Jamie R. Stevens

Accurate detection of hybridization and introgression is critical not only for basic research, but also for fisheries management. In many species, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the introduced H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs originally developed for population genetic analyzes in H. gammarus and subsequently applied to distinguish H. gammarus, H. americanus, and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we evaluated this panel's performance under the allele-frequency distributions and marker properties observed in the empirical dataset it was based on, using individual-based resampling to generate genotypes with known ancestry proportions. We show that the panel retains discriminatory power for broad ancestry classes and early-generation hybrids, but with reduced accuracy for later-generation backcrosses and especially high uncertainty in distinguishing backcrosses toward H. gammarus from variation within the H. gammarus parental reference. These findings provide an assessment of hybrid classification performance for this specific panel and demonstrate the value of empirical resampling simulations for identifying both the utility and the limitations of existing marker panels in fisheries-relevant species.

Mining pollution is an important stressor of freshwater communities worldwide. Persistence in these environments requires adaptation, yet identifying the mechanisms responsible in wild systems remains challenging due to differing water chemistries and genetic backgrounds. Parallel evolution presents a powerful framework for identifying adaptive mechanisms through repeated directional change. Here, we seek to understand the mechanisms that enable brown trout ( Salmo trutta ) to survive in metal-polluted rivers. Using low-coverage Whole Genome Resequencing (lc-WGS) we analyse paired metal-polluted and non-polluted brown trout populations across the British Isles. Metal-impacted populations show reduced nucleotide diversity and increased genomic divergence from paired control populations. We observe strong signatures of parallel adaptation in populations with shared geography, emphasising the importance of standing genetic variation in rapid adaptation to pollution. We identify a candidate region of 0.5 Mb on chr25 that shows strong parallel adaptation across multiple pairwise comparisons, including a shared signal among populations experiencing highly divergent water chemistries. The chr25 region contains the genes oestrogen receptor ( esr2b ) and a potassium-gated ion channel ( kcnh5b ), both of which are linked to developmental and osmoregulatory functions known to be disrupted by metals. Using population branch statistics (PBS) and scans for selective sweeps, we also identify population-specific candidate loci, yet putatively selected regions repeatedly converge on shared gene families and functional pathways. Our findings reveal both parallel and unique evolutionary responses to anthropogenic pollution in wild fish, highlighting convergent adaptive pathways to diverse pollutants in teleosts.

Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the European lobster (H. gammarus), despite its ecological significance and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6% (96.8% single-copy, 0.8% duplicated). As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry (3.18 to 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the European lobster assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterized gene expression across ten tissues to generate a tissue gene expression atlas, available at www.LobsterGeneX.com. Using single-copy orthologues, we estimated a divergence time of 26 Mya between H. gammarus and H. americanus, corresponding to the Oligocene–Miocene boundary. We also identified lobster-specific gene duplications with roles in immunity and longevity, including telomere maintenance. These genomic resources will facilitate future research into lobster biology, supporting sustainable fisheries and aquaculture, while enabling investigations of homarid evolutionary adaptations.

As populations decline under climate change and other stressors, survivors become increasingly isolated. Allee effects in such fragmented populations may arise during reproduction, particularly for sessile organisms such as corals, reducing fertilisation potential and increasing the probability of recruitment failure. However, the critical distances between corals needed to maintain viable populations remains uncertain. We experimentally investigated fertilisation patterns in the broadcast spawning coral Acropora cf. hyacinthus using a manipulated patch, spacing colonies at increasing distances downstream from a central spawning aggregation. Field samples showed a steep decline in fertilisation with increasing intercolonial distance and genetic paternity analysis indicated most parents were located within 3 m of each other. Colony position relative to the current direction also influenced fertilisation success, with 81% of sequenced progeny sired by upstream colonies. Simulations projecting natural population distributions onto a virtual grid, incorporating experimental results, indicated that populations remained well-mixed at typical adult densities. Yet at reduced densities approaching 0.01 colonies m ⁻² , reproductive isolation and patchy breeding units emerged. These findings demonstrate that colony isolation substantially impairs reproductive connectivity, with additional influence from the spatial arrangement of colonies. Conservation strategies should prioritise maintaining colony density and spatial connectivity to support viable coral populations on degraded reefs.

Populations of Atlantic salmon continue to suffer marked declines in abundance due to stressors acting in both their freshwater and marine habitats. It is therefore an imperative to identify populations in need of increased conservation intervention, with the aim of preserving as much as possible the genetic diversity present within the species. Previous microsatellite‐based analyses have shown the chalk rivers of southern England and northern France to hold genetically distinct populations of salmon. However, these salmon populations have never been investigated in the same study. Using a suite of 93 single nucleotide polymorphism loci and samples from 42 British Isles and French rivers, we demonstrate the French and English chalk salmon to be closely related and confirm their distinction from salmon inhabiting non‐chalk rivers. The identification of a small number of significant F _ST outliers and loci associated with environmental variables suggests that this distinction is driven by local adaptation. We propose that the chalk and non‐chalk salmon be designated as two distinct Evolutionarily Significant Units that each contain multiple Management Units. The chalk river salmon, especially those from southern England, are identified as making a significant contribution to the overall diversity of the species within the English Channel region. Accordingly, we suggest that the salmon populations of the chalk streams could be considered as meeting the criteria for recognition as a distinct subspecies of salmon, Salmo salar calcariensis . Taken together, our findings highlight the urgent need for a better understanding of the intraspecific diversity of the species and the importance of such information in enhancing the conservation and protection of Atlantic salmon populations inhabiting the chalk rivers of southern England and northern France.

Accurate detection of hybridization and introgression is critical for both evolutionary research and applied conservation. In many systems, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the invasive H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs previously developed to distinguish species between American and European lobsters and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we present a resampling-based evaluation of this panel’s performance under realistic introgression scenarios, using individual-based population genetic models informed by empirical data. We show that the panel retains discriminatory power across multiple hybrid classes, with diminishing accuracy in second-generation backcrosses. These findings validate the panel’s utility for applied monitoring and highlight the broader potential of resumpling-anchored frameworks to benchmark hybrid detection tools in a wide range of species. Article summary: This study tests how well a reduced panel of genetic markers can detect hybridization across multiple generations. Using empirical genetic data of a 79-SNP panel from European and American lobsters, the authors generated individuals with known ancestry proportions through a resampling framework that preserves observed genetic variation. These data were analysed using model-based genetic assignment and ordination. The results show that the marker panel reliably identifies pure species and first-generation hybrids, but has reduced power to distinguish later backcross generations, mainly between adjacent hybrid classes. The study provides a practical benchmark for evaluating reduced marker panels used in applied monitoring and conservation genetics.

Wrasse species are widely used as cleaner fish in salmon aquaculture but their performance as cleaner fish may be impacted by thermal and ontogenetic changes. Understanding the conditions in which each species of wrasse is most productive as cleaner fish is hugely valuable to make informed decisions on the management of fisheries. To do this, we use a novel geochemical proxy to reconstruct ontogenetic trends in thermal habitat and field metabolic rate for six species of wrasse from two sampling locations from the Isle of Skye (Scotland) and Dorset (southern England). We describe consistent ontogenetic transitions from warmer to cooler thermal habitats across all species, and demonstrate reductions in activity levels associated with ontogenetic habitat shifts after accounting for body size and temperature effects. Field metabolic rates were not significantly different between Dorset and Skye after accounting for body size and temperature. Ontogenetic shifts in thermal habitat and activity level have implications for the effectiveness of wrasse as cleanerfish, as well as providing evidence to support size-based harvesting rules. More broadly, this work highlights the potential of otolith isotope analyses to recover field-based, context-specific data on physiology and thermal ecology, advancing fisheries conservation and management strategies.

Maerl beds, formed by free‐living coralline red algae, are biodiversity‐rich and carbon‐storing habitats of high conservation value but remain understudied at the genomic level. Here, we present the first draft genomes and population genomic analyses for two dominant maerl‐forming species in the north‐east Atlantic, Phymatolithon calcareum and Lithothamnion corallioides . Using maerl samples genotyped at over 15,000 single nucleotide polymorphisms (SNPs) across England, Wales and additional European sites, we assessed clonal diversity, population structure and potential adaptation to environmental gradients. P. calcareum generally showed moderate clonal diversity, though extreme clonality driven by a single genet (multi‐locus lineage) was detected at certain sites. In comparison, L. corallioides displayed high clonal diversity, with most maerl samples representing distinct genets, although local dominance of a single genet was occasionally observed. Contrasting clonal dynamics have important implications for resilience, as populations dominated by a few clones may be more sensitive to environmental change. Population structure analyses in both species revealed strong genetic differentiation between sites, consistent with limited dispersal, while genomic associations identified candidate SNPs linked to climate in P. calcareum , albeit explaining only a small proportion of the observed genetic variation. Genomic offset analyses suggested that certain populations may require greater shifts in allele frequencies to avoid being maladapted to mid‐century climate scenarios. Together, these findings highlight both genetically diverse and potentially vulnerable maerl populations, some of which fall within existing marine protected areas. Integrating genomic insights with ecological monitoring will help inform conservation and restoration strategies for these irreplaceable, high natural capital value habitats.

The European lobster ( Homarus gammarus ) and its sister species, the American lobster ( Homarus americanus ), are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster, but not yet for the European lobster, despite its ecological significance, and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6%. As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry, performed using independently sampled European lobsters (3.18 - 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the H. gammarus assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterised gene expression across ten tissues to generate a tissue-level gene expression atlas, available at www.LobsterGeneX.com . Using single-copy orthologs, we estimated a divergence time of 26 Mya (95% HPD 22 - 30 Mya) between H. gammarus and H. americanus , corresponding to the Oligocene-Miocene boundary. We also identified Homarus -specific gene duplications with roles in immunity and longevity, including telomere maintenance. The reported genomic resources can facilitate future research into lobster biology, support sustainable fisheries and aquaculture management practices, and enable investigations of the evolutionary mechanisms underlying basic biological processes, notably immunity and longevity in Homarid lobsters. Significance Statement: The European lobster ( Homarus gammarus ) and the American lobster ( Homarus americanus ) are large benthic decapod crustaceans with significant seafood value, known for their remarkable longevity, with typical lifespans of 30-55 years in the wild and maximum lifespans of up to 80 years. Lobsters grow, reproduce and regenerate limbs throughout their life, and there are very few reports of tumours or age-related diseases. We generated and herein share a high-quality genome assembly and annotation for the European lobster alongside a tissue expression atlas, LobsterGeneX , which enables the visualisation of gene expression profiles across ten tissue types. Based on the genetic information generated, we also provide an estimated time for the divergence between H. gammarus and H. americanus (26 Mya) and identify duplication events for genes related to immunity and longevity. The European lobster reference genome will facilitate further research for investigations into local adaptation in lobster populations, genomic mixing in Homarid hybrids, and identification of genes of interest in aquaculture, ageing, regeneration, disease and cancer resistance.

Populations of Atlantic salmon continue to suffer marked declines in abundance due to stressors acting in both their freshwater and marine habitats. It is therefore an imperative to identify populations in need of increased conservation intervention, with the aim of preserving as much as possible the genetic diversity present within the species. Previous microsatellite-based analyses have shown the chalk rivers of southern England and northern France to hold genetically distinct populations of salmon. However, these salmon populations have never been investigated in the same study. Using a suite of 93 single nucleotide polymorphism loci and samples from 42 British Isles and French rivers, we demonstrate the French and English chalk salmon to be closely related and distinct from salmon inhabiting non-chalk rivers. The identification of a small number of significant F _ST outliers suggests that this distinction is driven by local adaptation. We propose that the chalk and non-chalk salmon be designated as two distinct Evolutionarily Significant Units that each contain multiple Management Units. The chalk river salmon, especially those from southern England, are identified as making a significant contribution to the overall diversity of the species within the English Channel region. As a consequence, we propose that the salmon populations of the chalk streams may meet the criteria for recognition as a distinct subspecies of salmon, Salmo salar calcariensis . Taken together, the results presented here highlight the urgent need for enhanced conservation and protection for the Atlantic salmon populations inhabiting the chalk rivers of southern England and northern France.