DOI: 10.5061/dryad.c59zw3rm2
title: Subyearling Chinook salmon diets in Lower Columbia River estuarine habitats

description: The Lower Columbia River and Estuary is critical rearing habitat for
 juvenile Pacific salmon. Extending from the river mouth to Bonneville Dam
 235 river kilometers upstream, the Estuary has been altered by dams,
 dikes, and habitat loss due to deforestation and wetland removal. Since
 2008, a science group has monitored five sites to identify the long-term
 status and trends in Lower Columbia River and Estuary juvenile salmon
 rearing habitat. Here, we address predominantly natural origin juvenile
 Chinook Oncorhynchus tshawytscha diets and identify spatial and temporal
 trends in prey consumption, stomach fullness, energy consumption, and the
 metabolic costs associated with fish size and water temperatures. Juvenile
 Chinook diets consisted mainly of corophiid amphipods, chironomid
 dipterans, and cladocerans, with other insects filling in most of the
 remainder of their diets. Juvenile Chinook salmon diets were stable, and
 stomach fullness and caloric intake was comparable among the sites where
 most salmon were collected. Juvenile Chinook salmon were frequently in
 water temperatures above fitness thresholds. Higher water temperatures
 raise metabolic rates, so increased foraging will be necessary for growth
 in rising water temperature regimes. Reduced growth, earlier migration,
 and prey production timing mismatches are near term possibilities.
 Juvenile salmon rearing resiliency in the estuary can be aided by
 maintaining sufficient river discharge levels for salmon, and by restoring
 habitat and habitat connectivity to the mainstem channel.
description: # Subyearling Chinook salmon diets in Lower Columbia River estuarine
 habitats Dataset DOI: [10.5061/dryad.c59zw3rm2](10.5061/dryad.c59zw3rm2)
 ## Description of the data and file structure Title: Subyearling Chinook
 salmon diets in Lower Columbia River estuarine habitats This dataset
 contains 2008-2021 juvenile Chinook salmon diet data. Each row represents
 one salmon and its stomach contents, including total prey weight, total
 prey energy density, and metabolic costs. Additional data include water
 temperature at time of sampling, mark status, i.e., natural or hatchery
 origin fish, and the best estimate of fish origin.  ### Files and
 variables #### File: data\_2025\_LCEP\_EMP\_diets\_manuscript.xlsx
 **Description:** 2008-2021 subyearling Chinook diet data ##### Variables |
 Site | EMP site name | | :------------------------ |
 :---------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Month | month of year | | SalmonidID | unique ID for each salmon | | length.mm. | fork length of salmon | | field.wt.g | weight of fish in the field | | fullness | categorical descriptor of fullness of stomach (1=low) | | digestion | categorical descriptor of digestion of stomach contents (1=low) | | length.mm.\_bin | categorical length bin assigned to fish (30-59mm, 60-79mm, 80-99mm) | | Sum.of.wt.g. | sum of weight of prey contents in stomach (g) | | Instantaneous.Ration..IR. | ratio of total prey weight (sum of weights of all individual taxa in the diet) to total fish mass | | Energy.Ration..ER. | individual prey taxon masses for each fish multiplied by the energy density (kJ g−1 wet mass) of each prey taxon, summed, and divided by the individual fish mass | | MarkOrTag | presence/absence of form of fish tag | | BestEstimate | best estimate of fish origin | | AvgOfTempC | water temperatures at time of fish sampling | | MarknoMark | 1=marked (adipose fin absent), 0=unmarked (adipose fin present, i.e., unclipped)  | | lengthbin2 | categorical length bin assigned to fish (30-65mm, 66-99mm) | | jm | mass specific maintenance costs at 0º C (0.003) | | edt | e^dt (d is the temperature coefficient for biomass assimilation (0.68); t is water temperature in ºC) | | MM | maintenance metabolish: jm\*e^dt\*W (W=fish mass (g)) | ## Code/software Our statistical analyses were calculated using R Statistical Software [version 4.2.2.] and R Studio. Final models were developed using the package ‘glmmTMB’ [version 1.1.7] and were chosen considering corrected Akaike information criterion (wiqid version 0.3.3). Multivariate analyses on prey taxa were conducted using the package ‘vegan’ [version 2.6.4]. We organized data using “dplyr” [version 1.1.2]. Post-hoc analyses of mixed models included pairwise comparisons of estimated marginal means and calculating the effect size of the comparison, using “emmeans” [version 1.8.8]. We used “ggplot2” [version 3.4.4] for data visualization. ## Access information Other publicly accessible locations of the data: * Data is available to view at [https://public.tableau.com/app/profile/ecosystem.monitoring.program/viz/FY23-MacroinvertebrateCommunities/WelcometotheMacroinvertebrateEcosystemMonitoringDashboard](https://public.tableau.com/app/profile/ecosystem.monitoring.program/viz/FY23-MacroinvertebrateCommunities/WelcometotheMacroinvertebrateEcosystemMonitoringDashboard)