Anthropogenic influences and climate change are warming rivers in New Brunswick and threatening the cold water habitats of native salmonids. When ambient river temperatures in summer exceed the tolerance level of Atlantic salmon and brook trout, individuals behaviourally thermoregulate by seeking out cold water refugia. These critical thermal habitats are often created by tributaries and concentrated groundwater discharge. Thermal infrared imagery was used to map cold water anomalies along a 53 km reach of the Cains River on 23 July 2008. Although efficient and useful for mapping surface temperature of a continuous stream reach, the fish did not use all identified thermal anomalies as refugia. Overall, 100 % of observed large brook trout >35 cm in length were found in 30 % of the TIR-mapped cold water anomalies. Ninety eight percent of observed small brook trout 8 – 30 cm in length were found in 80 % of the mapped cold water anomalies and their densities within anomalies were significantly higher than densities outside of anomalies. Fifty nine percent of observed salmon parr were found in 65 % of the mapped anomalies; however, they were dispersed within study sites and their densities were not significantly different within anomalies compared to outside of the anomalies. No brook trout were observed at the seven noncold water study sites that were investigated. Preference curves for various habitat variables including velocity, temperature, depth, substrate, and deep water availability near cold water anomalies were developed based on field investigations during high temperature events (ambient river temperature >21 oC). Combined with thermal imagery, managers can use the physical descriptions of thermal refugia developed here as a tool to help conserve and restore critical thermal refugia for Atlantic salmon and brook trout on the Cains River, and potentially similar river systems.

Thesis (Ph. D.)--West Virginia University, 2010. / Title from document title page. Document formatted into pages; contains xii, 492 p. : ill. (some col.), maps. Includes abstract. Includes bibliographical references.

Thesis (M.S.)--West Virginia University, 2005. / Title from document title page. Document formatted into pages; contains xi, 155 : ill., maps (some col.). Includes abstract. Includes bibliographical references (p. 80-91).

The aim of the present work, based on two experiments, was to evaluate the impact of photostimulation as a prevention for delaying the sexual maturation of brook trout (Salvenilus fontinalis). Another additional experiment was to describe which effect has photostimulation on the consequences of aggressive behaviour of males. Two experimental groups were established and differed in illumination sources: the metal halide lamps (HAL) and the light emitting diodes (LED). The photostimulation timing (photoperiod) was tested in following experiment. In both tested groups (HAL and LED) the photoperiod was prolonged to 18L:6D in comparison to the control group with natural photoperiod. The results shows that before spawning females and males in both tested groups (HAL and LED) reached significantly higher body weight up to 100 g (=0.05) due to desirable delayed sexual maturation (up to one month). By obtaining the same results in both groups, clearly profitable source of illumination was LED and the time for sufficient application before spawning was 67 days. Moreover photostimulation had also positively reflected in the elimination of aggressive behaviour of males. The results of the present study suggest that photostimulation may be applicable in the intensive culture systems of salmonids in the Czech Republic.

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Improperly designed road-stream crossings can fragment stream networks by restricting or preventing aquatic organism passage. These crossings may also be more vulnerable to high flow events, putting critical human infrastructure at risk. Climate change, which will require access to suitable habitat for species persistence, and is also predicted to increase the frequency and magnitude of extreme floods, underscores the importance of maintaining stream connectivity and resilient infrastructure. Given the large number of road-stream crossings and the expense of replacement, it is increasingly important to prioritize removals and account for the multiple benefits of these management actions. I developed an aquatic barrier prioritization scheme that combines potential habitat gain, stream thermal resilience, aquatic organism passage, and culvert risk of failure. To assess relative thermal resilience, I deployed paired air-water thermographs in several New England watersheds and analyzed relative thermal sensitivity (relationship of water to air temperature) and exposure (duration, frequency, and magnitude of warm stream temperature episodes) among streams. These were combined into a single metric of thermal resilience corresponding with the distance of that stream’s sensitivity and exposure from the watershed median. To test the relationship between risk of failure, culvert dimensions, and stream connectivity, I developed a logistic regression to predict risk of failure using data from two watersheds that experienced extreme flooding from Hurricane Irene (2011). Finally, I applied the resultant prioritization scheme to 66 road-stream crossings in the Westfield River watershed (MA). Thermal habitat quality varied considerably within and among watersheds. Stream sensitivity was generally lower than the widely accepted 0.8 ̊C increase in stream temperature for every 1 ̊C increase in air temperature (Westfield median sensitivity = 0.44), with substantial differences among streams. Exposure also varied widely among streams, indicating that some headwater streams in New England are more thermally resilient than previously thought. Risk of infrastructure failure was predicted with a logistic regression using culvert constriction ratio and predicted aquatic organism passage as predictors (Likelihood ratio test, X2=59.1, df=3, p- value=9.2e-13), indicating that underdesigned culverts were more likely to be barriers to passage and more likely to fail in extreme flow events. To prioritize culverts, this study ultimately used a piecewise approach that identified culverts opening the longest reaches of thermally resilient habitat, and then ranked those culverts by infrastructure replacement need. In the Westfield River, the prioritization clearly identified crossing replacements most likely to yield multiple benefits. The scheme I developed can accommodate changes in the relative weights of the different criteria, which will reflect differences in management and conservation concerns in the confidence of inputs. In conclusion, increasing connectivity by removing barriers may be one of the most effective ways to mitigate the effects of climate change on aquatic systems, but it is important to remove the right barriers.

Populations of anadromous brook trout can be found from northern Canada into New England. It is believed that the extent of anadromy exhibited by coastal brook trout populations decreases with latitude, but the ecology and movements of the more southern populations are less studied. A 33-month acoustic telemetry study of anadromous brook trout (Salvelinus fontinalis) was conducted in a restored coastal stream and adjacent marine system in southeastern Massachusetts. Movement and migration patterns of 54 brook trout were investigated for individual differences and common features. Individuals exhibited a range of movement patterns. Some were more resident and only moved short distances, while others moved great distances covering the entire stretch of the stream (7.25 km) and moving into the marine environment. General Additive Mixed Models revealed that date was the major influence on brook trout movement between habitats and predicted peaks in movement in the spring and fall. Downstream movement peaked in the spring and in the fall, suggesting post-spawning feeding migration. Fish transitioned between habitats more often at new and full moons and when stream temperature was between 8 and 12 °C. Upstream transitions peaked as temperatures declined in winter 2011. Fifty percent of tagged brook trout were detected in the estuary during the study, suggesting that it is an important habitat for the population. In summer 2012, 14 tagged brook trout (20% of active tags) resided near one receiver at the head of the tide, which contained a thermal refugium in the form of a cold-water spring seep. Of the 84 tagged brook trout, 9.5% moved to the marine environment. Warm temperatures in saline Buttermilk Bay in the summer and cold temperatures in winter probably discourage some individuals from entering the marine environment. Compared to more northern coastal populations of brook trout, the Red Brook population appears to be less anadromous.

For a sexually reproducing species, the two major decisions facing all individuals are when and with whom to reproduce. When scaled to the population level, the outcome from all individual decisions determines reproductive variance, and age-class contribution to population growth rate. Both of these attributes determine a population‟s effective size (Ne), which is directly correlated with its fitness, persistence probability, and adaptability. The questions of when and with whom to reproduce, and their subsequent effects on Ne and age-at-maturity were assessed for wild brook trout (Salvelinus fontinalis) populations. Mating pairs were significantly size-assortative, with individual length accounting for 37% of the variation. This pattern of size assortative mate choice resulted in a reproductive strategy closer to monogamy than polygamy. Of all reproducing adults (n=157), 80% (n=126) produced only one full-sibling family, and only 6% (n= 9) contributed to more than two full-sibling families. The number of families and offspring contributed increased with length for both males and females. Comparison of the effective population size estimate to the adult census size (Nc) estimate returned an Ne:Nc ratio of 0.49 averaged over both populations. This value is nearly five times greater than the average reported across 165 (0.14) and 102 (0.10) different species. Age-at-maturity ranged from 0 to 2 years, with the proportion of age-0 and age-1 individuals maturing in a given year dependent upon growth opportunities determined primarily by environmental conditions. Mature fish were significantly larger than immature fish within an age-class, however, survival rates of mature and immature fish were similar. Furthermore, parental length did not influence offspring survival. These data suggest that the cost of early maturation is instead manifested through a reduction in egg number for females, and a reduced ability to acquire mates for males, both determined by an individual‟s size. Indeed, fecundity predicted by mean length of immature and mature fish within an age-class would result in mature fish producing an average of 38% (age-0) and 33% (age-1) more eggs than immature fish. These findings are discussed in the context of population persistence given the trend of increasing habitat fragmentation and looming climate change.

Density and standing stock of brook trout within the Hazel River, Shenandoah National Park, declined sharply between 1982 and 1989. Most of the reduction occurred within the middle and lower reaches, where density of brook trout declined 66% and 920/0, respectively. This study characterized the movement, growth, and mortality of the Hazel River brook trout population in 1989-1990 and examined the role of these phenomena in the recovery of that population. Physical habitat appeared excellent throughout the stream, with adequate pools, cover, and spawning substrate in all sections. Results from visible implant tag recoveries established that the majority (60%) of adult and yearling trout were sedentary during the one year study period. Brook trout exhibiting movement tended to move upstream during the fall over relatively short distances ( < 250 m). Movements of up to 700 m (up- and downstream) were observed in less than 5% of post-juvenile trout. Young-of-the-year (YOY) trout moved more frequently than other age groups and tended to move downstream; they are probably the primary vehicle of downstream recolonization. Growth and condition of Hazel River brook trout were typical of other streams within Shenandoah National Park. Poor growth occurred during the summer months, which is typical of southeast stream trout populations. Generally, growth was higher in areas where density was lowest. Estimated mortality over summer was highest (400/0) for yearling and adult trout within the upper reaches. Despite closure of the Hazel River to angling for two years, its brook trout population remained depressed in 1989. The study demonstrated that recovery of depleted trout stocks through intrastream migration may be slow. Reasons for the continued depression of the brook trout population in the Hazel River may include predation by American eels, illegal angIer harvest, the sedentary nature of stream-dwelling trout, or a combination of these factors / Master of Science

Brook trout invasion into bull trout streams is variable, and likely influenced by a suite of biotic and abiotic factors. Field observations revealed that brook trout dominated the fish community over bull trout in warmer sites that had undercut banks; in contrast, bull trout dominated in colder sites that had a high amount of large substrate cover, and where alternate non-native species were present. Laboratory studies of competition between the two species revealed that bull trout use a scramble foraging tactic, whereas brook trout use a territorial tactic. Bull trout outcompeted brook trout when fish density was low and habitat complexity was high, as this scenario reduced the effectiveness of the aggressive territorial foraging strategy of brook trout. Bull trout from a migratory population competed more successfully against brook trout and had higher rates of oxygen consumption than those from a resident population. This combined field-lab study points to some of the abiotic and biotic factors that affect competition between the two species, and may influence the outcome of brook trout invasion into bull trout streams. / xiv, 184 leaves : ill. ; 29 cm