Genetic Considerations for Sourcing Steelhead Reintroductions: Investigating Possibilities for the San Joaquin River

Steelhead trout (Oncorhynchus mykiss) historically occurred in all major watersheds along the west coast of the United States. They can be a vital part of a healthy riverine ecosystem, are highly valued for fishing, and have been greatly affected by human activities. Given these traits, and that the San Joaquin River in the Central Valley of California is under consideration for steelhead reintroduction, emphasis has recently been placed on conservation efforts to reintroduce steelhead into streams in which they were once native. There are many issues to consider when deciding how, where, and in what manner to reintroduce steelhead, including genetic considerations. One primary factor is determining the source population for reintroduction. In this paper, we consider the many important genetic aspects to consider when determining the source for steelhead reintroduction, and outline the genetic data needs when determining sources for reintroduction. We discuss the lessons learned from previous reintroductions in relation to a reintroduction scenario in the San Joaquin River, and recommend potential source populations

Genetic Considerations for Sourcing Steelhead Reintroductions: Investigating Possibilities for the San Joaquin River

Steelhead trout (Oncorhynchus mykiss) historically occurred in all major watersheds along the west coast of the United States. They can be a vital part of a healthy riverine ecosystem, are highly valued for fishing, and have been greatly affected by human activities. Given these traits, and that the San Joaquin River in the Central Valley of California is under consideration for steelhead reintroduction, emphasis has recently been placed on conservation efforts to reintroduce steelhead into streams in which they were once native. There are many issues to consider when deciding how, where, and in what manner to reintroduce steelhead, including genetic considerations. One primary factor is determining the source population for reintroduction. In this paper, we consider the many important genetic aspects to consider when determining the source for steelhead reintroduction, and outline the genetic data needs when determining sources for reintroduction. We discuss the lessons learned from previous reintroductions in relation to a reintroduction scenario in the San Joaquin River, and recommend potential source populations

Meek_et_al_EandE_Seq_Count_data

File contains the sequence counts for each individual in the RAD-seq study at each SNP locus, showing the counts for both allele 1 and allele 2, separated by a comma

Meek_et_al_EandE_Sequence_Data

File contains the sequences for the 24,198 SNP loci discovered. Sequence names are followed by "_1" or "_2" to denote the two different alleles of the same locus

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="fielddata.csv">fielddata.csv</a> (MD5: 2f2331b6bc827cf6a99dda99e3699b22)</p> <p><a href="genotypedata.csv">genotypedata.csv</a> (MD5: 448e3586babd9a48ea52357e214d9df5)</p> </div><h2>Description</h2><div> <p>This data set includes genotypes for 5000 chinook salmon individuals collected from throughout California's Central Valley between 1998–2013. We genotyped these samples using a panel of 96 single nucleotide polymorphism (SNP) markers. This is the most comprehensive, published genetic characterization to date across all of the California Central Valley Evolutionary Significant Units (ESUs) and includes all major river drainages within each ESU (total of 17 rivers and 5 hatchery populations). These populations are the foci of considerable basic and applied scientific research given the ecological, economic, and cultural importance of salmonid species. Moreover, all Central Valley ESUs are listed as either federally threatened, endangered, or species of concern. This data set improves our ability to study basic ecological questions about salmonid biology, including testing hypotheses about population structure, genetic diversity, introgression between ESUs, and levels of gene flow among populations. Additionally, it provides a baseline to test for changes in genetic diversity due to anthropogenic and natural environmental change. For conducting individual genetic assignment testing, the data set will serve as a baseline to allow identification of future unknown samples, such as juveniles, which are not easily identified and often mix on rearing grounds, allowing us to better study migration patterns and understand fitness and survivorship. Given that many of these loci are employed by chinook researchers across the species’ range, this data set will be useful to researchers studying chinook salmon at both broad and local (Central Valley specific) scales. We hope that publication of this data set will encourage others to build upon it and share similar salmonid data sets from other regions, increasing our understanding of salmonid ecology and improving our ability to sustainably manage and restore these important species. </p> <p> <i>Key words</i>: <i>California; Central Valley; chinook salmon; single nucleotide polymorphisms; genetic diversity.</i> </p> </div

Meek_et_al_EandE_LocusMapNamesAndSequence

File contains the Sequence ID and corresponding Map ID for loci used in the linkage map. The sequence provided is for one of the two alleles at each locus

Meek_et_al_EandE_LocusMapNamesAndSequence

File contains the Sequence ID and corresponding Map ID for loci used in the linkage map. The sequence provided is for one of the two alleles at each locus