Dataset DOI: 10.5061/dryad.zs7h44jq2

This README was generated on 2026-06-01 by K. Arai.

Author (Name, Institution, Email):
K. Arai, University of California Davis, kohmaarai@gmail.com

This README is in reference to the data sets and R codes (.Rmd) needed to recreate the figures and analyses in “Thermal bottlenecks constrain early-life survival of native fish in regulated rivers”, submitted by K. Arai.

There are four primary analyses in this manuscript:

1. Mapping historical and current habitats.
   The script 01_map_2026-05-07.Rmd generates maps of historical and contemporary habitat availability for Central Valley winter-run Chinook salmon in the Sacramento River and visualizes the spatial and temporal distribution of salmon redds overlaid on 2D water temperature contours.
2. Reconstructing pre-emergence temperatures.
   The script 02_otolith_temp_2026-05-07.Rmd reconstructs pre-emergence temperatures for juvenile Chinook salmon using SIMS-derived otolith δ¹⁸O measurements.
3. Predicting natal redd origin.
   The script 03_redd_probability_2026-05-07.Rmd estimates the probability of redd origin for juvenile survivors based on hatch dates and reconstructed pre-emergence temperatures.
4. Identifying the critical thermal window.
   The script 04_critical_window_2026-05-07.Rmd uses a moving-window generalized linear model (GLM) approach to identify the life stage most sensitive to thermal stress.

Additional code and data for supplementary analyses are not included here to maintain clarity and manage file size, but are available upon reasonable request.

Description of the data and file structure

Data list:

1. map_objects_2025-11-19.rds
2. temp_raft_interpolate_2025-11-19.csv
3. redd_distribution_2025-11-19.csv
4. WR_water_data_2025-02-12.csv
5. sims_d18O_2025-11-19.csv
6. fractionation_equation_data_2025-09-10.csv
7. sac_mainstem_sf_2025-11-21.rds
8. spatial_redds_2025-11-24.rds
9. spatial_redds_temp_time_2025-11-24.rds
10. hatch_data _2025-11-19.csv

Script list:

1. 01_map_2026-05-07.Rmd
2. 02_otolith_temp_2026-05-07.Rmd
3. 03_redd_probability_2026-05-07.Rmd
4. 04_critical_window_2026-05-07.Rmd

Map objects for generating Central Valley winter-run Chinook salmon habitat maps in the Sacramento River (map_objects_2025-11-19.rds)

This list contains all spatial data used to generate Figure 1 and related mapping outputs in the manuscript. It includes sf (simple features) objects representing contemporary and historical stream networks, key point locations, and supporting geographic layers. Missing or unavailable values are indicated by NA.

1. Contents:

stream_main: Simple feature collection of the mainstem Sacramento River.

stream_hist: Simple feature collection representing the historical distribution of winter-run Chinook salmon in the Sacramento River.

stream_current: Simple feature collection representing the current distribution of winter-run Chinook salmon in the Sacramento River.

lakes: Simple feature collection of lakes in California.

terrain: Data frame containing California terrain elevation data used for background shading.

red_bluff: Simple feature point representing the juvenile winter-run Chinook salmon collection site at the Red Bluff rotary screw trap.

keswick: Simple feature point representing the location of Keswick Dam.

shasta: Simple feature point representing the location of Shasta Dam.

Interpolated water temperature data for the Sacramento River from the RAFT model (temp_raft_interpolate_2025-11-19.csv)

This dataset contains daily interpolated water temperatures along the Sacramento River generated using the RAFT model. Missing or unavailable values are indicated by NA.

1. Number of variables: 5
2. Number of cases/rows: 38400
3. Variables:

date: Calendar date.

Distance_Below_Keswick_km: Distance below Keswick Dam (km).

temp: Water temperature (°C).

year: Calendar year.

plot_date: Date formatted for visualization.

Spatiotemporal distribution of winter-run Chinook salmon redds from aerial survey (redd_distribution_2025-11-19.csv)

This dataset contains the spatiotemporal distribution data of winter-run Chinook salmon redds from the aerial redd survey. Missing or unavailable values are indicated by NA.

1. Number of variables: 4
2. Number of cases/rows: 169
3. Variables:

year: Year of observation.

Redd_Obs: Redd observation date.

Distance_Below_Keswick_km: Location of the redd measured as the distance downstream from Keswick Dam (km).

n: Number of redds observed at the same spatiotemporal point.

Water stable oxygen isotope data from Sacramento River (WR_water_data_2025-02-12.csv)

This dataset contains the water stable oxygen isotope values measured in the Sacramento River. Missing or unavailable values are indicated by NA.

1. Number of variables: 14
2. Number of cases/rows: 113
3. Variables:

LabID: Unique laboratory identifier.

Sample_ID: Collection site identifier.

Type: Sample type (surface or subsurface collection).

Date. Water collection date.

Year: Collection year.

Month: Collection month.

d18O_w_vpdb: δ¹⁸O of water (VPDB scale).

d18O_w_vsmow: δ¹⁸O of water (VSMOW scale).

Comment: Notes or comments (all NA).

Lat: Latitude of the collection site.

Long: Longitude of the collection site.

Location: Name of the collection site.

Temperature_C: Water temperature (°C).

Salinity: Salinity.

SIMS otolith stable oxygen isotope data for winter-run juvenile Chinook salmon (sims_d18O_2025-11-19.csv)

This dataset contains otolith stable oxygen isotope (δ¹⁸O) measurements from juvenile winter-run Chinook salmon using secondary ion mass spectrometry (SIMS). Missing or unavailable values are indicated by NA.

1. Number of variables: 24
2. Number of cases/rows: 1213
3. Variables:

date_session: SIMS session identifier.

date: Date δ¹⁸O measurement was made.

analysis Type of δ¹⁸O measurement (line or cluster).

puck: SIMS puck identifier.

fish_id_short: Unique fish identifier.

spot_seq. SIMS spot sequence number.

X_coord: X coordinate of the SIMS measurement spot.

Y_coord: Y coordinate of the SIMS measurement spot.

d18O_vsmow_final: Final otolith δ¹⁸O (VSMOW scale).

d18O_vsmow_final_2se: Two standard errors associated with the otolith δ¹⁸O measurement.

distance_from_core: Standardized distance of the SIMS spot from the otolith core.

region: Otolith region where the SIMS spot was measured.

side: Otolith region where the SIMS spot was measured (dorsal or ventral).

hatch_um_dorsal: Location of the hatch check on the dorsal side of the otolith measured from the core (µm).

exog_um_dorsal: Location of the exogenous feeding check on the dorsal side of the otolith measured from the core (µm).

edge_um_dorsal: Otolith edge (dorsal side) measured from the core (µm).

hatch_um_ventral: Location of the hatch check on the ventral side of the otolith measured from the core (µm).

exog_um_ventral: Location of the exogenous feeding check on the ventral side of the otolith measured from the core (µm).

edge_um_ventral: Otolith edge (ventral side) measured from the core (µm).

collect_date: Collection date of the fish.

year: Collection year.

fork_length: Fork length (mm).

hatch date: Estimated hatch date from otolith microstructure.

exog_date: Estimated date of first exogenous feeding from otolith microstructure.

Temperature-dependent fractionation equation slope and intercept coefficient data (fractionation_equation_data_2025-09-10.csv)

This data contains the coefficient estimates of the fractionation equation slopes and intercepts of various fish species (including winter-run Chinook salmon). Missing or unavailable values are indicated by NA.

1. Number of variables: 19
2. Number of cases/rows: 11
3. Variables:

author: First author’s name from the original study.

year: Publication year of the study.

structure: Biological structure analyzed.

carbonate: Type of carbonate measured.

species_cap: Common name of species.

latin_name: Latin (scientific) name of the species.

life_stage: Life stage of the species.

analy_method: Instrumentation used for isotope analysis.

min_t: Minimum temperature of experiment (°C).

max_t: Maximum temperature of experiment (°C).

range: Temperature range of experiment (°C).

slope_1000lna: Estimated slope coefficient for the general fractionation equation.

slope_1000lna_se: Standard error of the slope estimate.

int_1000lna: Estimated intercept coefficient for the general fractionation equation.

int_1000lna_se: Standard error of the intercept estimate.

slope_d18O: Estimated slope coefficient for the fractionation equation based on the difference between carbonate and water δ¹⁸O values.

slope_d18O_se: Standard error of the slope estimate.

int_d18O: Estimated intercept coefficient for the fractionation equation based on the difference between carbonate and water δ¹⁸O values.

int_d18O_se: Standard error of the intercept estimate.

Spatial data of the mainstem Sacramento River (sac_mainstem_sf_2025-11-21.rds)

This dataset contains a simple feature collection of the mainstem Sacramento River. Missing or unavailable values are indicated by NA.

Observed winter-run Chinook salmon redd spatiotemporal data from aerial surveys (spatial_redds_2025-11-24.rds)

This dataset contains the observed spatiotemporal distribution of winter-run Chinook salmon redds collected from aerial surveys. Missing or unavailable values are indicated by NA.

1. Number of variables: 6
2. Number of cases/rows: 1045
3. Variables:

id: Unique redd identifier.

year: Year of redd observation.

Redd_Obs: Observation date of the redd.

Redd_Emerge_Date: Expected fish emergence date calculated using accumulated temperature units (ATU).

Distance_Below_Keswick_km: Location of the redd measured as the distance downstream from Keswick Dam (km).

geom: Spatial coordinates of the observed redd.

Daily experienced water temperatures for observed winter-run Chinook salmon redds (spatial_redds_temp_time_2025-11-24.rds)

This dataset contains the estimated daily water temperature experienced by individual observed redd. Missing or unavailable values are indicated by NA.

1. Number of variables: 10
2. Number of cases/rows: 94050
3. Variables:

id: Unique redd identifier.

year: Year of redd observation.

Redd_Obs: Redd observation date.

Redd_Emerge_Date: Expected fish emergence date calculated from accumulated temperature units (ATU).

Distance_Below_Keswick_km: Location of the redd measured as the distance downstream from Keswick Dam (km).

Days_pd: Days post redd observation.

Temperature: Estimated water temperature from the RAFT model (°C).

Temperature_sd: Standard deviation of the RAFT temperature estimate.

Date_pd: Calendar date corresponding to each day post-observation.

geom: Spatial coordinates of the observed redd.

Otolith microstructure data of juvenile winter-run Chinook salmon (hatch_data_2025-11-19.csv)

This dataset contains otolith microstructure-derived data for juvenile winter-run Chinook salmon collected in 2021 and 2022. Missing or unavailable values are indicated by NA.

1. Number of variables: 8
2. Number of cases/rows: 224
3. Variables:

Sample_ID: Unique fish identifier.

year: Year of sample collection.

collect_date: Date of sample collection.

hatch_date: Estimated hatch date based on otolith microstructure.

exog_date: Estimated date of first exogenous feeding.

fork_length: Fork length (mm).

abs_diff: Absolute difference in daily increment counts among readers.

cv: Coefficient of variation among age readers.

Code/Software

All analyses were conducted in R. The output assumes that the .Rmd scripts are placed in a scripts folder along with a data folder that contains the supplied data, a figures folder that is now empty but will contain output figures, and a outputs folder that is now empty but will contain outputs of the analyses. Please run the scripts in sequential order from 01 to 04.