Publications
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Brieuc, Marine Servane Ono; Besnier, Francois; Harvey, Alison C.; Andersen-Fjeldheim, Per Tommy; Andersen-Fjeldheim, Kaja Christine & Wennevik, Vidar
[Show all 14 contributors for this article]
(2026).
No significant change in domestication-admixture during the marine phase of an Atlantic salmon population.
Communications Biology.
9(1).
doi:
10.1038/s42003-026-10051-z.
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Domesticated organisms have been pivotal in food-production and human evolution. Yet, interbreeding between domesticated and wild conspecifics may have significant negative impacts on native populations. Atlantic salmon, subjected to more than 50 years of domestication and extensive escapes from aquaculture, represents a flagship example of this type of interaction. However, currently no data documents the influence of introgression on survival of a naturally-recruiting wild population during the marine phase of the life-cycle. Following analysis of 885 out-migrating smolts and 7275 adults returning to a Norwegian river in the period 2016–2023, we find no statistical evidence that marine survival varies with domestication-admixture, as admixture levels are not significantly different between out-migrating smolts and returning adults. As this wild population is highly admixed (25–30%) following extensive intrusion of escapees during 1989–2012, we conclude that in the current evolutionary state of this population, i.e. several generations after introgression started, there is no statistical evidence of strong selection against admixed fish during the marine phase. This is likely to be driven by natural selection purging mal-adapted individuals during the freshwater stage where fitness differences are well-documented, and potentially, also in the marine stage during the initial generation(s) following introgression.
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Purcell, Catherine M.; Wringe, Brendan F.; Boudry, Pierre; Brieuc, Marine Servane; Coulson, Mark W. & Kess, Tony
[Show all 9 contributors for this article]
(2025).
States of development and application of genetic and genomic tools in aquaculture and conservation programs: A guide for strengthening dialogue among practitioners of aquaculture and genetics.
Aquatic Living Resources.
ISSN 0990-7440.
38.
doi:
10.1051/alr/2025006.
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Araya, Robin Aasegg; Reinar, William Brynildsen; Tørresen, Ole K; Goubert, Clément; Daughton, Tara Jane & Hoff, Siv Nam Khang
[Show all 12 contributors for this article]
(2025).
Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.
Genome Biology and Evolution (GBE).
17(8).
doi:
10.1093/gbe/evaf131.
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Chromosomal inversions play a crucial role in evolution by influencing phenotypes through the linkage of coadapted alleles. While inversions have been found across a large number of taxa, mapping and characterizing inversion breakpoint regions remain challenging, often due to the presence of complex tandem repeats and transposable elements. Here, we identify and quantify transposable elements in the breakpoints of the four large-scale inversions previously reported in Atlantic cod, leveraging on three high-quality long-read-based reference genome assemblies for the Norwegian Coastal cod, the Northeast Arctic cod, and Celtic cod ecotypes. We detected a significant enrichment of transposable element orders and superfamilies with terminal inverted repeats within the inversion breakpoint regions of chromosomes 1, 7 and 12. Notably, we discovered a tandem accumulation of miniature inverted-repeat transposable elements belonging to a family of hAT transposons, exclusively residing in the breakpoints of the inverted haplotype on chromosomes 1 and 7 found in the Northeast Arctic cod. The accumulation of tandemly arranged transposable elements with high sequence similarity in breakpoint regions suggests that they have driven the appearance of inversions through ectopic recombination, further supporting the potential of transposable elements in facilitating chromosomal reorganizations with large evolutionary implications.
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Helmerson, Cecilia; Durant, Joël; Hoff, Siv Nam Khang; Brieuc, Marine Servane Ono; Berg, Paul Ragnar & Jorde, Per Erik
[Show all 14 contributors for this article]
(2025).
A century of anthropogenic perturbations impact genomic signatures of the iconic migratory Atlantic cod.
Science Advances.
11(31).
doi:
10.1126/sciadv.adp3342.
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Anthropogenic stressors have led to marked ecosystem perturbations, including population declines and shifts in habitat range for key marine fish species. Understanding how these changes affect genome-wide characteristics, causing long-term evolutionary responses, is still in its infancy. Genome-wide retrospective assessment of the iconic migratory Atlantic cod ( Gadus morhua ) from the Barents Sea, unraveled varying degree of admixture with the nonmigratory coastal ecotype throughout the 20th century, and intriguingly more intensified during recent decades. These genomic changes were supported by an increased number of individuals displaying the heterozygous state of the chromosomal inversion coupled to migratory behavior in Atlantic cod. Ecological models and genome-wide scans identified that some of the observed frequency shifts, coupled to neural development, metabolic, and growth regulation, covaried with intensified fisheries, reduced generation time, and ocean warming. Our results demonstrate how anthropogenic perturbations impact the dynamics between two well-known ecotypes of Atlantic cod and thus, their genomic signatures, with potential implications for future management programs.
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Jansson, Eeva; Ayllon, Fernando; Rubin, Carl-Johan; Casas, Laura; Saborido-Rey, Fran & Furmanek, Tomasz
[Show all 12 contributors for this article]
(2025).
Genomic Landscape of Divergence in Ballan Wrasse (Labrus bergylta).
Molecular Ecology.
ISSN 0962-1083.
34(21).
doi:
10.1111/mec.17732.
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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. Differences between morphs dominated in Spain in accordance with sympatric divergence, whereas in Norway allopatric differentiation was prominent and repeated genomic signals of local divergence were found. Chromosomes had large low-recombining areas shared across all populations. Within the Spanish morphs, these areas contained large islands of divergence, totalling ~11% of the genome, and showed high morph specificity and strong selection. The same regions showed frequent admixture in the French morphs and no differentiation in Norway. In contrast, divergent regions observed between sampling localities in Norway were shorter and found throughout the genome. High inbreeding and lower diversity were observed in the Norwegian samples, consistent with the proposed recolonisation bottleneck and subsequent drift. Several genomic regions were significantly associated with morphs and contained tens of genes of diverse functions, suggesting that colouration is unlikely to be the sole driver of divergence. Our results do not support the hypothesis of shared larger genomic features underlying intraspecific colour divergence. Instead, we observe gradual accumulation of differences into low-recombining regions, likely when additional factors like assortative mating and/or lack of gene flow favour their development.
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Helmerson, Cecilia; Weist, Peggy; Brieuc, Marine Servane Ono; Maurstad, Marius Filomeno; Schade, Franziska Maria & Dierking, Jan
[Show all 14 contributors for this article]
(2023).
Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s).
Evolutionary Applications.
16(7),
p. 1359–1376.
doi:
10.1111/eva.13575.
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Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)—indicative of a range expansion westwards—during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long-lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.
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Konstantinidis, Ioannis; Sætrom, Pål; Brieuc, Marine Servane Ono; Jakobsen, Kjetill Sigurd; Liedtke, Hannes & Pohlmann, Caroline
[Show all 8 contributors for this article]
(2023).
DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden.
Epigenetics.
ISSN 1559-2294.
18(1).
doi:
10.1080/15592294.2023.2282323.
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Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study indicates that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Matschiner, Michael; Barth, Julia Maria Isis; Tørresen, Ole K.; Star, Bastiaan; Baalsrud, Helle Tessand & Brieuc, Marine Servane Ono
[Show all 10 contributors for this article]
(2022).
Supergene origin and maintenance in Atlantic cod.
Nature Ecology and Evolution.
6(4),
p. 469–481.
doi:
10.1038/s41559-022-01661-x.
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Abstract 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 environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.
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Pinsky, Malin L.; Eikeset, Anne Maria; Helmerson, Cecilia Jenny Margareta Thomas; Bradbury, Ian R.; Bentzen, Paul & Morris, Corey
[Show all 17 contributors for this article]
(2021).
Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic.
Proceedings of the National Academy of Sciences of the United States of America (PNAS).
ISSN 0027-8424.
118(15).
doi:
10.1073/pnas.2025453118.
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The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.
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Garcia, Lourdes Martinez; Ferrari, Giada; Oosting, Tom; Ballantyne, Rachel; Jagt, Inge van der & Ystgaard, Ingrid
[Show all 20 contributors for this article]
(2021).
Historical demographic processes dominate genetic variation in ancient Atlantic cod mitogenomes.
Frontiers in Ecology and Evolution.
9,
p. 1–14.
doi:
10.3389/fevo.2021.671281.
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Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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Boudry, Pierre; Allal, François; Aslam, Muhammad Luqman; Bargelloni, Luca; Bean, Tim P. & Brard-Fudulea, Sophie
[Show all 18 contributors for this article]
(2021).
Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries.
Aquaculture Reports.
20,
p. 1–14.
doi:
10.1016/j.aqrep.2021.100700.
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Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic
species. Recent developments of high throughput genotyping technology now enable the implementation of
genomic selection, a method aiming to predict the breeding value of candidates based on their genotype at
genome-wide markers. In this review article, we review the state of the arts, challenges and prospects for the
application of genomic selection in aquaculture species. The particular focus is on the status of genomic selection
in several major aquaculture species of International Council for the Exploration of the Sea (ICES) member
countries: Atlantic salmon, rainbow trout, Atlantic cod, American catfish, Pacific oyster, European sea bass and
gilthead sea bream. While the potential of genomic selection is clear, tailored species-specific applications will be
needed to maximise its benefit for the aquaculture sector.
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Croft, Naomi; Solbakken, Monica Hongrø; Brieuc, Marine Servane Ono; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Qiao, Shuo Wang
(2020).
Single-Cell Transcriptome Profiling of Immune Cell Repertoire of the Atlantic Cod Which Naturally Lacks the Major Histocompatibility Class II System.
Frontiers in Immunology.
11.
doi:
10.3389/fimmu.2020.559555.
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Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael & Baalsrud, Helle Tessand
[Show all 12 contributors for this article]
(2020).
Evolution of male pregnancy associated with remodeling of canonical vertebrate immunity in seahorses and pipefishes.
Proceedings of the National Academy of Sciences of the United States of America (PNAS).
ISSN 0027-8424.
117(17),
p. 9431–9439.
doi:
10.1073/pnas.1916251117.
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A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.
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Brieuc, Marine Servane; Waters, Charles D.; Drinan, Daniel P. & Naish, Kerry A
(2018).
A practical introduction to Random Forest for genetic association studies in ecology and evolution.
Molecular Ecology Resources.
ISSN 1755-098X.
18(4),
p. 755–766.
doi:
10.1111/1755-0998.12773.
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Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd
[Show all 9 contributors for this article]
(2018).
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.
BMC Genomics.
19(240),
p. 1–17.
doi:
10.1186/s12864-018-4616-y.
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Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group.
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Brieuc, Marine Servane Ono; Besnier, Francois; Harvey, Alison C.; Andersen-Fjeldheim, Per Tommy; Andersen-Fjeldheim, Kaja Christine & Wennevik, Vidar
[Show all 14 contributors for this article]
(2026).
No selection against domestication-admixture during the marine phase of an Atlantic salmon population.
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The data in this record includes all data used for the analyses described in the MS titled "No selection against domestication-admixture during the marine phase of an Atlantic salmon population ".
Microsat_genotypes.xlsx contains all the genotypes for the individuals in the study, both adults and smolts
Admixture_adults_smolts.txt contains the admixture values for all the individuals in the study
Metadata_Adults_SmoltYear2016-2020.txt contains the metadata for all adults in the study
Metadata_smolts_2016-2020_genotyped.txt contains the metadata for all smolts in the study
Marine_Survival_code.Rmd is the R code to recreate most of the data analyses and figures (to the exception of the comparison of admixture estimates between the SNP chip and the SNP panel)
adm_2000_SNPs_and_SNP_panel.txt contains the admixture values using 2000 SNPs from the SNP chip and the 130 SNP panel, for the individuals previously genotyped on the 50K SNP chip (Besnier et al. 2022).
Comparisons_Adm_2000SNPs_SNPpanel.Rmd is the R code to produce the analysis and figures related to the comparison between the admixture values obtained with 2000SNPs vs 130SNP panel
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Harvey, Alison C.; Skaala, Øystein; Besnier, Francois; Østebø, Britt IrenTjelle; Sørvik, Anne Grete Eide & Andersen-Fjeldheim, Per Tommy
[Show all 12 contributors for this article]
(2025).
Domestication-admixed Atlantic salmon (Salmo salar) establish a productive population within a single generation.
doi:
https:/hdl.handle.net/11250/3214122.
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The data in this record includes all data used for the analyses decsribed in the MS titled "Domestication-admixed Atlantic salmon (Salmo salar) establish a productive population within a single generation". Manuscript has been submitted to Ecology Letters, a Wiley journal, in August 2025.
dataset1 is the data pertaining to the spawners: . Each row is one spawner
off.assign is each offpsring (row) and whether it was assigned to a spawner parent for figure S3
SpawnerN is the number of spawners in each spawner year and whether that spawner was a recruit (identified as a smolt) for figure 2
SmoltN is the number of smolts in each smolt year class and whether that smolt was recruited as a spawner for figure 2
SpawnerNall is all the spawners that entered the river from 2000 to 2021for figure S2
MS is the collated marine survival data for the supplementary figure S8
spawner.genetic is the microsatellite data used to check for duplicated spawners in the dataset
dataset1
ID Unique identifier of each spawner
Date Date on which the spawner entered the river
Year Year of river entry
Length Length of the spawner in cm
Weight Weight of the spawner in kg
Admix Admixture estimate of the spawner
Sex Genetically determined sex of the spawner
OffN Number of offspring assigned to the spawner
Repro Reproductive success, yes = reproduced, no = did not reproduce
Rsucc Reproductive success, 1 = reproduced, 0 = did not reproduce
River River assigned to the spawner
Threshold whether the river assignment was above or below the 0.80 probability of assignment threshold
off.assign
OffspringID Unique identifier of each offspring
Off.Year Year of migration of the offspring
Assign Whether the offspring was assigned to a parent or not
SpawnerN
Year Spawner year
Number Number of spawners in that year
Recruit How many were recruited from smolts
SmoltN
Year Smolt year class
Recruit Number of smolts that were then recruited back to the river as spawners
Number Number of smolts in the smolt year class
SpanwerNall
Fish number for each fish, continuous
Year Spawner year
MS
SYC Smolt year class
MS The marine survival (proportion)
Origin Whether that population is wild or of hatchery origin
River Which river the data comes from
Age Which age the marine survival relates to (1 sea winter SW, 2 sea winter SW)
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Pearse, Devon E.; Barson, Nicola; Nome, Torfinn; Gao, Guangtu; Campbell, Matthew A. & Abadía-Cardoso, Alicia
[Show all 32 contributors for this article]
(2020).
Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout (Nature Ecology & Evolution, (2019), 3, 12, (1731-1742), 10.1038/s41559-019-1044-6).
Nature Ecology and Evolution.
4(1),
p. 170–170.
doi:
10.1038/s41559-019-1076-y.
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Published
Dec. 8, 2021 10:37 AM
- Last modified
Dec. 8, 2021 10:37 AM