Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm

Seasonal migrations of the European sea bass (Dicentrarchus labrax L.) in UK and surrounding waters

The movements and behaviour of mature European sea bass (Dicentrarchus labrax L.) in UK waters have not been studied extensively since a series of mark-recapture experiments during the 1970s, 80s and 90s. To better understand the timing and extent of seasonal migrations, 171 mature sea bass > 42 cm were internally tagged with floated electronic tags programmed to record temperature and depth, and released in the English Channel, in the southern North Sea and in the Irish Sea. Among the 48 tags returned to date, sea bass were at liberty for 370 ± 337 days and were recovered 172 ± 200 km from their respective release locations. Most tags were recovered from beaches (54%), or via the fishery (44%). A comparison of the reconstructed tracks from returned electronic tags with the recapture locations of 237 mark-recapture returns (6.5%) from 3615 sea bass released between 1970 and 2020 showed strong overlap. Seasonal movements between shallow areas (Q2-Q3) and deeper spawning areas (Q4-Q1) were accompanied by elevated vertical swimming speeds and average water temperatures of 8.5 °C in the English Channel and Irish Sea, but lower temperatures in the North Sea. Movements between the Celtic Sea/Irish Sea and the North Sea and vice versa demonstrate high levels of connectivity in UK waters. We demonstrate that a proportion of sea bass remained resident within the North Sea throughout the year, with a strong suggestion that spawning might be occurring. These data have significant implications for the future sustainable management of sea bass stocks in UK and surrounding waters.

Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus

The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.

The spatial scale of dispersal revealed by admixture tracts

Evaluating species dispersal across the landscape is essential to design appropriate management and conservation actions. However, technical difficulties often preclude direct measures of individual movement, while indirect genetic approaches rely on assumptions that sometimes limit their application. Here, we show that the temporal decay of admixture tracts lengths can be used to assess genetic connectivity within a population introgressed by foreign haplotypes. We present a proof-of-concept approach based on local ancestry inference in a high gene flow marine fish species, the European sea bass (Dicentrarchus labrax). Genetic admixture in the contact zone between Atlantic and Mediterranean sea bass lineages allows the introgression of Atlantic haplotype tracts within the Mediterranean Sea. Once introgressed, blocks of foreign ancestry are progressively eroded by recombination as they diffuse from the western to the eastern Mediterranean basin, providing a means to estimate dispersal. By comparing the length distributions of Atlantic tracts between two Mediterranean populations located at different distances from the contact zone, we estimated the average per-generation dispersal distance within the Mediterranean lineage to less than 50 km. Using simulations, we showed that this approach is robust to a range of demographic histories and sample sizes. Our results thus support that the length of admixture tracts can be used together with a recombination clock to estimate genetic connectivity in species for which the neutral migration-drift balance is not informative or simply does not exist.

The European sea bass: a key marine fish model in the wild and in aquaculture

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.

Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L

Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). We found less females than males in the progeny, both in the global dataset (32.5%) and within each paternal group (from 25.1% for NEM to 39.0% for WEM), with significant variation among populations, dams, and sires. Sex, body weight (BW), and body length (BL) showed moderate heritability (0.52 ± 0.17, 0.46 ± 0.17, 0.34 ± 0.15, respectively) and sex was genetically correlated with BW and BL, with r_Asex/BW = 0.69 ± 0.12 and r_{A sex/BL} = 0.66 ± 0.13. A weighted GWAS performed both on the global dataset and within each paternal group revealed a different genetic architecture of sex determination between Atlantic and Mediterranean populations (9 QTLs found in NAT, 7 in WEM, 5 in NEM, and 4 in SEM, with a cumulated variance explained of 27.04%, 21.87%, 15.89%, and 12.10%, respectively) and a more similar genetic architecture among geographically close populations compared to geographically distant populations, consistent with the hypothesis of a population-specific evolution of polygenic sex determination systems in different environments.

The role of the Strait of Gibraltar in shaping the genetic structure of the Mediterranean Grenadier, Coryphaenoides mediterraneus, between the Atlantic and Mediterranean Sea

Population genetic studies of species inhabiting the deepest parts of the oceans are still scarce and only until recently we started to understand how oceanographic processes and topography affect dispersal and gene flow patterns. The aim of this study was to investigate the spatial population genetic structure of the bathyal bony fish Coryphaenoides mediterraneus, with a focus on the Atlantic-Mediterranean transition. We used nine nuclear microsatellites and the mitochondrial cytochrome c oxidase I gene from 6 different sampling areas. No population genetic structure was found within Mediterranean with both marker types (mean ΦST = 0.0960, FST = -0.0003, for both P > 0.05). However, within the Atlantic a contrasting pattern of genetic structure was found for the mtDNA and nuclear markers (mean ΦST = 0.2479, P < 0.001; FST = -0.0001, P > 0.05). When comparing samples from Atlantic and Mediterranean they exhibited high and significant levels of genetic divergence (mean ΦST = 0.7171, FST = 0.0245, for both P < 0.001) regardless the genetic marker used. Furthermore, no shared haplotypes were found between Atlantic and Mediterranean populations. These results suggest very limited genetic exchange between Atlantic and Mediterranean populations of C. mediterraneus, likely due to the shallow bathymetry of the Strait of Gibraltar acting as a barrier to gene flow. This physical barrier not only prevents the direct interactions between the deep-living adults, but also must prevent interchange of pelagic early life stages between the two basins. According to Bayesian simulations it is likely that Atlantic and Mediterranean populations of C. mediterraneus were separated during the late Pleistocene, which is congruent with results for other deep-sea fish from the same region.

Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)

Describing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.

Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, shaped by a complex interaction of historical and contemporary, physical and nonphysical drivers

Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long-distance dispersal triggered by extreme environmental conditions (e.g. population crashes).

Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone

The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (F_ST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation.

The European sea bass is an economically important fish species, which is subject to intense selective breeding. Here, the authors sequence the genome of the European sea bass and highlight gene family expansions underlying adaptation to salinity change, as well as the genomic architecture of speciation between two divergent sea bass lineages.