Ben J G Sutherland

Sutherland Bioinformatics

Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, around 65 million years ago, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but...

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self‐sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery‐farmed) or naturalized/wild oysters to move onto a farm (na...

Temperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind‐driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO2 (pCO2) and its associated microbial communities to the surface. Anecdotally, these events impac...

The harbour seal Phoca vitulina is a marine mammal predator with potentially significant ecological impacts. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean, and P. v. concolor in the Atlantic. Across the coastal ranges of the harbour seal, strong natal philopatry results in fine-scale genetic structure and isolation-by-...

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic di...

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive output, founder effects, and rapid genetic drift. However, it is important to consider for retaining adaptive potential and avoiding inbreeding depression, particularly in species with high mutational load. To support management of...

Pacific oysters (Magallana gigas, also known as Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. Consequently, for three weeks, we exposed early-developm...

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic di...

Clam gardens traditionally established and maintained by coastal Indigenous Peoples of northwest North America are habitat modifications that enhance intertidal clam productivity and therefore provide secure and reliable local food resources. In this study, transcriptomic and phenotypic responses of Pacific littleneck clams ( Leukoma staminea ) wer...

Genetic stock identification (GSI) and parentage-based tagging (PBT) are being increasingly applied to salmon fisheries and hatchery broodstock management and assessment in Canada. GSI and PBT with single nucleotide polymorphisms (SNPs) were applied in assessment of 2020 Chinook salmon fisheries and hatchery broodstocks in British Columbia (BC), Ca...

Variation among populations in life history and intrinsic population characteristics (i.e., population diversity) helps maintain resilience to environmental change and dampen interannual variability in ecosystem services. As a result, ecological variation, and the processes that generate it, are considered central to strategies for managing risks t...

Genetic stock identification (GSI) from genotyping‐by‐sequencing of single nucleotide polymorphism (SNP) loci has become the gold standard for stock of origin identification in Pacific salmon. The sequencing platforms currently applied require large batch sizes and multiday processing in specialized facilities to perform genotyping by the thousands...

Temperate coastal marine waters are often thermally stratified from spring through fall, but can be dynamic and disrupted by tidal currents and wind-driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO 2 (pCO 2 ), and its associated microbial communities to the surface. Anecdotally, there have be...

Genetic stock identification (GSI) and parentage-based tagging (PBT) are being increasingly applied to salmon fisheries and hatchery broodstock management and assessment in Canada. GSI and PBT were applied to assessment of 2019 coho salmon fisheries and hatchery broodstocks in British Columbia (BC), Canada, with 8208 individuals successfully genoty...

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilitie...

Abstract Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies hav...

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline c...

When barriers to migration are removed, anadromous fishes from other rivers may colonize accessible habitat, or landlocked forms of the species may resume anadromy if conditions allow. For example, two large hydroelectric dams on the Elwha River, in Washington, USA, were removed, between 2011 and 2014, to restore Pacific salmon populations after a...

Re: Facets-2020-0025 The title of the paper was published incorrectly. The correct title of the paper is Comparing metabarcoding and morphological approaches to identify phytoplankton taxa associated with harmful algal blooms The article has been corrected accordingly. The publisher apologizes for this error.

Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report in Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), and metabarcoding with multiple marke...

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 RADseq-derived markers to construct an...

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal...

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes....

Direct DNA sequencing is powering a revolution in the application of genetics to resource management, with parentage-based tagging (PBT) increasingly applied to salmon fisheries and hatchery broodstock management and assessment. Genetic stock identification (GSI) and PBT were applied to assessment of 2018 coho salmon ocean fisheries and hatchery br...

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 RADseq-derived markers to construct a...

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal...

Pacific oyster Crassostrea gigas , endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). The oyster aquaculture industry depends on commercially available seed (hatchery-farmed) or naturalized oysters that can be moved onto a farm (naturalized-farmed),...

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes....

Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report in Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), and metabarcoding with multiple marke...

Environmental DNA (eDNA) detection is a revolutionary approach that aims to determine the presence of organisms, and other population parameters, by extracting the genetic material released from living and dead organisms in environmental samples, such as water. The rapid development of tools and technologies associated with eDNA has generated an un...

Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to chara...

This protocol comes with no guarantees, and is primarily used for the authors’ purposes. This protocol is an adaptation from the work in the following publications: Mascher M, Wu S, Amand PS, Stein N, Poland J (2013) Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ord...

Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the paleopolyploid salmonid Brook Charr Salvelinus font...

This protocol comes with no guarantees, and is primarily used for the authors’ purposes. This protocol is an adaptation from the work in the following publications: Mascher M, Wu S, Amand PS, Stein N, Poland J (2013) Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ord...

Ararose (1%) gel electrophoresis for genomic DNA quality checking. This protocol comes with no guarantees from the authors.

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for loca...

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for loca...

Background: Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress to death. The microsporidian Facilispora margolisi infects the Pacific salmon louse (Lepeophtheirus salmonis oncorhynchi), an eco...

Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous man...

Salmon lice (Lepeophtheirus salmonis) are important ectoparasites of wild and farmed salmonids and cause major losses to the salmon farming industry throughout the Northern Hemisphere. With the emergence of resistance to several commonly used parasiticides, novel control strategies and integra- tion of multiple treatment options are needed, includi...

Whole genome duplication can have large impacts on genome evolution. However, much remains unknown about these impacts, such as the mechanisms of coping with a duplicated sex determination system, which may result in increased sex determination mechanism diversity. Sexual conflict (i.e. alleles having different optimums in each sex) can result in s...

Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and...

Background Outcomes of infections with the salmon louse Lepeophtheirus salmonis vary considerably among its natural hosts (Salmo, Oncorhynchus spp.). Host-parasite interactions range from weak to strong host responses accompanied by high to low parasite abundances, respectively. Parasite behavioral studies indicate that the louse prefers the host A...

Using massively parallel sequencing data from two species with different life history traits-American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus)-we highlighted how an unbalanced sex ratio in the samples combined with a few sex-linked markers may lead to false interpretations of population structure and thus to potentially err...

Background: Salmon lice, Lepeophtheirus salmonis (Copepoda: Caligidae), are highly important ectoparasites of farmed and wild salmonids, and cause multi-million dollar losses to the salmon aquaculture industry annually. Salmon lice display extensive sexual dimorphism in ontogeny, morphology, physiology, behavior, and more. Therefore, the identific...

Whole genome duplication (WGD) can provide material for evolutionary innovation. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species, but can res...

Sockeye Salmon are an iconic species widely distributed throughout the North Pacific. A devastating pathogen of Sockeye Salmon is infectious hematopoietic necrosis virus (IHNV, genus Novirhabdovirus, family Rhabdoviridae). It has been postulated that IHNV is maintained in salmon populations by persisting over the life of its host and/or by residing...