynthesis. Sampling for molecular studies included in this research enabled assessment of two taxonomic sections: Luzuloidei and Diclidium. The New World section Luzuloidei, which is composed of C3 members, is strongly supported as monophyletic. A morphological synapomorphy in section Luzuloidei is the presence of two-keeled floral scales. Section Diclidium, which is diagnosed as having spikelets which break into one- to two-fruited segments upon maturity, is polyphyletic. Therefore, this unique mode of spikelet shattering arose independently at least twice. Results provided some insight into several taxonomic problems in the Umbellati group and in section Strigosi; however, a greater number of samples are needed to assess these problems. The suspected relationship of the North American prairie species Cyperus cephalanthus to the South American Cyperus rigens species group was confirmed by the molecular phylogenetic analyses, as was the monophyly of the C. rigens group. Cyperus cephalanthus strongly resembles the South American C. impolitus. It was hypothesized that these taxa were morpholically indistinguishable. Morphometric analysis showed that several characters are statistically different, includeing floral scale dimensions, achene width, and achene shape. However, results of Principal Components Analisis (PCA) suggest that Cyperus cephalanthus and C. impolitus are the same morphological species. Results of PCA of Cyperus rigens and several of its infraspecific taxa were inconclusive, highlighting the need for more work with this highly variable South American taxon. Coastal prairie is one of the most imperiled habitats in North America. It is in this habitat where Cyperus cephalanthus is found, with fewer than 20 known populations in North America (Louisiana and Texas). This research included a floristic survey of wet coastal prairie sites in southwestern Louisiana. This work was partly stimulated by the preference of Cyperus cephalanthus for this habitat, and further motivated by the discovery of several promising prairie remnants quadrupaling the aerial extent of known coastal prairie in Louisiana. The wet coastal prairie flora included 512 minimum-rank taxa, with 461 being native. A total of 255 were estimated to be ecological conservative and characteristic of coastal prairie, with the balance consisting of weedy elements taking advantage of disturbance and habitat alteration. The wet coastal prairie was rich in sedges, with 72 species among nine genera. Cyperus was the most species rich genus in the entire wet prairire flora with 20 species. Coefficients of conservatism (C-values) were assigned to each taxon in the wet prairie flora. These C-values will allow computation of various Floristic Quality Indices (FQI) for sites ranging from unplowed prairie remnants to de novo restorations.