Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean

The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.

Graphical abstract

Innovation to limit seafood fraud post-COVID-19

Seafood is an important source of protein and micronutrients, but fishery stocks are increasingly under pressure from both legitimate and illegitimate fishing practices. Sustainable management of our oceans is a global responsibility, aligning with United Nations Sustainable Development Goal 14, Life Below Water. In a post-COVID-19 world, there is an opportunity to build back better, where locally sourced food via transparent supply chains are ever-more important. This article summarises emerging research of two innovative case studies in detecting and validating seafood provenance; and using alternative supply chains to minimise the opportunity for seafood fraud in a post-COVID-19 world.

EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries

A fishery’s structure and connectivity are priors to its effective management. A successful description of such processes depends on both the sampling design and the choice of adequate genetic markers. EST markers are perfusing the studies of marine metapopulations and are believed to provide access to functional polymorphisms. However, the assumed adaptive role of outlier EST loci might not be generalizable. EST-microsatellites represent the upper polymorphic boundary in these regions because of their high mutation rate. We have subclassified the polymorphisms of EST-microsatellites to assess their structural contribution in the European hake, a paradigmatic and highly mobile marine species (HMMS). Because of the counterbalanced forces between directional markers (15%) and balanced markers (23%), the whole marker set offers the same structural situation as the one observed with neutral markers (62%), i.e., k = 2 gene pools. In contrast to outlier EST- microsatellites, neutral EST subsets allow one to measure crucial population phenomena for fisheries’ management. The high inter-population divergence of outlier EST-microsatellites is compatible with drifted post-selection genomic regions rather than with ongoing local selective pressures. The structural scenario in hake is explainable by a limited gene flow across the Almería-Oran Front (AOF) and by the within-basin IBD pattern of connectivity plus drift-related demographic events. This study highlights how polymorphic properties of EST-microsatellite types can be useful to address mutually excluding research tasks in fisheries, i.e., to address its evolutionary history (directional markers or FAPS: Fossil Adaptive Polymorphic Systems); to delineate management units (neutral markers or NAPS: Non Adaptive Polymorphic Systems); or to ensure sustainability (balanced markers or APS: Adaptive Polymorphic Systems).

Genetic hypervariability of a Northeastern Atlantic venomous rockfish

BACKGROUND

Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins.

METHODS

In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron.

RESULTS

The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.

Into the Deep: New Data on the Lipid and Fatty Acid Profile of Redfish Sebastes mentella Inhabiting Different Depths in the Irminger Sea

New data on lipid and fatty acid profiles are presented, and the dynamics of the studied components in muscles in the males and females of the beaked redfish, Sebastes mentella, in the depth gradient of the Irminger Sea (North Atlantic) is discussed. The contents of the total lipids (TLs), total phospholipids (PLs), monoacylglycerols (MAGs), diacylglycerols (DAGs), triacylglycerols (TAGs), cholesterol (Chol), Chol esters, non-esterified fatty acids (NEFAs), and wax esters were determined by HPTLC; the phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylcholine (PC), and lysophosphatidylcholine (LPC) were determined by HPLC; and fatty acids of total lipids were determined using GC. The Chol esters prevailed in muscles over the storage TAGs, and the wax ester content was high, which is a characteristic trait of vertically migrating species. Specific dynamics in certain PL in redfish were found to be depended on depth, suggesting that PLs are involved in the re-arrangement of the membrane physicochemical state and the maintenance of motor activity under high hydrostatic pressure. The high contents of DHA and EPA were observed in beaked redfish muscles is the species' characteristic trait. The MUFAs in muscles include dietary markers of zooplankton (copepods)-20:1(n-9) and 22:1(n-11), whose content was found to be lower in fish sampled from greater depths.

Drivers for genetic structure at different geographic scales for Pacific red snapper (Lutjanus peru) and yellow snapper (Lutjanus argentiventris) in the tropical eastern Pacific

The tropical eastern Pacific (TEP) is a highly dynamic region and a model system to study how habitat discontinuities affect the distribution of shorefishes, particularly for species that display ontogenetic habitat shifts, including snappers (Lutjanidae). To evaluate the genetic structure of the Pacific red snapper (Lutjanus peru) and the yellow snapper (Lutjanus argentiventris) throughout their distribution range along the TEP, 13 and 11 microsatellite loci were analysed, respectively. The genetic diversity of L. peru (N = 446) and L. argentiventris (N = 170) was evaluated in 10 and 5 localities, respectively, showing slightly higher but non-significant values in the Gulf of California for both species. The genetic structure analysis identified the presence of significant genetic structure in both species, but the locations of the identified barriers for the gene flow differed between species. The principal driver for the genetic structure at large scales >2500 km was isolation by distance. At smaller scales (<250 km), the habitat discontinuity for juveniles and adults and the environmental differences throughout the distribution range represented potential barriers to gene flow between populations for both species.

Combining genotypic and phenotypic variation in a geospatial framework to identify sources of mussels in northern New Zealand

The New Zealand green-lipped mussel aquaculture industry is largely dependent on the supply of young mussels that wash up on Ninety Mile Beach (so-called Kaitaia spat), which are collected and trucked to aquaculture farms. The locations of source populations of Kaitaia spat are unknown and this lack of knowledge represents a major problem because spat supply may be irregular. We combined genotypic (microsatellite) and phenotypic (shell geochemistry) data in a geospatial framework to determine if this new approach can help identify source populations of mussels collected from two spat-collecting and four non-spat-collecting sites further south. Genetic analyses resolved differentiated clusters (mostly three clusters), but no obvious source populations. Shell geochemistry analyses resolved six differentiated clusters, as did the combined genotypic and phenotypic data. Analyses revealed high levels of spatial and temporal variability in the geochemistry signal. Whilst we have not been able to identify the source site(s) of Kaitaia spat our analyses indicate that geospatial testing using combined genotypic and phenotypic data is a powerful approach. Next steps should employ analyses of single nucleotide polymorphism markers with shell geochemistry and in conjunction with high resolution physical oceanographic modelling to resolve the longstanding question of the origin of Kaitaia spat.

Otolith chemical fingerprints of skipjack tuna (Katsuwonus pelamis) in the Indian Ocean: First insights into stock structure delineation

The chemical composition of otoliths (earbones) can provide valuable information about stock structure and connectivity patterns among marine fish. For that, chemical signatures must be sufficiently distinct to allow accurate classification of an unknown fish to their area of origin. Here we have examined the suitability of otolith microchemistry as a tool to better understand the spatial dynamics of skipjack tuna (Katsuwonus pelamis), a highly valuable commercial species for which uncertainties remain regarding its stock structure in the Indian Ocean. For this aim, we have compared the early life otolith chemical composition of young-of-the-year (<6 months) skipjack tuna captured from the three main nursery areas of the equatorial Indian Ocean (West, Central and East). Elemental (Li:Ca, Sr:Ca, Ba:Ca, Mg:Ca and Mn:Ca) and stable isotopic (δ13C, δ18O) signatures were used, from individuals captured in 2018 and 2019. Otolith Sr:Ca, Ba:Ca, Mg:Ca and δ18O significantly differed among fish from different nurseries, but, in general, the chemical signatures of the three nursery areas largely overlapped. Multivariate analyses of otolith chemical signatures revealed low geographic separation among Central and Eastern nurseries, achieving a maximum overall random forest cross validated classification success of 51%. Cohort effect on otolith trace element signatures was also detected, indicating that variations in chemical signatures associated with seasonal changes in oceanographic conditions must be well understood, particularly for species with several reproductive peaks throughout the year. Otolith microchemistry in conjunction with other techniques (e.g., genetics, particle tracking) should be further investigated to resolve skipjack stock structure, which will ultimately contribute to the sustainable management of this stock in the Indian Ocean.

Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure.

Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus)

Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ¹³C and δ¹⁸O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12-18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ¹⁸O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ¹⁸O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.

Using multiple natural tags provides evidence for extensive larval dispersal across space and through time in summer flounder

Dispersal sets the fundamental scales of ecological and evolutionary dynamics and has important implications for population persistence. Patterns of marine dispersal remain poorly understood, partly because dispersal may vary through time and often homogenizes allele frequencies. However, combining multiple types of natural tags can provide more precise dispersal estimates, and biological collections can help to reconstruct dispersal patterns through time. We used single nucleotide polymorphism genotypes and otolith core microchemistry from archived collections of larval summer flounder (Paralichthys dentatus, n = 411) captured between 1989 and 2012 at five locations along the US East coast to reconstruct dispersal patterns through time. Neither genotypes nor otolith microchemistry alone were sufficient to identify the source of larval fish. However, microchemistry identified clusters of larvae (n = 3-33 larvae per cluster) that originated in the same location, and genetic assignment of clusters could be made with substantially more confidence. We found that most larvae probably originated near a biogeographical break (Cape Hatteras) and that larvae were transported in both directions across this break. Larval sources did not shift north through time, despite the northward shift of adult populations in recent decades. Our novel approach demonstrates that summer flounder dispersal is widespread throughout their range, on both intra- and intergenerational timescales, and may be a particularly important process for synchronizing population dynamics and maintaining genetic diversity during an era of rapid environmental change. Broadly, our results reveal the value of archived collections and of combining multiple natural tags to understand the magnitude and directionality of dispersal in species with extensive gene flow.

Comparative influence of genetics, ontogeny and the environment on elemental fingerprints in the shell of Perna canaliculus

The trace elemental composition of biogenic calcium carbonate (CaCO₃) structures is thought to reflect environmental conditions at their time of formation. As CaCO₃ structures such as shell are deposited incrementally, sequential analysis of these structures allows reconstructions of animal movements. However, variation driven by genetics or ontogeny may interact with the environment to influence CaCO₃ composition. This study examined how genetics, ontogeny, and the environment influence shell composition of the bivalve Perna canaliculus. We cultured genetically distinct families at two sites in situ and in the laboratory. Analyses were performed on shell formed immediately prior to harvest on all animals as well as on shell formed early in life only on animals grown in the laboratory. Discriminant analysis using 8 elements (Co, Ti, Li, Sr, Mn, Ba, Mg, Pb, Ci, Ni) classified 80% of individuals grown in situ to their family and 92% to growth site. Generalised linear models showed genetics influenced all elements, and ontogeny affected seven of eight elements. This demonstrates that although genetics and ontogeny influence shell composition, environmental factors dominate. The location at which shell material formed can be identified if environmental differences exist. Where no environmental differences exist, genetically isolated populations can still be identified.