Laura Casas

Fisheries management relies on accurate stock assessments, which in turn depend on precise age information. Recent molecular tools called ‘epigenetic clocks’ harness age‐related DNA methylation changes to build accurate and precise age‐prediction models. However, the influences of intrinsic and extrinsic factors on clock performance remain uncertain. In this study, we examined Atlantic cod aged 0 to 7 years, sampled from various locations across the North Sea, and developed an epigenetic clock using DNA methylation data of 73 CpG sites from fin clips obtained by bisulfite restriction‐site associated DNA sequencing (bis‐RAD‐seq). This clock predicted age with 97.5% accuracy and a precision of 2.8 months and generalised well in unseen data. Further, we addressed critical variables such as sex and maturity status, which are often overlooked, and we showed that clock performance was unaffected by sex‐specific differences in growth, and it was lower in advanced sexually mature individuals, reflecting a slight bias towards younger fish. A key finding of our study is the discovery of a latitudinal cline in global DNA methylation patterns. We found that DNA methylation varied with latitude, despite the absence of genetic differences, while our clock maintained consistent performance across geographic locations. This resolves a major question regarding how generalizable epigenetic clocks are within the distribution of a species. Our clock demonstrates extensive applicability and enhanced practicality for real‐world fisheries management. It provides accurate and precise age prediction for Atlantic cod irrespective of intrinsic differences or environmental influences associated with geographic locations.

European hake is an economically important fishery resource with known declines in population abundances and biomass in the last decades. However, little is known about the effect of these abundance declines on the genetic diversity levels of the stocks. In this study, we analysed genomic data of Atlantic and Mediterranean European hake populations, representing the main fishery stocks. The results indicate that abundance declines have likely affected the levels and patterns of genetic diversity within and among the three analysed populations. The Mediterranean population shows lower genetic diversity than the Atlantic ones and can be slightly genetically differentiated from them. Results indicate significant deviations from neutral expectations for constant population sizes, and substantial population declines in all three populations. Estimates of recent and ancestral effective population size (Ne) obtained from coalescence, linkage disequilibrium and sibship methods were coherent with each other. Historical Ne estimates suggest drastic declines of more than 90% in all three populations within the last 15 generations (i.e. nearly 50 years). Positive correlations observed between historical Ne and stock parameters indicative of abundances support the historical trends of estimated Ne. Since genetic variation is essential for populations facing anthropogenically induced environmental changes, this study demonstrates the importance of population genetic estimates for planning management strategies targeting the long-term sustainability of European hake fisheries.

Sex determination is exceptionally diverse and shows a high evolutionary rate in fish. European hake (Merluccius merluccius) is a species of great commercial value distributed throughout European coasts, which displays a significant sexual growth dimorphism. We present a chromosome-level genome of M. merluccius, composed of 215 contigs using long- and short-read sequencing, further scaffolded into the species’ 21 chromosomes using Hi-C technique (715 Mb). RNA-seq on several tissues from pooled individuals improved annotation (26,625 protein-coding genes and 11,083 ncRNAs). Five males and 5 females from an Atlantic population were re-sequenced at 30× depth to look for association with sex across the whole genome. Genetic differentiation between males and females (FST) and intrapopulation fixation index (FIS) pointed to a region on chromosome 9 spanning ∼10 Mb which included several genes related to gonad differentiation and showed strong linkage disequilibrium associated with a putative inversion. Near sox3 gene (∼25 kb), SNPs were mostly heterozygous in males and homozygous in females, consistent with an XX/XY sex-determining (SD) system. These SNP markers were validated in a larger sample of 56 males and 63 females from the same population using MassARRAY. Other genomic regions that were differentiated between males and females and suggestive of sexual conflict were also explored across the genome. Results support a candidate master SD gene in M. merluccius and indicate some differentiated regions potentially under sexual conflict. This information will be useful for the fisheries management of M. merluccius in the context of climate change, where noninvasive sex identification tools are essential.

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.

Editorial: Prospects and challenges for the implementation of HTS genetic methods in fisheries research surveys and stock assessments

Knowing the number of individuals in a population is fundamental for the sustainable management of exploited marine resources but estimating this parameter is often extremely challenging, especially in large, highly mobile and dispersed populations. Abundance estimation traditionally relies on multiple data types that include the relationship between fishery catches and effort (Catch Per Unit Effort or CPUE), scientific research surveys and demographic models that are developed to estimate past and current stock dynamics, but uncertainty is often high. Close-kin mark-recapture (CKMR) is an alternative method for estimating abundance and other demographic parameters (e.g. population trend, survival rates, connectivity), using kinship relationships determined from genetic samples. This methodology is based on a simple concept - the larger the population the less likely to find relatives and vice versa - and was proposed two decades ago although regained considerable attention recently. Refinements in the statistical methodology and advances in high throughput sequencing methods have boosted the efficiency of genomic analysis, promising to revolutionize the field of fisheries stock assessments. In theory, it can be applied to almost any species, provided that there is sufficient information about the life-history/biology of the organism and that the populations are not so small as to be almost extinct or so large that finding relatives becomes extremely difficult. Thus, it has the potential to provide baseline data for the many exploited fish stocks that remain largely unassessed and to reduce uncertainty in those that are regularly evaluated. Here, we provide an overview of the method in the context of fisheries assessments, analyze the advances and synthetize the field studies published in the last five years. Moreover, we evaluate the readiness, viability and maturity of the method to infer demographic parameters in species spanning diverse life histories. We evaluate technical considerations and requirements for a successful application and analyze the main challenges and limitations preventing a broader implementation.

Stock assessments serve to monitor the condition of fish stocks and exploit them sustainably but require accurate data such as growth and mortality rates as input parameters. Most species fished worldwide lack the data needed to assess their status and even those closely assessed are often based on parameters that are known to contain uncertainty. This has resulted in an increased share of overfished stocks over the last half century, demanding urgently innovative methodologies that can provide novel means to reduce uncertainty of fish stocks assessments and expand the range of assessed species. CKMR has emerged recently attracting a great interest due to its potential to provide accurate demographic parameters of interest in stock assessments. The method is at the crossroads between fisheries science and genomics, requiring specialized knowledge that is usually outside of the experience of fisheries scientist and modellers, complicating the application of the method and its uptake in regular fisheries assessments. In this review, we provide useful information to perform the genomics and bioinformatics steps required to complete successfully a CKMR study. We discuss the most suitable genomics assays, considering the amount of information they provide, their easiness of use and cost of genotyping accurately the large number of individuals needed to assess most fish stocks. We provide an overview of methods of analysis and statistical methodologies that can be used to infer kinship with the accuracy required in a large population setting with sparse sampling, where most individuals are unrelated, determining a low probability of finding closely related individuals. We analyse potential sources of biases and errors and provide recommendations to facilitate the application of CKMR to a wider range of fish stocks.

An increasing number of studies using marine environmental DNA (eDNA) approaches are showing its potential application in marine fisheries management by helping and simplifying some of the labor-intensive traditional surveys required to assess exploited populations and ecosystem status. eDNA approaches (i.e. metabarcoding and targeted) can support to ecosystem-based fisheries management by providing information on species composition; surveillance of invasive, rare and/or endangered species; and providing estimates of species abundance. Due to these potential uses in fisheries and conservation sciences, the number of studies applying eDNA approaches in marine habitats has expanded in the very last few years. However, a lack of consistency across studies when applying pipelines for data analyses, makes results difficult to compare among them. Such lack of consistency is partially caused by poor knowledge in the management of raw sequences data, and analytical methods allowing comparative results. Hence, we review here the essential steps of eDNA data processing and analyses to get sound, reproducible, and comparable results, providing a set of bioinformatics tools useful for each step. Altogether this review presents the state of the art of eDNA data analyses towards a comprehensive application in fisheries management promoting sustainability.

Increasing anthropogenic pressures on the coastal marine environments impact these ecosystems via a variety of mechanisms including nutrient loading, leading to eutrophication and increases in algal blooms. Here, we use a metagenomics approach to assess the taxonomic and functional changes of the microbial community throughout a nutrient enriched mesocosm phytoplankton bloom. We tested four different nutrient treatments consisting of either nitrate and phosphate or nitrate, phosphate and silicate, administered on the first day or continuously for the first two weeks of the experiment. Our results show a shift in the taxonomic composition of the community over time that is dependent on the nutrient addition regime. Significant differences in the functional potential of the communities were detected, with an interaction between bloom period (pre-bloom, bloom and post-bloom) and nutrient treatment (p = 0.004). A sharp drop in functional similarity was observed in the first week in all treatments and after 20 days had not returned to pre-bloom levels. Changes within energy metabolism pathways showed a remarkable enrichment of the dissimilatory nitrate reduction pathway in the post-bloom period. Eukaryotic oxidative phosphorylation and photosynthetic antenna proteins were more abundant during the bloom, especially in the continuous treatment with silicate. Our results suggest that continuous (i.e. chronic) nutrient enrichment has a larger effect on the functioning of marine systems compared to a single (i.e acute) addition. A deep understanding of the functional and taxonomic shifts in the community during blooms is essential to reverse or mitigate human impacts on coastal environments.

Fishes are the only vertebrates that undergo sex change during their lifetime, but even within this group, a unique reproductive strategy is displayed by only 1.5% of the teleosts. This lability in alternating sexual fate is the result of the simultaneous suppression and activation of opposing male and female networks. Here, we provide a brief review summarizing recent advances in our understanding of the environmental cues that trigger sex change and their perception, integration, and translation into molecular cascades that convert the sex of an individual. We particularly focus on molecular events underpinning the complex behavioral and morphological transformation involved in sex change, dissecting the main molecular players and regulatory networks that shape the transformation of one sex into the opposite. We show that histological changes and molecular pathways governing gonadal reorganization are better described than the neuroendocrine basis of sex change and that, despite important advances, information is lacking for the majority of hermaphrodite species. We highlight significant gaps in our knowledge of how sex change takes place and suggest future research directions.