Date of Award

Summer 8-2025

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Doctor of Philosophy (PhD)

Department

Wildlife Ecology and Wildlife Conservation

First Committee Advisor

Joseph Zydlewski

Second Committee Member

Christina Murphy

Third Committee Member

Erik Blomberg

Additional Committee Members

Hamish Greig

Sydne Record

Abstract

Atlantic salmon (Salmo salar), once abundant across northeastern North America, have experienced significant declines in recent decades. In the United States, the Gulf of Maine Distinct Population Segment (DPS) represents the last remaining wild population and was listed under the Endangered Species Act in 2000. Recovery of this iconic species remains a top conservation priority, particularly in Maine, where restoration and research efforts are concentrated. Each spring, most of the adult Atlantic salmon return to the Penobscot River, the largest river within the Gulf of Maine DPS to spawn and begin the next generation. Following spawning, juvenile Atlantic salmon (parr) remain in freshwater for one to three years. During this period, they face a suite of threats that contribute to high mortality even before reaching the smolt stage. Predation, competition for space and food, and disruptions to

natural flow and temperature regimes challenge their survival. Habitat alterations, particularly those resulting from impoundments, further reduce habitat quality and connectivity. These threats compound over time and can significantly reduce the number of individuals that survive to undergo smoltification, a critical physiological transformation that prepares salmon for their first migration to the ocean. As smolts leave freshwater, they encounter additional challenges, including passage delays at dams that increase predation risk and exposure to new marine predators. Layered on top of these life stage specific threats is the growing impact of climate change, which poses an emerging risk to this thermosensitive species throughout its range. High levels of predation and competition may be significant limiting factors in the recovery of Atlantic salmon. Of particular concern is the growing presence of smallmouth bass (Micropterus dolomieu), a non-native, thermally tolerant predator that may negatively impact juvenile salmon through both direct predation and competition. As a generalist species with broad environmental tolerances, smallmouth bass are expected to expand their range and become more ecologically influential under future warming scenarios. This anticipated range expansion raises concerns about increasing spatial and temporal overlap with thermally sensitive Atlantic salmon, potentially intensifying predator-prey and competitive interactions as climate change progresses. In this study, we used multiple modeling approaches to quantify the consumption potential of migrating smolts, identify shifts in habitat suitability and species distribution of juvenile freshwater life stages of Atlantic salmon and smallmouth bass under historical and future climate scenarios, and model water temperature dynamics across the state of Maine. To

investigate these concerns, we developed an integrated framework combining temperature modeling, bioenergetics, habitat suitability and species distribution models. We developed a Random Forest model to estimate daily water temperatures across Maine’s river networks from 1990 to 2090. The modeling process began with point-based water temperature observations, where missing temporal gaps were filled using regression-based interpolation. These completed time series were then used to train the Random Forest model, which incorporated key environmental predictors such as temperature points, precipitation, baseflow, river depth, and flow. The model was applied at the river reach scale across the state under two climate change scenarios (RCP 45 and RCP 85). Results revealed a consistent warming trend, with projected increases in river temperatures ranging from 0.7°C to 1.5°C by the end of the century. Notably, winter months exhibited the most pronounced warming. These projections highlight the growing vulnerability of freshwater ecosystems, particularly during colder seasons and emphasize the importance of adaptive management strategies in the face of climate change. To evaluate predation risk, we used a bioenergetics model to simulate smolt migrations through the Weldon Dam headpond, a known high-mortality zone. The model incorporated variables such as smolt size, smallmouth bass stomach capacity and consumption rate, and temperature-driven encounter probabilities. We simulated migrations for wild (20–50 g) and hatchery (51–150 g) smolts over a range of migration sizes, from 2,500 to 1,000,000 individuals. Simulations demonstrated that predation risk decreased with larger migration sizes but increased substantially with migration delays, particularly at low smolt densities. These results highlight how even localized areas of predator concentration can pose significant threats to broader freshwater migrations. Specifically, individual predation risk decreased as overall smolt numbers

increased (from 38.3% at the lowest densities to just 0.2% at the highest densities), while cumulative smolt consumption increased with migration size (ranging from 605 to 10,618 individuals). Larger hatchery fish were consumed less frequently than wild smolts, suggesting potential differences in vulnerability. We consistently observed that delays in migration led to increased consumption, with the most pronounced effects occurring at lower smolt densities. We also developed a Habitat Suitability Index (HSI) model to evaluate how habitat suitability for juvenile Atlantic salmon (parr) and smallmouth bass may change over time. The model incorporated key habitat variables such as water velocity, depth, substrate composition, temperature, and proximity to dams to calculate HSI scores. These scores were mapped across the Gulf of Maine DPS for both current and future conditions under climate change scenarios. Results revealed divergent habitat trends between the species: under future climate conditions, Atlantic salmon experienced a decline in high suitability, particularly in stream orders 2 and 3, while low suitability areas, absent historically, emerged in stream orders 5 and 6. Moderate suitability for salmon increased slightly, with a noticeable shift toward stream order 4. In contrast, smallmouth bass showed a substantial increase in high suitability under climate change, with suitable habitat shifting from stream orders 2 and 4 historically to stream orders 3 through 6 in future scenarios. Moderate suitability for bass became more concentrated at stream order 2, with a drop-off in higher stream orders. These findings suggest a likely expansion of favorable habitat for smallmouth bass under warming conditions and a reduction of suitable habitat for Atlantic salmon. Comparing the two species, smallmouth bass consistently had higher proportions of high suitability across both time periods, with the disparity widening under climate change. To assess the potential impacts of climate change on the distribution and overlap of Atlantic salmon and smallmouth bass, we employed four species distribution models (SDMs):

Random Forest, GLM, GAM, and MaxEnt. These models predicted the occurrence probability of both species across historical and future climate scenarios, incorporating key environmental variables such as temperature, substrate, and river flow with temperature as the dominant factor. Model outputs were combined into an ensemble focused on the critical summer and fall periods, with MaxEnt and Random Forest outperforming the other models. The SDM results showed shifts in predicted species presence across stream orders. Smallmouth bass exhibited an overall proportional increase in predicted presence, with peak occurrence shifting from stream order 3 to stream order 2 under climate change. Atlantic salmon, conversely, showed a slight overall decrease, with peak presence moving from stream order 2 to stream order 3. Across both historical and climate scenarios, smallmouth bass occurred at greater proportions than Atlantic salmon, and this disparity increased under climate change. These findings suggest that warming conditions may favor smallmouth bass range expansion and dominance, posing an increasing risk of competition and predation for juvenile Atlantic salmon in future stream ecosystems.

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