Remnant salmon life history diversity rediscovered in a highly compressed habitat

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under rapidly changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life history still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There currently is a concerted effort to protect federally listed spring run populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River system. To understand t..., Samples were collected through three main sampling efforts, a hook-and-line survey, an acoustic telemetry project, and a carcass survey, conducted by the RMT between the years 2009-2011 as part of their annual surveys to characterize Chinook salmon migration up the Yuba River to the spawning reaches. For the hook-and-line survey and acoustic telemetry effort, genetic samples were collected from all adult fish caught via hook-and-line sampling, targeting fish in the lowermost reaches from the confluence of the Yuba and Feather Rivers to DPD from May to October, 6 days a week during the years 2010-2011. Fin clips were collected from all captured fish (N=122), but only fish that were determined to be in “good condition” (showing no signs of disease or injury) were selected to be acoustically tagged as part of the acoustic tagging survey effort (N=42, we refer to these as the “acoustic tagging samples'' and those that were just fin clipped but not tagged as “hook-and-line survey samples'')...., , # Data from: Remnant salmon life history diversity rediscovered in a highly compressed habitat

[https://doi.org/10.5061/dryad.fj6q57436](https://doi.org/10.5061/dryad.fj6q57436)

This repository includes the raw data (genotype consensus calls, raw genotypes at each genetic position, and date of sampling in the different methods) for the publication 'Remnant salmon life history diversity rediscovered in a highly compressed habitat'.

## Description of the data and file structure

The dryad file Yuba_compiled.dryad.csv contains the genotypes and survey data for Chinook salmon (Oncorhynchus tshawytscha) collected in the Yuba River of California, USA during the year 2009-2011. Single Nucleotide Polymorphisms (SNPs) were called from fin clip DNA extracted and called using Fluidigm genotyping methods. Fin clip samples were collected during two efforts--hook and line sampling for acoustic surveys (in which some fish were then selected for acoustic tagging) and carcass surveys after fish spawn...