Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.

The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems.

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%).

Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome.

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly.

Re-evaluating Coho salmon () conservation units in Canada using genomic data.

Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic data sets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection.

Strong Parallel Differential Gene Expression Induced by Hatchery Rearing Weakly Associated with Methylation Signals in Adult Coho Salmon (O. kisutch).

Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction.

Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon.

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range.

Correction: The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.

[This corrects the article DOI: 10.1371/journal.pone.

Chinook and Coho salmon hybrids linked to habitat and climatic changes on Vancouver Island, British Columbia.

Between 2013 and 2019, 63 presumed Chinook salmon sampled primarily in the Strait of Georgia (0.63% of total sample) were identified as potential Chinook-Coho () hybrids by the presence of anomalous microsatellite genotypes. Their hybrid origin was confirmed by single nucleotide polymorphism amplification of two species-specific amplicons.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle.

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years.

Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration.

Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human-induced genomic variation, human-induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations.

Correction: Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon.

[This corrects the article DOI: 10.1371/journal.pgen.

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.

Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes-the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes.

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon.

A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives.

Insights on the concept of indicator populations derived from parentage-based tagging in a large-scale coho salmon application in British Columbia, Canada.

For Pacific salmon, the key fisheries management goal in British Columbia (BC) is to maintain and restore healthy and diverse Pacific salmon populations, making conservation of salmon biodiversity the highest priority for resource management decision-making. Salmon status assessments are often conducted on coded-wire-tagged subsets of indicator populations based on assumptions of little differentiation within or among proximal populations. In the current study of southern BC coho salmon () populations, parentage-based tagging (PBT) analysis provided novel information on migration and life-history patterns to test the assumptions of biological homogeneity over limited (generally < 100 km) geographic distances and, potentially, to inform management of fisheries and hatchery broodstocks.

Variation in migration pattern, broodstock origin, and family productivity of coho salmon hatchery populations in British Columbia, Canada, derived from parentage-based tagging.

In salmonid parentage-based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently, progeny can be nonlethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e., age).

Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada.

Wild Pacific salmon, including Coho salmon , have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed.

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome.

When unifying genomic resources among studies and comparing data between species, there is often no better resource than a genome sequence. Having a reference genome for the Chinook salmon (Oncorhynchus tshawytscha) will enable the extensive genomic resources available for Pacific salmon, Atlantic salmon, and rainbow trout to be leveraged when asking questions related to the Chinook salmon. The Chinook salmon's wide distribution, long cultural impact, evolutionary history, substantial hatchery production, and recent wild-population decline make it an important research species.

Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon.

Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented.

Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages.

Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.

Harnessing the Power of Genomics to Secure the Future of Seafood.

Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration.

Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka).

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites.

Subtle population genetic structure in yelloweye rockfish (Sebastes ruberrimus) is consistent with a major oceanographic division in British Columbia, Canada.

The boundaries between oceanographic domains often function as dispersal barriers for many temperate marine species with a dispersive pelagic larval phase. Yelloweye rockfish (Sebastes ruberrimus, YR) are widely distributed across the northeastern Pacific Ocean, inhabiting coastal rocky reefs from the Aleutian Islands in Alaska through southern California. This species exhibits an extended pelagic larval duration and has the capacity for long distance larval transport.

Detection of quantitative trait loci (QTL) related to grilsing and late sexual maturation in Atlantic salmon (Salmo salar).

In Atlantic salmon aquaculture, early sexual maturation represents a major problem for producers. This is especially true for grilse, which mature after one sea winter before reaching a desirable harvest weight, rather than after two sea winters. Salmon maturing as grilse have a much lower market value than later maturing individuals.

Male nest site fidelity and female serial polyandry in lingcod (Ophiodon elongatus, Hexagrammidae).

Nest site fidelity and serial polyandry were examined in lingcod, Ophiodon elongatus, a teleost fish in which the nest-guarding male parent invests more heavily in parental care than the elusive female parent. Lingcod parental and progeny genotypes were established for fish spawning on a 200 m(2) section of Snake Island reef, British Columbia in two successive years to evaluate male and female mate choice (monogamy or polygamy) and nest site reuse by the same parents (nest site fidelity) and/or different parents (nest site affinity). Thirteen nests (egg masses) guarded by nine males and 14 nests guarded by seven males were observed in 2002 and 2003, respectively.