DOI: 10.5061/dryad.fj6q57436
title: Data from: Remnant salmon life history diversity rediscovered in a highly compressed habitat

description: 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 this diversity, we collected migration timing data and GREB1L
 genotypes from hook-and-line, acoustic tagging, and carcass surveys of
 Chinook salmon in the Yuba River between 2009-2011. Variation in the
 GREB1L region of the genome is tightly linked with run timing in Chinook
 salmon throughout the range, but the relationship between this variation
 and entry on spawning grounds is little explored in the Central Valley. We
 found that the date Chinook salmon crossed the lowest barrier to Yuba
 River spawning habitat (Daguerre Point Dam) was tightly correlated with
 their GREB1L genotype. Importantly, our study confirms that ESA-listed
 spring run Chinook salmon are spawning in the Yuba River, promoting a
 portfolio of life history and genetic diversity, despite spawning in a
 compressed habitat. This work highlights the need to identify and protect
 this life history diversity in heavily impacted systems to maintain
 healthy Chinook salmon metapopulations in those systems. Without this, we
 run the risk of losing the last vestiges of important variation.
description: 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''). The acoustic tagging samples were tagged with VEMCO
 V13-1L acoustic transmitters via esophageal/gastric insertion and were
 detected via two ultrasonic receivers located in the north and south side
 of the top of the fish ladder to detect fish successfully passing DPD from
 both sides (PSMFC,
 2011; VEMCO, 2010). The most upstream area was sampled via
 carcass surveys that occurred upstream of the DPD on a weekly basis during
 the years 2009-2010, starting 10-15 days after the first spawning redds
 were detected each year. Only fresh carcasses (possessing at least one
 clear eye and gills that are red or pink) were sampled to avoid sampling
 fish that had degraded DNA and had already been in the system for a long
 period of time. In 2009 and 2010, tissue samples were taken from carcasses
 throughout the river reach between the DPD and Englebright Dam.
 To genotypically assign run-type, we extracted DNA from fin clips
 using the DNeasy® Blood and Tissue extraction kit (Qiagen, Valencia, CA).
 We genotyped fish at a specific region of GREB1L previously shown to be
 the most highly associated with Chinook salmon run timing in Central
 Valley populations (Thompson et al 2020) by selecting five Single
 Nucleotide Polymorphisms (SNPs) across this region that had been
 identified as strongly associated with run timing in previous analyses
 (Koch
 and Narum, 2020; Thompson et al., 2020).
description: # 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 spawning. The dataset includes the date each sample was surveyed by their associated method (Sample Date) and then and additional date was recorded if any fish included in hook and line sampling was detected at a later point at the Daguerre Point Dam (DPD).  ## Abbreviations: YFO = Yuba Field Office MSU = Michigan State University DPD = Daguerre Point Dam EE = Early Early genotype for the associated SNP, or homozygous early EL = Early Late genotype for the associated SNP, or heterozygous LL = Late Late genotype for the associated SNP, or homozygous late ## Column names: SampleID = unique identifier for each individual fish GREB1L.call = overall consensus call for the 5 SNPs  Survey.Date = initial date of sampling in one of two categories--Hook.and.line or Carcass.sampling River.Mile = a measure of distance upriver from the mouth of a river, in this case, the Yuba River Floy.Tag = unique numeric number assigned to the floy tag, a tag used to identify the fish in the wild if re-sampled Fin.Clip.location = physical location where the fin piece used for genetic analysis is stored Hook.and.line = column indicating whether or not the sample was part of hook and line surveys, indicated with Y or N for yes or no DPD.Passage = column indicating whether or not the sample was detected passing the DPD, indicated with Y or N for yes or no Acoustic.ID = unique identifier for the acoustic tag implanted in individual fish, NA if the fish was not given an acoustic tag DPD.Passage.Date = date at which acoustically tagged fish (from the hook and line sampling method) were acoustically detected at the Daguerre Point Dam (DPD) Carcass.sampling = column indicating whether or not the sample was part of carcass surveys, indicated with Y or N for yes or no