Nelson-Chorney, H. (2019) Paleolimnological reconstruction of Westslope Cutthroat Trout (Oncorhynchus clarki lewisi) in alpine lakes using a next-generation sequencing platform.

Thesis Title: Paleolimnological Reconstruction of Westslope Cutthroat Trout (Oncorhynchus clarki lewisi) in Alpine Lakes using a Next-Generation Sequencing Platform (link; co-supervisors: R. Vinebrooke, M. Taylor)

Author: Hedin Nelson-Chorney

Abstract

Understanding historical species distributions is vital to the conservation and restoration of native species, yet such information is often qualitative. Here, we show that the paleolimnological history of threatened freshwater fishes can be reconstructed using species diagnostic markers amplified from environmental DNA deposited in lake sediments (lake sediment DNA). This method was validated through the detection of lake sediment DNA from non-native trout (Yellowstone cutthroat trout; Oncorhynchus clarkii bouvieri), which corroborated historical records of human-mediated introductions. Moreover, we discovered native trout (westslope cutthroat trout; Oncorhynchus clarkii lewisi) lake sediment DNA that predated human-mediated introductions of freshwater fishes in a watershed with high topographical relief. This unexpected result revealed that the population was of native origin and requires immediate conservation protection. Our findings demonstrate that lake sediment DNA can be used to determine the colonization history of freshwater fishes and the structure of ecosystems, aiding in the identification of native ranges, novel native diversity, and introductions of non-native species.

Banting, A. L. K. (2018) Impacts of a novel predator on aquatic invertebrates in fishless lakes: Implications for conservation translocation

Thesis Title: Impacts of a novel predator on aquatic invertebrates in fishless lakes: Implications for conservation translocation

Author: Allison L.K. Banting

Abstract

Fishless mountain lakes hold important ecological and conservation value. As such, managers are establishing conservation goals (e.g., non-native fish removal) to restore the naturalness to many of these lakes. Simultaneously, managers who are recovering native (coldwater) fish populations threatened by climate change (e.g., Westslope Cutthroat Trout, Oncorhynchus clarki lewisi and Bull Trout, Salvelinus confluentus) are exploring conservation strategies involving the intentional translocation of native fish species to more suitable areas. These areas include unoccupied, or naturally fishless, stream and lake habitat within their native range or favorable habitats outside their native range. This action presents a potential threat for fishless mountain lakes as conservation managers view these as recovery habitat for imperiled native fish species. The purpose of my study was to inform native fish recovery efforts by assessing the potential consequences of translocating native fishes to naturally fishless lakes, thus outside their historic distribution. Forty alpine and sub-alpine lakes in Banff National Park, Alberta and Kootenay National Park, British Columbia were sampled and divided into three lake types, including 13 naturally fishless lakes, 13 native fish-bearing or native fish-stocked lakes, and 14 non-native fish-stocked lakes historically unoccupied by fish. Littoral invertebrate community composition, density and diversity were examined among lake types to 1) quantify the impacts of introducing non-native fishes into historically fishless lakes, and 2) quantify the differences between native fish lakes and naturally fishless lakes. These comparisons provided context for the scale of impact between two predators of different geographic origins (native vs. non-native) introduced to fishless lakes. The variation in environmental gradients amoung lake types was controlled for, suggesting fish presence strongly influenced changes to invertebrate community density and composition. Native and non-native fishes have the capacity to similarly alter littoral invertebrate community composition of fishless lakes, yet non-native fishes appear to have the greatest impact on littoral invertebrate density. Although impacts vary between native and non-native predators, the introduction of any novel fish predator to a fishless lake will result in a negative impact to key littoral macroinvertebrates, such as Gammaridae, Ephemoptera and Plecoptera, and a positive impact to burrowing taxa, such as Oligochaeta, Nemata and Chironomidae. While the introduction of non-native fishes has been repeatedly shown to affect invertebrate communities, the translocation of native fishes similarly has the potential to alter the ecology of a naturally fishless lake. With considerations for possible aquatic-terrestrial cross boundary effects, this study suggests that conservation ecologists consider the entire ecosystem when building resilience for climate change.

Medinski, N. (2018) Assessing the impacts of multiple ecological stressors on an endangered native salmonid, the Athabasca Rainbow Trout, in the foothills of the Canadian Rocky Mountains.

Thesis Title: Assessing the impacts of multiple ecological stressors on an endangered native salmonid, the Athabasca Rainbow Trout, in the foothills of the Canadian Rocky Mountains.

Author: Nathan Medinski

Abstract

Freshwater fish face a multitude of ecological stressors, which has resulted in substantial declines in aquatic biodiversity. The loss of aquatic biodiversity can lead to changes in ecosystem function, productivity and food web dynamics. One such imperiled freshwater fish is the Athabasca Rainbow Trout (Oncorhynchus mykiss), a unique Rainbow Trout ecotype found in the upper reaches of the Athabasca River watershed, forming the only native Rainbow Trout population in Alberta. Athabasca Rainbow Trout have experienced widespread declines in abundance, with losses of approximately 90% over the last three generation, or approximately 15 years. Two of the main ecological stressors impacting Athabasca Rainbow Trout are competition with invasive Brook Trout (Salvelinus fontinalis) and habitat degradation associated with natural resource extraction developments in the region. For example, in 2013 the accidental breach of a tailings dam at the Obed coal mine near Hinton, Alberta, Canada, released 670,000 m³ of coal tailings material into Athabasca Rainbow Trout habitat. My goal in this thesis was to improve our understanding of ongoing impacts from multiple ecological stressors on Athabasca Rainbow Trout abundance and food resource use, inferred from sampling seven streams in the upper Athabasca River watershed. The specific objectives of this thesis were therefore to: 1) determine how this ecological stressor gradient has influenced Athabasca Rainbow Trout abundance in the foothills of west-central Alberta, and 2) understand how food resource utilization by Athabasca Rainbow Trout populations has been affected along a disturbance gradient associated with habitat degradation from the Obed mine tailings release and competition with invasive Brook Trout.

To meet my first study objective, I compared Rainbow Trout abundance with metrics associated with mining impacts to aquatic systems, landscape level stressors, abundance of invasive species and general stream habitat parameters between waterbodies along a gradient of ecological stressors. I determined that Athabasca Rainbow Trout abundance was not significantly different between groupings of streams impacted by the Obed mine tailings release compared with reference streams but was lowest in streams that were both highly turbid and had high abundance of invasive Brook Trout. To answer my second study objective, I used stable isotope analysis to determine trophic position, carbon source pathways, diet composition, niche width and resource use overlap to infer if food resource use changed along a disturbance gradient. I found that Athabasca Rainbow Trout in tailings disturbed waterbodies were utilizing a wider breadth of dietary resources and had substantially higher niche overlap with Brook Trout than in waterbodies not impacted by the tailings release, indicative of greater competition for food resources.

This thesis contributes to our understanding of how endangered Athabasca Rainbow Trout populations have been impacted by multiple ecological stressors and quantifies important interactions between these stressors with fish abundance and food resource use. Fisheries managers may wish to pursue additional measures to prevent subsequent declines in Athabasca Rainbow Trout populations by minimizing the detrimental impacts associated with landscape level habitat degradation and competition with invasive Brook Trout.

Rudolfsen, T.A. (2017) Characterizing adaptive morphological features and resource selection of Rocky Mountain Sculpin (Cottus sp.), a species at risk in Canada

Thesis Title: Characterizing adaptive morphological features and resource selection of Rocky Mountain Sculpin (Cottus sp.), a species at risk in Canada

Author: Tyana Rudolfsen

Abstract

Freshwater biodiversity is presently one of the world’s largest conservation concerns. Both direct and indirect human activities contributing to waterway modifications, climate change, and habitat alteration are causing major declines in freshwater fish species richness and abundance. While these impacts are well studied for pelagic fishes, little is known about how to best direct management efforts toward benthic, dispersal-limited fishes. The Rocky Mountain Sculpin (Cottus sp.), a benthic, sedentary, and federally listed species at risk in Canada, was used to address the following objectives: 1) to identify its susceptibility to varying flow regime, and whether or not it displays morphological adaptation to flow, and 2) to characterize hybrid zones and the driving environmental factors that lead to their persistence. Using geometric morphometrics and meristic counts of fin rays/spines and sensory pores, phenotype was compared across the four river populations in Canada. Systems with higher flow regimes generally had Rocky Mountain Sculpin that were more dorso-ventrally compressed and had meristic features better suited to positioning themselves among cobble substrate and detecting prey in fast moving water. Biogeographic isolation contributed to phenotypic variation, indicating that the Rocky Mountain Sculpin might not be able to quickly adapt to human-induced flow alterations. To achieve the second objective, hybrid zones between the westslope Rocky Mountain Sculpin population (Flathead River drainage, BC) and the Slimy Sculpin (Cottus cognatus) were studied. Using 731 genetic samples and 10 polymorphic microsatellite loci, two hybrid zones were identified more upstream than expected from previous studies. A logistic mixed-effects model revealed that habitat features relating to climate change and water quality were driving an upstream range expansion of Rocky Mountain Sculpin and movement of hybrid zones. While the Rocky Mountain Sculpin, despite their sedentary life history, appears to have more tolerance to anthropogenic habitat alterations that originally expected, their tolerance level likely has limits that can be widely detrimental to the species if tested. Further, given their high levels of phenotypic variation across populations, management efforts involving dispersal-limited species should be directed at the population level. In the event of hybrid zones, which are indicators of more localized environmental factors driving species presence, a more localized scale of management might be required.

Docherty, C. (2017) Establishment, spread and impact of Prussian Carp (Carassius gibelio), a new invasive species in Western North America.

Thesis Title: Establishment, spread and impact of Prussian Carp (Carassius gibelio), a new invasive species in Western North America.

Author: Cassandra Docherty

Abstract

Freshwater ecosystems are some of the most imperilled on the planet. Invasive species pose the second largest threat to freshwater organisms after habitat degradation. Aquatic introductions have led to extinctions, competition for resources, hybridization, the introduction of foreign pathogens and the alteration of ecosystem structure and function. One of the most recent invaders in western North America is Prussian Carp (Carassius gibelio). The first record of this species in North America was in 2000, in Alberta, Canada, yet little is known about its invasion, current distribution or effects on stream communities. In Eurasia, Prussian Carp have been assessed as one of the most harmful invasive fish species because of its ability to reproduce asexually, high environmental tolerances and preference for human modified habitats. The arrival of Prussian Carp in western North America poses concerns for many native freshwater species. Therefore, the objectives of this study were to assess the severity of Prussian Carp’s invasion in western North America by 1) mapping Prussian Carp distribution and rate of spread since its initial arrival; 2) analysing the impact of Prussian Carp on native fish species; and 3) identifying environmental parameters that predict Prussian Carp presence. Using kernel density functions, we found that the range of Prussian Carp increased in Alberta, Canada from approximately 500 km² since its arrival (estimated as 2000) to over 20,000 km² in 2014. The rate of spread is increasing at an exponential rate over five year increments (e.g. 1.6, 2.1, and 2.3 times), suggesting rapid expansion since first detection. Our results did not indicate that Prussian Carp have a negative effect on native fish species, which is likely due to its recent expansion into these areas and an already depauperate species community. The most important habitat variables that best predicted the presence of Prussian Carp were: dense aquatic vegetation, high conductivity, pH, high dissolved oxygen and low flow rates indicating preference for relatively slow, eutrophic streams. Successful management of this species in western North America will require the integration of all levels of government between neighbouring provincial and national borders, as well as the public. Prussian Carp are a highly mobile species and given the connection to other watersheds in Canada and proximity to the Missouri/Mississippi drainages in the United States, agencies throughout North America should be aware of this invasive species and the potential impacts on native biota

Neufeld, K.R. (2016) Improving our ability to assess the impacts of hydrologic alteration on stream fishes: An interdisciplinary approach to assess the Threatened Western Silvery Minnow Hybognathus argyritis in Canada

Thesis title: Improving our ability to assess the impacts of hydrologic alteration on stream fishes: An interdisciplinary approach to assess the Threatened Western Silvery Minnow Hybognathus argyritis in Canada

Author: Kenton Neufeld

Abstract

Human induced hydrologic alteration is ubiquitous in North American riverscapes. These alterations have been shown to impact fishes by modifying habitats, influencing movement patterns and driving changes in community structure. Understanding these impacts is an essential first step for the conservation of fish in these systems. We use Western Silvery Minnow Hybognathus argyritis and the Milk River of southern Alberta as a model system to develop and apply an interdisciplinary approach to assess the impacts of hydrologic alteration on capture efficiency and habitat suitability of stream fishes. The capture efficiency of sampling gear is a key component of many fish research programs, and understanding the link between hydrology and capture efficiency is critical to accurately assessing the impacts of hydrologic alterations on fish. We measured seine net capture efficiency in the Milk River, and investigated the effects of flow, species, and habitat variables on capture efficiency using mixed effects models. Flow state was an important driver of capture efficiency, which increased ~5 % during augmented flow compared to natural flow. Habitat suitability assessments are commonly used to determine the impacts of hydrologic alteration on fishes, but often rely on poorly understood relationships between fish and their habitat. We used the swimming performance of Western Silvery Minnow to measure the cost of movement between habitat patches in the Milk River and incorporated this cost into a graph theoretic metric of habitat suitability (Equivalent Connected Area). Compared to augmented flow, the proportion of suitable area was ~ 475 % higher during natural flow, the mean cost of movement between habitat patches was ~ 13 % higher and Equivalent Connected Area increased ~ 0.119 (95% C.I. 0.109-0.130). By including flow as a variable in modelling capture efficiency and swimming performance as a mechanism defining habitat suitability, we show the utility and benefits of taking an interdisciplinary approach to assessing the impacts of hydrologic alteration on stream fishes.

Veillard, M. (2016) Investigating fine-scale movement patterns and comparative swimming performance of the newly identified and threatened Rocky Mountain Sculpin (Cottus sp.) across its Canadian distribution

Thesis Title: Investigating fine-scale movement patterns and comparative swimming performance of the newly identified and threatened Rocky Mountain Sculpin (Cottus sp.) across its Canadian distribution

Author: Marie Veillard

Abstract

Cumulative anthropogenic impacts to the riverscape, including hydrologic alteration, have contributed to an escalated number of freshwater fish species at risk in North America. Species dispersal is an important mechanism underlying many ecological processes. Understanding the scale at which species carry out their life history can inform both conservation actions and recovery potential. Our study used the recently-identified Rocky Mountain Sculpin (Cottus sp.), a species federally listed as threatened, to investigate the (1) fine-scale movement potential and (2) comparative swimming ability of adults throughout their restricted Canadian distribution. Rocky Mountain Sculpin are a small-bodied, cryptic benthic species that utilizes interstitial spaces for shelter. To assess the fine-scale movement potential of Rocky Mountain Sculpin, I conducted a mark-recapture study on Lee Creek, Alberta using Passive Integrated Transponder (PIT) and Visible Implant Elastomer (VIE) tags. I assessed the abiotic and biotic factors influencing movement using Boosted Regression Tree models. In this study I found that 89% of sculpins moved less than 30 meters, while a few individuals moved up to 240 meters. Biotic factors indicated sculpins moved from high to low abundances of fish due to intra- and inter- specific competition from congeners and benthic competitors. The most important abiotic factor contributing to movement was abundance of cobble substrate at destination transects. Interestingly, there was a strong interaction between biotic and abiotic components indicating the importance of focusing restoration efforts on both biotic and abiotic factors. To address the second objective, comparative fish swimming performance and recovery potential was assessed in a laboratory on individuals sourced from drastically different hydrologic regimes in Alberta and British Columbia, including the flow augmented, North Milk River. Permutational ANOVAs were used to compare swimming performance between rivers using two aspects of swimming ability: (1) slip velocity, the point at which fish slipped and transitioned into swimming and 2) failure velocity, the point at which fish could no longer hold position against the flow without resting. While we expected swimming ability to be correlated with natal hydrologic regimes, our study found there were no differences in failure or slip velocity between rivers. However, resting oxygen uptake prior to swim tests was significantly higher for fish from the augmented, North Milk River, indicating there may be a physiological response to flow augmentation. Over repeated exercise, fish failure velocity decreased from 7.45 ± 3.10 body lengths per second (BL s-1) in the first test to 6.18 ± 2.56 BL s-1 by the third test suggesting the use of anaerobic metabolism to power swimming performance of this small-bodied species. Linear mixed-effects models developed using body characteristics showed caudal morphology to influence both failure and slip velocities, while body height was negatively correlated to slip velocity, demonstrating morphological selection for benthic living. Taken together, these studies suggest that while large-scale flow augmentation may come at an energetic cost to sculpins, fine-scale developments may be equally as detrimental to this dispersal-limited species. Conservation for this species may then require both fine-scale and regional management.

Thayer, D. (2016) Identifying seasonal Lake Sturgeon (Acipenser fulvescens) movement patterns and habitat selection in the South Saskatchewan River Basin

Thesis Title: Identifying seasonal Lake Sturgeon (Acipenser fulvescens) movement patterns and habitat selection in the South Saskatchewan River Basin

Author: Donnette Thayer

Abstract

Lake Sturgeon (Acipenser fulvescens Rafinesque 1817) have experienced population declines throughout their range. In Alberta, low density age-class distributions, irregular recruitment, critically low spawning potential ratios and other factors led to a 2007 designation of “Threatened” for this species under the Provincial Wildlife Act. As a protected species, efforts to develop a comprehensive recovery strategy require an understanding of species’ biology, behavior, and critical habitat requirements. My objectives were to a) identify movement behaviors and habitat changes before and after an extreme flood event, and b) ascertain overwintering movement behaviors and habitat selection of South Saskatchewan River Basin Lake Sturgeon. Multiple-receiver acoustic telemetry was used to obtain triangulated, fine-scale movement patterns at the confluence of the Bow and Oldman rivers, a potential critical spawning habitat site, before, during and after an extreme flood, and at a study site on the South Saskatchewan River known to be critical overwintering habitat, before, during, and after the ice-on period. Substrate analysis was performed pre- and post-flood for Grand Forks, and substrate, bottom velocity, and depth analyses were performed for the South Saskatchewan River overwintering study site. In the extreme flood event study, movement behaviors were captured by receivers positioned to triangulate movements and provide positions at a fine scale. Receivers had been deployed to assess spawning behavior when the 2013 Alberta ‘Flood of Floods’ occurred, providing an opportunity to document fine-scale Lake Sturgeon movement behaviors before, during and after an extreme disturbance event. Lake Sturgeon showed a tendency to avoid high water velocity areas. Increases in flow rate showed a significant negative relationship to mean positional distance from shore. Substrate assessment prior to and following the flood showed a significant change in substrate composition. Mean gravel- and larger-substrate area increased, providing evidence that high flow rates in 2013 and 2014 exposed larger particle fluvial substrate. Complexity as measured by patch density increased, indicating a measureable overall increase in heterogeneity. Lake Sturgeon benefitted from improved spawning habitat following the extreme flood by gaining larger, cleaner substrate with more complexity. Although extreme flood events may be costly to human life and infrastructure, they may be ecologically beneficial to some freshwater organisms, particularly plesiomorphic, long-lived species such as Lake Sturgeon whose survival has depended upon a capability to adapt to erratic and occasionally extreme peak flow events. In the overwintering study, fine-scale movements by adult and juvenile Lake Sturgeon were tracked for a previously identified overwintering habitat in the South Saskatchewan River using acoustic telemetry from late October 2013 through April 2014 for a 1.5 kilometer reach of the South Saskatchewan River identified in a previous study as overwintering habitat. Period-segmented movement rates, depth selection, aggregation behavior and preferential overwintering habitat selection by adult and juvenile Lake Sturgeon were evaluated for 23-26 individuals (20-23 adults and 3 juveniles, depending on residency during period assessed – individuals not present during all segments were excluded) detected within the study area. Environmental parameters included depth, depth standard deviation (rugosity), bottom velocity, bottom velocity standard deviation, and substrate type (silt, sand, and gravel or larger substrate). Boosted regression tree (BRT) analyses were performed to identify habitat selection for Lake Sturgeon for period-aggregated core (50th percentile) and range (95th percentile) positions. Movement rates paralleled temperature variation, becoming highly restricted during periods of deepest cold. Increased aggregation was also noted for these periods. The deepest habitat positions occurred during ice formation and breakup. Depth and bottom velocity were the most important variables used to identify sturgeon habitat for all periods assessed. Since Lake Sturgeon display site fidelity and aggregation behaviors independent of resource availability, winter habitat may limit the population. While spawning habitat is crucial to ensuring successful recruitment, data suggests that a substantial portion of the population spends the greater part of the year in overwintering locations, making this habitat potentially more critical to the survival of the population as a whole than any other habitat. If winter habitat is degraded or otherwise compromised, it could hinder species recovery, and should be considered critical habitat, receiving appropriate protection. This was the first study to use fine-scale acoustic telemetry analysis of movement behavior and habitat selection for a Lake Sturgeon population occupying fluvial winter habitat.

Maitland, B. (2015) Stream Crossings in the Western Boreal Forest: Assessing Impacts and Prioritizing Restoration for Native Freshwater Fishes

Thesis Title: Stream Crossings in the Western Boreal Forest: Assessing Impacts and Prioritizing Restoration for Native Freshwater Fishes

Author: Bryan M. Maitland

Abstract

Growing anthropogenic development in response to rising demands for natural resources is a major concern for freshwater fish, particularly in resource rich regions such as Canada’s boreal forest. Expanding networks of industrial resource roads has led to the installation of hundreds of thousands of stream-crossing structures that are becoming increasingly common anthropogenic features on North American riverscapes. These structures can reduce available fish habitat, deteriorate instream habitat, and disrupt ecological connectivity by acting as barriers to fish and aquatic organism movement. My objectives were (i) to determine the extent to which commonly installed stream crossings affect stream fish communities in a boreal forest watershed, and (ii) to assess the application of operational research tools that utilize an optimization framework for mitigating the effects of fragmentation on native freshwater fish and informing restoration planning in the boreal forest. I used mixed-effects modeling and multivariate analyses to determine the effects of stream crossings from 33 culverted, bridged, and reference streams in an industrializing region of the boreal forest in west-central Alberta. Instream habitat characteristics such as mean depth, percent fines, and turbidity showed significant between- as well as within-stream differences among stream crossings. I found that the majority of fish species exhibited significantly lower densities (n·m -2) in upstream habitats as compared to downstream habitats, including a significant reduction in Slimy Sculpin densities in streams with culverts compared to reference streams. Multivariate tests showed that fish assemblages differ as a function of stream type and location. The prioritization method utilized in this study suggests that large gains in potential connectivity could be realized with a moderate investment (~$200K to $500K). I found that the operational research tool can be used to develop cost-benefit curves from the study watersheds, which can be used to minimize overall restoration costs to achieve particular management objectives in watersheds of interest, as well as provide defendable evidence for budget planning to regulators and decision-makers. Additionally, varying model parameters that account for species-specific differences in habitat use (e.g. dispersal distance) affected prioritization solutions, and should be considered in future prioritization analyses. In addition to effecting fish passage and stream connectivity, my results suggest that culverts may also be altering fish habitat, further contributing to large-scale changes in stream fish communities in the boreal forest. Further, my research highlights the efficacy of a novel, easy to use optimization-based barrier prioritization toolset that has minimal data requirements, is applicable to both stream-resident and long-range migratory species, and significantly reduces the mathematical and technical expertise needed to perform relatively complex optimization analyses.