scholarly journals Survival of a threatened salmon is linked to spatial variability in river conditions

2021 ◽  
Author(s):  
Colby L. Hause ◽  
Gabriel P. Singer ◽  
Rebecca A. Buchanan ◽  
Dennis E. Cocherell ◽  
Nann A. Fangue ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Oncorhynchus Tshawytscha ◽  
Central Valley ◽  
Data Generation ◽  
Habitat Variability ◽  
River Habitat ◽  
San Joaquin River ◽  
The Pacific

AbstractExtirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-α, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

scholarly journals Spatial and temporal covariability in early ocean survival of Chinook salmon (Oncorhynchus tshawytscha) along the west coast of North America

2014 ◽  
Vol 71 (7) ◽  
pp. 1671-1682 ◽  
Author(s):  
D. Patrick Kilduff ◽  
Louis W. Botsford ◽  
Steven L. H. Teo
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Survival Rates ◽  
Central Valley ◽  
Vancouver Island ◽  
Regional Patterns ◽  
Migration Patterns ◽  
The Pacific ◽  
Spatial Coverage ◽  
Correlation Scale

Abstract Knowledge of the spatial and temporal extent of covariation in survival during the critical ocean entry stage will improve our understanding of how changing ocean conditions influence salmon productivity and management. We used data from the Pacific coastwide coded-wire tagging program to investigate local and regional patterns of ocean survival of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California to southeastern Alaska from 1980–2006. Ocean survival of fish migrating as subyearlings covaried strongly from Vancouver Island to California. Short-term correlations between adjacent regions indicated this covariability increased, beginning in the early 1990s. Chinook salmon survivals exhibited a larger spatial scale of variability (50% correlation scale: 706 km) than those reported for other northeast Pacific Ocean salmon. This scale is similar to that of environmental variables related to ecosystem productivity, such as summer upwelling (50% correlation scale: 746 km) and sea surface temperature (50% correlation scale: 500–600 km). Chinook salmon ocean survival rates from southeastern Alaska and south of Vancouver Island were not inversely correlated, in contrast to earlier observations based on catch data, but note that our data differ in temporal and spatial coverage from those studies. The increased covariability in Chinook salmon ocean survival suggests that the marine phase contributes little to the reduction in risk across populations attributable to the portfolio effect. In addition, survival of fish migrating as yearlings from the Columbia River covaried with Chinook salmon survival from the northernmost regions, consistent with our understanding of their migration patterns.

Spatially overlapping salmon species have varied population response to early life history mortality from increased peak flows

2021 ◽  
pp. 1-10
Author(s):  
Colin L. Nicol ◽  
Jeffrey C. Jorgensen ◽  
Caleb B. Fogel ◽  
Britta Timpane-Padgham ◽  
Timothy J. Beechie
Keyword(s):  
Climate Change ◽  
Life History ◽  
Pacific Northwest ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Early Life History ◽  
Climate Change Scenarios ◽  
Peak Flows ◽  
Multi Stage ◽  
The Pacific

In the Pacific Northwest, USA, climate change is expected to result in a shift in average hydrologic conditions and increase variability. The relative vulnerabilities to peak flow changes among salmonid species within the same basin have not been widely evaluated. We assessed the impacts of predicted increases in peak flows on four salmonid populations in the Chehalis River basin. Coupling observations of peak flows, emissions projections, and multi-stage Beverton–Holt matrix-type life cycle models, we ran 100-year simulations of spawner abundance under baseline, mid-century, and late-century climate change scenarios. Coho (Oncorhynchus kisutch) and spring Chinook salmon (Oncorhynchus tshawytscha) shared the highest projected increase in interannual variability (SD = ±15%). Spring Chinook salmon had the greatest reduction in median spawner abundance (–13% to –15%), followed by coho and fall Chinook salmon (–7% to –9%), then steelhead (Oncorhynchus mykiss) (–4%). Our results show that interspecies and life history variability within a single basin is important to consider. Species with diverse age structures are partially buffered from population variability, which may increase population resilience to climate change.

scholarly journals Comparison of Length-at-Date Criteria and Genetic Run Assignments for Juvenile Chinook Salmon Caught at Sacramento and Chipps Island in the Sacramento–San Joaquin Delta of California

2021 ◽  
Vol 19 (3) ◽  
Author(s):  
Patricia Brandes ◽  
◽  
Brian Pyper ◽  
Michael Banks ◽  
David Jacobsen ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Central Valley ◽  
River System ◽  
Population Status ◽  
Juvenile Chinook Salmon ◽  
Late Fall ◽  
San Joaquin River ◽  
Juvenile Chinook ◽  
Specific Timing

There are four distinct runs of Chinook Salmon (Oncorhynchus tshawytscha) in the Central Valley, named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, we use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit). Fin tissues were collected from approximately 7,500 juvenile Chinook Salmon captured in trawl samples between 2007 and 2011. Tissues were analyzed using 21 microsatellites to determine genetic run assignments for individuals, which we compared with LDC run assignments. Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.

Wild Chinook salmon productivity is negatively related to seal density and not related to hatchery releases in the Pacific Northwest

2019 ◽  
Vol 76 (3) ◽  
pp. 447-462 ◽  
Author(s):  
Benjamin W. Nelson ◽  
Carl J. Walters ◽  
Andrew W. Trites ◽  
Murdoch K. McAllister
Keyword(s):  
Pacific Northwest ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Maximum Sustainable Yield ◽  
Bayesian Hierarchical ◽  
The Pacific ◽  
Bioenergetics Modeling ◽  
Stock Recruitment ◽  
High Conservation ◽  
Conservation Concern

Predation risk and competition among conspecifics significantly affect survival of juvenile salmon, but are rarely incorporated into models that predict recruitment in salmon populations. Using densities of harbour seals (Phoca vitulina) and numbers of hatchery-released Chinook salmon (Oncorhynchus tshawytscha) smolts as covariates in spatially structured Bayesian hierarchical stock–recruitment models, we found significant negative correlations between seal densities and productivity of Chinook salmon for 14 of 20 wild Chinook populations in the Pacific Northwest. Changes in numbers of seals since the 1970s were associated with a 74% decrease (95% CI: −85%, −64%) in maximum sustainable yield in Chinook stocks. In contrast, hatchery releases were significantly correlated with Chinook productivity in only one of 20 populations. Our findings are consistent with recent research on predator diets and bioenergetics modeling that suggest there is a relationship between harbour seal predation on juvenile Chinook and reduced marine survival in parts of the eastern Pacific. Forecasting, assessment, and recovery efforts for salmon populations of high conservation concern should thus consider including biotic factors, particularly predator–prey interactions.

Thermal landscapes in a changing climate: biological implications of water temperature patterns in an extreme year

2019 ◽  
Vol 76 (10) ◽  
pp. 1740-1756 ◽  
Author(s):  
E. Ashley Steel ◽  
Amy Marsha ◽  
Aimee H. Fullerton ◽  
Julian D. Olden ◽  
Narasimhan K. Larkin ◽  
...  
Keyword(s):  
Water Temperature ◽  
Pacific Northwest ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Micropterus Salmoides ◽  
Network Models ◽  
Bull Trout ◽  
Stream Network ◽  
Salvelinus Confluentus ◽  
The Pacific

Record-breaking droughts and high temperatures in 2015 across the Pacific Northwest, USA, provide an opportunistic glimpse into potential future thermal regimes of rivers and their implications for freshwater fishes. We applied spatial stream network models to data collected every 30 min for 4 years at 42 sites on the Snoqualmie River (Washington, United States) to compare water temperature patterns, summarized with relevance to particular life stages of native and nonnative fishes, in 2015 with more typical conditions (2012–2014). Although 2015 conditions were drier and warmer than what had been observed since 1960, patterns were neither consistent over the year nor on the network. Some locations showed dramatic increases in air and water temperature, whereas others had temperatures that differed little from typical years; these results contrasted with existing forecasts of future thermal landscapes. If we will observe years like 2015 more frequently in the future, we can expect conditions to be less favorable to native, cool-water fishes such as Chinook salmon (Oncorhynchus tshawytscha) and bull trout (Salvelinus confluentus) but beneficial to warm-water nonnative species such as largemouth bass (Micropterus salmoides).

Stock specific variation in the probability of precocious male maturation in hatchery Chinook Salmon (Oncorhynchus tshawytscha)

2021 ◽  
Author(s):  
Donald A Larsen ◽  
Abby E. Fuhrman ◽  
Deborah L. Harstad ◽  
David A Venditti ◽  
Brian R Beckman
Keyword(s):  
Pacific Northwest ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Common Garden ◽  
Reaction Norm ◽  
Wild Fish ◽  
Natural Origin ◽  
The Pacific ◽  
History Of ◽  
Specific Variation

Age of maturation in many salmonid species is phenotypically plastic and dependent on exceeding a genetically set threshold in growth, often described as a probabilistic maturation reaction norm (PMRN). Hatchery supplementation programs for Chinook salmon in the Pacific Northwest US have been developed to minimize differences between hatchery and wild fish by integrating natural-origin adults into broodstock, potentially affecting PMRNs. We raised fish from 10 Chinook salmon stocks with variable levels of natural-origin integration in a common garden environment to explore potential genetic variation in PMRNs for precocious male maturation as age 2 minijacks. Proportion minijacks varied ≈10-fold (0.043 to 0.443) and the PMRN WP50 (predicted weight at 50% maturation) varied by ≈18 g (24.1 to 41.7g). The propensity for minijack maturation was generally higher in stocks with higher levels of natural origin integration. These findings demonstrate the effect of genotype by environment interactions on life history of salmonids and the need for stock specific tailoring of rearing regimes to regulate differences between hatchery and wild fish, when wild fish are used in broodstocks.

Estimating the influence of temperature on the survival of chinook salmon smolts (Oncorhynchus tshawytscha) migrating through the Sacramento – San Joaquin River Delta of California

1995 ◽  
Vol 52 (4) ◽  
pp. 855-863 ◽  
Author(s):  
Peter Fritz Baker ◽  
Franklin K. Ligon ◽  
Terence P. Speed
Keyword(s):  
Water Temperature ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Logistic Function ◽  
Laboratory Findings ◽  
Natural Systems ◽  
San Joaquin River ◽  
Influence Of Temperature On ◽  
The Relationship ◽  
Good Agreement

Data from the U.S. Fish and Wildlife Service are used to investigate the relationship between water temperature and survival of hatchery-raised fall-run chinook salmon (Oncorhynchus tshawytscha) smolts migrating through the Sacramento – San Joaquin Delta of California. A formal statistical model is presented for the release of smolts marked with coded-wire tags (CWTs) in the lower Sacramento River and the subsequent recovery of marked smolts in midwater trawls in the Delta. This model treats survival as a logistic function of water temperature, and the release and recovery of different CWT groups as independent mark–recapture experiments. Iteratively reweighted least squares is used to fit the model to the data, and simulation is used to establish confidence intervals for the fitted parameters. A 95% confidence interval for the upper incipient lethal temperature, inferred from the trawl data by this method, is 23.01 ± 1.08 °C This is in good agreement with published experimental results obtained under controlled conditions (24.3 ± 0.1 and 25.1 ± 0.1 °C for chinook salmon acclimatized to 10 and 20 °C, respectively): this agreement has implications for the applicability of laboratory findings to natural systems.

scholarly journals Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

2020 ◽  
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Alleé ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Bay ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon ( Oncorhynchus tshawytscha ) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.

Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year

2010 ◽  
Vol 67 (10) ◽  
pp. 1549-1565 ◽  
Author(s):  
R. Bruce MacFarlane
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Climate Models ◽  
Oncorhynchus Tshawytscha ◽  
Energy Content ◽  
Central Valley ◽  
Energy Dynamics ◽  
Period Data ◽  
Energy Gains ◽  
Engraulis Mordax

The greatest rates of energy accumulation and growth in subyearling Chinook salmon ( Oncorhynchus tshawytscha ) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kJ·day–1 and 0.8 g·day–1, representing 4.3%·day–1 and 5.2% day–1, respectively, relative to estuary exit values. Little gain in energy (0.28 kJ·day–1) or size (0.07 g·day–1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies ( Engraulis mordax ) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day–1) and about three per day immediately following ocean entry (15% body weight·day–1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler temperatures, lower sea level, and greater upwelling resulted in greater gains. These results suggest that greater freshwater flows, warmer sea temperatures, and reduced or delayed upwelling, all of which are indicated by some (but not all) climate models, will likely decrease growth of juvenile Chinook salmon, leading to reduced survival.

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