DOI: 10.5061/dryad.wm37pvmx4
title: Factors affecting the survival of Chinook salmon (Oncorhynchus tshawytscha) embryos in upper and middle Columbia River watersheds, Washington State, USA

description: A greater understanding of environmental effects on salmon survival during
 incubation can aid in prediction and facilitate population modeling at
 local and regional scales. Four basin-scale studies of Chinook salmon
 egg-to-fry survival were conducted between 2009 and 2021in spawning in
 tributaries of the upper and middle Columbia River; each study population
 is currently supplemented or have a recent history of supplementation, and
 most listed under the U.S. Endangered Species Act. Together, these studies
 provided a unique opportunity to assess factors influential to egg-to-fry
 survival, such as fine sediment infiltration and substrate scour, in the
 context of differences in survival among rivers and study years. We
 detected a 16.8% decrease in the odds of survival for every 1-cm increase
 in substrate scour, a 1.0% decrease in the survival odds with each
 one-unit change in the percentage of accumulated fines, distinct
 differences in survival within and among rivers (from 30.5% to 82.5%), and
 subtle effects of parentage in the presence of environmental factors. The
 causal and predictive relationships provided here will inform
 conservation, restoration, and further research.
description: # Factors affecting the survival of Chinook salmon (*Oncorhynchus
 tshawytscha*) embryos in upper and middle Columbia River watersheds,
 Washington State, USA
 [https://doi.org/10.5061/dryad.wm37pvmx4](https://doi.org/10.5061/dryad.wm37pvmx4) ## Description of the data and file structure We measured egg-to-fry survival and collected associated environmental data in the Methow, Entiat, Wenatchee, and Yakima river basins in Washington State, USA from 2009 to 2022. In total, the study area represents 380 river kilometers (rkm) of Chinook salmon spawning habitat in the middle and upper Columbia River system. Our study focused on spring Chinook salmon populations, i.e., those returning in the spring of the year, but spawning in the late summer and early fall. Our overall approach was as follows: We selected study sites representing the spatial range of spawning in each river system, fertilized eggs on-site, placed them in egg boxes, and buried them in areas routinely used by naturally spawning Chinook salmon at each study location. We measured substrate scour, fine sediment infiltration, substrate size and embeddedness, and temperature accumulation through the period of incubation at each site, and integrated parentage (i.e., sire and dam) into the study design. Refer to Johnson et al. (2012) for details on the methodology: Johnson, Christopher L., Philip Roni, and George R. Pess. "Parental effect as a primary factor limiting egg-to-fry survival of spring Chinook Salmon in the upper Yakima River basin." *Transactions of the American Fisheries Society* 141, no. 5 (2012): 1295-1309. ### Files and variables #### File: cjfas\_2024\_0250\_data\_and\_code.zip **Description:** This compressed file contains files in four directories: figures: code for figures 1-10 within the manuscript in .rmd file format  tables: code for tables: 2, 3, A1, A2, and A3 within the manuscript and Appendix 1 in .rmd file format models: causal and predictive models in .rmd file format. rds_files: data files to support the code listed above, and the raw data file: all_river_ef_dat. All are in .rds file format, and all are targeted by relative directories from within the figure, table, and model .rmd files. Data files are in the subdirectories for convenience: causal_desc_rds contains data files to support the causal model code, kfold_rds contains output used for model comparison, and pred_fit contains saved model fits as an alternative to running the code, which in some cases may take a very long time. as mentioned above the raw data are fully provided in the all_river_ef_dat.rds file. The dataframe consists of 25 columns and 1,197 rows. columns are as follows: include_exclude: a categorical column indicating if the data are considered sound with respect to the target analysis river: the river from which the data were collected brood_year: the year of Chinook spawning represented by the row of data reach: the categorical reach of the river from which the data were collected site: the categorical site (within reach) from which the data were collected lat: site latitude WGS84 lon: site longitude WGS84 redd: categorical index of the respective artificial redd at each site box_number: categorical index of the actual egg box placed within the artificial redd cross: a categorical index value representing the male and female from which eggs and milt were collected week: relative week of spawning/box placement stock_date: the date on which the egg box was placed in the gravel recovery_date: the date on which the egg box was recovered (or attempted recovery) days: the number of days at large (recovery_date - stock_date) atu: the number of accumulated thermal units from stocking to recovery (in degrees C) n_stocked: the number of eggs within each egg box n_survivors: the number of surviving fry following recovery of the egg box scour_cm: centimeters of scour measured over the period of deployment, negative values represent deposition. percent_fines: the percentage of particles =&lt; 2mm in the egg box following recovery d16: substrate size (mm) at the redd site for which 16% of the particles were smaller (see Wolman 1954; Kondolf et al. 2008) d50: median substrate size (mm) at the redd site (see Wolman 1954; Kondolf et al. 2008) d84: substrate size (mm) at the redd site for which 84% of the particles were smaller (see Wolman 1954; Kondolf et al. 2008) percent_embedded: the percentage of particles at the redd site considered to be embedded (see Chadd 2007). scour_loss: a categorical variable indicating if the egg box was lost and if so whether due to flow-related scour or redd superimposition egg_weight_g: egg weight (g) for the female used in each of the egg boxes Missingness in the data is indicated by an "NA" value. ## Code/Software Data and code were created using RStuido (Build 764), running R version 4.4.1. Model scripts were written using CmdStanR or Rstan packages in R (Gabry and Cešnovar 2022; Stan Development Team 2023). All scripts are saved in RStudio notebooks, *.rmd filetypes, and may be readily read and run using the freely available RStudio program. Specific packages necessary to execute the code are explicitly noted within each .rmd file.  this compressed file contains files in four directories: figures: code for figures 1-10 within the manuscript in .rmd file format  tables: code for tables: 2, 3, A1, A2, and A3 within the manuscript and Appendix 1 in .rmd file format models: causal and predictive models in .rmd file format. rds_files: data files to support the code listed above, and the raw data file: all_river_ef_dat. All are in .rds file format, and all are targeted by relative directories from within the figure, table, and model .rmd files. Data files are in the subdirectories for convenience: causal_desc_rds contains data files to support the causal model code, kfold_rds contains output used for model comparison, and pred_fit contains saved model fits as an alternative to running the code, which in some cases may take a very long time.