Linking aerobic scope to fitness in the wild reveals key opportunities to recover imperiled salmon populations

Published Jan 05, 2026 on Dryad. https://doi.org/10.5061/dryad.kprr4xhdr

Data files

Jan 05, 2026 version files 2.94 MB

DataS1_R1.csv

80.09 KB
DataS2.csv

468.67 KB
DataS3.csv

227.12 KB
DataS4.csv

1.37 MB
DataS5.csv

409.77 KB
DataS6.csv

3.51 KB
DataS7_R1.csv

375.67 KB
README.md

9.51 KB

Abstract

Aquatic ectotherms are hypothesized to be vulnerable to warming and deoxygenation associated with environmental change because temperature and oxygen (O₂) supply can restrict aerobic scope (AS) in captivity. However, evidence of a direct association between AS and fitness in the wild is lacking, inspiring debate about the circumstances under which AS is the primary driver of population fluctuations. Using the metabolic index (ɸ), we related AS to two Chinook salmon (Oncorhynchus tshawytscha) population bottlenecks in the wild, juvenile rearing and migration. We found that AS governed success probability for these bottlenecks only under a relatively narrow window of viable environmental conditions, depending on intraspecific metabolic trait diversity and hydrologic conditions. Opportunities for high-impact temperature- and O₂-specific conservation and management actions using existing hydraulic engineering infrastructure therefore exist when AS is between critical (ɸ_crit) and stable (ɸ_stable) values. Outside of this ecological threshold, increases in AS did not yield appreciable fitness benefits because successful rearing and migration were either exceptionally improbable (i.e., AS<ɸ_crit), or seemingly independent of AS (i.e., AS>ɸ_stable). In addition, AS impairments likely increased susceptibility to predation, and this may have been involved in the putative association between AS and fitness in the wild. We propose that ɸ_stable may serve as a more conservative benchmark than ɸ_crit to prevent extirpations and recover imperiled populations under a changing climate.

https://doi.org/10.5061/dryad.kprr4xhdr

Brief description

Data products are intended for use with the accompanying R code, and were derived from several data sources: Interagency Telemetry Advisory Group (ITAG) Central Valley Enhanced Acoustic Tagging Project (ITAG 2023), US Fish and Wildlife Service (USFWS) Chinook salmon and other species of pelagic organism decline (POD) caught by all DJFMP and EDSM gear types (USFWS 2023), U. S. Geological Survey (USGS) Water Data for California (USGS 2023), metabolic rates of juvenile Chinook salmon (Lo et al. 2022, McInturf et al. 2022, Zillig et al. 2023a, Zillig et al. 2023b), metabolic rates of largemouth bass (McInturf et al. 2022), and in situ predator-prey experiments using predation event recorders (Demetras et al. 2016, Michel et al. 2020a, Michel et al. 2020b, Michel et al. 2023).

References

Demetras, N. J., Huff, D. D., Michel, C. J., Smith, J. M., Cutter, G. R., Hayes, S. A., & Lindley, S. T. (2016). Development of underwater recorders to quantify predation of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river environment. Fishery Bulletin 114(2), 179–185.

ITAG (2023). Central Valley Enhanced Acoustic Tagging Project. https://oceanview.pfeg.noaa.gov/erddap/tabledap/FED_JSATS_detects.html

Lo, V. K., Martin, B. T., Danner, E. M., Cocherell, D. E., Cech, Jr, J. J., & Fangue, N. A. (2022). The effect of temperature on specific dynamic action of juvenile fall-run Chinook salmon, Oncorhynchus tshawytscha. Conservation physiology, 10(1), coac067.

McInturf, A. G., Zillig, K. W., Cook, K., Fukumoto, J., Jones, A., Patterson, E., Cocherell, D.E., Michel, C.J., Caillaud, D., & Fangue, N. A. (2022). In hot water? Assessing the link between fundamental thermal physiology and predation of juvenile Chinook salmon. Ecosphere 13(11), e4264.

Michel, C. J., Henderson, M. J., Loomis, C. M., Smith, J. M., Demetras, N. J., Iglesias, I. S., Lehman, B.M., & Huff, D. D. (2020a). Fish predation on a landscape scale. Ecosphere 11(6), e03168.

Michel, C. J., Nelson, T. R., Lehman, B. M., Demetras, N. J., Harrison, L. R., & Danner, E. M. (2023a). “Assessing the Impacts of Different Contact Points on Predation-Related Mortality of Juvenile Chinook Salmon in the Sacramento-San Joaquin Delta” (Tech. Rep. R18PG00077, U.S. Bureau of Reclamation, Washington, D.C.).

Michel, C. J., Smith, J. M., Lehman, B. M., Demetras, N. J., Huff, D. D., Brandes, P. L., Israel, J.A., Quinn, T.P., & Hayes, S. A. (2020b). Limitations of active removal to manage predatory fish populations. North American Journal of Fisheries Management 40(1), 3–16.

USFWS (U. S. Fish & Wildlife Service). (2023). Chinook salmon and other species of pelagic organism decline (POD) caught by all DJFMP and EDSM gear types; https://www.fws.gov/media/all-gears-chn-pod-species-2012-2022

USGS (U. S. Geological Survey). (2023). USGS Water Data for California; https://nwis.waterdata.usgs.gov/ca/nwis

Zillig, K. W., FitzGerald, A. M., Lusardi, R. A., Cocherell, D. E., & Fangue, N. A. (2023b). Intraspecific variation among Chinook Salmon populations indicates physiological adaptation to local environmental conditions. Conservation Physiology 11(1), coad044.

Zillig, K. W., Lusardi, R. A., Cocherell, D. E., & Fangue, N. A. (2023a). Interpopulation variation in thermal physiology among seasonal runs of Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences, 80(1), 1-13.

Description of derived data products

DataS1_R1.csv

Data for use with CodeS1_R2.R and CodeS2_R2.R. Empirical measurements used to determine metabolic traits that parameterized the metabolic index (ɸ) for juvenile Chinook salmon and largemouth bass. Each row represents measurements determined from individual fish. ref=reference (Zillig et al. 2023a, Lo et al. 2022, McInturf et al. 2022, or Zillig et al. 2023b), species=Oncorhynchus tshawytscha or Micropterus salmoides, lifestage=fry or smolt (if Chinook salmon), run=population of Chinook salmon (fall, late fall, winter, or spring), mass_kg=mass (kg), inv_T=inverse test temperature (eV), inv_accT=inverse acclimation temperature (eV), fas=factorial aerobic scope (unitless), pcrit_kPa=the oxygen required for standard metabolic rate (kPa). For raw data, see the relevant reference.

DataS2.csv

Data for use with CodeS2_R2.R. Beach seine sampling and environmental conditions used to determine Chinook salmon fry rearing probability in California’s Sacramento-San Joaquin Delta (Delta). Each row represents a unique sampling event. ref=reference (USFWS 2023), date_time = time when sampling event was conducted in %Y-%m-%d %H:%M:%OS format with time zone Etc/GMT+8, catch_bin=0 (no fry caught) or 1 (fry caught), Location=name of sampling location where repeat measurements occurred, sac=tidally filtered average daily discharge of the Sacramento River into the Delta (m3s-1), WaterTemp=water temperature (°C), phi_f=fry-specific ɸ. For raw data, see the relevant reference.

DataS3.csv

Data for use with CodeS2_R2.R and CodeS3_R2.R. Acoustic telemetry and environmental conditions used to determine through-Delta migration success probability of Chinook salmon smolts. Each row represents an acoustically tagged juvenile Chinook salmon smolt that attempted to migrate through the Delta to the Pacific Ocean. ref_fish=telemetry reference (ITAG 2023), ref_hydro=environmental conditions reference (USGS 2023), ben_or_ds=0 (unsuccessful migration) or 1 (successful migration), free_time=time when smolt entered (or was estimated to enter) Delta in %Y-%m-%d %H:%M:%OS format with time zone Etc/GMT+8, release_river_km=migration distance (km), fish_length=fork length (mm), flow=tidally filtered average discharge of the Sacramento River into the Delta (m3s-1), temp=water temperature (°C), phi=smolt-specific ɸ. For raw data, see the relevant reference.

DataS4.csv

Data for use with CodeS3_R2.R. Environmental conditions used to determine spatiotemporal patterns of ɸ in the Delta. Each row represents a daily measurement at a given location. ref=reference (USGS 2023 or USFWS 2023), lat=latitude, lon=longitude, Date=date in %Y-%m-%d format, water_year_doy=day of water year (1-366), phi_f=fry-specific ɸ, phi_s=smolt-specific ɸ, and phi_b=largemouth bass-specific ɸ. For raw data, see the relevant reference.

DataS5.csv

Data for use with CodeS3_R2.R. Beach seine sampling of Chinook salmon fry in the Delta used as overlay in Figure S2A. Each row represents a unique sampling event. As opposed to Data S2, these data include sampling from locations where fry were caught in fewer than 5% of sampling events over the entire 12-year sampling duration. ref=reference (USFWS 2023), lat=latitude, lon=longitude, Date=date in %Y-%m-%d format, and catch_bin=0 (no fry caught) or 1 (fry caught). For raw data, see the relevant reference.

DataS6.csv

Data for use with CodeS3_R2.R. Last detections of Chinook salmon smolts in the Delta aggregated by location and time used as overlay in Figure S2B. Each row represents a unique monitoring location over a unique time range. ref=reference (ITAG 2023), lat=latitude, lon=longitude, bin_lab=date bin for plotting, and morts=number of unique fish with last known detections at a given location over a given time period. For raw data, see the relevant reference.

DataS7_R1.csv

Data for use with CodeS3_R2.R. Predation event recorder (PER) deployments and environmental conditions used to determine predation risk of juvenile Chinook salmon by largemouth bass. Each row represents a unique PER deployment. refs=references (Demetras et al. 2016, Michel et al. 2020a, Michel et al. 2020b, or Michel et al. 2023), per_method=PER type and time period (per_2014_2015, sper_2017, pper_2022), Site=name of sampling location where repeat measurements occurred, predation=0 (not predated) or 1 (predated by largemouth bass), Temp_C=water temperature (°C), DO_mgL=dissolved oxygen concentration (mgL-1), dds_z=z-scored deployment duration (s), ds_z=z-scored median distance from shore (m), ttn_z=z-scored median time to night (min), and phi_b=largemouth bass-specific ɸ. For raw data, see the relevant reference.

Description of R code

CodeS1_R2.R

R code that determines metabolic traits of Chinook salmon and largemouth bass. Requires DataS1_R1.csv as an input. Produces Figure 1, Table 1, Figure S1, Figure S4, Figure S5, Figure S6, Figure S13, Figure S14, Table S1, Table S3, and Table S5.

CodeS2_R2.R

R code that associates the aerobic scope of Chinook salmon with ecological fitness in the wild. Requires DataS1_R1.csv, DataS2.csv, and DataS3.csv as inputs. Produces Figure 2, Figure 3, Figure S8, Figure S9, Figure S11, Figure S12, and Table S2.

CodeS3_R2.R

R code that determines the spatiotemporal patterns of aerobic scope, and assesses fitness detriments to Chinook salmon attributable to largemouth bass predation in an aerobic scope context. Requires DataS2.csv, DataS3.csv, DataS4.csv, DataS5.csv, DataS6.csv, and DataS7_R1.csv as inputs. Produces Figure 4, Figure 5, Figure S2, Figure S15, Figure S16, Figure S17, Figure S18, and Table S4.