Limited inbreeding avoidance at the gamete level despite inbreeding depression in Atlantic salmon (Salmo salar).

Inbreeding and the associated increase in homozygosity and potential accumulation of deleterious alleles may reduce fitness in a process known as inbreeding depression. Mechanisms to mitigate reproduction between close relatives, ranging from pre-mating mate choice to post-mating gamete selection, have evolved across taxa. In external fertilisers like Atlantic salmon (Salmo salar), where females have limited control over paternity, mechanisms of inbreeding avoidance can be expected to evolve at the gamete level.

Genetic Recovery of Two Wild Seatrout Populations Following Long-Term Stocking With Non-Native Conspecifics.

Predicting the long-term impact of releases and introgression from non-native strains into wild populations remains an important conservation issue, particularly in fishes where stocking and aquaculture escapes have led to widespread genetic admixture between wild and cultured conspecifics. Here, we investigated the genetic response of two wild sea trout, Salmo trutta L., populations following long-term stocking programmes with non-native conspecifics.

Validating Atlantic salmon (Salmo Salar) scale reading by genetic parent assignment and PIT-tagging.

Understanding changes in abundance and survival in Atlantic salmon populations requires knowledge of growth rates and age. Salmon are typically aged through scale reading, but such estimates are rarely validated against age-verified fish from the wild. Here, we present a unique dataset of scales from 254 PIT-tagged Atlantic salmon with known sea-age.

Genomic Landscape of Divergence in Ballan Wrasse (Labrus bergylta).

The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric colour morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-level reference genome and thereafter investigated genomic divergence among 152 individuals including both morphs, from two localities in Spain and Norway each and one in France.

Haemoglobin revisited: delineating population structure with the world's first molecular genetic marker used in fisheries research.

When haemoglobin genotyping was implemented in the early 1960s to investigate population genetic structure in Atlantic cod (), it became one of the first molecular genetic markers deployed in fisheries research worldwide. However, its suitability was questioned due to its potential for selection. While the issue of neutrality concerned the first population geneticists, markers under selection are now routinely used to study population genetic structure.

Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish.

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e.

Chromosomal aberrations and early mortality in a non-mammalian vertebrate: example from pressure-induced triploid Atlantic salmon.

In commercial aquaculture, the production of triploid fish is currently the most practical approach to prevent maturation and farm-to-wild introgression following escapes. However, triploids often exhibit poor welfare, and the underlying mechanisms remain unclear. Inheritance issues associated with sub-optimal hydrostatic pressure treatments used to induce triploidy, or the genetic background of parental fish, have been speculated to contribute.

A genetic method to infer ploidy and aberrant inheritance in triploid organisms.

Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce 'failed triploids' displaying diploidy, aneuploidy and aberrant inheritance.

Introgression affects juvenile life-history traits generations after stocking with non-native strains.

Introgression of non-native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long-term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout (, L.

Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing.

Most of the escaped farmed salmon entering a river during a 5-year period were infected with one or more viruses.

Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses.

DNA and scale reading to identify repeat spawning in Atlantic salmon: Unique insights into patterns of iteroparity.

Iteroparity represents an important but often overlooked component of life history in anadromous Atlantic salmon. Here, we combined individual DNA profiling and scale reading to identify repeat spawners among ~8000 adult salmon captured in a fish trap in the river Etne, Norway, in the period 2015-2019. Additionally, 171 outward migrating kelts were captured in the spring of 2018-2020 and identified using molecular methods to estimate weight loss since ascending the river to spawn.

Pre-fertilization gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic salmon ().

The environment gametes perform in just before fertilization is increasingly recognized to affect offspring fitness, yet the contributions of male and female gametes and their adaptive significance remain largely unexplored. Here, we investigated gametic thermal plasticity and its effects on hatching success and embryo performance in Atlantic salmon (). Eggs and sperm were incubated overnight at 2°C or 8°C, temperatures within the optimal thermal range of this species.

Aquaculture-driven evolution of the salmon louse mtDNA genome.

Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000-2002 "pre-resistance") and contemporary (2014-2017 "post-resistance") samples.

Overruled by nature: A plastic response to environmental change disconnects a gene and its trait.

In Atlantic salmon, age at maturation is a life history trait governed by a sex-specific trade-off between reproductive success and survival. Following environmental changes across large areas of the Northeast Atlantic, many populations currently display smaller size at age and higher age at maturation. However, whether these changes reflect rapid evolution or plasticity is unknown.

Global, regional, and cryptic population structure in a high gene-flow transatlantic fish.

Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations.

Geographic variation in gene flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod ( L.).

Identifying how physical and biotic factors shape genetic connectivity among populations in time and space is essential to our understanding of the evolutionary trajectory as well as the management of marine species. Atlantic cod is a widespread and commercially important marine species displaying several ecotypes with different life history strategies. Using three sets of SNPs: neutral, informative, and genome-inversion linked, we studied population genetic structure of ~2500 coastal Atlantic cod (CC) from 40 locations along Norway's 2500 km coastline, including nine fjords.

Introgression of domesticated salmon changes life history and phenology of a wild salmon population.

The release of domesticated conspecifics into the natural environment, whether deliberate or accidental, has the potential to alter the genetic integrity and evolutionary trajectory of wild populations. This widespread challenge is of particular concern for wild Atlantic salmon. By investigating phenotypic differences between the offspring of domesticated, hybrid, and wild Atlantic salmon released into the natural environment, earlier studies have documented the short-term consequences of introgression from domesticated fish into wild salmon populations.

Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon ( L.).

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits.

The salmon louse genome: Copepod features and parasitic adaptations.

Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish.

Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run.

Background: In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region.

The potential for cleaner fish-driven evolution in the salmon louse : Genetic or environmental control of pigmentation?

The parasitic salmon louse represents one of the biggest challenges to environmentally sustainable salmonid aquaculture across the globe. This species also displays a high evolutionary potential, as demonstrated by its rapid development of resistance to delousing chemicals. In response, farms now use a range of non-chemical delousing methods, including cleaner fish that eat lice from salmon.