The story so far: an in situ pairing of chemical oceanography and physiology

Climate change is a pressing environmental concern, and understanding how abiotic variation contributes to population dynamics and persistence may ultimately predict the fates of species. Ocean acidification negatively impacts a range of species, including those using calcium carbonate for shell formation such as shellfish, which are important as ecosystem engineers and for food security. While much is known about carbonate chemistry and impacts of ocean acidification on the U.S. Pacific coast, there is limited regional information in British Columbia (BC), especially in socio-economically important coastal zones for aquaculture and migrating fisheries populations. Laboratory experimentation mimicking future climate scenarios provide valuable information on biological impacts under controlled conditions, but do not take into account the natural environmental fluctuations of coastal environments that may influence population persistence. This research program combines lower trophic level monitoring (plankton analysis), physiological responses (functional genomics of commercial bivalves) and high speed near real-time oceanographic monitoring at a field site in the northern Salish Sea, to provide information on system variability and its biological impacts on coastal ecosystems. Site abiotic variability will be discussed in the context of pre-industrial to current condition effects on species. Shellfish gene expression data will focus on population plasticity or microevolutionary adaptation to seasonal, optimal and sub-optimal calcium carbonate conditions over the short and long-term

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 (WGBS), we show that of hatchery and wild born adult Coho Salmon (Oncorhynchus kisutch) originating from two previously studied river systems, early-life hatchery rearing environment induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 co-expressed genes were down-regulated in parallel in hatchery born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpG displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 month spent in a common environment (i.e. the sea). Finally, the differentiation is observed in parallel in two different river system, highlighting the fact that early life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs

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

Abstract 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. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.</jats:p

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. We performed whole genome bisulfite sequencing (WGBS) on the sperm of genetically indistinguishable hatchery and wild born migrating adults of Coho salmon (Oncorhynchus kisutch) from two geographically distant rivers at different epigenome scales. Our results showed that coupling WGBS with fine scale analyses (local and chromosomal) allows the detection of parallel early‐life hatchery‐induced epimarks that differentiate wild from hatchery‐reared salmon. Four chromosomes and 183 differentially methylated regions (DMRs) displayed a significant signal of methylation differentiation between hatchery and wild born Coho salmon. Moreover, those early‐life epimarks persisted in germ‐line cells despite about 1.5 year spent in the ocean following release from hatchery, opening the possibility for transgenerational inheritance. Our results strengthen the hypothesis that epigenomic modifications environmentally‐induced during early‐life development persist in germ cells of adults until reproduction, which could potentially impact their fitness

Physiological responses coupled with plankton productivity and chemical oceanographic monitoring in a dynamic coastal BC environment.

Coastal margins are under increasing human-induced pressures including eutrophication and ocean acidification, which interact with natural environmental fluctuations in ways that can exacerbate calcium carbonate (CaCO3) mineral corrosivity. The temporal and spatial patterns of these pressures are in general very under-studied. Ocean acidification negatively impacts a range of species, especially those dependent on CaCO3 saturation states for shell formation like marine shellfish. Marine shellfish are socio-economically important as worldwide aquaculture organisms and bioindicator species, used for generating indicators of coastal health. The capacity for marine populations to adapt to these changes is unknown, and the loss of dominant coastal and estuarine organisms such as shellfish may significantly alter marine ecosystem structure and function, as well as threaten food security. This research combines lower trophic level monitoring (plankton analysis), physiological responses (functional genomics of multiple species of shellfish) and oceanographic monitoring at a field site in the northern Salish Sea in British Columbia (BC), Canada. This initial project is a novel pairing of these technologies in situ, and provides information on coastal variability and impacts on ecosystem productivity in a poorly sampled portion of the BC coastal margin. This work is currently ongoing, but preliminary results of gene expression studies of multiple commercial shellfish species and accompanying plankton work will be discussed. In addition linkages of the biological research to variability of coastal carbonate chemistry will be discussed, with a view to determining the impact of ocean acidification on the long-term health and productivity of coastal ecosystems in BC

Population structure of eulachon (<i>Thaleichthys pacificus</i>) from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

Eulachon (Thaleichthys pacificus), a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published restriction site-associated DNA sequencing (RADseq)-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1989 individuals from 14 populations ranging from Northern California through central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel and thus will be used in future mixed-stock analyses of eulachon to provide new insights for management and conservation of eulachon.</jats:p

Population structure of eulachon (Thaleichthys pacificus) from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

Eulachon (Thaleichthys pacificus), a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published restriction site-associated DNA sequencing (RADseq)-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1989 individuals from 14 populations ranging from Northern California through central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel and thus will be used in future mixed-stock analyses of eulachon to provide new insights for management and conservation of eulachon.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Population structure of eulachon<i>Thaleichthys pacificus</i>from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

ABSTRACTEulachonThaleichthys pacificus, a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published RADseq-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1,989 individuals from 14 populations ranging from Northern California through Central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations, and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel, and thus will be used in future mixed-stock analyses of eulachon in order to provide new insights for management and conservation of eulachon.</jats:p