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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 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 histories still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon 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. 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 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in Californias 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 the highly compressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems, to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can fill an unoccupied niche between real-time, inexpensive, but error-prone visual identification and more expensive or time-consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR-based SHERLOCK assays capable of rapidly (

The Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater Cutthroat Trout O. clarkii ssp. complex and is federally listed as threatened under the Endangered Species Act. However, genetic studies to date have revealed very little genetic differentiation between the PCT and its closest relative, the Lahontan Cutthroat Trout (LCT) O. clarkii henshawi. These results casted doubt on whether the PCT is a genetically distinct subspecies or merely a phenotypic variant of the LCT. Here, we present a genomic analysis of Cutthroat Trout subspecies and populations to resolve the genetic and phylogenetic relationship between PCT and LCT. Our results demonstrate substantial genetic structure and differentiation between PCT and LCT populations. In contrast to current thinking, our phylogenetic reconstructions show the PCT to be a distinct evolutionary lineage that diverged from LCT before the LCT differentiated into its current populations (i.e., rather than PCT divergence due to geographic isolation from an LCT population in the Carson River). We conclude that the PCT is genetically distinct from the LCT.

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring‐run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%–73%) of spawners across six return years (2009–2011, 2018–2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba‐origin spawners, on average, 30% (range 14%–50%) exhibited the spring‐run genotype. The Yuba‐origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early‐migrating fry dominated the returns (mean 59%, range 33%–89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non‐natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in‐river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring‐run are reproducing, surviving, and returning to the Yuba River every year suggests that re‐establishment of an independent population is possible, although hatchery‐wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience. [ABSTRACT FROM AUTHOR]

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.

Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture ( R: AD c APTURE: ). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.

Biocomplexity is an important mechanism for population resilience in changing environments. However, we are just beginning to understand how to identify biocomplexity so that species management efforts promote resilience and stability. Genomic techniques are emerging as an important method for identifying biocomplexity. Central Valley (CV) Chinook salmon are an example of a species at risk of extinction if better methods for identifying and protecting biocomplexity are not employed. To address this knowledge gap, we employed restriction site associated DNA sequencing to conduct the first genomic study of all major populations of CV Chinook salmon. We found greater population structure across the Central Valley than previously documented. Additionally, we show evidence for differentiation and adaptation within migratory phenotypes despite high levels of gene flow. We also determined that genomic data can vastly improve our ability to assign individuals to their natal populations, even as they mix during migration, a finding that will assist management practices. These results demonstrate how genomic study can greatly improve our ability to identify and conserve biocomplexity. La biocomplexite est un mecanisme important pour la resilience des populations dans des milieux changeants. Nous ne faisons toutefois que commencer a comprendre comment circonscrire la biocomplexite pour nous permettre de gerer les especes d'une maniere qui favorise leur resilience et leur stabilite. De nouvelles techniques de genomique constituent une approche importante pour circonscrire la biocomplexite. Le saumon quinnat de la vallee centrale (VC) est un exemple d'espece a risque de disparition en l'absence de meilleures methodes pour circonscrire et proteger sa biocomplexite. Afin de combler ces lacunes dans les connaissances, nous avons utilise le sequenqage d'ADN associe a des sites de restriction pour realiser la premiere etude genomique de toutes les grandes populations de saumons quinnat de la VC. Nous avons ainsi constate que les populations a la grandeur de la vallee centrale presentent une structure plus importante que ce qui avait deja ete rapporte. Nous presentons egalement des preuves de differentiation et d'adaptation au sein de phenotypes migratoires, et ce, malgre des niveaux eleves de flux genetique. En ce qui concerne les pratiques de gestion, nous constatons egalement que les donnees genomiques peuvent grandement ameliorer la capacite d'affecter les individus a leurs populations natales, meme s'ils se melangent durant la migration. Ces resultats demontrent comment l'approche genomique peut ameliorer considerablement la capacite de circonscrire et de conserver la biocomplexite. [Traduit par la Redaction], Introduction Biocomplexity reflects the amount of intraspecific diversity within and among populations and is important for the stability and resilience of metapopulations (Hilborn et al. 2003). Identifying the factors that [...]

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.

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.

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.

This article summarizes the Special Issue of Evolutionary Applications focused on "Advances in Salmonid Genetics." Contributions to this Special Issue were primarily presented at the Coastwide Salmonid Genetics Meeting, held in Boise, ID in June 2023, with a focus on Pacific salmonids of the west coast region of North America. Contributions from other regions of the globe are also included and further convey the importance of various salmonid species across the world. This Special Issue is comprised of 22 articles that together illustrate major advances in genetic and genomic tools to address fundamental and applied questions for natural populations of salmonids, ranging from mixed‐stock analyses, to conservation of genetic diversity, to adaptation to local environments. These studies provide valuable insight for molecular ecologists since salmonid systems offer a window into evolutionary applications that parallel conservation efforts relevant and applicable beyond salmonid species. Here, we provide an introduction and a synopsis of articles in this Special Issue, along with future directions in this field. We present this Special Issue in honor of Fred Utter, a founder and leader in the field of salmonid genetics, who passed away in 2023. [ABSTRACT FROM AUTHOR]

Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley (CV) historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of CV Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of CV Chinook salmon that allows inclusion of relatively low‐quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late‐fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in CV Chinook salmon, and demonstrates the power of genomics‐based population assignments to aid the study and management of intraspecific diversity. [ABSTRACT FROM AUTHOR]

Objective: Managers can modify river flow regimes using fish monitoring data to minimize impacts from water management infrastructure. For example, operation of the gate-controlled Delta Cross Channel (DCC) in California can negatively affect the endangered Sacramento River winter-run Chinook Salmon Oncorhynchus tshawytscha. Although guidelines have been developed for DCC operations by using real-time juvenile fish sampling count data, there is uncertainty about how environmental conditions influence fish occupancy and the extent to which those relationships are affected by sampling and identification error. Methods: We evaluated the effect of environmental conditions, imperfect detection, and misidentification error on salmon occupancy by analyzing data using hierarchical multistate occupancy models. A total of 14,147 trawl tows and beach seine hauls were conducted on 1058 sampling days between October and December from 1996 to 2019. During these surveys, 2803 juvenile winter-run Chinook Salmon were identified, and approximately 29% of the sampling days had at least one winter-run juvenile detected. Result: The probability of misidentifying an individual juvenile winter-run Chinook Salmon in the field was estimated to be 0.056 based on fish identification examinations and genetic sampling. Occupancy varied considerably and was related to flow characteristics, water clarity, weather, time of year, and whether occupancy was detected during the previous sampling day. However, these relationships and their significance changed considerably when accounting for imperfect detection and the probability of misidentifying individual juvenile salmon. Detection was <0.3 under average sampling conditions during a single sample and was influenced by flow, water clarity, site, and volume sampled. Conclusion: Our modeling results indicate that DCC gate closure decisions could occur on fewer days when imperfect detection and misidentification error are not accounted for. These findings demonstrate the need to account for identification and detection error while using monitoring data to assess factors influencing fish occupancy and inform future management decisions. [ABSTRACT FROM AUTHOR]

We characterized 10 new microsatellite markers in each of two species of hydromedusae, Maeotias marginata and Moerisia sp. Genetic diversity was estimated using 20–41 individuals collected from Suisun Marsh within the San Francisco Estuary, CA. Allelic richness ranged from 5–9 in M. marginata and 2–10 in Moerisia sp. with average expected heterozygosities of 0.71 and 0.57 respectively. One locus in M. marginata and two in Moerisia sp. deviated from Hardy–Weinberg equilibrium expectations, likely due to null alleles.

A rapid renewable energy transition has facilitated the development of large, ground‐mounted solar energy facilities worldwide. Deserts, and other sensitive aridland ecosystems, are the second most common land‐cover type for solar energy development globally. Thus, it is necessary to understand existing diversity within environmentally sensitive desert plant populations to understand spatiotemporal effects of solar energy siting and design. Overall, few population genomic studies of desert plants exist, and much of their biology is unknown. To help fill this knowledge gap, we sampled Mojave milkweed (Asclepias nyctaginifolia) in and around the Ivanpah Solar Electric Generating Station (ISEGS) in the Mojave Desert of California to understand the species' population structure, standing genetic variation, and how that intersects with solar development. We performed Restriction‐site Associated Sequencing (RADseq) and discovered 9942 single nucleotide polymorphisms (SNPs). Using these data, we found clear population structure over small spatial scales, suggesting each site sampled comprised a genetically distinct population of Mojave milkweed. While mowing, in lieu of blading, the vegetation across the solar energy facility's footprint prevented the immediate loss of the ISEGS Mojave milkweed population, we show that the effects of land‐cover change, especially those impacting desert washes, may impact long‐term genetic diversity and persistence. Potential implications of this include a risk of overall loss of genetic diversity, or even hastened extirpation. These findings highlight the need to consider the genetic diversity of impacted species when predicting the impact and necessary conservation measures of large‐scale land‐cover changes on species with small population sizes. [ABSTRACT FROM AUTHOR]

Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species' trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world. [ABSTRACT FROM AUTHOR]