<p>The truffle genus Tuber (Ascomycota, Pezizales, Tuberaceae) produces underground mushrooms widely sought as edible fungi. Tuber species are distributed throughout Northern hemisphere forests and form obligate ectomycorrhizal symbiosis with trees within the Pinaceae, Fagaceae, Betulaceae, and Juglandaceae. </p><p>The transition to a truffle form (from an epigeous form) has occurred independently, multiple times in both the Ascomycetes and Basidiomycetes. One instance has given rise to the Tuberaceae, which is composed entirely of obligate ectomycorrhizal species. Attempts to cultivate European truffle species T. melanosporum, T. aestivum, and T. borchii are underway in North America and other parts of the world and have been met with mixed success.</p><p>The overarching goal of my dissertation is to address the systematics, ecology, and biogeography of Tuber within a phylogenetic framework. Multiple loci were sequenced from Tuber ascoma collected worldwide including ectomycorrhizae, though an emphasis was placed on sampling taxon within North American. Maximum likelihood, maximum parsimony, and Bayesian inference were used for phylogenetic reconstructions. </p><p>A taxonomic and phylogenetic overview of the family Tuberaceae is presented in Chapter 1. Tuber is resolved as monophyletic. In Chapter 2, through greater taxon sampling including epigeous and hypogeous Helvellaceae outgroups and related South American taxa, a resolved multi-gene phylogeny of the Tuberaceae and putative epigeous ancestor of Tuber is presented. A previously unknown South American lineage that contains both epigeous and hypogeous taxa is resolved as sister to the Tuberaceae. Chapter 3 is focused on issues of cryptic speciation and taxonomy within the Tuber gibbosum clade. The four species resolved in the Gibbosum clade appear to be endemic to the Pacific Northwest and associated primarily with Gymnosperms. Chapter 4 is a meta-analysis of all known Tuber ITS rDNA sequences (e.g. from Genbank and generated from herbarium collections) available at the time. These were placed within the Tuber phylogeny to assess species diversity, long-distance dispersal, and host associations. In total, 120 phylotypes were detected (based on a 96% similarity criterion). Tuber shows high levels of continental endemism. I hypothesize that species shared between continents and having low ITS variability (<1%) are the result of recent human-mediated introduction events. Chapters 5 and 6 are focused on the ectomycorrhizal ecology of the economic truffle T. lyonii, which is native to Eastern and Southern North America. There is a phenomenon of Tuber lyonii fruiting in pecan orchards. Pecans (Carya illinoinensis) are in the Juglandaceae, an understudied ectomycorrhizal plant family. I sampled the ectomycorrhizal communities of pecan orchards (associated with the production of the North American truffle species Tuber lyonii). In Chapter 5 I discuss four Tuber taxa discovered in these pecan orchards, their abundance and haplotype diversity. Chapter 6 examines the ectomycorrhizal communities across the five pecan orchards sampled. I show that multiple Tuber species, including Tuber lyonii, are dominant in the ectomycorrhizal community. Chapters 7 and 8 focus on black truffles in the Melanosporum clade. In Chapter 7 I document that Tuber indicum has been introduced into North America multiple times, and through ectomycorrhizal synthesis I demonstrate that this Asian species can associate readily with angiosperm and gymnosperm hosts endemic to North American. In Chapter 8 I describe a quick and reliable method for the determination of Tuber melanosporum. The method is based on direct PCR and species-specific primers and is very useful for rapid diagnostics. I have adapted this approach for other truffle and mushroom species. </p><p>Three major findings emerge from my dissertation research: 1) Tuber is more diverse than previously realized; 2) Tuber exhibits high levels of regional and continental endemism; 3) Taxonomic issues remain in many species complexes worldwide (including the Tuber candidum complex in North America, the Tuber excavatum complex in Europe, the Tuber indicum complex in Asia). Taxonomic challenges also remain regarding species known only from ectomycorrhizal or anamorphic states. The discovery of additional Tuber species is expected as the truffle flora of undersampled regions become better studied and incorporated into the Tuberaceae phylogeny.</p> / Dissertation

The first objective of this study was to investigate the role of an invasive grass species, Arundo donax (L.), on the hydrologic cycle. At a site on the Rio Grande in South Texas, we measured the gas exchange of carbon dioxide and water vapor at the leaf scale and structural characteristics, such as leaf area and shoot density, at the stand scale. In order to assess the effect of water availability, this study was conducted along transects perpendicular to the edge of the river along a potential moisture gradient. The second objective was to quantify the effect of two herbivores, an armored scale, Rhizaspidiotus donacis (Leonardi), and a stem-galling wasp, Tetramesa romana (Walker),on the photosynthetic and transpiration rates of A. donax. Leaf gas exchange measurements were made to determine the direction and magnitude of the effect on physiological processes and by what mechanisms any effects arose. Stands of A. donax used approximately 9.1 � 1.1 mm of water per day. This rate of water use was at the high end of the spectrum for plants. The major controls on stand scale transpiration were evaporative demand, leaf area index, and water availability. During two summer seasons, stand scale transpiration varied greatly, following the pattern of variability in precipitation, suggesting that recent rainfall constituted a significant proportion of the water taken up by this species. Herbivory by a stem-galling wasp and a sap-feeding scale, both separately and together, reduced the rates of leaf scale physiological processes in A. donax. The efficacy of the wasp was density dependent, and this herbivore reduced the carboxylation rate of Rubisco. The effect of the scale took approximately five months to manifest, which coincided with generation time. Scale reduced photosynthesis by decreasing the maximum rate of electron transport. When the two insects were both present, the effect of their herbivory seemed to be additive. These results will assist the responsible management agencies in evaluating the propriety of using one or both of the insect herbivores as biological control agents.

The non-game wildlife trade poses a risk to our natural landscape, natural heritage, economy, and security. Specifically, the trade in non-game reptiles and amphibians exploits native populations, and is likely not sustainable for many species. Exotic amphibian and reptile species pose risk of invasion and directly or indirectly alter the native landscape. The extent of non-game amphibian and reptile trade is not fully understood and is poorly documented. To quantitatively describe the trade in Texas, I solicited data from the United States Fish and Wildlife Service's (USFWS) Law Enforcement Management Information System (LEMIS) and Texas Parks and Wildlife Department's (TPWD) non-game dealer permits. I surveyed amphibian and reptile pet owners, breeders, Internet sites, pet shops, and meat and seafood establishments by visits, electronic surveys, and observations. The trade in exotic species of amphibians and reptiles in the state of Texas was found to be popular in two ways; the importation of wildlife products and sale of live specimens for pets. Persisting in the pet trade were species known to be exotic, a problem made worse by lack of regulations governing the import, export, and keeping of exotic species. Trade in wild collected native species was primarily for export to foreign countries. Collection of turtles from the wild in Texas was heavy until 2008, when TPWD restricted collection to private waters. Collection of other species from the wild was minimal, with the exception of the Western Diamond-backed Rattlsnake (Crotalus atrox) for rattlesnake roundups. Native species were found to exist in the pet trade, but primarily as genetic color variants that do not occur in the wild, an indication that captive breeding may be relieving pressures on wild caught specimens. Minor changes in reporting requirements and permitting systems at the state and federal level would improve the management of exotic and native amphibians and reptiles that persist in the trade. Changes that include standardized taxonomic reporting requirements at state and federal level, streamlined permitting system for individuals wishing to collect from the wild in Texas, bag limits and seasons for wild collection, increased reporting requirements for owners of exotics, and enforcement of reporting errors would aid in management of exotic and native amphibians and reptiles in the trade.

Life history traits such as growth, survival, and clonality can vary within a population. When such variation exists in a population of an invasive species, it can affect population dynamics, and if any part of the variation has a genetic basis the population can evolve in response to control regimes. Evolutionary responses to control efforts may shift the population towards a few more resilient genotypes, or towards different types in different microenvironments, depending on the scale of gene flow with respect to the patchiness of the environment. The purpose of this study is to examine whether the application of stress similar to control efforts (light level manipulation and biomass removal) results in varying emergence, growth, and survival rates between samples taken from spatially separated patches of the invasive clonal grass Imperata cylindrica. Accelerated Failure Time (AFT) and logistic regression models were fit to survival, emergence and growth data collected from two experiments in which samples collected from four spatially separated Imperata cylindrica patches were exposed to light level manipulation and biomass removal. Patch identity plays a large role in explaining variation in time-to-emergence, time-to-death, and probabilities of emergence and survival, especially under stressed conditions. Rhizome and above ground biomass characteristics also play substantial roles in explaining variation in emergence, survival, and growth, though more so under non-stressed conditions. Our results warrant further study of heterogeneous responses to stressful conditions, especially those imposed under control and management regimes. This heterogeneity may have important impacts on population processes such as maintenance, expansion, and gene flow.

Although the process by which fertilization occurs in bryozoans is well described, the ability to self-fertilize and the subsequent ecological consequences are poorly understood. Culturing experiments were conducted examining the effects of selfing on offspring survival and reproduction in the simultaneous hermaphrodite Bugula stolonifera collected from Eel Pond, Woods Hole, MA. Results from these experiments document significant decreases in survival and fecundity of selfed offspring, compared to outcrossed controls, suggesting that these animals are not routinely self-fertilizing in Eel Pond. How these arborescent colonies minimize selfing remains unclear, but it is hypothesized that conspecific aggregations could serve to minimize the chances that a colony utilizes its own sperm for fertilization. The genetic composition of these aggregations was investigated using a newly developed microsatellite library. As larvae routinely metamorphose on conspecific colonies, the possibility that larvae select or avoid their maternal colony was also investigated. Analyses of genetic structure document homogeneity throughout these aggregations on extremely small spatial scales, suggesting high amounts of larval dispersal within aggregations. When combined with results from parentage-exclusion and kinship analyses, these results indicate that a colony's nearest neighbors are not composed of siblings, potentially minimizing inbreeding. Molecular analyses were then used to determine if the high larval dispersal within aggregations resulted in high mixing between aggregations. Sites within Eel Pond separated by 100-300 m were routinely sampled from 2009 to 2011, and analyses were conducted to investigate potential inter- and intra-annual genotypic differentiation within and between aggregations. Results document that although low levels of mixing could result in increased homogeneity between some aggregations, barriers to genetic exchange prevent mixing between most sites. Further, inter-annual comparisons within sites document that significant differentiation can occur between reproductive seasons. Hence, any potential homogeneity achieved between sites during one reproductive season will likely be lost by the beginning of the next reproductive season. Additionally, while sampling in Eel Pond in 2010, I document the first occurrence from the western Atlantic Ocean of another aggregating arborescent bryozoan, Tricellaria inopinata. The growth and reproductive biology of these animals was monitored throughout 2011; results suggest that this introduction is likely to persist.

The historically introduced House Rock Valley bison herd has, in recent years, migrated from the eastern Arizona Strip onto the Kaibab Plateau within Grand Canyon National Park. Bison are considered a nonnative species to the southern Colorado Plateau, and the animals adversely impact sensitive ecosystems prompting National Park Service wildlife managers to pursue their removal. Archaeofaunal evidence of bison in the Grand Canyon and neighboring regions, however, raises concern that bison may in fact be native. Assessing the evidence within a zooarchaeological interpretive framework is critical since mere presence/absence lists of bison remains do not address the potentially complex cultural processes involved in the formation of archaeofaunal assemblages. Inter-assemblage comparisons illustrate a decline in relative abundance and skeletal completeness correlated to distance from traditionally understood historical bison distribution. If bison were present in the Southwest, as the evidence suggests, they likely entered the region only occasionally as small, dispersed herds.

Invasive species such as quagga mussel (Dreisseina bugensis) alter native ecosystems around the world. This study uses genetic markers to examine historical lineages for quagga mussels in lakes (reservoirs) of the Colorado River System. Specimens were collected from Lake Mead, Lake Mohave, Lake Pleasant, Lake Havasu, Lower Otay Reservoir, Yuma Area, and two Central Arizona Project pumping stations. Objectives of this project were to perform analyses of genetic variability within populations and determine if relatedness among individuals could resolve whether they originate from a single, or multiple, invasion events and genetically distinguish the populations at each water body. Analyses examined the mitochondrial DNA COI region and eight microsatellite DNA markers. Three populations were characterized in the study area and compelling information gathered about gene flow between them. Results indicate that microsatellite markers are useful to track quagga mussel invasions and provide insights into migration patterns that would otherwise be missed.

Shifting patterns of precipitation associated with climate change may affect water-limited ecosystems to a greater degree than atmospheric CO2 or temperature changes, yet we lack a mechanistic understanding of the effects of water in these ecosystems. In water-limited ecosystems, annual net primary productivity correlates strongly with total annual precipitation. However, precipitation in these ecosystems arrives in episodic events, suggesting that biophysical investigations should focus on the implications of discrete precipitation events. Further, examining dynamics of ecosystem processes over a period of days or weeks promises to link our leaf-level mechanistic understandings with larger scale patterns and temporal dynamics of ecosystem photosynthetic CO2 uptake, respiration and evapotranspiration.The objectives of this dissertation were to quantify: (1) the influence of biotic and abiotic features of an ecosystem (e.g., species composition and soil physical characteristics) on short-term patterns of resilience and resistance to a precipitation pulse; (2) the role of antecedent climatic conditions and the seasonal timing of rainfall in limiting ecosystem carbon exchange in response to precipitation events; and (3) the effect of changes in woody plant abundance on seasonal ecosystem carbon dynamics in relation to the North American Monsoon.Major findings and contributions of this research include defining the concepts of ecosystem functional resistance and resilience and their implications in the presence of a dominant nonnative bunchgrass in semi-arid grasslands (Appendix A); a better understanding of the influence of warm-season precipitation variability and the seasonal timing of rainfall on ecosystem carbon dynamics in a semi-arid grassland (Appendix B); the use of flux duration analysis, a novel approach to analyzing ecosystem carbon and water flux time-series data to distinguish between "pulse-driven" or "steady-state" ecosystems (Appendix C); and, finally, the application of flux duration analysis to quantify the sensitivity of ecosystem carbon exchange in response to seasonal rainfall in a riparian grassland and shrubland and the role that plant functional type diversity may play in constraining carbon exchange sensitivity (Appendix D).

Species distribution models must balance the need for model generality with that for precision and accuracy. This is critical when modelling range-expanding species such as invasive species. Given the increased use of species distribution models to study invasive species-landscape relationships, a better understanding of the effect of spatial scales, sampling biases, model transferability and discrepancies between different models’ future predictions is necessary. This dissertation addresses these knowledge gaps using mute swans (Cygnus olor) as a case study species. I specifically examine mute swan’s distributions in parts of their native range of Britain and their non-native range of Ontario, Canada. I first investigate which environmental variables at which spatial scales best explain mute swan’s distribution in its non-native range. Second, I perform a sample selection bias study to examine predictive accuracy when species distribution models are built using varying ranges of environmental variables and applied to broader spatial extents. Third, I examine the potential for, and limitations of model transferability between native and non-native regions. Finally, I use two different modelling approaches and three different climate change and land use change scenarios to predict future mute swan habitat suitability. The results indicate that (1) models with better predictive accuracy include environmental variables from multiple ecologically-meaningful scales and measured at spatial extents that include a broad range of environmental variable values; (2) models can exhibit asymmetrical transferability; (3) climate change will facilitate mute swan range expansion in the future more than land use change; and (4) mute swans are often found near urban waterbodies. When modelling invasive species distributions, I suggest that ecologists consider: (I) spatial scale of the underlying landscape processes and species’ use of the landscape; (II) variability and range of each environmental variable used for building models; and (III) stage of establishment of the invasive species.

Species distribution models must balance the need for model generality with that for precision and accuracy. This is critical when modelling range-expanding species such as invasive species. Given the increased use of species distribution models to study invasive species-landscape relationships, a better understanding of the effect of spatial scales, sampling biases, model transferability and discrepancies between different models’ future predictions is necessary. This dissertation addresses these knowledge gaps using mute swans (Cygnus olor) as a case study species. I specifically examine mute swan’s distributions in parts of their native range of Britain and their non-native range of Ontario, Canada. I first investigate which environmental variables at which spatial scales best explain mute swan’s distribution in its non-native range. Second, I perform a sample selection bias study to examine predictive accuracy when species distribution models are built using varying ranges of environmental variables and applied to broader spatial extents. Third, I examine the potential for, and limitations of model transferability between native and non-native regions. Finally, I use two different modelling approaches and three different climate change and land use change scenarios to predict future mute swan habitat suitability. The results indicate that (1) models with better predictive accuracy include environmental variables from multiple ecologically-meaningful scales and measured at spatial extents that include a broad range of environmental variable values; (2) models can exhibit asymmetrical transferability; (3) climate change will facilitate mute swan range expansion in the future more than land use change; and (4) mute swans are often found near urban waterbodies. When modelling invasive species distributions, I suggest that ecologists consider: (I) spatial scale of the underlying landscape processes and species’ use of the landscape; (II) variability and range of each environmental variable used for building models; and (III) stage of establishment of the invasive species.