Variation in estuary use patterns of juvenile Chinook salmon in the Fraser River, BC
Publication: Canadian Journal of Fisheries and Aquatic Sciences
20 August 2024
Abstract
Juvenile Pacific salmon (Oncorhynchus spp.) use estuary habitats to varying degrees with some species and populations thought to rely heavily on these areas for early growth. In the Fraser River, British Columbia, there are 18 distinct conservation units of Chinook salmon (O. tshawytscha), and all but one is of conservation concern. Our study compares the outmigration timing, size, and habitat use of juvenile Chinook salmon in the Fraser River estuary. Over 5 years (2016–2020), we captured 6493 juvenile Chinook salmon, with 3318 sampled for stock identification. Fraser River Chinook salmon extensively used estuary habitats, but patterns varied considerably by population. Juvenile Chinook salmon from the Lower Fraser River were most abundant and present the longest, arriving the smallest in late March and early April, and captured until July. South Thompson ocean-type Chinook salmon entered the estuary later, starting to arrive in late May or early June and remaining present until mid-August. Overall, juvenile Chinook salmon varied considerably in their estuary use across populations. Understanding this variation can inform differences in productivity and guide recovery actions.
Introduction
Estuaries connect freshwater and ocean environments for Pacific salmon, providing important habitats during a crucial transition period for juveniles, yet considerable variation exists in the extent of estuary reliance across species and populations. All anadromous Pacific salmon migrate through estuaries twice during their lifespan and many will reside for days to months during their downstream migrations (Healey 1982; Moore et al. 2016). Subyearling migrants of Chinook (Oncorhynchus tshawytscha), chum (O. keta), and pink salmon (O. gorbuscha) are thought to be more estuary reliant, while yearling migrants, typically lake-type sockeye (O. nerka) and coho (O. kisutch), move through estuaries more quickly (Groot and Margolis 1991). Chinook and chum salmon that migrate downstream in their first year of life are known to rear in estuaries from a few days up to a few months (Volk et al. 2010; Carr-Harris et al. 2015; Chalifour et al. 2019). Estuary rearing is particularly common for juvenile Chinook salmon with “ocean-type” life histories that migrate at small sizes as subyearlings, relative to “stream-type” populations that spend a year in freshwater before migrating downstream as yearlings (Chalifour et al. 2021).
Research in estuary systems across the Pacific Northwest has demonstrated the importance of estuary rearing for juvenile Chinook salmon. In the Fraser River, Chinook salmon can rely on tidal-marsh habitats in the estuary for extended periods of rearing and feeding before ocean entry (Levy and Northcote 1982). In the Skeena River estuary, 25% of juvenile Chinook salmon spent at least 33 days in the estuary, with larger Chinook salmon residing for longer durations and growing at an estimated 0.5 mm·day−1, providing evidence that estuary residency supports growth opportunities (Moore et al. 2016). In the Columbia River estuary, many juvenile Chinook salmon remained in the marsh for 2–4 weeks and increased their fork length by 10–20 mm during this time, with an average growth rate of 0.53 mm·day−1 (McNatt et al. 2016). Similarly, as part of the current study, Chalifour et al. (2021) reported Harrison River Chinook salmon in the Fraser River estuary had an average estuary residence period of 41.8 days with a mean growth rate of 0.57 mm·day−1. For juvenile Chinook salmon with estuary-reliant life histories, growth rates during the estuary residence period are likely the most important factor determining size at ocean entry and early marine survival (Woodson et al. 2013).
Although estuary rearing has been shown to be important for Chinook salmon, considerable variation exists in estuary use, entry timing, and size at entry, which could relate to subsequent marine survival. In the Columbia River, Weitkamp et al. (2015) reported significant variation in ocean entry timing and size of different Chinook salmon populations that was associated with variation in early marine growth rates. Early arrival timing in the estuary is thought to confer a benefit in some populations, for example, Chinook salmon that entered the ocean from the Snake River earlier in the season were shown to have consistently better survival (Scheuerell et al. 2009). Conversely, Beamish et al. (2010) suggested that Chinook in the Fraser River were benefitting from a later ocean entry timing. Variation in survival may be related to match–mismatch dynamics of timing of local ocean productivity (Wilson et al. 2021). For California’s Central Valley fall run Chinook population, survival of hatchery-produced Chinook salmon has been shown to directly relate to the timing of spring productivity (Satterthwaite et al. 2014), and in British Columbia, Wilson et al. (2021) found that juvenile steelhead marine survival was lower in years where they reached the marine environment prior to the increase in spring upwelling. Overall, understanding this variation in outmigration timing and estuary use can help to guide population-specific restoration and management actions, as well as identify changes in estuary productivity.
The Fraser River estuary in British Columbia (BC) is home to a diverse assemblage of salmon populations, including two distinct (South Thompson summer and Lower Fraser fall) groups of ocean-type Chinook salmon and three groups of stream-type Chinook salmon (CTC 2021). Stream-type Chinook make up the majority of individual populations (16 of 18); however, most populations of Fraser Chinook salmon have experienced persistent declines in abundance and survival over the past several decades, leading to 17 of 18 assessed populations classified as Threatened or Endangered by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC 2018), with only the South Thompson ocean-type listed as Least Concern. This decline has negative economic, social, and ecological consequences, including impacts to the endangered Southern Resident Killer Whales whose spring to fall diet is heavily dependent on Chinook from the Lower, Middle, Upper, and Thompson River portions of the Fraser watershed (Hanson et al. 2010; Stewart et al. 2023).
Harrison River fall ocean-type Chinook salmon was historically the largest population in the Fraser River and one of the most abundant Chinook salmon populations worldwide (Atlas et al. 2023). However, escapements since 2005 have generally been poor, declining by approximately 6% per year for the last 35 years and are currently considered Threatened (Atlas et al. 2023). Conversely, the South Thompson ocean-type population is the sole Fraser River population assessed as not at risk of extinction, experiencing an increase in abundance of +243% in the past 5 years relative to the long-term average (CTC 2021; Atlas et al. 2023). Beamish et al. (2010) reported that the South Thompson ocean-type population individuals were arriving in the marine environment much later than those from the Harrison River, yet little other information exists regarding differences in life histories that could help explain this variation in productivity. This highlights knowledge gaps regarding aspects of the South Thompson population life history, and whether it differs from the other populations of Chinook salmon in the Fraser River experiencing lower productivity.
Here we compare the outmigration timing, size, and habitat use of a broad array of populations of juvenile Chinook salmon in the Fraser River estuary. This study deepens our understanding of the ecology of juvenile Chinook salmon in estuary habitats, with the hypothesis that important variation exists even within designated life-history groups such as stream-type versus ocean-type Chinook salmon. Our goal was also to confirm and further investigate the rearing periods of ocean-type Chinook salmon in the Fraser River observed by Levy and Northcote (1982), with the addition of genetic techniques to compare population-specific trends. We also further compare these trends with juvenile Chinook populations with stream-type life histories and hatchery-produced individuals. As ocean-type Chinook populations are thought to be more reliant on estuaries for critical growth periods before ocean entry, we focused our analysis primarily on the difference between the Harrison and South Thompson populations of juvenile ocean-type Chinook in the Fraser River that are experiencing considerable differences in survival despite their similar life history. This work will help us understand estuary use across all populations of Fraser River Chinook salmon and inform recovery planning for these populations. Understanding Chinook salmon use of this major delta system provides a significant contribution to our broader understanding of the early life-history strategies and, more broadly, helps inform managers of Chinook salmon populations in other systems.
Materials and methods
Study system
The Fraser River is the largest salmon-producing river on the west coast of Canada, with a watershed area of 233 000 km2 (Northcote and Atagi 1997). The Lower Fraser River has four arms; the majority of water flow exits into the South Arm (78%) and its distributary at Canoe Pass, with the remaining flow exiting into the North Arm and its tributary, the Middle Arm, before reaching the outer estuary (Fig. 1). The Lower Fraser River is a low-gradient environment with a salt wedge which extends upstream 50 km and tidal influence which extends at least 65 km upstream. The estuary includes brackish marsh habitats dominated by sedges (Carex spp.) and expansive tidal sand and mud flats. The southern part of the estuary also has extensive beds of native (Zostera marina) and non-native (Z. japonica) eelgrass. These habitats follow similar trends in water temperatures over the season but vary considerably in salinity with marsh habitats generally freshwater to brackish (∼0–5 ppt), sand and mud flat sites showing generally brackish conditions, and eelgrass habitats generally representing higher salinity conditions (∼20–25 ppt) (Chalifour et al. 2019). The estuary has been highly modified since the early 1900s, including 85% of marsh habitat that has been lost, diked, drained, or isolated from the river (Finn et al. 2021). Additionally, numerous jetties and causeways alter the natural movement of freshwater, sediment, invertebrates, and fish.
Fig. 1.
The Pacific Salmon Commission plays a role in the management of Chinook salmon by facilitating cooperative agreements between Canada and the United States to manage shared Chinook salmon stocks. Fraser River Stock management units are aggregates of conservation units that share similar geography, life history, and run timing that are used for implementing fisheries management (See CTC 2021). These stock management units group stream-type Chinook salmon into Spring 4.2, Spring 5.2, and Summer 5.2 units, and ocean-type Chinook salmon into South Thompson Summer 4.1 and Lower Fraser Fall 4.1 (CTC 2021). The Summer 4.1 unit also includes Maria Slough Chinook salmon in the lower Fraser; however, they occur in very low abundance and only one was captured in our study and not included in our data. The Spring 4.2 management unit generally spawn in the Thompson River and tributaries and return to spawn in the spring at 4 years of age, while the Spring 5.2 management unit generally spawn in Middle and Upper Fraser as well as Thompson River tributaries and return in the spring at 5 years of age. The Summer 5.2 management unit generally spawn from the Lower and Middle Fraser to the North Thompson River and return in the summer at 5 years of age. Over the course of our study, the Summer 4.1 unit consistently had the highest spawning abundance, followed by the Lower Fraser Fall 4.1, and stream type Spring 4.2, Spring 5.2, and Summer 5.2 units had much lower spawning abundances (Table A1).
Study sites
We selected 30 sites that span the North, Middle, and South Arms of the inner estuary, and Roberts and Sturgeon Banks that make up the outer estuary (Fig. 1). These sites encompass three habitat types: brackish marsh (M1-14 and HF1-8) located in the inner estuary, sand and mud flats (SF1-7) in the middle estuary, and eelgrass beds (E1-7) in the outer estuary. Sites were chosen to provide broad spatial coverage and represent the diversity of habitat types across the estuary, as well as their ability to be safely accessed and surveyed at mid-to-high tide levels. In 2016 and 2017, we sampled 17 sites (M1-M5, SF1-6, and E1-7). In 2018 and thereafter, 13 sites were added (totaling 30) and sampling was expanded to the North and Middle arms of the inner estuary (M7-8,11-12, and 14) and high intertidal marsh areas (HF1-8), as part of baseline monitoring for a restoration project. Our sites are all located in areas that experience significant diurnal tidal fluctuation (a 4 m tidal range), allowing boat access at mid to high tide. Generally, all sites de-water at low tides.
Sampling methods
We conducted an extensive field sampling program over 5 years (2016–2020), capturing fish using beach seine, purse seine, and fyke net methods. We sampled bi-weekly throughout the spring and summer starting in mid-to-late March and continuing until mid-July in 2016–2017. We extended sampling until mid-August in 2018–2020. Beach seines were deployed in intertidal marsh channels (M1-14) with sufficient depth and width to deploy the net. A beach seine (20 m × 2 m with a 2 m deep bag, 6.3 mm stretch mesh) was deployed from a small boat using the round-haul method. A purse seine was used in sandflat and eelgrass sites. The purse seine (40 m × 3 m, 6.3 mm stretch mesh bunt, 12.7 mm stretch mesh wings) was set from a boat and towed for 1 min. The purse seine therefore generally sampled an area twice as large as each beach seine set. Beach and purse seining was done with three repeated non-overlapping sets on each sampling occasion. For marsh sites in the high intertidal (HF1-8) where it is too shallow to beach seine, we used a fyke net which consists of one lead wing (30 m x 1 m) two side wings (20 m × 1 m; 6.3 mm mesh) and a trap box (1 m wide × 1 m long × 1 m high; 6.3 mm mesh). The fyke net was set along the marsh leading edge approximately 2 h prior to high tide and was then pulled as the tide was falling, approximately 1 h after high tide. All sampling of fish was conducted following the protocols and guidelines of the Canadian Council on Animal Care (CCAC) and an approved animal use protocol with the University of British Columbia.
Genetic stock identification
We used genetic stock identification to determine the spawning location of origin of estuary-caught juvenile salmon. We collected a small fin clip from the top of the caudal fin of up to 30 individual juvenile Chinook from each sampling site on each sampling location. Clips were then placed onto Whatman sheets for preservation. Samples were analyzed at the Pacific Biological Station by Fisheries and Oceans Canada using microsatellite DNA analysis from 2016 to 2018 and single nucleotide polymorphisms (SNPs) from 2019 to 2020. Initial analyses from 2016 to 2018 were performed by the best method of the time, using 15 microsatellite markers (variants based on sizing of sequence repeats); while subsequent years transitioned to a larger marker panel based on 389 SNPs, which are anticipated to be more accurate at the individual level, and allow parental genotypes of lower Fraser broodstock to be used for parentage-based tagging assignments to hatchery and brood year of origin (Beacham et al. 2022). This allowed the identification of juvenile salmon to the population or conservation unit scale by running samples against an existing genetic baseline. These results were then used to group populations into Fraser River management units (aggregates of populations based on life history and run timing) established by the Pacific Salmon Commission (CTC 2021). Genetic origin was assigned with a high degree of confidence with most matches reaching 95%–100% confidence levels. We also chose to use a cut-off value of 80% for the probability of assignment for our genetic results (Gilbey et al. 2016), and any samples with weaker matches were not considered further.
During our study, the application of SNPs began in 2019, coupled with parental-based tags (PBTs) of hatchery origin fish (Beacham et al. 2021). This development allowed us to identify unmarked hatchery Chinook in 2019 and 2020. As the majority of hatchery-produced Chinook salmon releases in the Fraser River are unmarked (∼90%), this greatly improved our ability to compare juvenile wild and hatchery Chinook salmon. The Harrison River population has low enhancement from hatcheries (∼300 000 juvenile fish annually, all visually marked and released in June) within the spawning boundaries of the Harrison at the Chehalis River hatchery (Shaun Spenard, Chehalis River Hatchery, B.C. (personal communication, 2021)). The Chilliwack River hatchery, located in the Lower Fraser River basin, produces approximately 1.5 million juvenile Chinook salmon annually, of which only 10% are adipose clipped thereby making identification of hatchery-produced individuals challenging. These fish are consistently released on 15 May each year at much larger sizes (∼5–6 g) than wild origin fish (Jeremy Mothus, Chilliwack Hatchery Manager (personal communication 2019)). A small proportion of the ocean-type Chinook salmon that we captured were identified as originating from the Chilliwack River system, a population which was initially established using brood stock from the Harrison River population. The Chilliwack River now also supports wild production, therefore we broadly grouped Harrison River and Chilliwack River Chinook salmon together in our analysis as Lower Fraser Fall Chinook salmon. Microsatellite-based methods, which were utilized from 2016 to 2018, could not distinguish between natural-origin Harrison and hatchery-origin Chilliwack Chinook salmon, therefore there may have been a few hatchery fish captured during this time, which are classified as Lower Fraser; however, the majority of these captures represented Chinook with fork lengths representative of wild production. Fortunately, along with expanding our collection of genetic samples in 2020, SNP technology coupled with PBTs has allowed us to further understand the variation in estuary utilization between hatchery and wild fish in our system in a way which was not previously possible.
Statistical analysis
We grouped our data at the management unit scale to examine differences in fork lengths between management units of Chinook salmon. We also compared fork lengths between different habitat types for ocean-type Chinook salmon management units. To compare fork lengths, we grouped Fraser Chinook populations according to Pacific Salmon Commission management units (CTC 2021). For this analysis, only the subset of marsh sites sampled with the beach seine (M1–14) were included and high marsh sites (HF1–8) were excluded as they were only sampled beginning in 2018. As previously discussed, Harrison River and Chilliwack River Chinook salmon were grouped together within the Lower Fraser Fall Management Unit. Pair-wise comparisons (Tukey honestly significant difference (HSD); function “TukeyHSD” in R:: stats) were performed to test for differences in fork lengths across management units of Chinook, and across habitat types for ocean-type Chinook salmon. We used an alpha level of 0.0033 to determine statistically significant results after applying the Bonferroni correction (Lee and Lee 2018) based on 15 pairwise comparisons in each test. We completed statistical analyses in R version 3.5.1 (R Core Team 2019).
Results
We sampled Fraser River estuary habitats across the spring and summer outmigration season over 5 years (2016–2020) and captured a total of 141 741 fish including 17 490 juvenile salmon. Juvenile chum were the most-abundant salmon species across the study (n = 8965), captured in large numbers from late March to early May and completely absent by June (Fig. 2). Juvenile Chinook (n = 6496) were the second-most abundant, but the most consistently captured salmon in the estuary from late March through to mid-August (Fig. 2). We captured juvenile pink salmon (n = 1169) only in even-numbered years, and they were captured in high densities in April and May (Fig. 2). We captured juvenile sockeye salmon (n = 724, Fig. 2) at yearling sizes in April and May, and subyearling sizes in June and July, and rarely captured juvenile coho salmon (n = 185). Overall, while we captured individuals from five different salmon species, there was considerable variation in our capture rates and timing, with juvenile chum and Chinook salmon having the highest rates of capture during our study.
Fig. 2.
Our genetic sampling results demonstrated that ocean-type Chinook salmon from the Lower Fraser were captured at the highest rates, followed by ocean-type South Thompson Chinook salmon. We captured limited numbers from stream-type populations and hatcheries. We retained 3244 tissue samples from juvenile Chinook that were subsequently analyzed and successfully identified to their origin population. The number of genetic samples varied considerably each year, with the fewest samples collected in 2016 (n = 285), 2017 (n = 544), and 2019 (n = 406), and larger numbers collected in 2018 (n = 917) and 2020 (n = 1092) (Table A2). Juvenile Chinook salmon from the Lower Fraser River, representing the Harrison River and Chilliwack River populations, were captured at the high rate (n = 2363) and present for the longest period each year (Figs. 3 and 4). They were the first to arrive in late March or early April and captured until late June or early July. We typically captured ocean-type Chinook salmon from the South Thompson River (n = 535) in the estuary beginning in late May or early June, and they became the most captured population captured from July through to mid-August (Figs. 3 and 4). South Thompson Chinook salmon were generally captured in much lower densities relative to Lower Fraser Chinook salmon (Figs. 3, 4, and Table A2). Stream-type Chinook salmon were primarily captured during early May with a few individuals captured in late April and early June, and a few in late July of 2020 (n = 216, Figs. 3, 4, and Table A2).
Fig. 3.
Fig. 4.
We found that juvenile Chinook salmon from the Lower Fraser were the smallest individuals when they were captured in the estuary (mean FL = 57.2 mm, sd = 15.9 mm, range = 34–128 mm), and had significantly smaller fork lengths on average than ocean-type Chinook salmon from the South Thompson that entered later and at larger sizes (mean FL = 67.4 mm, sd = 11.8 mm, range = 38–106 mm; TukeyHSD, p < 0.0001) (Fig. 5). Conversely, South Thompson Chinook salmon were consistently smaller than Lower Fraser Chinook salmon for a given Julian date when they overlapped (Fig. 4c). Stream-type (yearling) juvenile Chinook salmon originating from Spring Run 4.2, Spring Run 5.2, and Summer Run 5.2 populations in the Thompson, Middle Fraser, and Upper Fraser rivers were captured at relatively low abundance (n = 280) (Figs. 3 and 4), but at significantly larger sizes than ocean-type individuals (Figs. 4 and 5; TukeyHSD, p < 0.0001). Spring 4.2 individuals were captured in the lowest abundance but were the largest (n = 21; mean FL = 111.0 mm, sd = 12.6 mm, range = 84– 132 mm; Tukey HSD, p < 0.001). The only groups which were not significantly different from each other were Summer 5.2 (n = 87; mean FL = 95.2 mm, sd = 15.4 mm, range = 57–132 mm) and the Spring 5.2 Chinook salmon, which was most-abundant stream-type population across years (n = 108; mean FL = 93.0 mm, sd = 13.9 mm, range = 42–134 mm) (Fig. 5). There were five individuals from the Summer 5.2 group which were captured at subyearling fork lengths (<70 mm) in late July in 2020, which were the only individuals assigned to stream-type populations captured outside of the typically seen migration period and at smaller fork lengths over the course of the study.
Fig. 5.
We captured low numbers of hatchery origin individuals relative to wild individuals, with parentage-based tagging revealing only 107 hatchery-produced individuals in 2019 (n = 42) and 2020 (n = 65). Most hatchery Chinook salmon captured were sub-yearlings produced from the Lower Fraser (n = 100), with a small number of yearlings produced in the Lower Fraser (n = 6) and at other Fraser River hatcheries on the Nicola River (n = 1) and Spius Creek (n = 2). We also captured a few individuals from outside the Fraser River watershed, originating from the nearby Capilano River Hatchery (n = 4), all of which were captured in sandflat and eelgrass habitats. Lower Fraser hatchery Chinook salmon were mostly from the Chilliwack hatchery (n = 77), with a smaller number captured from the Chehalis hatchery (n = 23). The earliest captured hatchery Chinook was on 26 April 2020 and came from Spius Creek and the Chehalis River; however, the majority captured in marsh habitats occurred during May sampling periods. Chinook produced at the Chilliwack River hatchery arrived in the estuary soon after their release date on 15 May, arriving in the marsh on 23 May in 2019 and 20 May in 2020. Hatchery-produced Chinook salmon (mean FL = 85.1 mm, sd = 11.2 mm, range = 55–119 mm) were also significantly larger than wild ocean-type Chinook but significantly smaller than wild stream-type populations (Fig. 5; A3; TukeyHSD, p < 0.003). Hatchery Chinook were captured in larger numbers in marsh habitats (n = 73) relative to sandflat (n = 17) and eelgrass habitats (n = 16); however, they were captured over a shorter period in the marsh habitats primarily in May, while they were captured in outer estuary habitats from late May through mid-July (Fig. 4).
Juvenile Chinook were predominantly captured in marsh habitats (n = 5771) with relatively few captured in eelgrass habitats (n = 327) or sand flats (n = 269), a trend consistent across both ocean-type populations (Fig. 4, Chalifour et al. 2021). Although our effort was not equal, with 521 sampling occasions in marsh habitats, compared to 168 sampling occasions in eelgrass and 173 in sand flat habitats, we believe this still demonstrates a large difference in capture rates between habitat types. Despite the reduced effort, the total number of fish captured was highest in eelgrass (n = 66 385), followed by marsh (n = 62 489), with much lower capture rates in sand flat areas (n = 12 867). We also found that juvenile ocean-type Chinook salmon had significantly shorter fork lengths in marsh habitats (Figs. 4 and 6; Tukey HSD, p < 0.001) relative to sandflat and eelgrass habitats. The exception to this were South Thompson Chinook captured in eelgrass habitat, which did not significantly differ from those captured in marsh habitats; however, the lack of statistical significance was likely due to our very low sample size. We found that juvenile ocean-type Chinook from the Lower Fraser and South Thompson did not significantly differ in fork lengths in sandflat and eelgrass habitats, although Lower Fraser Chinook were generally smaller particularly in sand flat habitats (Fig. 6).
Fig. 6.
Discussion
We captured juvenile Chinook from late March through to mid-August, extending the previously established Fraser River estuary residence period of late March through early June (Levy and Northcote 1982). Our results confirm that juvenile Chinook salmon use the Fraser River estuary extensively throughout the spring and summer and for longer periods than any other Fraser watershed salmon species. We observed similar trends in abundance of other juvenile salmon species to those reported by Levy and Northcote (1982), with high densities of juvenile chum salmon in April and May, as well as high catches of pink salmon in April of even-numbered years. Juvenile sockeye salmon were captured in relatively low numbers, with yearling migrants captured typically in May and sub-yearling migrants captured later in June and July. Our findings strengthen the evidence suggesting that Fraser juvenile Chinook salmon with ocean-type life histories rely heavily on estuary habitats, as we documented their presence in the estuary for 6 months over the spring and summer season each year.
Migration timing and estuary utilization
Genetic stock identification showed significant variation in estuary timing and use between Fraser River Chinook salmon populations. We confirmed that the first juvenile ocean-type Chinook salmon to arrive in the estuary originated from the Lower Fraser, and individuals from this population were present for the longest period, as late as July. Building upon Levy and Northcote's (1982) work, we found that juvenile ocean-type Chinook salmon arrived in two separate waves, with Lower Fraser individuals arriving from late March and present until July, and South Thompson individuals arriving late May and present until July and August. Similarly, Chinook salmon in the Nanaimo River have been shown to migrate in two distinct sub-yearling strategies, with a group spawning in the lower river moving quickly to the estuary upon emergence and a second upriver population that spreads its rearing equally between natal streams and the estuary (Carl and Healey 1984; Copeland and Venditti 2009). Our findings of distinct timing were also observed by Beamish et al. (2010), who saw a similar trend in entry to the Strait of Georgia with Harrison Chinook salmon; they were most abundant in July and replaced almost entirely by South Thompson Chinook by September. Overall, our data reveal distinct patterns for the arrival and duration of estuary residence of these two ocean-type Chinook populations in the estuary.
These results build on previous literature which has demonstrated considerable variation within outmigration timing and early life history of juvenile salmon populations that migrate as subyearlings. A review by Bourret et al. (2016) found that the stream-type and ocean-type classifications fail to fully represent the variation demonstrated both within and among populations of Chinook salmon. Apgar et al. (2021) found significant variation in migratory strategies across ocean-type Chinook salmon populations from California to Washington, driven by factors such as habitat availability, population abundance, and variations in flow patterns. Similarly in a study of coho salmon in coastal Oregon, three distinct subyearling life histories were observed which also varied in their contribution to the population across years (Jones et al. 2021). As well, as demonstrated by Sturrock et al. (2020), anthropogenic impacts can result in homogenization of juvenile outmigration timing and our understanding of life-history diversity relative to what would be observed in un-impacted systems. Overall, our results build on this literature that demonstrates the need to better understand variation in juvenile salmon life-history strategies beyond just yearling and subyearling designations. We found consistent variation in fork length and capture rates during estuary residence between Fraser River ocean-type Chinook salmon stock groups. Lower Fraser individuals moved quickly to the estuary and arrived the earliest and with the smallest fork lengths, while South Thompson individuals arrived in the estuary later, after a longer freshwater rearing period and migration. South Thompson Chinook salmon were significantly larger in marsh habitats (diff = +13.24, upper = +15.95, lower = +10.54, p < 0.001), demonstrating freshwater growth; however, in sandflat and eelgrass habitats, they were not significantly different, indicating that both populations appear to have a similar growth trajectories and potentially size threshold for ocean entry, potentially related to smoltification.
We found that stream-type Chinook salmon populations moved through the estuary quickly and were captured in low abundances throughout our study period relative to ocean-type populations. Stream-type Chinook salmon were captured primarily in early May, a trend that was consistent across all three stream-type management units over the 5 years, potentially indicating a fixed outmigration timing shared by all stream-type Chinook in the Fraser River. As stream-type Chinook salmon are thought to be vulnerable to seal predation during their downstream migration (Thomas et al. 2017), this may represent a predator-swamping tactic to reduce overall predation (Furey et al. 2016). However, stream-type populations in the Fraser River are currently at low abundances relative to historical data and ocean-type populations, which could result in the reduced variation in outmigration timing observed. Also, although we found that individuals identified as originating from stream-type populations were typically captured at fork lengths that would represent yearlings, there were smaller individuals captured, as well as ocean-type Chinook at larger fork lengths, which demonstrates that there is potential variation within these life-history strategies.
The application of cutting-edge genetic stock identification techniques revealed limited use of the estuary by hatchery origin Chinook salmon from the Lower Fraser River. Parentage-based tagging is proving to be a valuable tool that greatly improves the understanding of hatchery contributions to a wild or integrated population (Hargrove et al. 2021). In our study, it allowed us to observe overlap in habitats occupied by wild and hatchery fish in the estuary. Hatchery production of Lower Fraser Chinook salmon increased in 2019 to 2.5 million annually to enhance overall abundance of Fraser Chinook, with further increases desired by some stakeholder groups. Hatchery-produced fish could potentially represent competition for wild Chinook salmon in estuary habitats, resulting in reduced growth (Weber and Fausch 2005) and complicating efforts to increase abundance of the fall Lower Fraser aggregate. Despite being released as sub-yearlings, hatchery practices result in these fish growing to smolt sizes faster than their wild counterparts before they are released mid-May. These results aligned with those seen in Puget Sound (Rice et al. 2011), which showed greater use of estuary habitats by wild Chinook salmon, which also tended to be smaller than marked hatchery fish. If hatchery practices are modified to resemble wild fish life histories more closely, as some have suggested (Nelson et al. 2019), careful consideration will need to be taken to understand potential increases in density-dependent effects through competition with wild fish.
Habitat use
Building on the data of Chalifour et al. (2019, 2021), we found little variation between Chinook salmon populations in their apparent habitat preference. The vast majority of juvenile Chinook were captured in brackish marsh habitats and relatively few, proportionally, were captured in sand flat or eelgrass habitats. This was particularly true for South Thompson Chinook salmon, with less than 10 individuals captured in eelgrass habitats across the entire study period. Juvenile Chinook relied on marsh areas as their primary rearing area, where they were consistently captured earlier and at smaller sizes relative to those captured in the outer estuary sand flat and eelgrass habitats.
These results are consistent with those reported by others including Maier and Simenstad (2009), who found that juvenile ocean-type Chinook salmon in the Columbia River estuary relied heavily on marsh productivity. Duffy et al. (2010) found that ocean-type Chinook salmon in Puget Sound that migrated quickly to the estuary upon emergence remained in nearshore habitats before moving to the outer estuary from July to September. Hatchery-produced juvenile Chinook salmon were the exception, as they moved quickly through marsh habitats and were present for a longer period in outer estuary eelgrass habitats. This pattern was likely due to their large size and late release relative to wild ocean-type Chinook salmon. As marsh habitats present a variety of salinities, from freshwater to brackish saline conditions, wild ocean-type Chinook salmon that are not yet physiologically adapted to salt water may be remaining in these areas until they achieve a size threshold before undergoing smoltification.
We observed limited juvenile Chinook salmon use of the sand flat and eelgrass habitats, which was perhaps related to the numerous jetties and causeways that interrupt the natural migration pathways of juvenile salmon in the Fraser estuary. Chalifour et al. (2019) found that eelgrass habitats supported the highest relative abundance and diversity of fish relative to sand flat and marsh habitats. In the Fraser estuary, access to sand flat habitats is altered by numerous training structures across the flats that support the maintenance of navigation channels between the river and deeper marine waters (Levings 1985). Access to eelgrass habitats in the southern estuary is altered by two causeways that block fish migration and disconnect patches of habitat (Levings 1985), instead of forcing juveniles to migrate into Georgia Strait’s deeper more saline waters with a higher likelihood of predation. These jetties likely interrupt the movement of salmon between high-tide foraging areas in eelgrass and nearby deeper channels used as low-tide refugia. Juvenile Chinook salmon in the Skeena River have been found primarily in eelgrass habitats (Sharpe et al. 2019), which are known to provide important prey items such as decapod larvae (Kennedy et al. 2018). Juvenile Chinook salmon in less degraded estuaries have also been shown to rely on the full continuum of habitats as they move from inner estuary to outer estuary habitats (Kennedy et al. 2018; Woo et al. 2019). Additionally, mudflat habitats in other estuaries have high productivity and low predation risk (Seitz et al. 2020). As these habitats are typically used by juvenile salmon in other estuaries, it may be that the limited use of outer estuary habitats demonstrated in the current study is related to numerous connectivity barriers that currently exist throughout the Fraser estuary.
Potential implications for early marine growth and survival
Our study observed considerable variation in early life-history strategies between the two distinct stock groups of ocean-type Chinook salmon in the Fraser River. This aligns with other information regarding variation between these two populations, which noted that Harrison Chinook were unique in their immediate downstream migration after emergence, as was their variation in adult run timing and ocean distributions between these stocks (DFO 1999). This result could help to explain the observed differences in productivity between these populations. Lower Fraser Chinook salmon arrive in the estuary at much smaller sizes relative to South Thompson Chinook salmon and are present for a longer period. Lower Fraser Chinook have also been shown to rely on non-natal habitats in the Lower Fraser as their primary rearing areas (Murray and Rosenau 1989). However, as the majority of the historical habitat which was once accessible in the Lower Fraser has now become lost or disconnected (Finn et al. 2021), they may be arriving in the estuary earlier. Therefore, Lower Fraser Chinook salmon which arrive at small sizes appear to be much more reliant on the degraded Fraser estuary for growth prior to ocean entry.
We found that abundance of juvenile Lower Fraser Chinook declined rapidly each year after an initial peak, possibly indicating that the estuary is an area of high initial mortality for this population. As marsh habitats in the Lower Fraser and estuary have been mostly lost or highly modified over time (Levings 1985; Finn et al. 2021), the estuary may not be able to support high densities of juvenile salmon. The Lower Fraser also contains levels of contaminants (Hall and Schreier 1996) that have been shown to cause decreased growth rates in Chinook salmon populations in the Upper Willamette River in Oregon (Lundin et al. 2021), and contaminants have been found in concentrations that could impact health in wild Chinook salmon in the Snohomish River in nearby Washington (O'Neill et al. 2020). As such, habitat restoration initiatives in the estuary may be of particular benefit to Lower Fraser Chinook salmon, contributing to reduced densities and competition during the critical early growth period.
Lower Fraser Chinook may be exposed to higher degrees of competition in the estuary relative to South Thompson Chinook due to their migration timing. Lower Fraser Chinook salmon show a similar peak in their estuary abundance as juvenile chum and pink salmon that can reach high densities while overlapping in inner estuary marsh habitats. In Puget Sound, Chinook salmon showed consistently lower survival in even-numbered outmigration years when juvenile pink salmon are present, an interaction that Ruggerone and Goetz (2004) suggest has also occurred in the lower Strait of Georgia. Also, Lower Fraser Chinook salmon typically emigrate from the estuary after 6 weeks (Chalifour et al. 2021). This suggests that high numbers of fish that enter the estuary in March and April may be entering the ocean in May, aligning with the peak outmigration timing we observed for stream-type populations and the release of hatchery Chinook. High densities of juvenile chinook during early spring could cause Lower Fraser Chinook to migrate to sandflat and eelgrass habitats at smaller sizes, which is exacerbated by the high degree of habitat loss and degradation in marsh habitats of the Lower Fraser and estuary (Chalifour et al. 2022). Conversely, recent work by Sawyer et al. (2023) found that smaller juvenile coho salmon reared for longer in the Koeye River estuary relative to larger individuals. As such, competition in the early marine environment between Lower Fraser hatchery and wild Chinook salmon may also occur. In contrast, South Thompson Chinook had limited overlap with other salmon species and populations in the Fraser estuary, arriving in the marsh and early marine environment later (Beamish et al. 2010) and potentially experiencing reduced competition for prey resources.
South Thompson Chinook salmon may also benefit from a later arrival to the early marine environment if it is better aligned with the timing of estuary and ocean productivity. South Thompson Chinook arrived in the estuary to generally warmer waters and greater marsh vegetation growth relative to Lower Fraser Chinook, which may result in higher growth rates. Beamish et al. (2010) suggested that South Thompson Chinook salmon were conferring a survival benefit from a later ocean entry timing and suggested that there has been a reduction in the Strait of Georgia’s spring productivity. However, a recent analysis by Johannessen et al. (2021) found no long-term changes in primary productivity across the Salish Sea, suggesting that other factors are controlling variation in productivity in these populations. South Thompson Chinook salmon may also be benefiting from avoiding periods of peak predation, which has been shown to be the highest for avian predators in April and May in the Columbia River (Collis et al. 2002). Overall, there may be multiple benefits to the longer freshwater residence and later migration timing exhibited by the South Thompson ocean-type Chinook salmon.
Conclusion
Our 5-year study provides a deeper understanding of variation in juvenile Chinook salmon estuary entry timing and duration for Fraser River populations of high conservation concern. Recently, Fisheries and Oceans Canada has invested tens of millions of dollars of public funds into restoration projects aimed at reversing declines in Chinook salmon populations across British Columbia, with a focus on estuary life stages. Our study demonstrates the importance of understanding early life histories of individual salmon populations when prioritizing investments in restoration opportunities. In the Fraser River, investments in estuary restoration are likely to be beneficial to ocean-type populations but may do little to reverse the declines in stream-type populations exhibiting lesser estuary reliance. However, protecting and restoring estuary habitats may be critical to ensuring the ongoing productivity of the threatened Harrison River Chinook salmon population, which we observed to rely heavily on estuary habitats. Rebuilding this population would be beneficial both for fishers in British Columbia and to the critically endangered Southern Resident Killer Whales whose body condition and survival are correlated with abundance of Fraser River Chinook salmon (Stewart et al. 2021). In conclusion, conserving estuary habitats is crucial to preserving the diversity in run timing, habitat use, and migration strategies that can ensure population persistence amid global change.
Acknowledgements
We gratefully acknowledge support from the following agencies: Fisheries and Oceans Canada’s Coastal Restoration Fund, the Natural Sciences and Engineering Research Council of Canada, the Marine Environmental Observation, Prediction and Response Network (MEOPAR), the Pacific Salmon Foundation, and the Raincoast Conservation Foundation. We thank Allison Dennert, Jonathan Moore, John Richardson, and Brian Hunt for their helpful reviews of this manuscript and Riley Finn for producing our site map. We thank our boat captains Steve Stark from the Tsawwassen First Nation and Lindsey Wilson for their guidance in site selection, fishing techniques, and a 5-year safety record of purse seining. We thank field assistants Paige Roper, Emily Seimens, Samantha Scott, Jack Hall, Dylan Cunningham, Eric Perlett, Kyle Armstrong, Samantha Rhodes, and many volunteers for their assistance in field data collection. We acknowledge and thank the Stó:lō and Coast Salish Peoples in whose territories this research was conducted. This is Publication No. 85 from the Salish Sea Marine Survival Project (marinesurvivalproject.com).
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Appendix A
Table A1.
Table A2.
Information & Authors
Information
Published In
Canadian Journal of Fisheries and Aquatic Sciences
Volume 81 • Number 9 • September 2024
Pages: 1264 - 1278
History
Received: 12 January 2024
Accepted: 3 May 2024
Version of record online: 20 August 2024
Copyright
© 2024 Authors Scott, Chalifour, Baum, and Hinch; the Raincoast Conservation Foundation; and The Crown. This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
Data Availability Statement
The data collected and analyzed as part of this study is available upon reasonable request from the corresponding author.
Key Words
Authors
Author Contributions
Conceptualization: DCS, LC, MM, JKB, SGH
Data curation: DCS
Formal analysis: DCS
Funding acquisition: DCS, LC, MM, JKB, SGH
Investigation: DCS, LC, MM, TB, ER
Methodology: DCS, LC, MM, JKB, TB, ER
Project administration: DCS, MM, JKB, SGH
Resources: MM, JKB, TB, ER, SGH
Supervision: MM, JKB, SGH
Validation: TB, ER
Visualization: LC, MM
Writing – original draft: DCS
Writing – review & editing: DCS, LC, MM, JKB, TB, ER, SGH
Competing Interests
The authors declare there are no competing interests.
Funding Information
Fisheries and Oceans Canada: BCSRIF_2020_268, C1-PAC-80
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David C. Scott, Lia Chalifour, Misty MacDuffee, Julia K. Baum, Terry Beacham, Eric Rondeau, and Scott G. Hinch. 2024. Variation in estuary use patterns of juvenile Chinook salmon in the Fraser River, BC. Canadian Journal of Fisheries and Aquatic Sciences.
81(9): 1264-1278. https://doi.org/10.1139/cjfas-2024-0012
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