The expansion and industrialization of humanity has caused many unforeseen consequences to the natural world. Due to the importance of freshwater for people, rivers have been particularly altered to meet human needs, often at the expense of the natural world. Supplying water for farms, industries, and cities has reshaped the natural state of rivers by altering river paths, chemistry, and species compositions. These changes have harmed many species that prospered before widespread human alterations, including the native trout and salmon of western North America. As human populations continue to grow, new threats will surface for rivers, and the trout and salmon that call rivers home. As a result, many scientists have considered how to assess and counter-act threats to trout and salmon. Often, efforts focus around rehabilitating stretches of river, but do not consider large-scale watershed conditions,which may be responsible for chronic stream degradation. Tools have been developed to guide decision making for coordinating conservation efforts that consider the multitude of risks facing trout and salmon. In this thesis I implemented these tools to help managers and decision makers understand how risks affect their conservation efforts. Two examples are provided, with the first considering development and resource extraction risks to Pacific salmon spawning habitat in Alaska. The second example considers climate, development, and competition risks for cutthroat trout, throughout Utah. Results from both examples clarify that managers who consider risks while conducting conservation yield greater results than managers who attempt to avoid risks. The findings here intend to inform future conservation effort for trout and salmon, and also clarify the importance of risk management in conservation.

Zooplankton samples were collected from 166 Oregon lakes. The lakes included a wide range in size, trophic status, and water quality. Lakes were located throughout the state. Zooplankton were identified using standard taxonomic keys and counted. Seventy-four species were identified from the 200 total samples, including 32 species of cladocera, 22 copepods, and 11 rotifers. Two species of copepod were recorded for the first time in Oregon: Diaptomus mississippiensis and Diaptomus pallidus. Seven species had widespread distributions throughout most of the watersheds in the state. Seventeen other species had distributions restricted to eastern, central, or western Oregon. The remaining species were either rare or had random distributions.

Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus. Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing previously unknown or unaddressed aspects of the biology of Omus. Both morphometric and behavioral analysis was used to address specific questions regarding niche partitioning and mating behaviors in the genus. On the basis of the competitive exclusion principle, I predicted that these closely related species with similar ecological requirements would experience selective pressure to minimize niche overlap and competitive pressures through morphological character displacement. In particular, the mandibles of male tiger beetles serve a dual role: one as tools for feeding-- including prey capture and prey processing--and another role as secondary sexual organs whereby the males use their mandibles to grasp the female and maintain amplexus. A geometric morphometric approach was used to evaluate and compare shape differences between the two species as well as identify trends of sexual dimorphism and species differences in context of prey base. Tiger beetles obligatorily engage in male-superior mounted mating behavior. Body size was used to first address trends of female-biased sexual size dimorphism within the Carabid subfamily Cicindelinae. Female tiger beetles may be expected to experience proportionally greater stress during mating among larger bodied than smaller bodied species and selection would favor increasingly pronounced female-biased sexual size dimorphism among larger-bodied species. The mating duration of Omuswas anecdotally reported as an order of magnitude greater than any other tiger beetle but has never been experimentally confirmed. I performed a series of pairings under laboratory setting to (1) establish a baseline of mating duration for the two species and test the effects of (2) time of day mating was initiated, (3) food deprivation and (4) operational sex ratio on mating duration. Morphometric analysis suggested niche partitioning existed between the two species due to an average body size scaling factor of x1.3 and an average mandible length scaling factor of x1.5, i.e. "Hutchinsonian Ratios"-- an observed minimum scaling threshold of niche differentiation seen in several natural predator populations. Similar minimum values were not seen between the sexes of either species suggesting an absence of sexual niche dimorphism. Geometric morphometric analysis of the mandibles revealed two distinct regions subject to selective adaptation: the distal region of the mandible (including the apical incisor) was consistently sexually dimorphic between the examined species while the proximal region involving the terebral teeth showed interspecific differences independent of sex and likely associated with prey processing, further supporting the hypothesis of niche partitioning between the two species but not necessarily between the sexes. The magnitude of sexual size dimorphism was found to be constant within Cicindelinae regardless of species body size. Behavioral analysis of mating established thatO. audouiniandO. dejeaniihave average (± SD) mating durations of 10.6 (± 1.8) and 29.4 (± 5.6) hours, respectively. Time of initiation of mating (whether morning or evening), food deprivation and operational sex ratio did not have any statistically significant effect on mating duration for either species. The absence of effect operational sex ratios on mating duration by suggests that mate guarding may not be a universal factor for all tiger beetles and, instead, syn- copulatory courtship, as opposed to pre- or post-copulatory courtship, as a female-choice reproductive mechanism may serve as a better explanation for the mating behaviors seen in Omus.

The Florida Everglades presents a model setting for studying animal-habitat relationships in a dynamic landscape that is heavily influenced by seasonal hydrology and water management. I used dynamic, high-resolution habitat classification maps and radio-telemetry to examine habitat preference of Largemouth Bass, Bowfin, and Florida Gar before and after a field-scale manipulation was established to address uncertainties with Everglades restoration and water management practices. Results indicate preference for the canal habitat by all three species, which represents only a small portion of the submerged landscape even in the driest conditions. Bowfin and Florida Gar were more likely to be relocated within marsh habitats than Largemouth Bass. Preference for the canal habitat increased after landscape alteration and was influenced by water management practices rather than hydrological or environmental factors. Partial canal backfilling may assist with accomplishing restoration goals while maintaining preferred habitat for economically and ecologically valuable predatory fishes.

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The mining industry has over the last few decades seen a drastic increase in the usage of laser scanning technologies as a way of creating 3D maps of the mines being exploited. Underground mapping in places such as mines has become more prevalent as the technology has progressed and made it easier to generate highly detailed point clouds faster. A newer and faster method of generating point clouds is using a simultaneous localization and mapping (SLAM) based mobile laser scanner (MLS). With the help of complex algorithms, it enables instant point cloud registration and allows for continuous mapping of the surrounding environment while tracking the device location without needing a connection to GPS. As the accuracy and speed of SLAM based MLS continues to improve, its use is becoming far more widespread within the mining industry. Although studies have been conducted previously investigating the differences in quality between SLAM based MLS and terrestrial laser scanners (TLS), there is still a need for further studies conducted in mining environments. This case study aims to investigate the quality differences between two point clouds generated using an Emesent Hovermap HF1, which is a SLAM based MLS, and a Faro Laser Scanner Focus 3D X 330 TLS. Parameters like root mean square (RMS) were investigated. Volume calculations were carried out for both point clouds and compared to each other as well the calculated volume of a theoretical model. To conduct this study data from LKAB’s Kiruna mine was collected and provided by Blå Projekt, Process & GIS AB. The result of this study concludes that the Faro TLS is superior in terms of point cloud quality, with five times better RMS values and higher point density than the Hovermap MLS. It also shows that both scanners allowed for accurate volume calculations with only roughly 1% difference in the estimated volumes. The TLS method yielded a much more readable point cloud with clearer visual details than the SLAM based MLS method. This may however be a result of SLAM drift since no loop closure was performed when collecting the MLS data which otherwise could’ve minimized the errors. It was concluded that due to the amount of data processing required and the longer work time of TLS, SLAM based MLS is a method that is worth further development as it provides unparalleled flexibility, safety improvements and work time efficiency.

Dams are relatively simple hydraulic structures that provide vital services to communities in the United States (U.S.). However, many of the dams in the (U.S.) have surpassed their design life. Dams experience changes from external threats that result in deformation of the structure. Traditional surveying techniques provide limited information on deformation in pre-determined areas of a structure, but the collection effort can often be lengthy. In this research, different instruments used for change detection were reviewed and Terrestrial Laser Scanning (TLS), also known as ground-based Light Detection and Ranging (LiDAR), was selected as the most probable method to accurately evaluate deformation in dams. TLS is a remote sensing instrument that uses light to form a pulsed laser to measure ranges to variable targets, and it provides the ability to measure displacement with high accuracy using dense point clouds collected in a short amount of time. Deformation is identified by measuring changes in point clouds generated by TLS. The accuracy of TLS to identify deformation was tested on a thin arch dam at the Big Black Test site in Vicksburg, Mississippi, using the TLS system, Terrestrial Laser Scanner RIEGL VZ-400, for data collection and for registering scan positons between a pre-test condition and a post-test condition. Final data analysis was performed using Microstation TopoDOTTM Wall Monitoring Tool.

Phenotypic plasticity is hypothesized to facilitate colonization by enabling rapid adaptive responses to novel environments. The colonization of land exposed ancestrally aquatic animals to new ecological and physiological challenges, including toxic waste disposal in dry environments. The repeated evolution of terrestrial breeding in frogs creates opportunities to study developmental adaptations that may facilitate aquatic-to-terrestrial transitions. My dissertation examines the regulation of nitrogen excretion by early life stages in three anuran lineages that independently evolved terrestrial development. First, to assess developmental and environmentally cued changes, I measured N-waste accumulation over development in wet and dry environments in four species, then determined ammonia LC50 values to assess their risk of toxicity on land and the adaptive role of urea excretion. Ammonia accumulates developmentally in clutches or nests of all species and I found urea from both parental and embryonic larval sources. Embryonic larval urea excretion increased in response to dry conditions, and with ammonia accumulation, in the two species with longer terrestrial periods, and their urea excretion appears adaptive, preventing exposure to potentially lethal levels of ammonia. Where early life stages did not risk ammonia toxicity, they excreted no urea. Next, I examined biochemical mechanisms of ammonia detoxification. Urea excretion involves early onset of activity of two ornithine-urea cycle enzymes, arginase and carbamoyl phosphate synthetase, with regulatory plasticity in response to ammonia level during prolonged terrestriality and experimentally high aquatic ammonia. Glutamine synthetase activity provides another mechanism to detoxify ammonia during terrestrial development. Finally, I examined effects of prolonged terrestriality and the larval foam-making activity that supports it on larval physiology, development, and metamorphosis in Leptodactylus fragilis. Even young larvae effectively produced multiple foam nests. I found high ammonia concentrations in new larval nests, high urea excretion by developmentally arrested older larvae, and faster growth of larvae in water than while constructing nests. Larval foam-making extended terrestriality affected the aquatic larval period and age at metamorphosis, while metamorph size decreased with aquatic larval period, but increased with sibship size. Overall, my results suggest that, along with high ammonia tolerance, urea synthesis facilitates terrestrial development but carries physiological costs that may favor plasticity. Dehydration and ammonia accumulation are common, linked risks of terrestrial development. Along with parental adaptations, the evolved traits and plastic responses of early life stages are critical for transitions from aquatic to terrestrial breeding.

Understanding the movement phenology of the four-toed salamander (Hemidactylium scutatum) is essential to guide management practices. I examined the relationship between environmental variables and the directionality, timing, and magnitude of four-toed salamander movements at two locations in eastern Massachusetts. Four-toed salamanders move from upland habitats to wetland areas in early spring and move away from wetlands in late spring. Adult movements increased with more precipitation and less moon light. Juvenile movements were similarly affected, and in addition they were more likely to move when temperatures were warm and days long. My results can be used to implement management strategies aimed at reducing human-related impacts on migrating four-toed salamanders (e.g., road closures to reduce road mortality). In addition, I developed and evaluated the accuracy of classification and regression tree (CART) models at multiple spatial scales to predict suitable habitat and potential species occurrences of the four-toed salamander (Hemidactylium scutatum) in Massachusetts. I analyzed four-toed salamander Element Occurrence (EO) observations reported during 1990-2009 in response to fifteen environmental predictor variables at six different local and landscape-scales. The landscape-scale model measured at 2000 m was most successful at predicting four-toed salamander habitat. It correctly classified 92.4% of the training data and 87.7% of the verification data. When the 2000 m model was applied statewide, 30,195 wetlands were determined to be potentially suitable habitat for the four-toed salamander. The results of this study confirm the potential and value of classification and regression tree models for identifying potential habitat for rare or cryptic species.