Early evidence for establishment of a Chinook salmon population in a restored watershed

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 s..., , , # 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...