DOI: 10.5061/dryad.0vt4b8h5c
title: Data from: Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population

description: Chinook salmon (Oncorhynchus tshawytscha) are ecologically, culturally and
 economically important across their native range. The once-abundant
 spring-run Chinook salmon in California have declined due to habitat loss
 and water diversions. Understanding the genetic composition and life
 history types being expressed in the few remaining populations is
 essential for their effective management and conservation. In this study
 we combined genetics and otolith (fish ear stone) biochronologies to
 describe the genotypic and phenotypic diversity of Chinook Salmon in the
 Yuba River, California, comparing cohorts that experienced a range of
 hydroclimatic conditions. Yuba River salmon have been heavily impacted by
 habitat loss and degradation, and large influxes of unmarked hatchery fish
 each year have led to concern about introgression and uncertainty around
 the viability of its wild populations, particularly the rarer spring-run
 salmon. Our study found that Yuba River origin fish represented on
 average, 42% of spawners across six return years with large interannual
 variability. The remaining spawners were primarily strays from the nearby
 Feather River hatchery, and since 2018, also from the Mokelumne River
 hatchery. Among the Yuba-origin spawners, on average, 30% exhibited the
 spring-run genotype. The Yuba-origin fish also displayed a variety of
 outmigration phenotypes that differed in the timing and size at which they
 left the natal river. Early-migrating fry dominated the returns and their
 contribution rates were negatively correlated with flow. It is unlikely
 that fry survival rates are elevated during droughts, suggesting that this
 trend reflects disproportionately poor survival of larger later migrating
 parr, smolts, and yearlings along the migratory corridor in drier years.
 Otolith daily increments indicated generally faster growth rates in
 non-natal habitats, emphasizing the importance of continuing upstream
 restoration efforts to improve in-river growing conditions. Together,
 these findings show that the Yuba River maintains intraspecific
 biodiversity that should be taken into account in future management,
 restoration and reintroduction plans. 
description: # Data from: **Integrating otolith and genetic tools to reveal
 intraspecific biodiversity in a highly impacted salmon population**
 [https://doi.org/10.5061/dryad.0vt4b8h5c](https://doi.org/10.5061/dryad.0vt4b8h5c) This dataset contains the raw data and scripts for the analyses performed in "**Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population."** ## 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` contains all figures and tables generated in this project. Files in the `outputs folder` will get overwritten with subsequent runs of the scripts and should thus not be edited manually. **Scripts** Scripts are numbered and need to be run in sequence to generate the output files used in subsequent scripts. `1_yuba_data_prep`: Data preparation, homogenization of variable types and names, and otolith strontium isotope data reduction. `2_age_validation`: Otolith and scale age validation from multiple readers. `3_natal_origin_prediction`: Strontium isotope based predictions of natal origins. `4_data_analysis`: The main script for the project including data analysis of genetic and phenotypic data. `5_growth_analysis`: Analysis of daily growth form otolith increments for a subset of the fish. `6_floy_tagged_fish`: Additional analysis of floy tagged fish with known return timings. `7_escapement_scaling`: Scaling of the proportional data from natal origins and genetics based on escapement estimates for the Yuba River. **Data files** `IsoFishR-master`: The data reduction script for the otolith laser-ablation strontium isotope data. This folder contains a copy of the IsofishR script (Willmes et al., 2018) and there are several subfolders. *Example **runfiles *contains a set of example strontium isotope runfiles from the Nu Plasma mass spectrometer of White Seabass and Chinook Salmon otoliths to try out the data reduction.  The *Projects* folder has an example project called Default which uses the example runfiles and the *Yuba_2022* project that has the reduced data for the Yuba River salmon. To open the project start the IsofishR script and select the Yuba Project in the analyze data tab. The *plots* subfolder contains the individual isotope profiles for each fish generated by the data reduction script (83Kr, 85Rb88Sr, totalSr, 87Sr86Sr_reduced, 87Sr86Sr_analyzed). To redo the entire data reduction choose the reduce data tab and use the provided runfiles. To use the current data reduction open the csv files in the *Data* subfolder. The output for the following scripts is the Yuba_2022_04_analyzed_data.csv file which contains all isotopes measured in long format. For further details on 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. `runfiles`: The original raw runfiles from the Neptune mass spectrometer. These files were produced by the NuPlasma MC-ICPMS and can be used as input to carry out data reduction for example in IsoFishR or other software (e.g., Iolite). `floy_tagged_fish_yuba`: An excel sheet that contains the information about the floy tagged fish on the Yuba River. `PhysicalSampleInventory20220720`: Fish data provided by the Yuba RMT. `rmis_agesize_data`: An export from the Regional Mark Information System (RMIS) database subset for Chinook salmon in California. This information is used to provide known ages for the tagged hatchery reared salmon for otolith annual age validations. See the Regional Mark Processing Center web page (https://www.rmpc.org/) and specifically the user guide (https://www.rmis.org/files/RMIS_UserGuide_V3.pdf) for detailed explanations of all variable names and units. Missing values are indicated by empty cells. `tsc_sr87sr86_run_notes_20220825`: The run notes associated with the laser-ablation data. Run notes are being generated by the operators of the laser-ablation mass spectrometer and contain comments about sample quality and reference materials. `yuba_annuli_20220822`: Annual age counts from otoliths. `scale_ages`: Annual age counts from scales. `Yuba_genetics`: Genetic data for the analyzed fish in this project. `Yuba_sturrock`: Data from the Yuba River reports from Sturrock et al. for the sample years 2009, 2010 and 2019. `waterisoscape`: The strontium isoscape for the Central Valley based on water samples and juvenile Chinook Salmon. `sac_wy`: Water Year classifications for the Sacramento River watershed by CDFW. `LYR_Annual Abundance Estimate`: Yuba River escapement estimates. `targeted_3_yo_from_2010`: Age 3 fish from 2010 targeted sampling. `RST_percent_fry_sac_index`: RST data for years available from RMT interim report with Sac water index. `yuba_growth_data`: Otolith growth increment data for a subset of Yuba River origin samples. ## Code/Software All scripts were written in R using R studio and all packages are cited in the text and script files.