Data from: Diversity under pressure: Long-term genetic decline in California’s Central Valley Chinook salmon ESA listed runs
Data files
Aug 05, 2026 version files 126.91 MB
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cv_juv_1kaln_cutoff.snp_panel.IBSonly.sites.ibs
126.91 MB
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README.md
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Abstract
Intraspecific diversity enables populations to persist under stochastic and extreme environmental conditions. One system that is representative of notable intraspecific diversity is Chinook salmon (Oncorhynchus tshawytscha) in the Central Valley of California, USA. It is the only place in the species range where four distinct migration timings (Winter, Spring, Fall, Late-fall) co-occur. These populations are declining, with Winter run listed as Endangered and Spring run as Threatened under the Endangered Species Act (ESA). To quantify temporal changes in genetic diversity of the different runs, we genotyped outmigrating juveniles using RAD-sequencing across 20+ years of annual sampling. Tajima's D revealed significant shifts in neutral genetic variation over time in Spring and Winter runs. Effective population size (Ne) declined in all listed populations, and the historical Ne estimates indicate severe plummets in genetic diversity 25-50 generations ago. Our results demonstrate how anthropogenic forces have eroded the genetic diversity of ESA listed Chinook salmon populations over the past century. Moreover, this study demonstrates how an organism with genetically-based life history variation (migration timing), traditionally advantageous under natural environmental variability, struggles to persist when faced with anthropogenically altered habitat and changing climate.
Dataset DOI: 10.5061/dryad.tht76hfdr
Description of the data and file structure
All Chinook salmon in the Central Valley of California, USA (CV) are spawned in tributaries to the Sacramento and San Joaquin Rivers and migrate out to the ocean as juveniles through the CV Delta, passing by Chipps Island. We utilized archived samples collected from Chipps Island during the juvenile outmigration over a twenty-year period (1996-2018) to evaluate intraspecific-level diversity in listed CV Chinook salmon (see Fig. 1 in the associated article). The subpopulations of interest are the Mill Creek, Deer Creek, and Butte Creek populations within the Spring run (Fig. 1). The outmigrating juvenile Chinook salmon collected for this study were sampled from the territories of Miwok, Patwin, Me-Wuk (Bay Miwok), and the Confederated Villages of Lisjan and the individuals collected were spawned across the Central Valley, which covers the territory of over 100 tribes (Native Land Digital).
To evaluate genetic diversity and effective population sizes in CV Spring and Winter run Chinook salmon over the last 20 years, we utilized data from a previously published study (Thompson et al. 2024). This dataset genetically sequenced approximately 622 Chinook salmon juveniles sampled while outmigrating past Chipps Island in the lower Sacramento River Delta (Fig. 1) using a RAD-sequencing protocol (Ali et al., 2016), then assigned each sample to one of the major demographic groups in the CV (Winter, Spring, Fall, and Late-Fall runs), as well as to subpopulations within the Spring-run (Mill/Deer Creek, and Butte Creek; Fig. 1). In total, 325 samples confidently assigned to the Spring-run (159 Mill/Deer and 166 Butte Creek) and 220 samples confidently assigned to the Winter run, and these samples were included in the current study.
Files and variables
File: cv_juv_1kaln_cutoff.snp_panel.IBSonly.sites.ibs
Description:
The first column is the chromosome, the second column is the position, the third column is the major allele, the fourth column is the minor allele, and the rest of the columns are the genotype likelihood data for each individual.
The allele calling samples a single allele instead of calling genotypes (it picks a single read at the position and takes the allele from that read). Nothing is homozygous or heterozygous, it's just a single allele. Effectively, it down samples everything to 1x at each position, which greatly reduces technical artifacts from differences in coverage (something that doesn't matter much in relatively high coverage data because genotype calls are all pretty good once you get a little over about 5x, but can matter a lot for low coverage data that have a lot of uncertainty in genotype calls).
1 corresponds to the major allele, 0 to the minor, and -1 to missing.
Code/software
Sequencing data alignment and initial processing is described in Thompson et al. (2024). Briefly, raw fastq files were mapped to the Chinook salmon reference genome (Otsh_v2.0; GCA_018296145.1; Christensen et al., 2018) with bwa-mem (Vasimuddin et al. 2019), and samtools (Danecek et al. 2021) was used to quality filter the mapped reads. Only reads that mapped uniquely, had mapping qualities > 30, base qualities > 30, properly-paired reads, and > 1,000 final aligned reads were retained. Thompson et al. (2024) identified a panel of single nucleotide polymorphisms (SNPs) present in at least 50% of samples from that study with minor allele frequencies > 0.05, and that panel of SNPs was used for analyses in this current study. We filtered the samples by missingness by population according to Supplemental Table 2 in Thompson et al. (2024). To get the most information from the 20 years of samples with varying quality, Thompson et al. (2024) called a single allele at each SNP locus instead of calling a genotype.