Ian Bradbury

Fisheries and Oceans Canada | DFO · Northwest Atlantic Fisheries Centre

Estimating egg deposition for Atlantic salmon population assessments is made difficult by their lack of sexual dimorphism prior to the autumn spawning season. We quantified the effect of sex misclassification from subjective examination of external morphology on egg deposition estimates in four Atlantic salmon populations across multiple years. Sex...

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at‐risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlif...

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure an...

Aim In northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high-resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern sp...

Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hind...

Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and gene flow throughout life history challenges the characterization of dispersal pathways within a three-dimensional mari...

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) h...

The Committee on the Status of Endangered Wildlife in Canada (COSEWIC) recognizes 16 designatable units (DUs) of Atlantic Salmon (Salmo salar) with 15 of those DUs representing extant anadromous populations. Last assessed by COSEWIC in 2010, this species is currently up for reassessment. As a primary generator and archivist of data related to Atlan...

Polymorphic species are useful models for investigating the evolutionary processes driving diversification. Such processes include colonization history as well as contemporary selection, gene flow, and genetic drift, which can vary between intraspecific morphs as a function of their distinct life histories. The interactive and relative influence of...

Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and geneflow throughout life history challenges the characterization of dispersal pathways within a three-dimensional marin...

Farming of Atlantic salmon Salmo salar has resulted in highly domesticated individuals, with notable genetic and phenotypic differences from their wild counterparts. Understanding how interbreeding with aquaculture escapees affects wild, often at-risk populations is increasingly essential to conservation efforts. Here, we used an experimental relea...

Adaptation to ocean climate is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often...

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) h...

An understanding of genetic differences in fitness-related traits for farm, wild, and hybrid Atlantic salmon (Salmo salar) is key for predicting impacts of aquaculture escapes on wild populations. Here we used lipid and fatty acid (FA) analyses to investigate differences in storage and foraging ability among Atlantic salmon juveniles of three cross...

Selection due to multi-generational domestication and genetically distinct origins raise concerns about potential fitness consequences of hybridization between farmed and wild Atlantic salmon. In Newfoundland (NF), Canada, the aquaculture industry uses the North American (NA) Saint John River strain, though site-specific permission has been granted...

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are...

Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depends both on the degree of domestication and the original source of the domesticated population. Atlantic Salmon, Salmo salar, used in North American aqu...

The escape of domesticated Atlantic salmon Salmo salar from aquaculture facilities represents a continued threat to the genetic and demographic stability of wild salmon stocks. Escaped farm-origin salmon have been shown to hybridize with wild conspecifics, yet the long-term genetic impacts are generally unknown. Theoretically, life history variatio...

The escape of Atlantic salmon Salmo salar from aquaculture has been identified as a significant threat to the persistence and stability of wild salmon populations. Yet the magnitude of phenotypic impacts due to hybridization remains largely unresolved. We evaluated the phenotypic consequences of hybridization using geometric morphometrics both unde...

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmen...

Due to multi‐generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the gene...

The potentially significant genetic consequences associated with the loss of migratory capacity of diadromous fishes that have become landlocked in freshwater are poorly understood. Consistent selective pressures associated with freshwater residency may drive repeated differentiation both between allopatric landlocked and anadromous populations and...

Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and maste...

Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non‐model organisms. In Atlantic Salmon...

Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important rol...

Arctic charr Salvelinus alpinus are a commercially and culturally valued species for northern Indigenous peoples. Climate shifts could have important implications for charr and those that rely on them, but studies that evaluate responses to ecosystem change and the spatial scales at which they occur are rare. We compare marine-phase habitat use, lo...

It has long been clear that interbreeding between domesticated and wild Atlantic salmon can lead to negative fitness consequences for native populations. Few studies, however, have examined these consequences at critical early life stages, particularly in the context of distinct geographical and ancestral relationships among populations as well dom...

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population...

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (> 50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydros...

A Correction to this paper has been published: https://doi.org/10.1038/s41558-021-01023-8.

Significance Both theory and experiments suggest that fishing can drive the evolution of an earlier maturation age. However, determining whether changes in the wild are the result of fisheries-induced evolution has been difficult. Temporal, genome-wide datasets can directly reveal responses to selection. Here, we investigate the genomes of two wild...

Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the...

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and reduced representatio...

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four large supergenes have been identified and linked to migratory lifestyle and environmental adapt...

Despite widespread biodiversity losses, an understanding of how most taxa will respond to future climate change is lacking. Here we integrate genomics and environmental modelling to assess climate change responses in an ecologically and economically important Arctic species. Environmentally associated genomic diversity and machine learning are used...

When escapee farmed Atlantic salmon Salmo salar interbreed with wild fish, the introgression of maladaptive genes can lower wild population productivity and alter key life history traits. To date, only a few European studies have compared wild, farm, and hybrid salmon under common conditions in the wild, isolating the influence of genetics on survi...

The ICES Working Group on Application of Genetics in Fisheries and Aquaculture (WGAGFA) is composed of 51 members from 17 ICES Member States. There is a high level of commitment by the WGAGFA members to their group: During the WGAGFA cycle 2018 to 2020, the annual working group meetings were attended in average by 26 delegates from 11 ICES Member S...

Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of domestication has resulted in significant behavioural, morphological, and allelic differences from wild populations. Substantial evidence indicates that direct genetic interactions or interbreeding between wild and escaped farmed Atlantic salmon occurs...

The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an i...

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated i...

Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to...

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such quantifying diversity is central to combatting ongoing wide spread reductions in biodiversity. With the advent of next‐generation sequencing, several methods now exist for resolving fine‐scale population structure, but...

Abstract Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long‐term threats to wild populations, particularly if genetic interactions occur between wild and hatchery...

Abstract Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the...

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct cha...

Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recom-bination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) acro...

To develop more reliable marine species distribution models (SDMs), we examine how genetic, climatic, and biotic interaction gradients give rise to prediction error in marine SDM. Genetic lineages with distinct ecological requirements spanning genetic gradients have yet to be treated separately in marine SDM, which are often constrained to modeling...

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 YBP, with the two lineages isolated in different southern refugia during glacial maxima, driving trans‐Atlantic genomic and karyotypic divergence....

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net‐pen salmon aquaculture. Although domestic‐wild hybrid offspring have shown reduced fitness in lab and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to pred...

Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isola...

ABSTRACT: Genetic interactions (i.e. hybridization) between wild and escaped Atlantic salmon Salmo salar from aquaculture operations have been widely documented, yet the ability to incorporate predictions of risk into aquaculture siting advice has been limited. Here we demonstrate a model-based approach to assessing these potential genetic interact...

A hierarchical Bayesian life cycle model is presented that considers spatial covariation of marine life history traits of Atlantic salmon (Salmo salar) populations in the North Atlantic. The model is based on a collective analysis of the dynamics of 13 stock units (SUs) from two continental stock groups (CSGs) in North America and Southern Europe i...

A survey of the Kapisillit River system was conducted in 2005 and 2012 to study the only indigenous Atlantic salmon Salmo salar population in Greenland. Little is known about its characteristics or its relationship with other S. salar populations across the species range. Juvenile S. salar were captured in all stations surveyed within the lower riv...

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although...

Restriction‐site associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly varies between datasets and can be difficult and computationally expensive t...

Hybridization of escaped farmed Atlantic salmon Salmo salar with wild populations occurs throughout their native range and can threaten wild population stability and persistence. The extent of hybridization is often population-specific and can drive changes in phenotype and genotype. Current understanding of the forces that contribute to the spatia...

Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a...

Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreedi...

Hybridization between wild and escaped cultured Atlantic salmon (Salmo salar) can threaten the stability and persistence of locally adapted wild populations. Here we describe the development and validation of a genomic-based approach to quantify recent hybridization between escapee and wild salmon in the western Atlantic. Based on genome-wide singl...

Intraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variati...

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences...

Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genet...