Biology subjects

Besnier, F.

Publications and source records attributed to Besnier, F..

6 recordsLinked to original sources

bioRxiv2025

Genome-wide differentiation and SNP-based identification of northeastern Atlantic Sebastes species

Sustainable fisheries require reliable species identification and understanding of the underlying genetic hierarchies within the targeted species. Three Sebastes species are commonly found in the northeastern Atlantic: Sebastes mentella (beaked redfish), Sebastes norvegicus (golden redfish), and Sebastes viviparus (Norway redfish). These species are morphologically similar and have largely overlapping distribution ranges. Besides, three cryptic species for S. norvegicus and three depth-defined ecotypes for S. mentella have been suggested. Genetic knowledge and methods are needed to identify and monitor these species and to look at their geographic distribution. Here, a total of 99 specimens of S. mentella, S. viviparus as well as S. norvegicus A and B were sequenced in pools and aligned against a reference genome from a sister species, S. fasciatus (Acadian redfish). The measured divergence between all pairs, including the cryptic species pair S. norvegicus A and B, was high (mean FST = 0.33-0.61) and encompassing throughout genomes. Several shared megabase-scale regions of elevated divergence were observed, likely representing regions of reduced recombination. Moreover, 2914 fish collected across the northeastern Atlantic were analysed with a discriminatory SNP panel of high resolution (mean FST= 0.60-0.91), revealed few possible hybrids, and supported further sub-structuring within mentella and S. norvegicus B. The latter was split into two groups, one of which was the previously recognized giant morph and confirmed here for the first time in Norway. Sebastes mentella had two to three groups, likely representing previously identified depth-related ecotypes. Our study shows high genetic distinctiveness between acknowledged northeast-Atlantic Sebastes species, and between the cryptic species S. norvegicus A and B. Previously identified, fast-growing giant seems to be closely related to S. norvegicus B. Only few SNP markers are necessary for accurate species determination, facilitating further studies and widely applicable monitoring.

genetics↗

bioRxiv2025

Genetics in the ocean's twilight zone: Population structure of the Mueller's pearlside across its distribution range

The large estimates of mesopelagic fish biomass have fuelled harvesting interests in the relatively untouched oceans twilight zone. The Muellers pearlside, one of the most abundant species inhabiting the north Atlantic mesopelagic layer, is a candidate to such fisheries despite its enormous ecological importance and the insufficient knowledge about its population genetic structure. To shed light on the latter, 863 individuals sampled across the North Atlantic and Mediterranean were genotyped using 170 genome-wide SNPs. Analyses revealed habitat-driven differentiation in three units: Mediterranean Sea, oceanic samples, and Norwegian fjords. These groups were not completely isolated to each other as a cline of Mediterranean admixture was detected in the Eastern Atlantic facade up to 47{degrees}N in an otherwise genetically homogeneous oceanic cluster. Temperature seemed to modulate the differentiation patterns, and in the Mediterranean added to the complicated topography of the Greek Seas to shape genetic structure. In the Norwegian coastline, sills did not hamper genetic exchange among fjords ranging 200 km apart, probably due to the position of the species in the water column together with its swimming capacity. This genetic information should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.

genetics↗

bioRxiv2024

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, the Mediterranean Sea as well as 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 fisherys 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 SNP-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism in the form of three sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.

genomics↗

bioRxiv2022

Overruled by nature: A plastic response to an ecological regime shift disconnects a gene and its trait

In Atlantic salmon, age at maturation is a life history trait ruled by a sex-specific trade-off between reproductive success and survival. Following an ecological regime shift in 2005, many North Atlantic salmon populations currently display smaller size at age and delayed age at maturation. However, whether this change reflects rapid evolution or plastic response is unknown. Some 1500 historical and contemporary salmon from river Etne (Western Norway) genotyped at 50k SNPs revealed three loci significantly associated with age at maturation. These included vgll3 and six6, which collectively explained 36 to 50% of the age at maturation variation in the 1983-1984 period. Strikingly, the combined influence of these genes was nearly absent in all samples from 2013-2016, despite allelic frequencies at vgll3 remaining unchanged. We conclude that the regime shift has led to the sudden bypassing of the influence of vgll3 and six6 on maturation through growth-driven plasticity.

genetics↗

bioRxiv2021

The salmon louse genome: copepod features and parasitic adaptations.

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assembly containing {approx}60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics validated annotation and revealed a marked shift in gene expression after host attachment, including downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of peroxisomes, numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

genomics↗

bioRxiv2020

Sex determining gene transposition as an evolutionary platform for chromosome turnover

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are the best studied family of fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of transposition, suggesting a recent and non-random sex chromosome turnover in this species. We hypothesized the existence of an autosomic pseudocopy of sdY that is transmitted in accordance with Mendelian inheritance. To test this we developed a qPCR methodology to detect the number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomic copies in addition to the Y-specific copy present in males. Copy number frequencies were consistent with Mendelian inheritance. Pseudocopy loci were mapped to different chromosomes evidencing non-random transitions of the sex determining gene in Atlantic salmon and the existence of functional constraints for chromosome turnover.

genetics↗