DOI: 10.5061/dryad.m905qfv9v
title: Data from: Early evidence for establishment of a Chinook salmon population in a restored watershed

description: As fish populations face compounding pressures under climate
 change, highly modified rivers are receiving increasing research and
 conservation attention as important sites for restoration. Across the
 North Pacific Ocean, Chinook salmon (Oncorhynchus tshawytscha) have
 experienced unprecedented declines and extirpations because of habitat
 loss and fragmentation and climate variability. Here, we studied a rare
 example of a novel salmon population developing in Putah Creek,
 California, a dam-controlled stream flowing through an area of intensive
 agriculture where salmon were unlikely to occur prior to the
 rehabilitation of a more natural flow regime. We used otoliths from adult
 Chinook salmon carcasses recovered from Putah Creek to determine river- or
 hatchery-of-origin for five spawning year classes. Our results provide
 evidence of successful salmon reproduction, outmigration survival, and
 natal homing of individuals back to Putah Creek in recent years. Although
 hatchery-origin fish that strayed to Putah Creek to spawn dominated
 returns each year, this study documents life cycle completion required for
 the potential development of a self-sustaining salmon population. This
 study demonstrates that targeted restoration and flow rehabilitation
 efforts can generate viable new salmon spawning habitat in dam-controlled
 river systems, which could help mitigate habitat lost to dams and
 developments. Further, successful anadromous life cycle completion can
 occur in new spawning habitat within the first several generations, which
 will help inform other efforts to restore or reintroduce salmon in altered
 river systems.
description: # Data from: Early evidence for establishment of a Chinook salmon
 population in a restored watershed ## Description of the data and file
 structure Files are in a single .zip file and need to be extracted. There
 is an R project file included and several subfolders that are referenced
 in the scripts. The `data folder` contains the raw data used for the
 analyses, the `scripts folder` contains the R scripts, and the `outputs
 folder` is empty but will be populated with subsequent runs of the
 scripts. ### **Scripts** All scripts were written in R using R studio and
 all packages are cited in the text and script files. Scripts are numbered
 and need to be run in sequence to generate the output files used in
 subsequent scripts. **01_putah_creek_oto**: Data preparation,
 homogenization of variable types and names, and fish length and weight
 analyses **02_putah_creek_data_reduction**: Otolith strontium isotope data
 reduction. This script makes use of the outputs from isofishR
 (PC_2017_2021_04_analyzed_data.csv) and performs a series of data
 reduction steps to prepare the data for further analyses.
 **03_TE_analyses**: Otolith trace element data reduction. This script
 makes use of the outputs from Iolite and performs a series of data
 reduction steps to prepare the data for further analyses.
 **04_natal_classification**: Stepwise natal classification of the otoliths
 using first strontium isotopes and then trace elements for any potential
 putah creek origin fish **05_data_analyses**: Data analyses and plotting
 for the manuscript. **Code/Software** All scripts were written in R using
 R studio and all packages are cited in the text and script files. ###
 **Data files** All .xlsx datafiles contain a readme sheet that describes
 the columns in detail. **PC_2017_2021_analyzed_data**: This csv file which
 contains all isotopes measured in otoliths in long format. The metadata
 for this file is called PC_2017_2021_04_analyzed_data_metadata. For
 further details on how the raw strontium isotope data was treated to
 create this file using the isofishR script see Willmes et al., 2018. 
 Willmes et al., 2018, "IsoFishR: An application for reproducible data
 reduction and analysis of strontium isotope ratios (87Sr/86Sr) obtained
 via laser-ablation MC-ICP-MS. PLOS One, 13,9.
 doi: 10.1371/journal.pone.0204519. **TE**: A folder containing the raw
 Trace Element data as well as the associated iolite projects and data
 exports. The individual iolite analytical sessions are stored as Project 1
 – Project 3. The resulting data follows the same format and is stored in
 the “timeseries” subfolder. Additional sample information is stored in
 putah_creek_trace_elements_run_notes_20230328.xlsx.
 **Flow_From_dam_78-17**: A data file of daily flow releases recorded by a
 flow gage from Putah Diversion Dam from 1978 through 2017, operated by
 Solano County Water Agency. This datafile was downloaded from the Zenodo
 open data repository
 ([https://zenodo.org/records/7822308](https://zenodo.org/records/7822308))
 associated with Jacinto et al. 2023
 ([https://doi.org/10.1002/eap.2868](https://doi.org/10.1002/eap.2868)). |
 **Column header** | **Description** | | :---------------- |
 :-------------------------------------------------------------------------------------------------------------------- | | Date | Date of flow release | | Month | Month of flow release | | Day | Day (of month) of flow release | | Day\_of\_year | Julian day (1-366) of flow release | | Year | Year of flow release | | Released\_cfs | Flow release measured in cubic feet per second | | Released\_cms | Flow release measured in cubic meters per second | | Accord status | Indicates whether this date is before or after the implementation of Putah Creek Accord (pre\_accord or post\_accord) | **Otolith_Inventory_2017-2021**: Fish data from the field collections of Chinook Salmon on Putah Creek 2017 - 2021. **PC_cwt_knownfish_2017_2018**: Data for Coded-Wire-Tagged fish from 2017 and 2018 which includes known ages and known natal origin. | **Column header** | **Description** | | :------------------------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Lab\_id | Unique identifier for each fish in study population | | Survey\_year | Year of fish collection | | sex | Sex of fish (Female or Male) | | FL\_mm | Fork length (FL) of fish in millimeters (measured from the tip of the snout to the fork of the tail) | | Grouped\_classification | Fish origin classification grouped from Classification and Regression Trees (CART) model. Origins abbreviations correspond to: MOH = Mokelumne River Hatchery, MEH = Merced River Hatchery, FRH = Feather River Hatchery, NIH = American River Nimbus Fish Hatchery, CNH = Coleman National Fish Hatchery | | Age | Age classification (in years), numeric | | Age\_f | Age classification (in years), factor | | Age\_f\_rev | Age classification (in years), factor, reversed factor levels (for plotting) | | Simplified\_classification | Simplified classification of each fish by natal origin: fish originating from hatcheries are classed as Hatchery-strays, fish originating from wild populations are classed as natural-origin, and unknown fish are classified as unknown. | | Simplified\_classification\_withputah | Simplified classification of each fish by natal origin (same as preceding column) but with the natural-origin classification split to distinguish wild-origin fish from Putah Creek versus from other rivers. | | Section\_alpha | Numeric code (A through F) corresponding to which segment of the river the fish carcass was recovered from | **PC_otolith_line_measurements**: Data file containing the laser-ablation and transect line measurements for all otolith samples. **PC_otolith_measurements_2017-2021**: Width and lengths measurements for whole otolith samples. **PC_otolith_weights**: Weights for whole otolith samples. **putah_willmes_etal2021**: Fish and strontium isotope data from Willmes et al., 2021 ([https://doi.org/10.1002/fsh.10516](https://doi.org/10.1002/fsh.10516)). | **Column Header** | **Description** | | :------------------------- | :---------------------------------------------------------------------------------------------------------------------- | | Run\_ID | Corresponding runfile name | | Sample\_type | Age class of individual (adult or juvenile) | | Capture\_date | Date of sample collection | | Section | Numeric code (A through F) corresponding to which segment of the river the fish carcass was recovered from | | Sex | Sex of fish (F = female, M = male, U = unknown) | | FL\_cm | Fork length (FL) of fish in millimeters (measured from the tip of the snout to the fork of the tail) | | CWT | California Department of Fish and Wildlife Coded Wire Tag identification number of a given fish (hatchery batch number) | | CWT\_release | Release location of the fish into the wild from the hatchery of origin (as determined by coded wire tag data) | | CWT\_hatchery\_location | Name of the hatchery of origin for a given fish (as determined by coded wire tag data) | | CWT\_age | Age of the fish in years (as determined by coded wire tag data) | | Age\_all | Age of the fish in years (determined either by coded wire tag data or by otolith annuli analysis) | | Known\_origin | Hatchery of origin for a given fish (as determined by coded wire tag data) | | Region\_mean | Mean strontium isotope ratio (87Sr/86Sr) for the specified region in the otolith (e.g. natal) | | Region\_sd | Standard deviation of the strontium isotope ratio (87Sr/86Sr) for the specified region in the otolith (e.g. natal) | | Grouped\_classification | Natal origin for a given fish | | Simplified\_classification | Classification of the natal origin for a given fish (e.g., hatchery-origin, unknown origin, wild-origin) | | AME | Probability that the natal origin of a given fish is the American River | | BAT | Probability that the natal origin of a given fish is Battle Creek | | BUT | Probability that the natal origin of a given fish is Butte Creek | | CNH | Probability that the natal origin of a given fish is the Coleman National Fish Hatchery | | DEE | Probability that the natal origin of a given fish is Deer Creek | | FEA | Probability that the natal origin of a given fish is the Feather River | | FRH | Probability that the natal origin of a given fish is the Feather River Hatchery | | MEH | Probability that the natal origin of a given fish is the Merced River Hatchery | | MER | Probability that the natal origin of a given fish is the Merced River | | MIL | Probability that the natal origin of a given fish is Mill Creek | | MOH | Probability that the natal origin of a given fish is the Mokelumne River Hatchery | | MOK | Probability that the natal origin of a given fish is the Mokelumne River | | NIH | Probability that the natal origin of a given fish is the American River Nimbus Fish Hatchery | | PUC | Probability that the natal origin of a given fish is Putah Creek | | SAC | Probability that the natal origin of a given fish is the mainstem Sacramento River | | STA | Probability that the natal origin of a given fish is the Stanislaus River | | THE | Probability that the natal origin of a given fish is the Thermalito Annex | | TUO | Probability that the natal origin of a given fish is the Tuolumne River | | YUB | Probability that the natal origin of a given fish is the Yuba River | **putahcreek_otolith_agescores**: Annual ages reconstructed from otoliths. This file includes the individual age estimates by reader as well as the final agreement age. **waterisoscape**: The strontium isoscape for the Central Valley based on water samples and juvenile Chinook Salmon. | **Column Header** | **Description** | | :---------------- | :-------------------------------------------------------------------------------------------------------------------------------- | | Site name | Name of water body | | Site | Alpha-code of site | | Site\_group | Grouped code for site | | SampleYear | Year of sample collection | | Sample | Description of sample (Water or juvenile Chinook Salmon) | | Sr8786\_rf | Reference proportion of Sr87/Sr86 isotopes in the water body | | Source | Source of data for Sr8786\_rf column | | Type | Category of water body (River or Hatchery) | | System | Alpha-code of the watershed system in which the site is located (SAC\_system = Sacramento River; SJQ\_system = San Joaquin River) | | Ordering | Ordering of Rivers based on location in the SAC and SJQ watershed | | Ordering\_boot | Ordering of Rivers based on location in the SAC and SJQ watershed for the bootstrapped dataset | | System\_type | Code combining the System and Type columns | | Comments | Comments on the location of the site |