Data from: Remnant salmon life history diversity rediscovered in a highly compressed habitat
Data files
May 10, 2024 version files 19.79 KB
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README.md
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Yuba_compiled_dryad.csv
Abstract
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.
README: Data from: Remnant salmon life history diversity rediscovered in a highly compressed habitat
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
Methods
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).