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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Article
  • Peer Reviewed
UC Merced Previously Published Works (2017)
    Cover page: Evolution of Ecological Niche Breadth
    • Article
    • Peer Reviewed
    San Francisco Estuary and Watershed Science, Volume 12, Issue 1 (2014)

    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.

      Cover page: Genetic Considerations for Sourcing Steelhead Reintroductions: Investigating Possibilities for the San Joaquin RiverCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      San Francisco Estuary and Watershed Science, Volume 12, Issue 2 (2014)

      Successful salmonid restoration efforts depend upon an understanding of the evolutionary processes that historically shaped population diversity, as well as the realities of currently available, altered river systems. Habitat alterations over the past century have dramatically changed the ecological forces that shaped salmonid speciation and evolution, bringing formerly separate and distinct populations into contact and in some cases leading to hybridization. Hybridization can threaten the genetic diversity within salmonid species and may affect the outcomes of restoration efforts. Here we use the San Joaquin River Restoration as a case study to discuss some of the genetic challenges of Chinook salmon restoration in a newly reopened habitat. We discuss a range of genetic management strategies—from passive reintroduction to tightly managed, active reintroduction—and the strengths and weaknesses of each approach.

       

        Cover page: Examining the Causes and Consequences of Hybridization During Chinook Salmon Reintroductions: Using the San Joaquin River as a Restoration Case Study of Management OptionsCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2016)
        Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well-chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site-associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.
          Cover page: Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2015)
          Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.
            Cover page: Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2022)
            The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions. To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.
              Cover page: Genomics facilitates evaluation and monitoring of McCloud River Redband Trout (Oncorhynchus mykiss stonei)
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