Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki. Chapter 2: C/EBP-delta is constitutively expressed in unstressed, field-acclimated (ca. -1.86°C) animals in a highly tissue-specific manner. White muscle tissue contains the highest C/EBP-delta concentration, which is further increased in response to sublethal heat stress at 2.0 or 4.0°C. This response is mostly acute and transitory, but a lesser upregulation was observed in fishes held for one month at 4.0°C. Chapter 3: The heat-induced nuclear translocation of C/EBP-delta--as determined by immunohistochemistry--appears to be time, tissue and species specific with spleen, heart and retinae being particularly responsive in certain situations. Chapter 4: Protein concentrations of proliferating cell nuclear antigen are tissue specific and variably heat responsive. Surprisingly, levels appear to be positively correlated with C/EBP-delta. Chapter 5: Flow cytometry revealed increasingly high temperatures reduce the proportion of G1 cells while increasing the abundance of apoptotic cells. Chapter 6: These findings are discussed in the context of global climate change and the cellular stress response.

Predators are key components of aquatic ecosystems and innovative approaches to understanding their spatial distribution are imperative for research, effective management, and conservation. Discontinuities, created by abrupt changes between two unlike entities, are irregularly-distributed, intermediate-scale features that can have a disproportionate effect on organismal distribution within the seascape. Here I use the discontinuity concept to relate the distribution of a predator, striped bass (Morone saxatilis), to physical features within Plum Island Estuary (PIE), MA. I mapped the distribution of 50 acoustically-tagged striped bass during four monthly surveys at 40 sites to evaluate if heterogeneity in physical features concentrated predators. All striped bass survived tagging, were coastal migrants, displayed seasonal residency within PIE, and moved freely throughout the estuary. However, these highly mobile predators were not evenly distributed. Specifically, striped bass were clustered in the middle region of PIE in response to sandbar area, intermediate bottom unevenness, channel networks, and, to a lesser extent, confluences and drop-offs. The highest predator counts occurred at sites with the greatest additive habitat complexity. I measured 23 geomorphic metrics at 40 sites within the seascape to characterize the spatial patterns of confluences, drop-offs, bathymetry and land features. Then, I mapped integrated measurements of multimetric physical features to reveal distinct spatial trends in physical complexity of the estuary. By expanding the discontinuity concept and combining irregularly-distributed, intermediate-scale physical features with smaller-scale, traditional fish habitat methodologies, I revealed consistent and ecologically-meaningful patterns within a north temperate estuarine seascape.

Channel catfish virus disease (CCVD) is the principal viral disease in the United States catfish industry. The CCVD is caused by channel catfish virus (CCV), with mortality reaching up to 100% in fingerlings. CCV is assigned taxonomically to the family Alloherpesviridae, genus Ictalurivirus, species Ictalurid herpesvirus 1 (IcHV-1). To date, virulence, immunogenicity, and genome plasticity of the CCV field isolates have not been investigated. Three genotypes of CCV (IcHV-1A, IcHV-1B, and BCAHV) were identified using restriction fragment length polymorphism (RFLP) analysis. Virulence assessment of three representative isolates of RFLP groups suggests that IcHV-1B (pooled survival [mean ± SE]: 58.3% ± 2.6) showed significantly lower survival than IcHV-1A (68.6% ± 2.4). Re-exposure of the survivors with a representative of IcHV-1A and IcHV-1B isolates indicates a robust cross-protective effect (relative percent survival [RPS]: 80-100%). Antigenic determinants against anti-CCV monoclonal antibody Mab-95 were conserved among IcHV-1A, and IcHV-1B; however, BCAHV possesses antigenically distinct epitopes (Neutralization index [NI] = 0). Although BCAHV and CCV have nearly colinear genomes (except for the absence of ORF16A in CCV), they represent distinct species, given that nucleotide identity is 93.9%. Moreover, infectivity trials indicated that channel and hybrid catfish fingerlings might be refractive to LD50 (1.3×105 TCID50/L) dosage of BCAHV. However, previous exposure to BCAHV has protected the channel and hybrid catfish against the subsequent infection with the ATCC strain of CCV (RPS:100%). Next, two discriminatory duplex probe-based qPCR assays were designed and validated to diagnose latent IcHV-1A and IcHV-1B. Spatio-temporal survey of six Mississippi catfish hatcheries indicated that the prevalence of latent CCV genotypes varied between 25-100%. Lastly, twenty one reference quality genomes of CCV field isolates were assembled, and phylogenomic analyses supported the monophyly of the CCV field isolates with BCAHV as their closest relative. The phylogenomic analyses confirmed the two distinct genotypes (IcHV-1A and IcHV-1B) identified in RFLP analysis and further allowed the segregation of the IcHV-1A genotype into two subgroups, IcHV-1A1 and IcHV-1A2. Results from the current studies lay the foundation for future research and will help formulate efficient management strategies to reduce the economic impact of CCV in the catfish industry.

One-hundred and three bottom samples taken at Fish Lake, Utah from July, 1969 to June, 1970 were analyzed to determine the abundance, distribution, and standing crop of the bottom fauna species and to relate their availability to the amount of food eaten by the trout. Twenty-three taxa, representing three phyla and 19 families were collected. An amphipod, Gammarus limnaeus, in the littoral zone, and a tubificid worm, Rhyacodrilus coccineus, in the sublittoral and profundal zones, were the most abundant species. All 23 species were unevenly distributed in the littoral zone, whereas, only eight were found in the sublittoral and five in the profundal zones. Standing crop of invertebrates was greatest in the littoral zone in November, 1969. Analysis of the stomach contents of 135 lake trout and 1105 rainbow trout revealed that bottom invertebrates contributed only small amounts to the diet; differing from previous studies where bottom invertebrates were of major importance in the trout's diet.

Amidst the amphibian extinction crisis, in situ and ex situ amphibian species conservation initiatives utilize assisted reproductive technologies for optimal genetic management of captive and wild populations. Development of effective, simple, low-cost methods for obtaining gametes for artificial fertilization, sperm biobanking, or natural breeding alleviates obstacles for institutions or programs to apply reproductive technologies. Objectives herein include investigating the efficacy of alternative hormones for inducing spermiation, an alternative hormone administration route for inducing ovulation, exploring the physiological effects of hormone therapy, and utilizing sperm from deceased animals for biobanking.

Gill nets and longlines were compared as shark nursery sampling methodologies in inshore waters of Georgia to (1) assess differences in gear selectivity, bias, and stress of capture and (2) determine potential relationships between habitat features and shark distribution and abundance. Gear selectivity varied between gears as a function of both species and life stage resulting in significantly different estimates of species and life stage compositions. Juvenile bonnetheads (Sphyrna tiburo) and young of the year blacktip sharks (Carcharhinus limbatus) experienced significantly higher stress from gill net capture than longline. Major sources of bias are thought to result from dietary preferences and individual size. Juvenile sandbar shark (C. plumbeus) distribution revealed a potential preference for creeks rather than sounds, between 0.32-0.8km wide and 4.02-8.05km from the ocean. Adult Atlantic sharpnose sharks (Rhizoprionodon terraenovae) appear to prefer larger, open sound waters closer to the ocean. A potential preference for locations in close proximity to jetties over those near oyster reefs was also observed for adult Atlantic sharpnose sharks, and while statistical significance was observed, a stronger pattern may exist, as sample sizes in this study were relatively small yet still able to detect a difference. Future investigations that quantify proportions of habitat availability and shark abundance in a given area may be more useful for identifying preferences for the structures observed in this study. This study also provides strong evidence of finetooth shark (C. isodon) primary and potentially secondary nursery habitat in areas that had not yet been documented. Findings from these investigations can be useful for managers seeking to maintain healthy coastal shark populations.

Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and isolate them in headwater stream reaches, with populations in the spatial margins of their distributions facing greater risk. Native salmonid populations are often separated or isolated by natural or artificial upstream migration barriers (i.e., waterfalls, culverts, etc.). Prior to continuing conservation and management actions targeting WCT, it is imperative to understand habitat requirements of this keystone species in fragmented areas. Field survey data were collected in the summer of 2015 on channel geomorphic characteristics and WCT presence/absence in 26 streams located in the Colville National Forest. A clear spatial separation was observed between Eastern Brook Trout (Salvenius fontinalis, EBT) and WCT above four culvert road crossings and the habitat in both of these areas was compared statistically to identify explicit differences. This dataset was also analyzed using logistic regression modeling to determine the best habitat predictors of the presence of isolated WCT populations existing upstream of these crossing. In general, stream habitat in the Middle and South Forks of Mill Creek had low large substrate, high fine sediments, and exhibited pool-riffle channel morphology. Pool habitat supporting isolated WCT was significantly smaller, in terms of volume and surface area, than pool habitat supporting sympatric populations of WCT and EBT, largely due to the headwater nature of channel units supporting isolated WCT populations. Additionally, due to the extreme drought conditions during 2015, stream flow was substantially diminished in the study area causing these reaches to be highly fragmented and largely disconnected from the rest of the stream channel. Fine sediments were generally higher in headwater reaches supporting isolated WCT, including in pools and riffles, which was unexpected, mainly because they exist above sediment delivery points in the longitudinal extent of the system. Logistic regression analysis indicated that the presence of isolated WCT populations was primarily positively associated with an increase in large wood and boulders, and negatively associated with increasing gravel, bedrock, habitat unit length, depth, and width (Significant x2, R2=0.174, misclassification rate = 14.9%, α=0.05). The final model correctly predicted 37.5% of isolated WCT presence observations and 96.5% of the WCT/EBT presence observations significantly better than by chance alone (k=0.81). This model, in fact, may be useful in identifying limited habitat due to the fragmented nature of the channel units supporting IWCT. Large wood and boulders were positively correlated to WCT presence, likely because both are important in the formation of pools and cascades. Channel unit length, width, depth, active channel width as well as gravel and bedrock substrates, were all negatively associated with WCT presence. This suggests that isolated WCT are primarily associated with small headwater cascades with complex shelter, which may provide greater thermal and predation refuge compared to shallow glide or large pool habitats. Future model analysis should include additional habitat variables such as water temperature, stream gradient, and species interactions to strengthen the prediction of Westslope Cutthroat Trout presence. Overall, I concluded that differences in stream habitat above and below blocking culverts are not driving Westslope Cutthroat Trout distributions in the study area due to confounding factors such as the presence of problematic barriers and small sample size. I also conclude that future conservation and management decisions specific to WCT should prioritize complex cascade habitat in headwater stream reaches because of the type and quantity of habitat they may provide, especially during severe drought or low flow conditions.

Beginning in the early 1600s, dam construction in New England obstructed anadromous fish access to spawning grounds during migration. As a result, anadromous forage fish populations have declined, which has impacted freshwater, marine, and terrestrial ecosystems. To determine the impacts of dams on anadromous forage fish and freshwater ecosystems, I used historical and current data to estimate population changes in alewives (Alosa pseudoharengus) from 1600-1900. A significant reduction in spawning habitat occurred in New England as a result of 1,642 dams constructed between 1600 and 1900, resulting in 14.8% and 16.6% lake and stream habitat remaining by 1900, respectively. In eight New England watersheds, this translates to an estimated cumulative annual loss of 30 B juvenile alewives available as freshwater forage and 538 M year 1, 2 and 3 alewives available as marine forage. The cumulative annual lost number of adult return spawners was conservatively 17 M fish, or 3,642 metric tons. Lost marine-derived nutrients from adult return spawners were 11 T phosphorus, 64 T nitrogen, and 410 T carbon. A comparison of predator fish growth and condition in alewife and non-alewife lakes showed that white perch (Morone Americana) and yellow perch (Perca flavescens) have higher condition in early summer in lakes with alewives. Predator growth rates (length-at-age) were significantly higher in early life stages (ages 1 and 2) when alewives were present, but significantly lower in late life stages (ages 3 and older). Results indicate a greater maximum length obtained by mature fish when alewives are absent, and an earlier age and length at maturity when alewives are present. These results indicate significant ecosystem impacts of lost anadromous forage fish, with bottom-up trophic effects across multiple time scales and biological processes. An ecosystem-based management approach should be used by inland and marine aquatic managers, and ecosystem connectivity and trophic interactions should be considered when managing migratory fish and prioritizing restoration goals.

As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams.