Forestry, Faculty of
DSpace
UBCV
Roper, Paige
Master of Science - MSc
University of British Columbia
The Fraser River is the major producer of Pacific salmon (Oncorhynchus spp.) in Canada with millions of juveniles out-migrating through its estuary each year. Estuaries provide critical rearing habitat for juveniles, in particular Chinook salmon (O. tshawytscha), which can reside in estuaries for several weeks. The diet of juvenile Chinook salmon in this habitat is a crucial component of their early development and survival. In 2021 and 2022, I examined size, stomach contents, and stomach fullness of 142 juvenile Chinook salmon of wild and hatchery origin from eelgrass habitat at Roberts Bank (Fraser River estuary). I examined an additional 37 wild Chinook salmon from marsh and sandflat habitats. GSI analyses revealed 83% of all wild fish originated from lower Fraser River populations and PBT analyses revealed 91% of all hatchery fish originated from lower Fraser River populations. In eelgrass habitat, hatchery fish were on average 6.1 mm (~7%) longer than wild fish. Stomach fullness increased with fish size and was ~34% higher in wild fish compared to hatchery fish. Wild fish trended towards fuller stomachs in marsh habitat and emptier stomachs in sandflat habitat compared to those in eelgrass habitat. Stomach content analysis suggested size and time of year were indicators of juvenile Chinookâs transition to a primarily piscivorous diet, which was seen in wild fish with fork lengths as small as 63 mm. Liver and dorsal muscle samples from 130 wild and hatchery Chinook salmon captured in eelgrass habitat were analyzed for Î´Â¹âµN and δ¹³C revealing overlapping trophic ellipses. Wild fish had greater niche widths compared to hatchery fish and tended to consume higher-quality prey and utilized more diverse habitats compared to hatchery fish highlighting the importance of conserving eelgrass and marsh habitats and the prey they support. To improve foraging competency of hatchery fish in estuaries, naturalization of feeding systems in rearing facilities should be implemented.
DIETARY ANALYSIS OF WILD AND HATCHERY JUVENILE CHINOOK SALMON (ONCORHYNCHUS TSHAWYTSCHA) IN THE FRASER RIVER ESTUARY REVEALS DIFFERENCES IN ONTOGENETIC SHIFTS by Paige Roper A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in The Faculty of Graduate and Postdoctoral Studies (Forestry) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) November 2025 © Paige Roper, 2025 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the thesis entitled: DIETARY ANALYSIS OF WILD AND HATCHERY JUVENILE CHINOOK SALMON (ONCORHYNCHUS TSHAWYTSCHA) IN THE FRASER RIVER ESTUARY REVEALS DIFFERENCES IN ONTOGENETIC SHIFTS submitted by Paige Roper in partial fulfilment of the requirements for the degree of Master of Science in Forestry Examining Committee: Dr. Scott Hinch, Professor, Forestry, UBC Supervisor Dr. Brian Hunt, Associate Professor, Institute for the Oceans and Fisheries, UBC Supervisory Committee Member Dr. Tara Martin, Professor, Forestry, UBC Supervisory Committee Member Dr. Evgeny A. Pakhomov, Professor, Institute for Oceans and Fisheries, UBC Additional Examiner iii Abstract The Fraser River is the major producer of Pacific salmon (Oncorhynchus spp.) in Canada with millions of juveniles out-migrating through its estuary each year. Estuaries provide critical rearing habitat for juveniles, in particular Chinook salmon (O. tshawytscha), which can reside in estuaries for several weeks. The diet of juvenile Chinook salmon in this habitat is a crucial component of their early development and survival. In 2021 and 2022, I examined size, stomach contents, and stomach fullness of 142 juvenile Chinook salmon of wild and hatchery origin from eelgrass habitat at Roberts Bank (Fraser River estuary). I examined an additional 37 wild Chinook salmon from marsh and sandflat habitats. GSI analyses revealed 83% of all wild fish originated from lower Fraser River populations and PBT analyses revealed 91% of all hatchery fish originated from lower Fraser River populations. In eelgrass habitat, hatchery fish were on average 6.1 mm (~7%) longer than wild fish. Stomach fullness increased with fish size and was ~34% higher in wild fish compared to hatchery fish. Wild fish trended towards fuller stomachs in marsh habitat and emptier stomachs in sandflat habitat compared to those in eelgrass habitat. Stomach content analysis suggested size and time of year were indicators of juvenile Chinookâs transition to a primarily piscivorous diet, which was seen in wild fish with fork lengths as small as 63 mm. Liver and dorsal muscle samples from 130 wild and hatchery Chinook salmon captured in eelgrass habitat were analyzed for Î´Â¹âµN and δ¹³C revealing overlapping trophic ellipses. Wild fish had greater niche widths compared to hatchery fish and tended to consume higher-quality prey and utilized more diverse habitats compared to hatchery fish highlighting the importance of conserving eelgrass and marsh habitats and the prey they support. To improve foraging competency of hatchery fish in estuaries, naturalization of feeding systems in rearing facilities should be implemented. iv Lay Summary The Fraser River is a major producer of Pacific salmon in Canada, with millions of juveniles migrating through its estuary each year. Estuaries provide critical stopover habitat for juvenile Chinook salmon, which can reside in these areas for over a month. Wild Chinook typically occupy marsh habitats in the fresher parts of the estuary before moving to the saline outer estuary. There, eelgrass beds offer diverse prey, predator refuge, and a transitional environment for ocean entry. Hatchery Chinook enter the estuary later and at larger sizes, spending less time in marsh habitat and primarily using outer estuary areas. To examine how these two groups utilize eelgrass habitat, I analyzed diet differences by assessing stomach contents and stable isotope ratios of hatchery and wild juvenile Chinook salmon. This approach provides insights into short- and long-term resource use during this critical stage of out-migration. v Preface The research in this thesis was conducted in collaboration with Raincoast Conservation Foundation and Mitacs. Field work was led by myself, with support from David Scott, Samantha Rhodes, Jack Hall, Lauren Mitchell, Taylor Marriott, and Christian Lackey. Lab processing of biological samples was led by myself, with support from Samantha Rhodes, Johanna Griggs, Jack Hall, and Gretchen Macnaughton. Aline Isabelle created my map. I held primary responsibility for the study design, data analysis and for the preparation of this manuscript for submission. Additional guidance for data analysis and interpretation was given by Stephanie Lingard and Noa Mayer. ChatGPT was used for grammar editing and RStudio code troubleshooting. I received invaluable support and supervision from my supervisor Dr. Scott G. Hinch, as well as numerous others. A version of this thesis is pending submission for publication [Roper P, Hinch S, Scott D]. All fish handling was conducted under Animal Use Protocol (A19-0193). vi Table of Contents Abstract .......................................................................................................................................... iii Lay Summary ................................................................................................................................. iv Preface............................................................................................................................................. v Table of Contents ........................................................................................................................... vi List of Tables ................................................................................................................................ vii List of Figures ................................................................................................................................. x List of Symbols ............................................................................................................................ xiv List of Abbreviations .................................................................................................................... xv Acknowledgements ..................................................................................................................... xvii Introduction ..................................................................................................................................... 1 Methods........................................................................................................................................... 7 Study area .................................................................................................................................... 7 Sampling...................................................................................................................................... 7 Stomach content analysis ............................................................................................................ 9 Stable isotope processing .......................................................................................................... 10 Data analysis ............................................................................................................................. 11 Results ........................................................................................................................................... 15 Discussion ..................................................................................................................................... 20 Chinook salmon size during estuary residency ......................................................................... 20 Stomach fullness of wild and hatchery Chinook salmon .......................................................... 21 Diet composition and isotopic niches........................................................................................ 22 Wild Chinook salmon and the broader estuary ......................................................................... 25 Limitations ................................................................................................................................ 26 Conclusions and implications ................................................................................................... 26 Tables ............................................................................................................................................ 31 Figures........................................................................................................................................... 42 Works Cited .................................................................................................................................. 58 Appendix ....................................................................................................................................... 74 vii List of Tables Table 1: Total number of sampling occasions for each date, site, and habitat type (eelgrass, sandflat, and marsh). ......................................................................................................................31 Table 2: Total number of Chinook captured for each date, site, and habitat type (eelgrass, sandflat, and marsh). ......................................................................................................................32 Table 3: GSI and PBT results for the genetic sources of individual wild and hatchery Chinook salmon captured in eelgrass, marsh, and sandflat habitat. .............................................................33 Table 4: Results from the two-way analysis of variance (ANOVA) examining differences in fork length between wild and hatchery fish and Julian day of juvenile salmon in eelgrass habitats. ...34 Table 5: GLM results for predictors of stomach fullness in juvenile Chinook salmon in eelgrass habitat. Response variable: stomach fullness (log-linked). ...........................................................34 Table 6: GLM results for predictors of stomach fullness in wild juvenile Chinook salmon across habitats. ..........................................................................................................................................34 Table 7: Results of PERMANOVA testing the effects of wild and hatchery origin and size class on proportional diet composition of juvenile Chinook salmon in eelgrass habitat. BrayâCurtis dissimilarities, 999 permutations. ..................................................................................................35 Table 8: SIMPER results for wild and hatchery Chinook salmon diets in eelgrass habtitat. Percent contribution is each prey groupâs share of total average dissimilarity; cumulative shows running total. ..................................................................................................................................35 viii Table 9: Results of PERMANOVA testing the effects of habitat and size class on proportional diet composition of wild juvenile Chinook salmon. BrayâCurtis dissimilarities, 999 permutations. ..................................................................................................................................36 Table 10: SIMPER results for wild juvenile Chinook salmon diets: eelgrass vs. marsh habitat. Percent contribution is each prey groupâs share of total average dissimilarity; cumulative shows running total. ..................................................................................................................................36 Table 11: SIMPER results for wild juvenile Chinook salmon diets: eelgrass vs. sandflat habitat.........................................................................................................................................................37 Table 12: SIMPER results for wild juvenile Chinook salmon diets: marsh vs. sandflat habitat...38 Table 13: Total percentage of diet composition for each month in wild and hatchery Chinook salmon in eelgrass habitat. .............................................................................................................39 Table 14: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon liver tissue samples captured in eelgrass habitat. .............................................................................................40 Table 15: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon dorsal tissue samples captured in eelgrass habitat. ...................................................................................40 Table 16: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon dorsal tissue samples captured in eelgrass habitat. ...................................................................................41 ix Table 17: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon dorsal tissue samples captured in eelgrass habitat and broken up into size classes. ................................41 x List of Figures Figure 1. Location of all sites sampled within eelgrass, marsh, and sandflat habitats in the Fraser River estuary in 2021 and 2022. Inset map (A) shows the study region in British Columbia, Canada (gray area) with the Fraser River watershed highlighted (blue), and the study locale indicated by a red dot. The large map (B) shows sampling sites in eelgrass habitat (E 1-5 and 7) and sandflat habitat (SF 1-3, 5, and 7), characterized by higher salinity and outer estuary conditions, whereas intertidal marsh and marsh channel sites (WB, HF1, M1, M8, and M16) were characterized by relatively freshwater conditions. Base layers from ESRI, UTM coordinate system projection zone 10 N, NAD83 datum. Habitat polygons adapted from Scott et al. (2024).........................................................................................................................................................42 Figure 2. Inset map (A) highlights (gray) location of British Columbia and Washington state within North America. Map of southern British Columbia and northern Washington state (B) show the relative abundance of Chinook salmon populations from different natal sources used for analysis in eelgrass, marsh, and sandflat habitat in the Fraser River estuary. Circles with a black outline represent PBT-verified hatchery Chinook salmon captured and analyzed (N=51), while circles with no outline represent GSI-verified wild Chinook salmon captured and analyzed (N=122). Two fish from the Middle Fraser River-summer and Upper Fraser River-spring population which were excluded from analysis but known in the figure. There was a total of 176 individual Chinook salmon with a known source, but 6 additional clipped hatchery Chinook were analyzed. ........................................................................................................................................44 Figure 3. Fork length of juvenile Chinook salmon captured in eelgrass habitat between May and August of 2021 and 2022. ..............................................................................................................45 xi Figure 4. Predicted effect plot showing stomach fullness by fork length, stratified by wild and hatchery types. The y-axis is predicted stomach fullness as a proportion of body weight, derived from stomach content weight divided by body weight. Solid lines represent the model-predicted mean stomach fullness for each production type across fork length. Shaded ribbons represent the 95% confidence intervals around the predicted means. .................................................................46 Figure 5. Proportional mass of stomach contents binned to size classes < 70 millimeters, 70-79 millimetres, 80-89 millimetres, 90-99 millimetres, and â¥ 100 millimetres, classified by the fork length of juvenile Chinook salmon. All individuals were captured in eelgrass habitat between May through July of 2021 and 2022. There was a total of 73 wild Chinook salmon analyzed and 40 hatchery Chinook salmon assessed. ..........................................................................................47 Figure 6. Proportional mass of stomach contents binned by month of juvenile Chinook salmon capture in eelgrass habitat in years 2021 and 2022. There was a total of 73 wild Chinook salmon analyzed and 40 hatchery Chinook salmon assessed. ....................................................................48 Figure 7. Proportional mass of stomach contents binned to size classes < 70 millimeters, 70-79 millimetres, 80-89 millimetres, 90-99 millimetres, and >100 millimeters classified by the fork length of juvenile Chinook salmon. All individuals were captured in eelgrass habitat in May (top), June (middle), and July (bottom) of 2021 and 2022. There was a total of 21 wild Chinook salmon analyzed and 3 hatchery Chinook salmon assessed in May, there was a total of 25 wild Chinook salmon analyzed and 24 hatchery Chinook salmon assessed in June, and there was a total of 28 wild Chinook salmon analyzed and 13 hatchery Chinook salmon assessed in July. ...49 Figure 8. Proportional mass of stomach contents of wild Chinook salmon binned by habitat. All individuals were captured in eelgrass habitat in July of 2021 and 2022. There was a total of 76 xii wild Chinook salmon captured in eelgrass habitat, 13 wild Chinook salmon captured in marsh habitat, and 5 wild Chinook salmon captured in sandflat habitat. .................................................51 Figure 9. Non-metric multidimensional scaling (NMDS) plot of juvenile Chinook salmon diet based on BrayâCurtis dissimilarities of proportional diet data for wild (circles) and hatchery (triangles) juvenile Chinook salmon captured in eelgrass habitat. Each point represents an individual fish, with color indicating the dominant prey taxon in its diet. Dietary ellipses represent 95% confidence regions around each wild and hatchery types (solid line = wild; dotted line = hatchery). .............................................................................................................................52 Figure 10. Non-metric multidimensional scaling (NMDS) plot of juvenile Chinook salmon diet based on BrayâCurtis dissimilarities of proportional diet data for wild Chinook salmon captured in eelgrass habitat (circles), marsh habitat (triangles), sandflat habitat (diamond). Each point represents an individual fish, with color indicating the dominant prey taxon in its diet. Dietary ellipses represent 95% confidence regions around each wild and hatchery types (solid line = eelgrass; dotted line = marsh; dashed line). ...................................................................................53 Figure 11. Stable isotope ellipses for wild and hatchery Chinook salmon liver tissue. δ15N permille is on the y-axis and δ13C permille is on the x-axis. ........................................................54 Figure 12. Posterior estimates of isotopic niche widths (SEAB) for wild and hatchery Chinook salmon liver and dorsal muscle tissue. Shaded boxes represent 50, 75, and 95% credible intervals from dark to light grey. Black dots represent the modes of the distributions and red Xs are SEAC point estimates. ..............................................................................................................................55 Figure 13: Posterior estimates of isotopic niche widths (SEAB) for wild and hatchery Chinook salmon liver tissue in 70-79 mm, 80-89 mm, 90-99 mm, and â¥100 mm size classes. Shaded xiii boxes represent 50, 75, and 95% credible intervals from dark to light grey. Black dots represent the modes of the distributions and red Xs are SEAC point estimates. ...........................................56 Figure 14: Posterior estimates of isotopic niche widths (SEAB) for wild and hatchery Chinook salmon dorsal tissue in 70-79 mm, 80-89 mm, 90-99 mm, and â¥100 mm size classes. Shaded boxes represent 50, 75, and 95% credible intervals from dark to light grey. Black dots represent the modes of the distributions and red Xs are SEAC point estimates. ...........................................57 xiv List of Symbols â°: Per mille δ13C: Delta thirteen carbon δ15N: Delta fifteen nitrogen xv List of Abbreviations AIC: Akaikeâs information criterion ANOVA: Two-way analysis of variance CU: Conservation Units DU: Designatable Unit EMMs: Estimated Marginal Means EVI: East Vancouver Island GLM: Generalized linear model GSI: Genetic stock identification LFR: Lower Fraser River LFR-fall: Lower Fraser River MCMC: Markov Chain Monte Carlo MFR: Middle Fraser River NPS: North Puget Sound PBT: Parental-based tagging PERMANOVA: Permutational multivariate analysis of variance QP: Quesnel Plateau SEA: Standard ellipse area xvi SEAB: Bayesian standard ellipses area SEAC: Corrected standard ellipse area SEP: Salmonid Enhancement Program SIMPER: Similarity percentage SNP: Single nucleotide polymorphisms SPS: South Puget Sound STh: South Thompson River STh-SHUR: South Thompson â Shuswap River TA: Total convex hull area UFR: Upper Fraser River xvii Acknowledgements Through my time at UBC I have had the pleasure and luck of getting support from many great minds and excellent friends. Thank you to my supervisor, Dr. Scott Hinch, who I met and admired as an undergraduate student in the Faculty of Forestry and has continued to support me as a student in his department and lab since. Dave Scott, thank you for hiring me, showing me the ropes (literally), and helping me through every step of my degree and beyond. Everyone at Raincoast Conservation Foundation, including Dave Scott, Misty MacDuffee, Chris Genovali, Kristen Walters, Allison Dennert, and Auston Chhor, thank you for your guidance and being exemplary researchers and advocates for salmon. Thank you to all the amazing captains at Tsawwassen Shuttles who took us where we needed to go, especially Lindsay Wilson who was always a positive force. I have made amazing friends through my fieldwork, including but not limited to Dave Scott, Samantha Rhodes, Jack Hall, Lauren Mitchell, Taylor Marriott, and Christian Lackey who not only helped me collect samples but were also the best people to trudge through the marsh with in the early morning hours. To my lab mates in the Pacific Salmon Ecology and Conservation Lab, thank you for years of support; Iâm so grateful to have shared this time with you, especially Noa Mayer, Stephanie Lingard, Dave Scott, and Samantha Rhodes for their endless help, and to my partner, Hollis Kinnard, for encouraging me to push through to the end. Samantha Rhodes, Jack Hall, Johanna Griggs, and Gretchen MacNaughton thank you so much for helping me in the lab and never complaining about the tedious nature of the work. To everyone who spent anywhere from one afternoon to many hours helping me dissect and process my samples in the lab, I am eternally grateful. Lastly to my family, thank you for your endless encouragement in this area of my life and in all others. Without your guidance, understanding, and support I probably wouldnât even know how xviii to read, let alone get this degree. Thanks for always making sure my homework was finished, and my science projects were ridiculously elaborate. 1 Introduction Coastal estuaries are dynamic, complex ecosystems which provide critical habitats for many fish species. Estuaries form where freshwater river-outflow meets the saline tides of the ocean, typically on river deltas where fine, nutrient-rich sediments accumulate (Dyer, 1997). Constant ebbing and flowing of tides and freshwater outflow promote the development of channel networks and off-channel habitat in estuaries, serving as pathways for movement and areas of refuge for fish species (Greene et al. 2017). Organic matter and nutrients including nitrogen, phosphorus, and silica are deposited into estuaries from rivers and support foundational phytoplankton, benthic, and diatom communities (Underwood and Kromkamp, 1999; Statham, 2012). Additionally, estuarine conditions vary with river discharge and tidal cycles, creating stratification or salt-wedge dynamics that influence nutrient mixing and phytoplankton growth (Kostaschuk et al., 1989; Yin et al., 1995). These physical and chemical interactions shape unique habitats such as marshes, sandflats, and eelgrass beds which support diverse communities (Pessanha et al., 2021). Globally, estuaries comprise a small portion of the coastal landscape but have an outsized importance for the species residing and migrating in and through these habitats. Approximately 38% of the global human population lives within 100 kilometers of a coastline and associated estuaries (Cosby et al., 2024), and resource extraction, dredging to facilitate navigation, urbanization, and agricultural development have led to the degradation of estuaries, fish habitat connectivity and quality (Gregory & Bisson, 1997; Sheer & Steel, 2006). In many degraded river systems, estuaries serve as the final sink for contaminants, pollutants, and excess nutrients transported downstream (Wollast, 2003). In Canada, southern catchments export the highest levels of nitrogen and organic carbon, linked to dense human populations (Clair et al., 2013). Increased pollution, such as heavy metals (Bendell-Young et al., 2004) and 2 sewage outfall (Arvai et al., 2002), reduces primary production in estuaries which can have cascading impacts on fish communities. All anadromous Pacific salmon (Oncorhynchus spp.) pass through estuaries, but Chinook (O. tshawytscha), sockeye (O. nerka), and chum (O. keta) salmon often rear in estuaries for weeks to months, unlike pink (O. gorbuscha) and coho (O. kisutch) which have a short estuary residency (Healey, 1991). Of all Pacific salmon species, Chinook salmon are the most reliant on estuarine habitats as juveniles (Moore et al., 2016) with residency extending up to 90 days (Miller & Simenstad, 1997; Volk et al., 2010; Moore et al., 2016; McNatt et al., 2016). Estuary residency is especially critical for âocean-typeâ Chinook salmon, which migrate to sea within their first year in late March and April, and rely on estuaries for feeding, predator refuge, and physiological transition to high salinity environments (Simenstad et al., 1982; Chalifour et al., 2021). The Fraser River has the largest estuary in Canada and juvenile Chinook salmon initially use its tidal marshes (Levy & Northcote, 1982) before migrating to outer-estuary eelgrass and sandflat habitats as they grow larger (Chalifour et al., 2021; Scott et al., 2024). However, habitats in the Fraser River estuary have been degraded for several decades due to channelization, dredging, bank hardening, log booms, and other industrial and urban development activities (Boyle et al., 1997). Further, floodplain infrastructure in the lower Fraser River has resulted in the loss of 85% of floodplain habitat and 64% of streams being lost or inaccessible to salmon (Finn et al., 2021). Pacific salmon species in the Fraser River that rely heavily on estuaries, like Chinook salmon, have experienced significant population declines in recent decades due to climate change and freshwater habitat degradation (Grant et al., 2019). In southern British Columbia, 19 3 of 28 Conservation Units (CUs) across all Pacific salmon species have been assessed as Threatened or Endangered (COSEWIC, 2018). CUs are the fundamental unit of Canadaâs Wild Salmon Policy (WSP) defined as a group of wild Pacific salmon isolated from others to the extent it would be very unlikely to be naturally recolonized within a meaningful timeframe. For Chinook salmon specifically, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) evaluates populations as Designatable Units (DUs) for assessment under the Species at Risk Act (SARA). DUs are distinct enough to be considered separate conservation or management entities. Of the 28 DUs for Chinook salmon in southern B.C., 13 have been designated Threatened or Endangered (COSEWIC, 2019, 2020). Two common approaches taken to mitigate these population declines involve restoring and creating marsh habitat, given the enormous extent of habitat loss for Chinook in the lower Fraser (Finn et al., 2021). Marsh habitat creation has been an approach used in the Fraser River estuary since the 1980s, but the success of these projects, measured through marsh recession and species dominance, has varied greatly (Stewart et al., 2024). Other recent efforts include improving connectivity from the estuary to important rearing areas by breaching dikes and restoring natural mud flats (Raincoast Conservation Foundation, 2025). Despite these efforts, there is a lack of knowledge on outer-estuary habitats and how they are used by juvenile Chinook salmon and therefor how to optimize restoration efforts. Another approach taken to mitigate these population declines has involved enhancement through hatchery programs. In British Columbia, hatcheries were established in 1963, leading to the creation of the Salmonid Enhancement Program (SEP) in 1977 (DFO, 1978) which aimed to supplement wild stocks and support fisheries (MacKinlay et al., 2004). Hatchery fish are reared in controlled environments and released as juveniles (Naish et al., 2007). Hatchery Chinook 4 salmon are generally released into freshwater after wild Chinook salmon have already out-migrated to reduce interactions and overlap in limited freshwater habitat (Fisheries and Oceans Canada, 2005). Since 2020, Canada has released 380 million hatchery salmon annually, including around 40 million Chinook salmon (Fisheries and Oceans Canada, 2024). In 2023, Canada accounted for 15% of global Chinook salmon hatchery releases, second to the United States at 84%, but contributed to only 4% of total global hatchery salmonid production (NPAFC, 2024). Despite its smaller share, hatchery production remains central to Canada's conservation strategy, especially for Chinook salmon. Hatchery supplementation can have unintended effects on wild populations. Interbreeding between hatchery and wild fish may reduce genetic fitness and diversity of wild stocks (Araki et al., 2007; Christie et al., 2012), increase vulnerability to disease (Arkush et al., 2002) and reduce adaptability to environmental change. Coordinating hatchery releases to minimize competition with wild fish is challenging, as both hatchery and wild fish respond to similar environmental cues and occupy overlapping habitats (Weitkamp et al., 2015). While there might be reduced overlap in freshwater outmigration, if both groups use the estuary for extended periods, space and resource use has potential to overlap. Density-dependent interactions can affect wild salmon growth, behaviour, and migration, potentially impacting wild fish survival (Einum & Fleming, 2001; Weber & Fausch, 2005). Despite their widespread use, evidence that hatchery programs improve wild salmon spawning returns remains limited (Araki et al., 2007), raising questions about their long-term effectiveness. Juvenile Chinook salmon diet and habitat use during estuary residency are shaped by life history, body size, and morphology (Beauchamp, 2007; Miller et al., 2020). Smaller-bodied wild juveniles in estuarine marshes primarily feed on chironomid larvae, cladocerans, and other small 5 benthic and planktonic invertebrates (Weitkamp et al., 2022; Levings et al., 2023). Ocean-type Chinook salmon populations begin rearing in these marsh habitats at earlier life stages and smaller sizes, but gradually transition to outer-estuary areas as they grow (Chalifour et al., 2021; Scott et al., 2024). Eelgrass habitats support greater species richness (Chalifour et al., 2019) and, along with increased body size, facilitate a dietary shift to larger prey such as small fish and eelgrass-associated species (Kennedy et al., 2018). This shift contributes to energy storage critical for surviving the transition to the ocean (Garcia & Sewall, 2021; Pearcy, 1992; Beamish & Mahnken, 2001). Hatchery-reared Chinook salmon, which generally are released at larger sizes than wild fish at the same ages, often bypass marsh habitats and instead reside in outer estuarine areas (Scott et al., 2024). The spatial overlap of wild and hatchery Chinook salmon in eelgrass habitats raises the potential of direct competition for prey, a situation that has never been studied. This research is intended to improve the understanding of out-migrating wild and hatchery Chinook salmon diets in the Fraser River estuary, particularly in eelgrass habitat. Stomach content analysis provides a âsnapshotâ of the consumers diet by showing high taxonomic resolution (Buckland et al., 2017), foraging ability, and relative selection of available prey (Schabetsberger et al., 2003: Duguid et al., 2021). Stomach contents provide detailed information from the time of sampling, but this data can be inaccurate in its representation of diet due to varying digestion rates, abnormalities in prey selection, and movement between habitat types (Polunin and Pinnegar, 2002). Alternatively, stable isotope analysis shows dietary sources for the consumer over a longer temporal scale (Hobson, 1999; Pinzone et al., 2017). Using both liver and muscle samples for stable isotopes improves accuracy of integration rates into tissue because liver tissue has a relatively shorter turnover rate of days, while dorsal muscle has a 6 turnover rate of weeks to months (Carter et al., 2019; Heady & Moore, 2013). Through analyzing stomach contents and nitrogen and carbon stable isotope values from wild and hatchery Chinook salmon, my study provides both short and long-term diet information, providing a broader perspective of diet similarities and differences between wild and hatchery fish. The objectives of this study were to: (i) characterize and compare stomach contents of juvenile wild and hatchery Chinook salmon captured in marsh, sandflat, and eelgrass habitats; (ii) investigate the effects of wild and hatchery Chinook salmon, seasonality, habitat type and body size on stomach fullness, and (iii) describe the dietary overlap of wild and hatchery Chinook salmon in eelgrass habitat using prey identified in stomach contents and trophic niche width from stable isotopes values. 7 Methods Study area The Fraser River watershed (233,000 km2) is one of the largest in Canada with the mainstem flowing 1,375 km from the Canadian Rocky Mountains to the Pacific Ocean (Northcote and Atagi, 1997) (Figure 1). The main stem is joined by several tributaries including the Nechako River in the upper portion of the river, Quesnel and Thompson rivers flowing from the east side, and West Road River flowing from the west side of the middle river portion. The tidal portions of the Fraser River extends ~ 50 km from the town of Mission, British Columbia to the estuary at the Strait of Georgia (Figure 1). The estuary consists of marsh, sandflat, and eelgrass dominated habitats and is a highly productive stopover area for many fish species to rear and acclimate to ocean conditions (Chalifour et al. 2019). Much of the estuaryâs intact eelgrass habitat is separated by the Deltaport causeway and Tsawwassen ferry terminal on Roberts Bank. My sampling focusses in this estuary area (Figure 1). Sampling From March to August of 2021 and 2022, I sampled sites similar to those in Chalifour et al. (2019), dominated by eelgrass, marsh, and sandflat habitat, and captured fish using beach and purse seining methods. Sites in marsh habitat were sampled using a beach seine (20 m x 2 m with a 2-meter-deep bag, 6.3 millimeter stretch mesh) which was deployed from a small boat using the round-haul method (Chalifour et al., 2019; Chalifour et al., 2021; Scott et al., 2024). Sites in eelgrass and sandflat habitat were sampled using a purse seine (30 m x 3 m, 6.3 millimeter stretch mesh bunt, 12.7 millimeter stretch mesh wings), which was set from a boat and towed for 1 minute, enclosing an area of the water and the fish within that area to be further 8 processed (Chalifour et al. 2019; Chalifour et al. 2021; Scott et al. 2024). Sampling was conducted during mid-to-high tide (2.4â3.7 metres), primarily on a rising tide. For each new sampling event, defined by a unique combination of habitat type, site, date, and tidal height, I typically conducted three sets, though this varied (Table 1). In total, there were 57 sampling events in eelgrass, 27 in sandflat, and 7 in marsh habitats. Once a set was complete, all fish were identified and counted, and size of all salmonids were measured to the nearest millimetre. A subset of up to 25 juvenile ocean-type Chinook was euthanized using blunt force. The subset of Chinook salmon were sacrificed and put on ice and taken to the University of British Columbia where they were placed in a -20 C freezer to be analyzed later. Fish sampling was carried out in accordance with the protocols and guidelines established by the Canadian Council on Animal Care (CCAC) and under an approved animal use protocol (A19-0193) with the University of British Columbia. I sampled a small amount of tissue from the top corner of the caudal fin of Chinook salmon in all habitat types. Fin clips were preserved on Whatman sheets and sent to Fisheries and Oceans Canada (DFO), Molecular Genetics Lab at the Pacific Biological Station in Nanaimo BC. Population identification was assessed using single nucleotide polymorphisms (SNPs; Shastry, 2004). This genetic stock identification (GSI) approach has been validated and used for many years to identify the natal origins of most BC salmon populations (Beacham et al., 2022; Beacham et al., 2021). GSI tracks the allelic frequencies of individuals to a genetic baseline dataset and then fish can be assigned to a specific Conservation Unit (CU) which is a meta-population classification approach that considers genetic population identification, life-history traits, biogeographic locations, and local knowledge. GSI was determined with most matches achieving confidence levels between 95 and 100%. I adopted a threshold probability of 9 population assignment of 80% and excluded any samples with lower matches in our analysis. Two wild Chinook salmon were omitted from further analysis as they were identified to be stream-type salmon, making the total number of known juvenile Chinook salmon assessed being 142 individuals in eelgrass habitat, 24 in marsh habitat, and 13 in sandflat habitat (Table 2). Hatchery-origin salmon were identified using a molecular-based approach (parental-based tagging (PBT)) which tracks parent-offspring relationships within known hatchery populations (Steele et al., 2019). Only 10-15% of hatchery individuals are marked by facilities in Canada, making PBT a useful tool for identification of unmarked salmonids. The majority of hatchery-origin juvenile Chinook from the Fraser River are unmarked. The Chilliwack River hatchery releases 1.5 million juvenile Chinook salmon each year with approximately 90% of individuals remaining unmarked for their release which is reliably on May 15th (Jeremy Mothus, Chilliwack Hatchery Manager (personal communication 2019)). Alternatively, the Harrison River has relatively low enhancement of hatchery fish (approximately 300,000 juvenile Chinook released annually), but approximately 90% of these fish are marked upon their June release (Jeremy Mothus, Chilliwack Hatchery Manager (personal communication 2019). Ocean-type Chinook salmon captured from the Chilliwack River system and the Harrison River were grouped as Lower Fraser Fall Chinook salmon in our analysis, as the Chilliwack River now also supports wild production following its initial establishment with broodstock from the Harrison River population. Six fish with failed origin assessments were classified as hatchery Chinook as they were clearly marked fish. Stomach content analysis I dissected and gathered stomach content data from 179 juvenile Chinook salmon. Frozen fish were partially thawed, blotted dry, and the mass and fork length were measured. Fish were 10 cut into on the left side of the body and the stomach was removed by cutting just below the esophagus. Intestines were also removed. After blotting the outside of the stomach dry, the stomach was weighed with contents inside, and then the stomach lining was reweighted after removing the contents inside. This provided a gross estimate of stomach fullness which included digested and unidentifiable material in the stomach. Stomach fullness was standardized as a percent of the fishâs total weight using the following formula (Litz et al., 2017): Stomach fullness = Stomach content mass (g) / (Total fish mass (g) - Stomach content mass (g)) * 100 Stomachs were considered as âemptyâ when fullness was <1% of the total body weight. Additionally, there were 24 Chinook salmon (n=10 hatchery; 14=wild) with fully empty stomachs. After stomach contents were weighed, contents were either immediately processed or preserved in formalin to be processed on a later occasion. Stomach contents were examined under a microscope at a scale precision of 60 μm, and prey items were identified to the lowest possible taxonomic level. Once prey items were identified, they were counted, and each prey group was weighed, and a mean value was calculated for each prey group. Terrestrial invertebrates were often unidentifiable due to breakage, so individuals were counted by head or not counted for this prey group. Stomach content analysis provides a short-term snapshot of juvenile Chinook salmon diet, typically reflecting prey consumed within the few hours prior to capture, depending on digestion rates. Stable isotope processing Stable isotope analysis was based on tissues removed during dissection. I analyzed Î´Â¹âµN and δ¹³C in both liver and dorsal muscle samples to characterize dietary overlap for hatchery and 11 wild Chinook salmon. Liver and muscle tissues (above the lateral line except in a few cases in the smallest size class, muscle was taken from the entire flank) were removed and samples were cleaned with distilled water, dried at 60°C for 48 hours, and ground to a homogenous powder with a stainless-steel mortar and pestle. A 1.0 ± 0.2 mg portion of the fine powder was packaged in a tin capsule and sent to UBCâs Stable Isotope Facility (SIF) in the Faculty of Forestry and the Stable Isotope Laboratory (SIL) in the Pacific Centre for Isotopic and Geochemical Research. At the SIL, bulk isotope samples were analyzed for their δ¹³C and Î´Â¹âµN values using a VarioMicroCube Elemental Analyzer (EA) coupled to an Isoprime 100 mass spectrometer. Data were corrected using a two-point normalization based on the international standards IAEA-600 and MCP (marine collagen peptides). Precision, assessed by the standard deviation of replicate analyses of standards, was regularly between 0.1â° and 0.2â°. Bulk isotope samples were analyzed for their δ¹³C and Î´Â¹âµN values at the SIF using a Vario Micro Cube elemental analyzer (Elementar) coupled to an Isoprime 100 isotope ratio mass spectrometer (Isoprime Ltd.). Data were corrected using a two-point normalization based on USGS-40 and USGS-41 (L-glutamic acid). Precision was â¤0.3â° for both δ¹³C and Î´Â¹âµN. The stable isotopes of carbon and nitrogen (Î´Â¹âµN and δ¹³C) were expressed in delta notation: ðð¡ðððð ð¼ð ðð¡ðððð = (ð ð ðððððð ð ð¡ððððððâ 1) â 1000 where R is 15N:14N or 13C:12C. Data analysis The intention of this study was to contrast hatchery and wild fish among habitat types however genetic analyses revealed only three hatchery fish were captured in marsh habitat and 0 in sandflat habitat. As a result, only wild fish were used in analyses that contrasted responses 12 among the three habitat types, and effects of wild and hatchery origin could only be examined in eelgrass habitat. A two-way analysis of variance (ANOVA) was conducted to examine differences in fork length between wild and hatchery fish and Julian day of juvenile salmon in eelgrass habitats. Assumptions of normality and homogeneity of variance were assessed using histograms, QâQ plots, the ShapiroâWilk test, and Leveneâs test; no major violations were detected, so the data were analyzed without transformation. I then performed a post-hoc pairwise comparison (Tukey-style) using Estimated Marginal Means (EMMs) to compare the effect of wild and hatchery types on fork length in eelgrass habitat, while controlling for the effects of Julian day. A generalized linear model (GLM) with a Tweedie distribution and log link function (Brooks et al., 2017) was used to examine the effects of population origin (wild or hatchery), fork length, and temperature on stomach fullness of juvenile Chinook salmon sampled in eelgrass habitat. Year was initially assessed as a random intercept to account for annual variability, but its inclusion resulted in a higher AICc and there was no significant differences between years, so it was excluded from the final model. The Tweedie distribution and log link were selected to accommodate the zero-inflated, non-negative, and right-skewed nature of the stomach fullness data. Simulated residuals from the DHARMa package indicated no evidence of model misspecification or overdispersion, supporting the appropriateness of the Tweedie distribution for these data. Julian day was not included in the final model due to its high correlation with temperature (r = 0.86), which could lead to multicollinearity and unstable coefficient estimates. Another generalized linear model (GLM) with a Tweedie distribution and log link function (Brooks et al., 2017) was used to examine the effects of habitat type and fork length on 13 stomach fullness of wild juvenile Chinook salmon sampled in marsh, sandflat, and eelgrass habitats. Year was initially assessed as a random intercept to account for annual variability, but its inclusion increased AICc and revealed no significant between-year differences, so it was excluded from the final model. Julian day and temperature were also excluded, as their inclusion did not improve model fit and temperature varied across sites and habitat use differed over time. To evaluate differences in juvenile Chinook salmon diets, I conducted a PERMANOVA on BrayâCurtis dissimilarities with 1000 model permutations (Legendre and Gallagher, 2001) derived from proportional diet data to understand the effects of wild and hatchery types and size class on stomach contents. A subsequent SIMPER analysis identified prey taxa contributing most to differences between wild and hatchery fish. The isotopic niche widths were compared between wild and hatchery juvenile Chinook salmon using the Stable Isotope Bayesian Ellipses with the SIBER package in R (Jackson et al. 2011). A multivariate normal model was fit to δ¹³C and Î´Â¹âµN values, and 95% Bayesian standard ellipse areas were estimated via Markov Chain Monte Carlo (MCMC) simulation (20,000 iterations, burn-in = 1,000, thin = 10, 2 chains). The following metrics were calculated to characterize trophic niche dimensions: 1. The total area (SEA) - the convex hull area that encompasses all individuals in δ¹³C and Î´Â¹âµN space (including outliers). 2. The Bayesian standard ellipses area (SEAB) â a posterior distribution calculated through Bayesian inference 3. The corrected standard ellipse area (SEAC) â a maximum likelihood estimate of the core isotopic niche area, which is corrected for a small sample size. 14 Bayesian posterior distributions of SEAB were compared between wild and hatchery fish to assess differences in niche breadth. Overlap between ellipses was used to infer niche separation and potential dietary divergence. This was done for both liver and dorsal tissue samples. For each statistical test, several models were assessed and the model with the lowest Akaikeâs information criterion (AIC) (Burnham and Anderson, 2002), unless there was a reason to include or exclude a variable due to its ecological importance or confounding nature with other variables. All analyses were done in R with RStudio (Posit Team, 2025) with a significance criteria level of α = 0.05. 15 Results Overall, I captured 179 Chinook across eelgrass (n=142), marsh (n=24), and sandflat habitats (n=13). Of these, 84.4% identified to lower Fraser River populations (LFR-fall, LFR-suppl; n=151; (Table 3). The South Thompson River was home to 6.0% of populations (STh-0.3, STh-SHUR; n=11; Table 3). Much smaller populations contributions were associated with two fish from Puget Sound (NPS, SPS) and four fish from Vancouver Island (QP-fall, EVI-fall) (Table 3). There were six additional clipped fish captured that were determined to be hatchery Chinook salmon but no further genetic determination was conducted. Hatchery fish were significantly larger than wild fish (F(1, 134) = 16.88, p < 0.001), and all fish increased in size with Julian day (F(1, 134) = 50.37, p < 0.001; Table 4). There was no significant interaction between wild and hatchery origin and Julian day (F(1, 134) = 0.87, p = 0.352; Table 4), indicating similar growth trends across groups (Figure 3). Estimated marginal means showed hatchery fish were on average 6.1 mm longer than wild fish (90.9 ± 1.73 mm vs. 84.6 ± 1.39 mm; t(134) = 2.71, p = 0.0075; Table 4). Wild and hatchery origin was a significant predictor of stomach fullness in eelgrass habitat (β = 0.29, SE = 0.13, z = 2.26, p = 0.024; Table 5), with wild juveniles having fuller stomachs on average (Figure 4). On the original scale (given the log link), this represents an estimated ~34% increase in expected stomach fullness for wild Chinook salmon compared to hatchery fish. Fork length was strongly positively related to stomach fullness (β = 0.0145, SE = 0.0044, z = 3.31, p < 0.001; Table 5), indicating that larger individuals tended to have fuller stomachs. Temperature had no detectable relationship with stomach fullness (β = 0.0066, SE = 0.0285, z = 0.23, p = 0.82; Table 5), suggesting that within the range observed, water 16 temperature did not influence feeding success. Although temperature was not statistically significant, its inclusion resulted in a model with stronger AICc support. For wild Chinook salmon, habitat type was marginally associated with stomach fullness, while fork length had no significant effect. Fullness tended to be higher in marsh habitat compared to eelgrass (β = 0.42, SE = 0.25, z = 1.68, p = 0.093; Table 6) and lower in sandflat habitat compared to eelgrass (β = â0.27, SE = 0.29, z = â0.95, p = 0.34; Table 6), although neither effect was statistically significant. Fork length was positively related to fullness (β = 0.0048, SE = 0.0057, z = 0.84, p = 0.40; Table 6), but the effect size was small. Year, Julian day, and temperature were not included in this model, as their inclusion did not improve fit. The histogram of scaled residuals and residual-vs-predictor plots (fork length and habitat) showed no significant deviation from expected distributions, with residuals appearing approximately uniform. However, a significant dispersion test (p < 0.001) indicated overdispersion, suggesting some unexplained variability remains in the model. Attempts to add additional variables did not improve fit, and the chosen model was used. A PERMANOVA using BrayâCurtis dissimilarities on proportional diet composition in eelgrass habitat revealed significant differences for fish based on wild or hatchery origin and fish size class (PERMANOVA: Fâ9,ââââ = 3.98, R² = 0.26, p = 0.001; Table 7). These two factors collectively explained 26.0% of the variation in juvenile Chinook salmon diet composition. A SIMPER analysis identified the prey groups contributing most to dietary dissimilarities between wild and hatchery fish. The top contributors were fish (38.3% of the average dissimilarity), decapoda (17.6%), and insecta (13.4%), which together accounted for approximately 69.3% of the group-level variation (Table 8). None of the prey groups contributed significantly to differences in diet composition between wild and hatchery Chinook salmon, except for plant 17 material (p = 0.038), which occurred more frequently in hatchery Chinook salmon diets. All other prey groups had non-significant relationships with wild and hatchery Chinook salmon populations: fish (p = 0.504), insecta (p = 0.920), crustacea (p = 0.456), decapoda (p = 0.202), digested material (p = 0.321), polychaeta (p = 0.410), amphipoda (p = 0.350), unidentified material (p = 0.153), and mollusca (p = 0.402) (Table 8; Figure 9). These differences indicate high within-group variability, with plant material being the only prey group showing a statistically significant difference. Of all the fish prey in stomach contents of wild and hatchery Chinook salmon, approximately 53% was identified as Ammodytes hexapterus (Pacific sand lance), approximately 38% was Clupea pallasii (Pacific herring), and 9% of fish prey was unknown (Appendix Table 3). A PERMANOVA using BrayâCurtis dissimilarities on proportional diet composition of wild juvenile Chinook salmon revealed significant differences by habitat and size class (PERMANOVA: Fâ6,80â = 4.55, R² = 0.254, p = 0.001; Table 9), indicating that these variables collectively explained ~25% of the variation in diet. A SIMPER analysis identified the prey groups contributing most to dietary differences among habitat types for wild fish. In comparisons between eelgrass and marsh habitats, fish prey and insecta were the most influential, with fish occurring only in eelgrass diets (p = 0.001) and insects more prevalent in marsh diets (p = 0.018); amphipoda (p = 0.040), crustacea (p = 0.002), and plant material (p = 0.016) also contributed significantly to the dissimilarity (Table 10; Figure 11). In comparisons between eelgrass and sandflat habitats, fish (p = 0.006) and decapoda (p = 0.011) emerged as key differentiators (Table 11). Fish were again unique to eelgrass diets, while decapods were more abundant in sandflat diets. In contrast, differences between marsh and sandflat diets were primarily driven by decapoda (p = 0.004), with insecta (p = 0.051) and unidentified material (p = 18 0.017) also contributing meaningfully (Table 12). Notably, fish were absent from both marsh and sandflat diets. Juvenile Chinook salmon captured in eelgrass habitat exhibited distinct isotopic niche widths based on wild and hatchery types, as measured from liver and muscle tissue. For liver tissue, maximum likelihood estimates of corrected standard ellipse area (SEAc) indicated that wild Chinook salmon had broader isotopic niches than hatchery Chinook salmon (9.35 vs. 5.07â°Â², respectively; Table 14; Figure 11). Bayesian estimates of ellipse area (SEAB) showed a similar pattern: in 99.8% of posterior draws, wild Chinook salmon had larger SEAB values than hatchery Chinook salmon. Total convex hull area (TA), a measure of the total isotopic niche space, was also notably higher for wild fish (40.43â°Â²) compared to hatchery fish (20.62â°Â²) (Table 14; Figure 11). For liver tissue, trophic niche metrics (TA, SEA, SEAc) decreased with increasing size class for both wild and hatchery Chinook salmon. In the 70â79 mm size class, wild fish had the largest trophic area (TA = 44.6) and ellipse width (SEA = 17.38, SEAc = 18.54), exceeding hatchery fish (TA = 19.72; SEA = 13.45; SEAc = 15.69; Table 15). In the 80â89 mm class, wild fish again had higher values (TA = 35.89; SEA = 13.82; SEAc = 14.63) than hatchery fish (TA = 30.75; SEA = 12.28; SEAc = 13.65), though differences were smaller (Table 15). In the 90â99 mm class, wild fish maintained broader niches (TA = 22.50; SEA = 10.73; SEAc = 11.92) compared to hatchery fish (TA = 10.6; SEA = 4.92; SEAc = 5.46; Table 15). In the â¥100 mm class, wild fish had the smallest niche overall (TA = 1.13; SEA = 0.76; SEAc = 0.91), while hatchery fish were slightly larger (TA = 5.38; SEA = 2.43; SEAc = 2.67; Table 15). Results for dorsal muscle tissues differed but showed similar trends for isotopic niches. Maximum likelihood estimates of corrected standard ellipse area (SEAc) indicated that wild 19 Chinook salmon had broader isotopic niches than hatchery Chinook salmon (13.68 vs. 8.64â°Â², respectively; Table 16; Figure 11). Bayesian estimates of ellipse area (SEAB) revealed a consistent pattern, with wild individuals having larger isotopic niches in 98.9% of posterior draws. Total convex hull area (TA), which represents the overall isotopic niche space, was also larger for wild Chinook salmon (59.86â°Â²) compared to hatchery Chinook salmon (43.75â°Â²) (Table 15; Figure 11). These results suggest broader trophic diversity among wild individuals occupying eelgrass habitat. For dorsal muscle tissue, isotopic niche metrics (TA, SEA, SEAc) also declined with increasing size class for both wild and hatchery Chinook salmon. In the 70â79 mm size class, wild fish had the largest niche (TA = 44.6; SEA = 17.38; SEAc = 18.54), exceeding hatchery fish (TA = 19.72; SEA = 13.45; SEAc = 15.69; Table 17). In the 80â89 mm class, wild fish maintained slightly higher values (TA = 35.89; SEA = 13.82; SEAc = 14.63) than hatchery fish (TA = 30.75; SEA = 12.28; SEAc = 13.65; Table 17). In the 90â99 mm class, wild fish again showed broader niches (TA = 22.50; SEA = 10.73; SEAc = 11.92) compared to hatchery fish (TA = 10.6; SEA = 4.92; SEAc = 5.46; Table 17). In the â¥100 mm class, wild fish had the narrowest niche (TA = 1.13; SEA = 0.76; SEAc = 0.91), while hatchery fish were slightly larger (TA = 5.38; SEA = 2.43; SEAc = 2.67; Table 17). 20 Discussion Hatchery Chinook salmon have lower marine survival rates than wild conspecifics (Beamish et al., 2012) and it has been understood that the early marine life stage is one of the main bottlenecks to survival over their life history (Atkinson et al., 2024; Bradford, 1995). This study examined several aspects of juvenile salmon growth and diets to better understand the role of estuarine rearing as a factor affecting juvenile survival in wild and hatchery Chinook salmon. This study contrasted size and diets in wild and hatchery fish in their common eelgrass habitat. Additionally, diet was assessed in marsh and sandflat habitats to compare diet in wild Chinook salmons extended use of the estuary. Chinook salmon size during estuary residency Hatchery Chinook salmon were larger than wild Chinook salmon, potentially contributing to their earlier use of eelgrass habitats. Although estuary habitat residence was not directly measured in this study, prior research indicates hatchery Chinook salmon more frequently occupy nearshore intertidal zones, whereas wild Chinook salmon tended to inhabit tidally influenced freshwater and emergent marsh habitats (Davis et al., 2018; Scott et al., 2024). Despite these differences in initial size and habitat preference, both groups exhibited steady, parallel growth over time within eelgrass habitat. Larger body size in early marine residence can reduce predation risk (Duffy & Beauchamp, 2011), so the poor marine survival of hatchery fish either manifests later in their marine life or suggests that their larger size is not translating to improved survival. Other contributing factors to relatively lower hatchery survival may include domestication-driven genetic changes (Howe et al., 2024), differences in growth rates, age at migration, or developmental timing between hatchery and wild fish (Knudsen et al., 2006), and behavioral differences associated with hatchery rearing (Jackson & Brown, 2011). 21 Stomach fullness of wild and hatchery Chinook salmon Despite their larger size and preference for eelgrass habitat, hatchery Chinook salmon had emptier stomachs than wild Chinook salmon in eelgrass habitat. This suggests potential differences in foraging efficiency or adaptation to estuarine conditions. Scott et al. (2024) found that wild South Thompson Chinook salmon exhibited the highest growth rates in Fraser River estuary marsh habitat, indicating sufficient prey availability to support rapid growth in this habitat type. This growth facilitates shifts in prey type and habitat use, suggesting that the diverse habitat mosaic supports wild salmon by matching their size and foraging capacity during outmigration (Woo et al., 2019). In contrast to wild fish, hatchery fish must quickly transition from consuming inert food pellets to actively hunting live prey (Olla et al., 1998). Hatchery Chinook salmon rapidly move into eelgrass habitat (Scott et al., 2024), which offers rich foraging opportunities (Kennedy et al., 2018) but may hinder foraging efficiency due to structural complexity that reduces predator-prey encounters (review by Heck & Orth, 2006). Without the gradual foraging experience gained in marsh habitats, hatchery Chinook salmon may not hunt as effectively in eelgrass environments. This idea is supported by Davis et al. (2018) who found wild Chinook salmon had stomachs twice as full as hatchery Chinook salmon in the Nisqually River delta. Stomach fullness increased over time in both wild and hatchery Chinook salmon in this study, likely reflecting gradual acclimation to the habitat and access to larger, more energy-dense prey. As juveniles shift to a piscivorous diet, fullness may increase due to the size of fish prey compared to smaller prey sources and the tendency of piscivores to binge-feed during prey pulses (Armstrong & Schindler, 2011; Furey et al., 2016). Despite this, even when both populations had switched to a fish dominated diet, hatchery Chinook salmon had less full stomachs compared to wild Chinook salmon. 22 In this study, water temperature did not significantly influence stomach fullness for either wild or hatchery Chinook salmon in eelgrass habitat. Although elevated temperatures can affect salmon feeding through physiological and ecological mechanisms, such as increased metabolic demands at moderate warming (Daly & Brodeur, 2015; Volkoff & Rønnestad, 2020) and potential oxygen limitations, impaired digestion, and reduced appetite at higher temperatures (Kindree et al., 2024; Volkoff & Rønnestad, 2020), the observed range in eelgrass habitat (10.9°C to 19.8°C) may not have exceeded thermal thresholds for juvenile Chinook salmon. Brett (1971) reported peak food intake for sockeye salmon near 17°C, with declines at higher temperatures and cessation around 24°C, suggesting that most temperatures during sampling were within a tolerable range. While warmer temperatures can also increase predation pressure from species with higher thermal tolerance (McInturf et al., 2022; Nobriga et al., 2021), such effects were not detectable in this dataset. Diet composition and isotopic niches Diet composition varied between wild and hatchery Chinook salmon in eelgrass habitat across size classes, with fish prey representing the most distinguishing group. Wild Chinook salmon consumed a higher average proportion of fish prey and terrestrial insects, while hatchery salmon consumed more decapods, consistent with previous findings (Davis et al., 2018). The presence of insects in wild Chinook salmon diets likely reflects foraging along land edges adjacent to eelgrass habitat. Given that terrestrial insects can have energy densities twice as high as crustaceans (Duffy et al., 2010), this dietary choice may provide energetic advantages. While not sourced directly from the eelgrass beds themselves, wild Chinook salmon may supplement their eelgrass-derived diet with insects allowing them to have their stomachs full of high energy content. Consumption of energy-rich prey such as insects and fish is associated with reduced 23 consumption rates overall, as fewer prey items are needed to meet metabolic demands (Davis et al., 1998). In this study, hatchery fish had less full stomachs and consumed fewer insects and fish than wild fish suggesting that, in addition to targeting less energy-rich prey, hatchery fish were less effective foragers compared to their wild counterparts. Faster consumption rates in the less energy-rich prey found in hatchery Chinook salmon stomach contents could misrepresent their total fullness if digestion occurred more rapidly, but it remains they would be disadvantaged based on their dietary choices. Although both groups consumed a similar range of prey in eelgrass habitat, reflecting the opportunistic foraging nature of juvenile Chinook salmon (Williams, 2010), wild fish exhibited a higher incidence of energy rich prey sources. This difference is ecologically meaningful and may indicate a more rapid or successful transition to piscivory in wild individuals. Duffy et al. (2010) observed piscivory in Chinook salmon as small as 70 mm in nearshore habitats. In this study, I detected piscivory in four wild individuals below that threshold, including one at 63 mm in fork length. This finding suggests that wild Chinook salmon may shift to piscivory at smaller sizes, an important transition for early marine growth and survival (Beauchamp & Duffy, 2011; Daly et al., 2009; Duffy et al., 2010, 2011; Daly et al., 2015; Litz et al., 2017). While hatchery Chinook salmon were larger than their wild counterparts upon initial ocean entry, benefits of their size may not be significant from the start or quickly disappear if they are relying on a more benthic diet (Davis et al., 2018). Daly et al. (2009) found that higher proportions of Pacific sand lance in juvenile diets were linked to increased adult returns, even when stomach fullness was low. In this study, Pacific sand lance dominated fish prey identified in stomach contents, highlighting its importance as an energy-rich resource. High availability of such prey can increase piscivory, as seen with northern anchovy in Willapa Bay (Litz et al., 24 2017) and may buffer against poor conditions by allowing growth with lower consumption (Garcia & Seawall, 2021). Davis et al. (2018) reported that hatchery Chinook consumed less energy-dense prey, possibly reflecting foraging inefficiency or weaker adaptation to estuarine habitat, which was similarly supported in this study. Liver and dorsal muscle derived δ¹³C and Î´Â¹âµN trophic niche width estimates revealed broader widths in wild Chinook salmon compared to hatchery counterparts. Liver tissue has a faster isotopic turnover rate than dorsal muscle (Heady and Moore, 2013), so isotopic signatures from hatchery feed or prey consumed in the upper estuary are less expressed in these samples. Although the difference in trophic niche width between wild and hatchery Chinook salmon was smaller in liver tissue, the difference remained significant across both tissue types. The broader niche observed in wild Chinook salmon likely reflects greater consumption of insects that were less common in eelgrass habitat and in hatchery Chinook salmon stomachs. In marsh habitat, Davis et al. (2018) similarly found lower trophic niche width in hatchery Chinook salmon, largely due to reduced time spent in forested tidal freshwater and transitional emergent marsh habitat. Having a broader trophic niche is a useful adaptive trait because as resources become less available, individuals with a broader diet range may be capable of accessing more resources (Bearhop et al., 2004). This becomes less relevant after the shift to piscivory, because an all-fish diet would be less diverse and result in a smaller trophic niche. This pattern is shown in this study through Chinook salmon above 100 mm; wild fish had smaller trophic niche ellipses which correlated to their entirely fish dominated diet (Table 16; Table 18). Hatchery Chinook salmon had smaller dietary range before a shift to piscivory, combined with less fish in their diet compared to wild Chinook salmon at the same sizes. Together, these findings suggest that wild 25 Chinook salmon may be better equipped to utilize diverse estuarine resources and switch to piscivory, potentially creating a survival advantage during this early life stage. Wild Chinook salmon and the broader estuary Although sampling of wild Chinook salmon across habitat types was limited, particularly in sandflat habitat, findings support the idea that wild juveniles benefit from a mosaic of connected estuarine habitats (Chalifour et al., 2021; Woo et al., 2019). Estuaries provide both opportunity and risk, serving as critical areas for acclimation, foraging, and predator avoidance, or conversely, as high-risk zones of predation and physiological stress (Quinn, 2018). Chalifour et al. (2021) found that wild Chinook salmon smaller than 54 mm were confined to low-salinity marsh habitats, suggesting early-estuary juveniles rely on marshes for gradual acclimation. Despite being large enough to consume fish, wild juveniles in sandflats had no fish prey in their stomachs and piscivory was only observed in eelgrass habitats. This aligns with findings from Chalifour et al. (2019) that overall fish species richness was highest in eelgrass beds compared to sandflat habitat. Despite lower stomach fullness and the absence of fish prey in stomach contents, this habitat serves as an ecologically important transition zone, linking vegetated marsh and eelgrass habitats (Chalifour et al., 2019). Its overlapping species composition suggests it functions as a connective corridor that facilitates movement and resource access across habitat types. Sandflat diets were dominated by decapod larvae, similar to patterns observed in intertidal zones by Davis et al. (2018), while amphipods and terrestrial insects were common in both sandflat and marsh diets. These findings reinforce the ecological value of estuarine habitat heterogeneity, where different habitats provide complementary functions that support growth, survival, and ontogenetic shifts in foraging strategy for wild Chinook salmon. 26 Limitations There are several limitations that may have influenced or constrained the interpretation of this studyâs findings. First, small sample sizes in certain habitats reduced the power and scope of analysis, particularly for wild fish captured in sandflat (n = 13) and marsh (n = 24) habitats. This limited ability to apply the same statistical comparisons that were conducted for fish captured in eelgrass habitat. Due to the small number of wild Chinook salmon in additional habitat types, trophic niche width analyses were not conducted in sandflat and marsh habitats. Limited numbers in sandflat habitat also made stomach content analysis less powerful, especially with the prevalence of empty or near-empty stomachs in sandflat fish (over half, n = 8). Stomach content analysis presents inherent limitations, as it captures only a snapshot of recent feeding and may underrepresent soft-bodied or rapidly digested prey items (Hyslop, 1980). Furthermore, although sampling was conducted during mid-to-high tide (2.4â3.7 metres), slight variations in tidal height and timing may have affected prey availability and salmon foraging behavior, which is known to be tide-dependent in estuarine systems (Levings, 1982). Finally, six fish lacked successful genetic assignments and were classified as hatchery-origin based on the absence of an adipose fin. While this is a standard field approach, adipose fin clipping is not always consistently applied and was not the primary method of identification in this research, introducing the possibility of misclassification. Conclusions and implications Although this study did not directly measure competition between wild and hatchery Chinook salmon, previous research has documented such interactions due to their potential negative effects on wild populations (Bohlin et al., 2002; Cline et al., 2019; Naish et al., 2007; Perry & Bjornn, 1996; Weber & Fausch, 2005). In resource-limited environments such as 27 streams, hatchery fish may exhibit more aggressive or territorial behavior than wild fish (Bohlin et al., 2002; Naish et al., 2007). While this does not always reduce growth or survival, high densities can exacerbate competitive impacts (Weber & Fausch, 2005). A review by Riddell et al. (2024) assessing the effectiveness of Pacific salmon hatcheries found if interactions were present between wild and hatchery salmon, they were more commonly negative, but these studies were primarily in stream habitats. Estuaries, by contrast, are typically more productive systems (Day et al., 1989), which may buffer effects of competition among populations. Because hatchery Chinook salmon spend less time in marsh habitat, eelgrass areas are critical for assessing competition. In this study, wild Chinook salmon consumed higher proportions of energy-rich fish and insect prey, especially in May and June, suggesting they may outcompete hatchery fish where spatial overlap occurs. Earlier shifts to piscivory in wild Chinook salmon may offset the size and abundance advantages of hatchery fish upon estuary entry. As both groups adopt piscivory, competition for forage fish may intensify depending on prey availability. Currently, there is no evidence that hatchery fish negatively affect wild Chinook salmon foraging in the Fraser River estuary's eelgrass habitat; if any effect exists, it is likely hatchery fish are at a dietary disadvantage. As the more successful predator, wild Chinook salmon might instead put hatchery Chinook salmon at a disadvantage if resources were scarce. Hatcheries, alongside broader efforts to improve water quality, habitat connectivity, and habitat conditions, are used to supplement wild salmon populations for purposes of conservation and/or fisheries harvest (Fisheries and Oceans Canada, 2018, 2005). Ideally, hatchery fish are reared in environments that prepare them for the challenges of natural ecosystems. Key survival skills such as predator avoidance and effective foraging are critical during outmigration, yet traditional hatchery facilities are typically uniform and predictable, offering little resemblance to 28 natural feeding or rearing habitats (Weber & Fausch, 2003). To address this, naturalized feeding systems, such as varied feeding schedules or the use of live prey, have been shown to improve foraging ability in hatchery-reared fish (Olla et al., 1998). The Oregon Hatchery Research Center has implemented programs that integrate natural processes into rearing practices for steelhead, coho, and Chinook salmon, including access to benthic food sources (Noakes & Corrarino, 2010). While hatchery fish may be used more heavily when wild populations decline and other recovery measures are lacking, long-term dependence on hatcheries will not necessarily aid in wild salmon recovery in terms of biodiversity goals (Bradford et al. 2025; Riddell et al., 2024). Hatcheries serve not only conservation goals but are also valued by recreational, commercial, and First Nations fisheries, and will likely continue to be used for diverse purposes in the future. Enhancing hatchery effectiveness through naturalized rearing, particularly improved feeding opportunities, may increase post-release survival, making hatchery fish a more ecologically aligned tool during critical low-survival periods. However, such improvements must be implemented alongside habitat protections to prevent additional pressure on vulnerable wild populations. As the final stopover before ocean entry, eelgrass habitat in the Fraser River estuary provides critical foraging grounds for juvenile Chinook salmon. These structurally complex areas offer refuge and concentrated prey, particularly energy-dense forage fish such as Pacific sand lance and Pacific herring, which were the only species detected in the stomachs of Chinook salmon sampled from eelgrass habitat in this study. This pattern aligns with findings by Kennedy et al. (2017) who emphasized the role of eelgrass beds in supporting prey availability for juvenile salmon. However, suitable spawning habitat for Pacific sand lance remains limited. Huard et al. (2022) estimated only 5.4% of the Salish Seaâs intertidal zone supports Pacific sand lance 29 spawning, with a small proportion located in the Fraser River estuary near the eelgrass sites sampled. The conservation of forage fish such as Pacific sand lance and Pacific herring is therefore essential not only for sustaining Chinook salmon populations, but also for supporting other predators including marbled murrelets and baleen whales (Huard et al., 2022). Although Chinook salmon exhibit generalist feeding behavior, access to abundant, high-quality prey early in estuarine residence can facilitate a more rapid transition to piscivory and support growth under suboptimal environmental conditions (Litz et al., 2017). Osgood et al. (2016) demonstrated that Pacific herring can serve as a dietary replacement for eulachon when the latter is scarce, maintaining lipid-rich energy intake for juvenile salmon. Despite the ecological importance of these habitats, the eelgrass beds at Roberts Bank are adjacent to areas of high industrial activity, including the existing Deltaport shipping terminal and the Tsawwassen ferry terminal. The planned Roberts Bank Terminal 2 (T2) expansion would add a new three-berth container terminal to this area, significantly increasing vessel traffic, noise, dredging, and wake energy near this critical habitat, posing potential threats to the species who utilize this area. Miller & Simenstad (1997) found created habitat may support less effective foraging due to reduced prey, so keeping existing habitat intact should be a priority. As such, conservation of eelgrass habitats and associated forage fish habitats must be considered a priority within the broader context of Chinook salmon recovery and ecosystem-based management of the Salish Sea. Additionally, wild Chinook salmon use marsh habitat early in their estuarine residence, benefiting from lower salinity and abundant insect prey that support rapid growth and acclimation (Chalifour et al., 2019; Scott et al., 2024). Despite its ecological value, much of the Fraser estuaryâs marsh habitat has been lost or degraded, making its restoration and protection essential for sustaining wild Chinook salmon populations. Marsh habitat supports rapid growth 30 and provides energy-rich food sources, so the conservation and restoration of lost marsh habitats will further support wild salmon. While this is not the first study to assess the differences of wild and hatchery Chinook diet in estuaries (Accola et al., 2025; Davis et al., 2018; Levings et al., 1986), it does provide novel and direct comparisons of diet between populations in the Fraser River estuaryâs eelgrass habitat. I found that wild Chinook had broader diets and greater use of diverse estuarine habitats and hatchery Chinook salmon may not fully exploit estuarine foraging opportunities. Additionally, access to high-quality prey like juvenile fish may offer growth advantages during early ontogeny. This is the first direct comparison of wild and hatchery Chinook diet in a Pacific Canadian estuary. Additional applications of stomach content and stable isotope analysis is needed for other salmonids (wild and hatchery populations) and in other estuaries. Additional bioenergetic modelling and Bayesian mixing models with Î´Â¹âµN and δ¹³C samples for prey types are needed to gain a comprehensive understanding of diet composition over a longer temporal range. Overall, these findings emphasize that Fraser River estuary conservation should prioritize maintaining intact eelgrass beds, restoring degraded marsh habitats, and safeguarding forage fish spawning grounds to sustain the prey base that supports ontogenetic shifts of juvenile Chinook salmon. For hatchery management, incorporating naturalized rearing strategies that improve foraging ability may increase post-release survival, but must be paired with habitat protections to aid wild populations. 31 Tables Table 1: Total number of sampling occasions for each date, site, and habitat type (eelgrass, sandflat, and marsh). Year Date E1 E2 E3 E4 E7 SF1 SF2 SF3 SF4 SF5 SF6 SF7 WB1 HF1 M1 M16 M805-10 2 305-20 3 3 305-25 3 306-02 106-03 3 3 3 3 306-07 3 3 3 3 3 3 306-08 3 3 3 3 306-17 3 3 3 3 306-22 2 2 3 3 306-30 407-05 3 3 3 3 307-06 3 3 3 3 307-19 1 2 3 2 307-21 2 3 3 3 307-30 2 2 1 105-13 3 3 3 3 305-16 205-17 105-24 105-25 3 3 2 2 305-26 3 2 3 3 306-10 3 3 3 3 306-29 5 207-06 3 407-07 307-11 3 3Eelgrass Sandflat Marsh2021202232 Table 2: Total number of Chinook captured for each date, site, and habitat type (eelgrass, sandflat, and marsh). Year Date E1 E2 E3 E4 E7 SF1 SF2 SF3 SF5 SF7 WB1 HF1 M1 M16 M805-10 1 1005-20 1 205-25 606-02 106-03 1 4 3 1 106-08 206-17 1 10 806-22 206-30 307-05 1 2 107-06 1 3 107-19 3 1 107-21 1007-30 405-13 205-16 1605-17 105-24 605-25 1 9 1 406-10 206-29 18 207-06 1 107-07 107-11 9 2320212022Eelgrass Sandflat Marsh33 Table 3: GSI and PBT results for the genetic sources of individual wild and hatchery Chinook salmon captured in eelgrass, marsh, and sandflat habitat. Habitat captured Source population Location Hatchery Wild Eelgrass LFR-fall Lower Fraser River 47 75 STh-0.3 South Thompson River 6 QP-fall Quesnel Plateau 3 STh-SHUR South Thompson â Shuswap River 1 EVI-fall East Vancouver Island 1 LFR-suppl Lower Fraser River 1 1 MFR-summer Middle Fraser River 1 UFR-spring Upper Fraser River 1 NPS North Puget Sound 1 SPS South Puget Sound 1 Marsh LFR-fall Lower Fraser River 20 STh-0.3 South Thompson River 4 Sandflat LFR-fall Lower Fraser River 4 STh-SHUR South Thompson â Shuswap River 2 Maria Maria Slough 1 STh-0.3 South Thompson River 6 Total 51 125 34 Table 4: Results from the two-way analysis of variance (ANOVA) examining differences in fork length between wild and hatchery fish and Julian day of juvenile salmon in eelgrass habitats. Predictors df F p Post-hoc difference (Hatchery and Wild) Hatchery and wild origin 1, 138 15.75 <0.001 +6.0 mm (90.4 ± 1.73 vs. 84.4 ± 1.39 mm), p = 0.008 Julian day 1, 138 54.67 <0.001 Hatchery and wild origin Ã Julian day 1, 138 0.89 0.346 Table 5: GLMM results for predictors of stomach fullness in juvenile Chinook salmon in eelgrass habitat. Response variable: stomach fullness (log-linked). Predictor β SE z p Origin (wild vs hatchery) 0.29 0.13 2.26 0.024 Fork length (mm) 0.0145 0.0044 3.31 <0.001 Temperature (°C) 0.0066 0.0285 0.23 0.820 Table 6: GLMM results for predictors of stomach fullness in wild juvenile Chinook salmon across habitats. Predictor β SE z p Marsh vs eelgrass 0.42 0.25 1.68 0.093 Sandflat vs eelgrass â0.27 0.29 â0.95 0.340 Fork length (mm) 0.0048 0.0057 0.84 0.400 35 Table 7: Results of PERMANOVA testing the effects of wild and hatchery origin and size class on proportional diet composition of juvenile Chinook salmon in eelgrass habitat. BrayâCurtis dissimilarities, 999 permutations. Factor df F R² p Model 9 3.98 0.256 0.001 Residual 102 0.740 Total 111 1.000 Table 8: SIMPER results for wild and hatchery Chinook salmon diets in eelgrass habtitat. Percent contribution is each prey groupâs share of total average dissimilarity; cumulative shows running total. Prey Group Percent Contribution (%) Cumulative (%) p Fish 38.2 38.2 0.547 Decapoda 17.6 55.8 0.187 Insecta 13.5 69.3 0.925 Digested material 11.3 80.6 0.321 Polychaeta 7.8 88.4 0.388 Amphipoda 7.6 96.0 0.426 Unidentified material 2.2 98.2 0.129 Crustacea 1.2 99.4 0.463 Plant material 0.4 99.8 0.056 Mollusca 0.1 99.9 0.382 Nematoda 0.1 100.0 0.354 Branchiopoda 0.0 100.0 0.371 36 Table 9: Results of PERMANOVA testing the effects of habitat and size class on proportional diet composition of wild juvenile Chinook salmon. BrayâCurtis dissimilarities, 999 permutations. Factor df F R² p Model 6 4.55 0.354 0.001 Residual 80 0.746 Total 86 1.000 Table 10: SIMPER results for wild juvenile Chinook salmon diets: eelgrass vs. marsh habitat. Percent contribution is each prey groupâs share of total average dissimilarity; cumulative shows running total. Prey Group Percent Contribution (%) Cumulative (%) p Fish 31.2 31.2 0.001 Insecta 23.8 55.0 0.016 Amphipoda 10.8 65.8 0.025 Crustacea 9.9 75.7 0.008 Digested material 9.4 82.2 0.348 Decapoda 6.0 88.0 1.000 Unidentified material 5.0 93.0 0.133 Plant material 4.5 97.5 0.022 Polychaeta 2.6 100.0 0.538 Nematoda 0.0 100.0 0.134 Mollusca 0.0 100.0 0.146 Branchiopoda 0.0 100.0 0.136 37 Table 11: SIMPER results for wild juvenile Chinook salmon diets: eelgrass vs. sandflat habitat. Prey Group Percent Contribution (%) Cumulative (%) p Fish 32.4 32.4 0.003 Decapoda 30.6 63.0 0.001 Insecta 20.6 83.6 0.261 Unidentified material 7.0 90.6 0.142 Digested material 3.8 94.4 0.701 Polychaeta 2.7 97.1 0.279 Amphipoda 2.7 99.8 0.970 Crustacea 0.6 99.9 0.979 Nematoda 0.0 99.9 0.075 Mollusca 0.0 99.9 0.068 Branchiopoda 0.0 100.0 0.068 Plant material 0.0 100.0 0.878 38 Table 12: SIMPER results for wild juvenile Chinook salmon diets: marsh vs. sandflat habitat. Prey Group Percent Contribution (%) Cumulative (%) p Decapoda 33.1 33.1 0.004 Insecta 27.4 60.5 0.051 Unidentified material 10.8 71.3 0.029 Amphipoda 9.8 81.1 0.270 Crustacea 9.2 90.3 0.115 Plant material 4.9 95.2 0.077 Digested material 4.8 100.0 0.664 Fish 0.0 100.0 NA 39 Table 13: Total percentage of diet composition for each month in wild and hatchery Chinook salmon in eelgrass habitat. Prey groups Hatchery Wild May June July May June July Fish 58.62 73.62 98.67 76.68 83.27 91.78 Amphipoda 39.66 1.24 0.04 6.19 0.05 0 Polychaeta 0 9.78 0 0 11.52 2.11 Decapoda 0 6.26 0.15 13.18 1.29 0.07 Digested material 0 4.18 1.14 1.59 2.53 2.84 Insecta 1.72 3.42 0 0 0.03 2.86 Crustacea 0 0.69 0 0.72 0 0 Unidentified material 0 0.35 0 1.05 0 0 Plant material 0 0.32 0 0 0 0.14 Nematoda 0 0 0 0 0 0.19 Mollusca 0 0.15 0 0 0 0 Branchiopoda 0 0 0 0.13 0 0 Stomachs processed 3 25 15 22 26 29 Prey count 5 249 22 221 327 89 40 Table 14: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon liver tissue samples captured in eelgrass habitat. Group TA (â°Â²) SEA (â°Â²) SEAc (â°Â²) Wild Chinook salmon liver tissue 40.43 9.16 9.35 Hatchery Chinook salmon liver tissue 20.62 4.91 5.07 Table 15: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon liver tissue samples captured in eelgrass habitat and broken up into size classes. Group TA (â°Â²) SEA(â°Â²) SEAc (â°Â²) 70-79 Wild 22.81 10.91 11.82 Hatchery 14.57 12.24 15.29 80-89 Wild 27.35 9.90 10.66 Hatchery 3.26 2.26 2.83 90-99 Wild 14.69 7.97 8.97 Hatchery 4.26 2.66 3.04 â¥100 Wild 0.44 0.35 0.43 Hatchery 3.45 1.35 1.37 41 Table 16: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon dorsal tissue samples captured in eelgrass habitat. Group TA (â°Â²) SEA (â°Â²) SEAc (â°Â²) Wild Chinook salmon liver tissue 59.86 13.47 13.68 Hatchery Chinook salmon liver tissue 43.75 8.44 8.64 Table 17: Isotopic niche metrics (total convex hull area (TA), standard ellipse area (SEA), and small-sample corrected SEA (SEAc)) for wild and hatchery juvenile Chinook salmon dorsal tissue samples captured in eelgrass habitat and broken up into size classes. Group TA (â°Â²) SEA (â°Â²) SEAc (â°Â²) 70-79 Wild 44.6 17.383 18.54 Hatchery 19.72 13.45 15.69 80-89 Wild 35.89 13.82 14.63 Hatchery 30.75 12.28 13.65 90-99 Wild 22.5 10.73 11.92 Hatchery 10.6 4.92 5.46 â¥100 Wild 1.13 0.76 0.91 Hatchery 5.38 2.43 2.67 42 Figures 43 Figure 1. Location of all sites sampled within eelgrass, marsh, and sandflat habitats in the Fraser River estuary in 2021 and 2022. Inset map (A) shows the study region in British Columbia, Canada (gray area) with the Fraser River watershed highlighted (blue), and the study locale indicated by a red dot. The large map (B) shows sampling sites in eelgrass habitat (E 1-5 and 7) and sandflat habitat (SF 1-3, 5, and 7), characterized by higher salinity and outer estuary conditions, whereas intertidal marsh and marsh channel sites (WB, HF1, M1, M8, and M16) were characterized by relatively freshwater conditions. Base layers from ESRI, UTM coordinate system projection zone 10 N, NAD83 datum. Habitat polygons adapted from Scott et al. (2024). 44 Figure 2. Inset map (A) highlights (gray) location of British Columbia and Washington state within North America. Map of southern British Columbia and northern Washington state (B) show the relative abundance of Chinook salmon populations from different natal sources used for analysis in eelgrass, marsh, and sandflat habitat in the Fraser River estuary. Circles with a black outline represent PBT-verified hatchery Chinook salmon captured and analyzed (N=51), while circles with no outline represent GSI-verified wild Chinook salmon captured and analyzed (N=122). Two fish from the Middle Fraser River-summer and Upper Fraser River-spring population which were excluded from analysis but known in the figure. There was a total of 176 individual Chinook salmon with a known source, but 6 additional clipped hatchery Chinook were analyzed. A B 45 Figure 3. Fork length of juvenile Chinook salmon captured in eelgrass habitat between May and August of 2021 and 2022. Hatchery Chinook salmon release dates are regularly released on May 15th, which explains the delayed representation of hatchery Chinook salmon before and shortly after that date. 46 Figure 4. Predicted effect plot showing stomach fullness by fork length, stratified by wild and hatchery types. The y-axis is predicted stomach fullness as a proportion of body weight, derived from stomach content weight divided by body weight. Solid lines represent the model-predicted mean stomach fullness for each production type across the fork lengths. Shaded ribbons represent the 95% confidence intervals around the predicted means. 47 Figure 5. Proportional mass of stomach contents binned to size classes < 70 millimeters, 70-79 millimetres, 80-89 millimetres, 90-99 millimetres, and â¥ 100 millimetres, classified by the fork length of juvenile Chinook salmon. All individuals were captured in eelgrass habitat between May through July of 2021 and 2022. There was a total of 73 wild Chinook salmon analyzed and 40 hatchery Chinook salmon assessed. 48 Figure 6. Proportional mass of stomach contents binned by month of juvenile Chinook salmon capture in eelgrass habitat in years 2021 and 2022. There was a total of 73 wild Chinook salmon analyzed and 40 hatchery Chinook salmon assessed. 49 50 Figure 7. Proportional mass of stomach contents binned to size classes < 70 millimeters, 70-79 millimetres, 80-89 millimetres, 90-99 millimetres, and >100 millimeters classified by the fork length of juvenile Chinook salmon. All individuals were captured in eelgrass habitat in May (top), June (middle), and July (bottom) of 2021 and 2022. There was a total of 21 wild Chinook salmon analyzed and 3 hatchery Chinook salmon assessed in May, there was a total of 25 wild Chinook salmon analyzed and 24 hatchery Chinook salmon assessed in June, and there was a total of 28 wild Chinook salmon analyzed and 13 hatchery Chinook salmon assessed in July. 51 Figure 8. Proportional mass of stomach contents of wild Chinook salmon binned by habitat. All individuals were captured in eelgrass habitat in July of 2021 and 2022. There was a total of 76 wild Chinook salmon captured in eelgrass habitat, 13 wild Chinook salmon captured in marsh habitat, and 5 wild Chinook salmon captured in sandflat habitat. 52 Figure 9. Non-metric multidimensional scaling (NMDS) plot of juvenile Chinook salmon diet based on BrayâCurtis dissimilarities of proportional diet data for wild (circles) and hatchery (triangles) juvenile Chinook salmon captured in eelgrass habitat. Each point represents an individual fish, with color indicating the dominant prey taxon in its diet. Dietary ellipses represent 95% confidence regions around each wild and hatchery types (solid line = wild; dotted line = hatchery). 53 Figure 10. Non-metric multidimensional scaling (NMDS) plot of juvenile Chinook salmon diet based on BrayâCurtis dissimilarities of proportional diet data for wild Chinook salmon captured in eelgrass habitat (circles), marsh habitat (triangles), sandflat habitat (diamond). Each point represents an individual fish, with color indicating the dominant prey taxon in its diet. Dietary ellipses represent 95% confidence regions around each wild and hatchery types (solid line = eelgrass; dotted line = marsh; dashed line). 54 Figure 11. Stable isotope ellipses for wild and hatchery Chinook salmon liver tissue. δ15N permille is on the y-axis and δ13C permille is on the x-axis. 55 Figure 12. Posterior estimates of isotopic niche widths (SEAB) for wild and hatchery Chinook salmon liver and dorsal muscle tissue. Shaded boxes represent 50, 75, and 95% credible intervals from dark to light grey. Black dots represent the modes of the distributions and red Xs are SEAC point estimates. 56 Figure 13: Posterior estimates of isotopic niche widths (SEAB) for wild and hatchery Chinook salmon liver tissue in 70-79 mm, 80-89 mm, 90-99 mm, and â¥100 mm size classes. Shaded boxes represent 50, 75, and 95% credible intervals from dark to light grey. 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Entrainment of Nitrate in the Fraser River Estuary and its Biological Implications. I. Effects of the Salt Wedge. Estuarine, Coastal and Shelf Science, 40(5), 505â528. https://doi.org/10.1006/ecss.1995.0035 74 Appendix Table A1. Model comparison based on AICc for Tweedie GLMs predicting juvenile Chinook salmon stomach fullness in eelgrass habitat (n = 142). Models include different combinations of fixed effects (wild and hatchery types, fork length, Julian day, temperature, and population) and a random effect for year where specified. Model Description K AICc ÎAICc AICc Weight LogLik Significant Effects Wild and hatchery types + Fork + Julian Day + Temp (no year) 7 -498.92 0.00 0.53 256.88 Wild â., Fork â, Julian Day â**, Temp â Wild and hatchery types + Fork + Julian Day + Temp (+ year) 8 -496.67 2.25 0.17 256.88 Wild â., Fork â, Julian Day â**, Temp â Wild and hatchery types + Fork + Julian Day (no year) 6 -496.12 2.79 0.13 254.37 Wild â, Fork â, Julian Day . Fork + Julian Day + Temp (+ year) 7 -495.66 3.26 0.10 255.25 Fork ., Julian Day â**, Temp â* Wild and hatchery types + Julian Day + Temp (+ year) 7 -494.38 4.54 0.06 254.61 Wild ns, Julian Day â**, Temp â Wild and hatchery types + Julian Day + Temp + Population (+ year) 16 -481.75 17.17 <0.01 259.05 Wild â., Fork â, Julian Day â**, Temp â â = positive effect, â = negative effect, *** p < 0.001, ** p < 0.01, * p < 0.05, . p < 0.1, ns = not significant. K = number of estimated parameters including random effects. 75 Table A2. Model comparison based on AICc for Tweedie GLMs predicting juvenile wild Chinook salmon stomach fullness in marsh habitat (n=24), sandflat habitat (n=13) andoli eelgrass habitat (n = 85). Models include different combinations of fixed effects (wild and hatchery types, fork length, Julian day, temperature, and population) and a random effect for year where specified. Model Description K AICc ÎAICc AICc Weight LogLik Significant Effects Habitat + Julian Day (no year) 6 -343.79 0.00 0.61 178.26 Marsh â, Sandflat â., Julian Day â Habitat + Julian Day (+ year) 7 -341.54 2.25 0.20 178.26 Marsh â, Sandflat â., Julian Day â Habitat + Fork (no year) 6 -340.56 3.23 0.12 176.65 Marsh ns, Sandflat ns, Fork ns Habitat + Julian Day + Fork (+ year) 8 -339.26 4.53 0.06 178.27 Marsh â., Julian Day â., Fork ns Habitat + Julian Day + Fork + Temp (+ year) 9 -335.79 8.00 0.01 177.71 Julian Day â*, all other variables ns Habitat + Julian Day + Fork + Temp +Population (+ year) 16 -321.98 21.81 <0.01 179.61 Julian Day â*, all other variables ns â = positive effect, â = negative effect, *** p < 0.001, ** p < 0.01, * p < 0.05, . p < 0.1, ns = not significant. K = number of estimated parameters including random effects. 76 Table A3. Prey taxa observed in juvenile Chinook Salmon stomach contents and the total percentage proportion of taxa category to total weight of prey in stomach contents. Taxon Total proportion (%) Amphipoda 0.89 Unidentified 0.40 Ampithoidae 0.01 Caprellidae 0.03 Corophiidae 0.09 Gammaridae 0.35 Hyperiidae 0.08 Branchiopoda 0.01 Cladocera 0.01 Crustacea 0.25 Unidentified 0.01 Copepoda 0.03 Cumacea 0.01 Euphausiacea 0.20 Decapoda 2.78 Unidentified 0.14 Decapoda zoea 0.63 Decapoda megolop 2.01 Digested material 2.71 Fish 84.94 Unidentified 32.46 Clupea pallasii 7.84 Ammodytes hexapterus 44.65 Insecta 3.39 Unidentified 2.17 Hemiptera 0.11 Trichoptera 0.01 Caelifera 0.15 Coleoptera 0.03 Diptera 0.12 Athericidae 0.22 Culicomorpha 0.30 Ceratopoginidae 0.00 Chironomidae 0.05 Lepidoptera 0.02 Arachnida 0.01 Tetramorium sp. 0.20 77 Taxon Total proportion (%) Mollusca 0.04 Nematoda 0.07 Plant material 0.19 Polychaeta 4.75 Glyceridae 4.73 Unidentified material 0.02 Table A4: Mean, standard deviation, and sample size of wild and hatchery Chinook salmon δ¹³C values from liver tissue samples. Hatchery Wild Size class (mm) Mean and standard deviation N Mean and standard deviation N <70 â â -17.90 ± 2.31 7 70-79 -20.10 ± 2.79 6 -20.30 ± 3.48 21 80-89 -19.50 ± 1.28 6 -20.10 ± 3.00 20 90-99 -17.70 ± 1.14 9 -18.20 ± 2.59 10 â¥100 -17.90 ± 0.92 13 -17.50 ± 0.40 6 78 Table A5: Mean, standard deviation, and sample size of wild and hatchery Chinook salmon δ¹5N values from liver tissue samples. Hatchery Wild Size class (mm) Mean and standard deviation N Mean and standard deviation N <70 â â 11.70 ± 1.05 7 70-79 11.50 ± 2.22 6 11.10 ± 1.78 21 80-89 11.60 ± 0.82 6 11.00 ± 2.00 20 90-99 13.00 ± 0.75 9 12.00 ± 1.33 10 â¥100 13.50 ± 0.49 13 13.70 ± 0.39 6 Table A6: Mean, standard deviation, and sample size of wild and hatchery Chinook salmon δ¹³C values from dorsal tissue samples. Hatchery Wild Size class (mm) Mean and standard deviation N Mean and standard deviation N <70 -17.60 ± 2.04 2 -20.00 ± 4.56 13 70-79 -19.00 ± 2.60 9 -20.40 ± 4.18 27 80-89 -19.80 ± 2.29 11 -19.90 ± 3.60 27 90-99 -18.40 ± 1.85 11 -17.70 ± 2.60 11 â¥100 -17.60 ± 1.39 12 -17.10 ± 0.61 7 79 Table A7: Mean, standard deviation, and sample size of wild and hatchery Chinook salmon δ¹5N values from dorsal tissue samples. Hatchery Wild Size class (mm) Mean and standard deviation N Mean and standard deviation N <70 12.80 ± 0.48 2 12.40 ± 2.20 13 70-79 12.60 ± 2.03 9 11.90 ± 2.21 27 80-89 12.50 ± 2.52 11 11.80 ± 1.95 27 90-99 13.70 ± 1.45 11 12.90 ± 1.81 11 â¥100 14.30 ± 0.67 12 14.30 ± 0.71 7 80 Figure A2: Boxplots of δ¹³C values in liver tissue from hatchery and wild juvenile Chinook salmon across size classes. Boxes show the interquartile range (25thâ75th percentiles), horizontal lines indicate medians, whiskers extend to the most extreme values within 1.5 times the interquartile range, and points represent outliers. 81 Figure A3: Boxplots of δ15N values in liver tissue from hatchery and wild juvenile Chinook salmon across size classes. Boxes show the interquartile range (25thâ75th percentiles), horizontal lines indicate medians, whiskers extend to the most extreme values within 1.5 times the interquartile range, and points represent outliers. 82 Figure A4: Boxplots of δ¹³C values in dorsal tissue from hatchery and wild juvenile Chinook salmon across size classes. Boxes show the interquartile range (25thâ75th percentiles), horizontal lines indicate medians, whiskers extend to the most extreme values within 1.5 times the interquartile range, and points represent outliers. 83 Figure A4: Boxplots of δ15N values in dorsal tissue from hatchery and wild juvenile Chinook salmon across size classes. Boxes show the interquartile range (25thâ75th percentiles), horizontal lines indicate medians, whiskers extend to the most extreme values within 1.5 times the interquartile range, and points represent outliers.
Thesis/Dissertation
eng
Forestry
Vancouver : University of British Columbia Library
Attribution-NonCommercial-NoDerivatives 4.0 International
Graduate
Hinch, Scott G.
Dietary analysis of wild and hatchery juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Fraser River estuary reveals differences in ontogenetic shifts
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