<p> Invasive tamarisk has many impacts in freshwater systems including increasing soil salinity, decreasing water content, and causing a shift in food web structure. Tamarisk species originally introduced to the US have hybridized and have been documented invading salt marsh systems in San Diego County, California. The main goals of this study were to determine the impacts of tamarisk within a salt marsh and among genetic types of tamarisk. Amplified Fragment Length Polymorphism was used to determine genetic identity of each individual salt-marsh invading tamarisk. Abiotic impacts depended on microhabitat, as did tamarisk tree morphology, and infauna community composition. Tamarisk altered abiotic factors in the upland and upstream microhabitats and altered infauna community composition in the marsh microhabitat. 17.8% of trees were hybrids of <i> T. ramosissima</i> x <i>T. chinensis.</i> The remainder were pure <i>T. chinensis.</i> Tamarisk genetic identity did not influence abiotic factors, although invertebrate diversity was lower beneath pure <i> T. chinensis</i> than the hybrid. The tamarisk invasion was not an <i> in-situ</i> hybridization and had the most pervasive impact on the infauna in the marsh microhabitat.</p>

<p> Bur oak (Quercus macrocarpa Michx.) savannas of the Great Plains have long been reported to be disappearing and/or progressing to other vegetative schemes. These losses are directly relatable to the arrival of European settlers and their subsequent suppression in natural prairie fires, along with the introduction of domestic livestock. A preliminary investigation of the floristic composition within remaining oak savannas of Custer County, Nebraska was conducted as a base means of documenting plant diversity within the remaining savannas of central Nebraska. The point-centered quarter method was used to determine species, density, relative density, frequency, relative frequency, dominance, relative dominance, and importance values (IV). The Swedish-increment boring method was applied to woody vegetation to document tree ages and compositional change in the savanna over time. Exclusion cages on oak seedlings, vegetative and soil sampling were also utilized. Results indicated a bleak future for the remaining savannas of Nebraska. Bur oak averaged an importance value of 159.10 out of 300.00, leaving a substantial portion of the importance values divided among several fire-sensitive species. The majority of bur oaks sampled were distributed among the higher size classes, indicating a low rate of recruitment. Age class distributions further support this conclusion with a minuscule number of oaks younger than 25 years of age and the majority of the species recorded over 100 years of age. Seedling survivability tests during summer months produced low survivorship (3.13%) due to drought and large/small mammal herbivory. Winter testing displayed similar results. Vegetation sampling indicated high percentages of exposed till and weedy plant species, indicating a long history of abuse. Soil tests resulted in significant differences in phosphorus and zinc concentrations. As oak recruitment failings continue on a near global scale, more research should be conducted to assist in the conservation and management of these vital ecosystems.</p>

<p>This project explores species boundaries, coevolution, biodiversity, parasite life cycles, and ecology using the cestode (tapeworm) fauna parasitizing the spiny dogfish, <i>Squalus acanthias</i>, and several of its close relatives. One of the aims was to verify the species identity of all the shark specimens from which cestodes were collected. Chapter 1 details use of the elasmobranch "barcoding" gene, NADH2, to verify host identifications, as well as to raise doubt about the wisdom of recognizing the Black Sea population of <i>S. acanthias</i> as a distinct subspecies. Chapter 2 examines diversity in the monotypic cestode genus, <i>Trilocularia</i>, throughout the widespread anti-tropical distribution of <i>S. acanthias</i> (i.e., the North and South Pacific, the North Atlantic, and the Black Sea), and in its congeners. An integrative approach, including morphological (i.e., light microscopy, histology, and scanning electron microscopy) and molecular methods (i.e., 28S, ITS1, 16S genes), was employed. Results reveal a large amount of undiscovered diversity in this genus and suggest that species of <i> Trilocularia</i> may be undergoing speciation more rapidly than their hosts. Chapter 3 describes one of the new species discovered, <i>Trilocularia eberti</i> n. sp. from <i>S.</i> cf. <i>mitsukurii</i>, and provides a prototype for future descriptions of species in this genus. Chapter 4 investigates microthrix variation in <i>Trilocularia</i> from the stomach and the spiral intestine of <i>S. acanthias</i> off Rhode Island. Results suggest that variation seen within a host individual is likely due to developmental changes rather than species differences. Chapter 5 aims to further the understanding of cestode infections in a marine environment through space and time by examining seasonal infection parameters in the cestode community of <i>S. acanthias</i> from Rhode Island across three years. While some general trends may be maintained across disparate localities, spatial variation is likely due to differences in accessibility to intermediate hosts and host diet across sites. The knowledge gained from understanding cestode infections in the vast ocean environment allows us to speculate about the factors driving fluctuations in parasite infections in elasmobranchs. </p>

<p> Abstract As invasive predators spread across landscapes, their sudden presence may have significant effects on the behavior patterns of their new found prey. Here, I examined how predator-naive foxes responded to colonization by non-native golden eagles on Santa Cruz Island, California. First, using radio-telemetry, I investigated the effects of this diurnal, aerial predator on fox activity patterns. In 1992, just prior to the arrival of golden eagles, foxes showed substantial diurnal activity, but diurnal activity was 37.0% lower in 2003-7, after golden eagle colonization; concurrently, overall activity declined and nocturnal activity increased. Moreover, on nearby Santa Catalina Island, where golden eagles were absent but where the fox population recently crashed due to a disease epidemic, remaining foxes were significantly more diurnally active than were those on Santa Cruz Island. The weight of evidence suggested that the change in activity pattern was a response to predation, not to low population density, and that this was probably a heritable, rather than a learned, behavioral trait. Second, I used radio-telemetry, camera traps, sightings to investigate spatial patterns and habitat use in the wake of eagle colonization. When comparing pre- and post-colonization conditions, foxes demonstrated an inverse home range-density relationship, as fox core areas and home ranges expanded significantly in the low-density conditions following eagle colonization. I found that diurnal ranges were 11% smaller than nocturnal home ranges in post-colonization conditions, perhaps reflecting restricted diurnal movement as a form of predator avoidance of the diurnally hunting eagles. In terms of habitat preference, foxes preferred shrubland &ndash; a habitat which provides cover from aerial predators &ndash; over other habitat types. This suggested a way in which foxes may have mitigated golden eagle predation risk. Finally, I examined changes in fox diet before and after colonization using scat analysis. Because this invasion reduced the endemic fox population by 95% in a decade, these dietary changes could have been be attributed to behavioral change (e.g., reduced diurnal activity and movement), demographic change (e.g., reduced intra-specific density), and/or community level change (e.g., increased intra-specific competition with island spotted skunks), all of which were shifts associated with eagle predation. Concurrently, there were marked changes in the island's vegetation community, with the removal of introduced grazers and the subsequent increase in recruitment of shrubland. I hypothesized that these effects would cause fox diets to differ from historic diets, as indicated by scat analysis. I also evaluated seasonal differences and dietary breadth in the post-eagle colonization period. Although I did not observe an overall large scale modification of fox dietary patterns, statistically significant dietary changes were observed before and after eagle colonization. Results suggested that all four factors may have had an effect on fox diet, although evidence suggested that grazer removal may have had a more pronounced effect. Seasonal patterns and dietary breadth reflected the seasonal availability of fruiting shrubs in the dry season, and an emphasis on other food items, primarily mice and insects, in the wet season, as expected. While this fox population has subsequently rebounded successfully, understanding how animals respond to the sudden arrival of an invasive predator is crucial to improving approaches to conserving endangered species in the future.</p>

<p> The widespread introduction of round goby (<i>Neogobius melanostomus </i>) throughout the Great Lakes basin has raised concerns regarding increased risk of egg predation on nesting fish species. Five-minute observation trials were conducted to determine the identity and number of nest predators on rock bass (<i>Ambloplites rupestris</i>), pumpkinseed (<i>Lepomis gibbosus</i>), and smallmouth bass (<i>Micropterus dolomieu</i>) nests following removal of the guarding male. Rock bass had a greater proportion of nests invaded (85.4 %) and average number of predators per nest (9.32, SE 1.7) than pumpkinseed (45.0%, 1.83, SE 0.64) in 2011. Similarly, rock bass had a greater proportion of nests invaded (52.5%) and average number of predators per nest (5.3, SE 1.7) than pumpkinseed (35.0%, 2.3, SE 1.1) and smallmouth bass (37.5%, 2.7, SE 0.94) in 2012. Principal components analysis and canonical correspondence analysis of habitat variables indicates some species are more vulnerable to nest predation due to preferred spawning habitat. </p>

<p> Six transgenic events (TEv) of <i>Castanea dentata,</i> each containing four to five transgenes with varying insertion numbers, were field-tested for non-target impacts on root symbiotic ectomycorrhizal fungi (EMF). Also included was the cloned plant used to create the TEv as a control, and a variety of seed-grown <i>C. dentata</i> and other <i>Castanea</i> species or hybrids to test natural variation and the effect of micropropagation procedures. The field sites included two open-field and two shelterwood sites. Two of the six TEv, both containing the transgene encoding the antimicrobial peptide ESF39, formed significantly less ectomycorrhizas than the control in their first season in the field; no differences were detected in the next season. No other differences in receptivity to EMF or between EMF communities were detected among the various experimental plants. No significant impacts on EMF of the transgenes encoding oxalate oxidase, GFP, BAR and NPTII were detected. Nor were impacts due to differences in insert copy number, insert position or micropropagation procedures. The shelterwood sites had significantly higher colonization than both of the open-field sites. Both open sites had relatively low diversity and communities composed of EMF typically found in pioneer communities. One of the shelterwood sites had significantly higher diversity and EMF typical of mature forest communities. The other did not; possible reasons for this are discussed. This study compared experimental plants with high numbers of gene inserts, differences found did not correlate with the number of insertion events or genes used, indicating that pleiotropic effects are rare in this species. Differences in colonization were temporally dependent which should be considered in future studies. Site characteristics affected both colonization by and community composition of EMF.</p>

<p> Noise associated with human activity is widespread and expanding rapidly in terrestrial environments, but there is still much to learn about its effects on animals. To determine the effect of introduced noise on lek attendance and strutting behavior, I played back recorded continuous and intermittent anthropogenic sounds associated with natural gas drilling and roads at leks of Greater Sage-Grouse (<i>Centrocercus urophasianus</i>). For 3 breeding seasons, I monitored sage-grouse abundance at leks with and without noise. Peak male attendance (i.e., abundance) at leks experimentally treated with noise from natural gas drilling and roads decreased 29% and 73% respectively relative to paired controls. Decreases in abundance at leks treated with noise occurred in the first year of the study and were sustained throughout the experiment. There was limited evidence for an effect of noise playback on peak female attendance during the experiment or on male attendance the year after the experiment ended. These results suggest that sage-grouse avoid leks with anthropogenic noise and that intermittent noise has a greater effect on attendance than continuous noise. To quantify the potential for noise from natural gas infrastructure to mask sage-grouse vocalizations over both long and short distances, I analyzed both the individual notes of mating vocalizations produced by male sage-grouse and recordings of such noise. Noise produced by natural gas infrastructure is predicted to mask sage-grouse vocalizations substantially, reducing the active space of detection and discrimination of all vocalization components, particularly impacting notes that are low frequency and low amplitude. Such masking could increase the difficulty of mate assessment for lekking sage-grouse. Significant impacts to sage-grouse populations have been measured at noise levels that predict little to no masking. I investigated whether male sage-grouse adjust the repetition and timing of their strut displays in response to playback of noise associated with natural gas development. I compared the signaling behavior of male sage-grouse on leks with long-term drilling and road noise playback to that of males on similar leks with no noise playback. Males exposed to long-term drilling noise playback strutted at higher rates and in longer bouts than males on control leks, while males on road noise leks strutted at lower rates and in shorter bouts than males on control leks; these differences were only observed during close courtship, when strut rate is most important in influencing female mate choice. I did a short-term playback of intermittent traffic noise and compared the strut timing of individuals during noisy and quiet periods. Males performed fewer struts overall during noisy periods, but male strutting behavior was related to female proximity. Males that were not closely approached by females strutted less during noisy periods than quiet periods and males that engaged in close courtship with females strutted at similar rates during noisy and quiet periods, even when females were far away. Introduced noise associated with natural gas development causes large declines in sage-grouse lek attendance and is likely to cause substantial masking of sage-grouse vocalizations. However, masking is not likely to be the only mechanism of noise impact on this species. Sage-grouse may at least partially reduce masking impacts through behavioral plasticity, adjusting the timing of their signals in a manner that may reduce the impacts of masking on communication.</p>

<p> To avoid unintended complications of invasive species eradication, it is important to understand the potential implications of the techniques used in species eradication efforts. This study aimed to compare how different methods of removing <i>Malephora crocea</i> affect the survivorship of planted seedlings of native perennial plants on Anacapa Island. Employing a randomized complete block design in an <i>M. crocea</i> stand, three removal treatments were tested: 1) hand-pull; 2) spray with herbicide and leave skeletons; and 3) spray and then remove skeletons after 2.5 months. In each treatment, seedlings of three species (<i>Leptosyne gigantea, Frankenia salina</i>, and <i>Grindelia stricta</i>) and seeds of two species (<i>L. gigantea</i> and <i>G. stricta</i>) were planted. Survivorship and seed establishment were monitored quarterly between March 2010 and January 2011. For transplanted seedlings, the spray-and-leave treatment resulted in higher survivorship, while no difference was observed between the pull-treatments. Seed establishment was very low overall, but results of seeding of <i>G. stricta</i> showed that the spray-and-pull treatment provided for higher establishment than other treatments. <i> L. gigantea</i> seed establishment was inconclusive. The spray-and-leave treatment also provided the highest relative soil moisture. My results suggest that the spray-and-leave treatment provided the most suitable conditions for survival of transplanted native perennial vegetation.</p>

<p> Stream temperature (ST) is a primary determinant of individual stream species distributions and community composition. Moreover, thermal modifications associated with urbanization, agriculture, reservoirs, and climate change can significantly alter stream ecosystem structure and function. Despite its importance, we lack ST measurements for the vast majority of USA streams. To effectively manage these important systems, we need to understand how STs vary geographically, what the natural (reference) thermal condition of altered streams was, and how STs will respond to climate change. Empirical ST models, if calibrated with physically meaningful predictors, could provide this information. My dissertation objectives were to: (1) develop empirical models that predict reference- and nonreference-condition STs for the conterminous USA, (2) assess how well modeled STs represent measured STs for predicting stream biotic communities, and (3) predict potential climate-related alterations to STs. For objective 1, I used random forest modeling with environmental data from several thousand US Geological Survey sites to model geographic variation in nonreference mean summer, mean winter, and mean annual STs. I used these models to identify thresholds of watershed alteration below which there were negligible effects on ST. With these reference-condition sites, I then built ST models to predict summer, winter, and annual STs that should occur in the absence of human-related alteration (r² = 0.87, 0.89, 0.95, respectively). To meet objective 2, I compared how well modeled and measured ST predicted stream benthic invertebrate composition across 92 streams. I also compared predicted and measured STs for estimating taxon-specific thermal optima. Modeled and measured STs performed equally well in both predicting invertebrate composition and estimating taxon-specific thermal optima (r² between observation and model-derived optima = 0.97). For objective 3, I first showed that predicted and measured ST responded similarly to historical variation in air temperatures. I then used downscaled climate projections to predict that summer, winter, and annual STs will warm by 1.6 &deg;C - 1.7 &deg;C on average by 2099. Finally, I used additional modeling to identify initial stream and watershed conditions (i.e., low heat loss rates and small base-flow index) most strongly associated with ST vulnerability to climate change.</p>

<p> Amphidromous species migrate between fresh water and the sea for larval development. Many caridean shrimps, especially <i>Macrobrachium </i> spp., are amphidromous, and some populations are found far-upstream within continental river systems. This project tested the hypothesis that populations of <i>Macrobrachium ohione</i> from the Atchafalaya and Mississippi Rivers are amphidromous. </p><p> In the laboratory, I tested the hypothesis that upstream populations of <i>M. ohione</i> have freshwater larval development. My results indicated that saline habitats are essential for <i>M. ohione</i> development, and larval mortality increased after 3-4 days of freshwater drifting. This provides indirect evidence that upstream populations have extended marine larval development. </p><p> Due to their limited freshwater survival, <i>M. ohione</i> must deliver larvae to the sea. Spatial-temporal analysis in the Atchafalaya and Mississippi Rivers reported an influx of reproductive-sized shrimps and females with near-hatching broods into coastal sites. This suggests that females are migrating downstream to hatch larvae in downstream habitats. </p><p> Stable isotope analysis indicated that the upstream juvenile migration originates from saline habitats. Video surveillance revealed that juveniles migrate throughout the night at an average speed of &sim; 0.56 km hr^-1, and swimming speeds were related to the water velocity they swam against. From these results, I estimated that juveniles are capable of migrating to far-upstream habitats within their life span (1-2 years). </p><p> Lastly, I investigated how dams affect the juvenile migration, and tested juvenile migrant climbing abilities. This study reported greater densities of juveniles downstream of dams than upstream of dams, indicating the dams impede the juvenile migration downstream of Old River Control. Shrimp climbing studies revealed that at various inclinations and water velocities, ~ 52% of the shrimps were climbing the shrimp ramp and ~ 12% completed the climb. These results demonstrated juveniles can climb bypass structures with detectable water flows. </p><p> My findings suggest that <i>M. ohione</i> populations within the Mississippi River System are amphidromous, because they require marine larval development and long-distance migrations are conducted to and from the sea. This study may serve as a general model for migrations of amphidromous shrimps in comparable large rivers, and potentially contribute to freshwater shrimp conservation.</p>