Heat shock proteins are highly conserved in nature and act as molecular chaperones for other proteins, repairing and preventing misfolding or inappropriate interactions. They also assist in transporting these molecules between cellular compartments. Although these functions are performed under physiological conditions, the loss of protein stability under stressful conditions increases the expression of HSPs (Wei et al., 2020).

The regulation of heat shock proteins (HSPs)—one of the most evolutionarily conserved cellular mechanisms—occurs through the expression of inducible genes, that is, genes expressed under the influence of a stressor, such as heat shock, or substance. When cells are subjected to such stressors, they experience proteotoxic stress and other cellular disturbances that trigger specific signaling pathways, ultimately leading to the activation of the heat shock response. The expression of HSPs involves transcriptional activation mediated by a specific transcription factor, HSF (Heat Shock Factor). Under normal conditions, cells contain HSF in both the cytoplasm and the nucleus in its monomeric form, which does not bind to DNA (Mikhailova et al., 2025). Under basal conditions, the transcription factor HSF1 (Heat Shock Factor 1) remains in the cytoplasm in an inactive monomeric form, complexed with chaperone proteins such as HSP70 and HSP90, which keep it repressed (Banfi et al., 2025). In response to heat shock and other physiological stresses, HSF is phosphorylated by protein kinases and forms trimers that accumulate within the nucleus. These trimers bind to Heat Shock Elements (HSE), specific DNA sequences that trigger the transcription of HSP70 mRNA. The mRNAs then translocate to the cytosol, where they promote the synthesis of additional HSP70 proteins. These newly synthesized HSP70 molecules bind to damaged proteins, aiding in their stabilization and repair (Singh et al., 2024).

These proteins are organized into families based on the similarity of their coding sequences and the molecular weight of the proteins, and are generally classified as HSP10, HSP40, HSP60, HSP70, HSP90, HSP100, and HSP110 (Makhoba, 2025). Examples of such stimuli include exposure to radiation or heavy metals, nutrient deprivation, hypoxia, infections, and inflammation, among others (Killian et al., 2020; Koyama et al., 2024). All known forms of stress, if sufficiently intense, induce the expression of these proteins. Associations of these groups with specific functions or phenotypes are also made, but this is questioned due to the difficulty in determining the stress to which the increased expression relates, since organisms rarely face a single adversity at a time (Chen et al., 2018; Jacob et al., 2017; Singh et al., 2024). Furthermore, since organisms face secondary impacts of multiple environmental stressors at a time, and the responses to stress are highly individual, and species-specific (Iyer et al., 2021; Singh et al., 2024).

Marine contamination by heavy metals (such as Cd, Pb, and Hg) and polycyclic aromatic hydrocarbons (PAHs) represents one of the major threats to the biological integrity of coastal ecosystems. These compounds interact with DNA and histone proteins, promoting hypermethylation of promoter regions of detoxification genes, such as those of the CYP450 family, and inducing epigenetic silencing of antioxidant pathways (Aluru, 2017; Brander et al., 2017; Marczylo et al., 2016; Suter and Aagaard-Tillery, 2009).

In studies conducted with the mussel Mytilus edulis, individuals from contaminated estuaries exhibited differential methylation patterns in genes associated with cellular defense and metal homeostasis, revealing the epigenome’s high sensitivity in reflecting chronic pollution exposure (Bjerknes et al., 2024; Corrochano-Fraile et al., 2024; Regan et al., 2024). These findings reinforce the use of epigenetic markers as early indicators of environmental impact, complementing traditional chemical and physiological assessments.

Global climate changes have been profoundly altering the conditions of marine ecosystems, impacting the metabolism, reproduction, and survival of species. Ocean acidification and water warming modify the epigenetic regulation of genes associated with energy metabolism and thermal tolerance (Alter et al., 2024; Liu et al., 2025; Putnam et al., 2016; Zetzsche and Fallet, 2024).

In corals of the genus Pocillopora, for example, hypomethylation of metabolic genes, such as PDK4, has been observed in response to prolonged acidification, which modulated phenotypic plasticity and favored local adaptation (Putnam et al., 2016). Similarly, in Atlantic killifish (Fundulus heteroclitus) chronically exposed to polycyclic aromatic hydrocarbons, resistance to contaminants is associated with extensive changes in hepatic gene expression and alternative splicing, including the aryl hydrocarbon receptor gene ahr2b, as well as a marked reduction in intra-population variance of metabolic gene expression (Harishchandra et al., 2024). These results suggest that epigenetics acts as a molecular mediator of physiological acclimatization, enabling flexible and potentially heritable responses (Luo et al., 2020; Zhou et al., 2025).

Hypoxia, common in eutrophic regions and estuarine zones, represents one of the most critical stressors for marine species (Figure 2). The reduction of dissolved oxygen activates epigenetic responses associated with the regulation of anaerobic metabolism and redox balance (Hindle, 2020; Liu et al., 2022; Johnston et al., 2025).

Johnston et al. (2025) analyzed fish models subjected to chronic hypoxia, identifying that demethylation of promoters of anaerobic metabolism genes (such as LDH-A and HIF-1α) is directly linked to tolerance to low oxygen. The authors demonstrate that epigenetic modifications act as “molecular switches” that reprogram redox balance, enabling survival in eutrophicated estuarine zones.

A study on coral larvae exposed to hypoxia revealed that histone acetylation (H3K27ac) modulates the expression of redox detoxification genes. This mechanism promotes phenotypic plasticity even under abrupt oxygen fluctuations, suggesting an analogous model to that observed in adult corals. The discovery is relevant to Pocillopora by explaining how reef species maintain metabolic functions in unstable environments (Alderdice et al., 2022).

A genetic-epigenetic focused study in marine mammals (such as elephant seals) identified positive selection in hypoxia-regulated genes (EPAS1, VHL), with conserved epigenetic signatures that modulate redox stress responses. The research offers evolutionary parallels to understand how epigenetics can accelerate adaptations in marine species under climate pressure (Hindle, 2020).

In Fundulus heteroclitus, exposure to hypoxia led to the deacetylation of histones H3 and H4, resulting in the repression of genes involved in oxidative processes and the activation of alternative metabolic pathways. These epigenetic adjustments allow the organism to optimize energy use and reduce oxidative stress, maintaining cellular homeostasis in unstable environments (Aluru et al., 2025; Chang et al., 2025).

Whole-genome bisulfite sequencing (WGBS) is regarded as the gold standard for DNA methylation analysis, enabling single-base resolution detection. In this method, DNA is treated with sodium bisulfite, which converts unmethylated cytosines into uracils, while methylated cytosines remain unchanged (Cao et al., 2023). Subsequent sequencing allows highly precise discrimination of genomic regions that exhibit specific methylation patterns (Kurdyukov and Bullock, 2016). However, the high cost, substantial sequencing depth requirements, and the need for sophisticated bioinformatic pipelines make WGBS technically and financially demanding, constituting a major methodological challenge for large−scale or non−model marine organisms (Agius et al., 2023; Klughammer et al., 2015).

Recent applications of WGBS in marine organisms, such as pearl oysters (Gu et al., 2023) and sea cucumbers (Chang et al., 2023), for mapping DNA methylation in responses to environmental stresses and immunity, with advances in high-resolution sequencing and phenotypic plasticity analysis. Reduced-representation approaches such as RRBS and targeted bisulfite sequencing offer a pragmatic compromise, lowering sequencing costs and analytical complexity by focusing on CpG-rich regions or predefined loci while retaining single-base resolution at the sites of interest (Moser et al., 2020). Although such methods inevitably miss part of the methylome, they are compatible with routine monitoring when combined with prior identification of informative loci and can deliver sufficiently fast and accurate measurements for biomarker applications in many marine systems (Panagopoulou et al., 2026; Tian et al., 2020; Vrba et al., 2020). At present, truly high-throughput, field-deployable epigenetic assays remain limited, but the combination of reduced-representation methods, targeted assays (e.g. locus-specific bisulfite PCR, ddPCR) and automated library preparation already allows for practical, relatively rapid and accurate detection of selected epigenetic markers in a monitoring context, especially when sample throughput is moderate rather than massive (Van den Ackerveken et al., 2025; Zhou et al., 2024).

In marine organisms, WGBS is especially valuable for mapping how extreme environmental conditions influence gene regulation. Bivalve mollusks and estuarine fish, for example, show phenotypic plasticity that appears to be mediated by dynamic DNA methylation patterns, enabling adaptive responses to chemical pollution and changes in water physicochemical parameters (Li et al., 2025; Nicolini et al., 2023; Regan et al., 2021; Suárez-Ulloa et al., 2013). Studies in bivalves have shown that methylation profiles are linked to the expansion and regulation of immune gene families, supporting adaptation to stressors such as hypoxia and chemical contamination (Martínez et al., 2023). However, the application of WGBS in non-model species is still limited by the scarcity of high-quality reference genomes, which complicates the annotation of methylated regions (Mc Cartney et al., 2024). To address this, de novo genome assemblies and comparative bioinformatic strategies are increasingly being adopted (Muñoz-Barrera et al., 2025; Satam et al., 2023).

In practice, the choice between genomic, transcriptomic, and epigenomic analyses depends on the type of question being addressed and on logistical constraints. Genomic data are most informative when the aim is to quantify standing genetic variation or identify hard selective sweeps, whereas transcriptomic approaches are preferable when the focus is on short-term changes in gene activity in response to specific stressors (Chen et al., 2022; Lancaster et al., 2022; Stark et al., 2019). Epigenomic analyses, in turn, are particularly useful when the goal is to detect environmentally responsive regulatory changes that may persist beyond immediate transcriptional responses, including potential carry-over and transgenerational effects (Turner, 2009; Walker et al., 2025). Routine multi-omics screening of wild populations is unlikely to be feasible in most monitoring programs due to cost and infrastructure requirements; instead, targeted epigenetic assays can be deployed once candidate loci or pathways have been identified through initial, more comprehensive studies (Balard et al., 2024; Han et al., 2020; Krassowski et al., 2020).

Another widely used technique is Chromatin Immunoprecipitation Sequencing (ChIP-seq), which enables the identification of post-translational modifications in histones, such as acetylation, methylation, or phosphorylation. Such modifications directly influence chromatin structure, modulating DNA accessibility and, consequently, gene expression (Kurdyukov and Bullock, 2016).

In the marine context, ChIP-seq enables an understanding of how organisms respond molecularly to environmental stressors (Fuller et al., 2025; Xu et al., 2022). Changes in histone marks can indicate genes that are activated or silenced in response to specific conditions, such as increased atmospheric CO₂ and the resulting ocean acidification. This approach is promising for revealing adaptive epigenetic signatures in marine populations, providing evidence of mechanisms of resilience or vulnerability.

However, the execution of ChIP-seq in marine species faces methodological challenges, primarily due to the need for highly specific antibodies and the complexity of obtaining suitable tissues in natural environments. Additionally, epigenetic patterns often vary between tissues of the same organism, which requires meticulous standardization in the selection of biological material (Bhute et al., 2025; Tahara and Ozaki, 2025).

Despite its great potential, epigenetic analysis in marine organisms still faces several challenges. A large portion of marine biodiversity lacks fully sequenced and annotated genomes, which complicates the interpretation of high-resolution epigenomic data. Additionally, different tissues may exhibit markedly distinct epigenetic profiles even within a single organism. This makes comparative analysis across multiple tissues necessary, thereby increasing experimental complexity (Abdelnour et al., 2024; Brennan et al., 2025; Liu et al., 2025).

These constraints are particularly acute in developing countries, where marine biodiversity losses are often severe but financial and technical resources for high-throughput sequencing are limited (Hestetun et al., 2020; Heuertz et al., 2023). In such contexts, cost-effective strategies based on sentinel species, reduced-representation or targeted assays, and regional reference datasets may provide an entry point for incorporating epigenetic tools into monitoring without requiring full-scale genomics infrastructure (Longtin et al., 2025; Šrut, 2022). Capacity-building initiatives and collaborative networks that share protocols, bioinformatic pipelines and reference epigenomes will be essential to ensure that the benefits of epigenetic biomonitoring are not restricted to well-resourced regions (Adebamowo et al., 2023; Kiosia et al., 2024; Subasinghe et al., 2026; Zare Jeddi et al., 2026).

Epigenetic marks are highly dynamic and can vary according to seasonality, pollution, temperature fluctuations, and other environmental factors. Distinguishing temporary changes from heritable alterations therefore remains a constant challenge. Many techniques were originally developed for “model organisms” such as Drosophila, mice, and humans, and their adaptation to marine organisms requires technical adjustments, including the development of DNA and chromatin extraction protocols specifically designed for tissues with high polysaccharide or salt content (Klibaner-Schiff et al., 2024; Suter and Aagaard-Tillery, 2009).

Thus, epigenetic analysis techniques such as WGBS and ChIP-seq are powerful tools for understanding the regulatory mechanisms that underpin phenotypic plasticity and adaptation in marine organisms (Bogan and Yi, 2024; Putnam et al., 2016). Recent advances in next-generation sequencing, bioinformatics, and comparative biology have substantially expanded the scope and resolution of marine epigenomics, enabling increasingly detailed characterization of environmentally responsive epigenetic variation (Satam et al., 2023). Understanding the epigenetic basis of adaptive responses in marine species is not only a scientific goal but also an urgent necessity in the context of global climate change, in which coastal and oceanic ecosystems are subjected to intensifying environmental pressures (Riancho et al., 2016).

Marine taxa exhibit distinct epigenetic response patterns to environmental stressors, reflecting their phylogenetic constraints and ecological niches. In bivalves like Mytilus edulis, chronic pollution exposure induces hypermethylation of detoxification gene promoters (e.g., CYP450 family), altering metal homeostasis pathways without immediate physiological deterioration (Hook et al., 2014). This taxon-specific epigenetic sensitivity positions mussels as robust bioindicators for coastal heavy metal contamination.

Conversely, corals (Pocillopora spp.) demonstrate stressor-specific histone modifications: thermal stress triggers H3K27ac redistribution in symbiosis-related genes, while acidification causes hypomethylation of metabolic regulators like PDK4 (Martinez-Haro et al., 2022).

Fish lineages reveal further divergence; hypoxia-tolerant species (e.g., Fundulus heteroclitus) exhibit rapid histone deacetylation in oxidative metabolism genes, whereas salmonids show gametic DNA methylation reprogramming transmitted intergenerationally under warming stress (Wernersson et al., 2015). These taxon-divergent patterns underscore that conservation strategies must account for epigenetic response variability when predicting species resilience.

Epigenetic biomarkers provide powerful advantages for environmental assessment because they function as early-warning indicators, exhibit high specificity to distinct stressors and offer a sensitive means of integrating molecular variation with ecosystem-level patterns. DNA methylation shifts in Mytilus gill tissue, for instance, detect pollutant exposure well before conventional physiological assays register a response (Hook et al., 2014), supporting their value as anticipatory diagnostic tools. Recent analyses of invertebrate methylomes further demonstrate that environmentally responsive CpG methylation can serve as a reliable signature of tolerance mechanisms and pollutant exposure levels, while also revealing important methodological biases that must be considered when applying these techniques in ecological contexts (Anastasiadi and Beemelmanns, 2022).

In corals, chromatin-level markers such as H3K9me3 and H3K27ac differentiate acidification-driven metabolic stress from thermal stress with high precision, illustrating the potential of histone landscapes to function as fine-scale fingerprints of environmental pressure. This pattern is consistent with growing evidence showing that gene-body and promoter methylation in scleractinian corals reflects both seasonal environmental variation and physiological acclimatization capacity (Rodríguez-Casariego et al., 2020). Similarly, non-coding RNA expression gradients in sediment-dwelling polychaetes correlate strongly with eutrophication levels across estuarine zones (Hagger et al., 2006), underscoring the ability of epigenetic markers to track spatial and temporal dimensions of ecosystem degradation.

Despite recent progress, important gaps remain (Figure 4). The lack of standardized baseline epigenomes for most marine taxa hampers cross-population comparisons, and high-resolution approaches such as ChIP-seq are difficult to implement in field conditions because obtaining high-quality chromatin from complex marine samples is technically challenging. Horizon-scan assessments highlight that, although epigenetic responses in marine animals are powerful tools for ecological monitoring, they are still underutilized, partly because robust functional links between methylation patterns and organismal performance require further validation (Hofmann, 2017). Emerging computational approaches may help address these gaps: machine-learning models capable of predicting environmentally responsive methylation hotspots from transcriptomic or reduced-representation methylation datasets are beginning to reduce dependence on whole-genome bisulfite sequencing, thereby enabling broader biomonitoring applications even in species lacking reference genomes (Trigg et al., 2022). Together, these advances position epigenetic biomarkers as promising components of next-generation marine monitoring frameworks (Figure 4), provided that technical, ecological and taxonomic challenges are progressively resolved.

Because the practical value of epigenetic biomarkers ultimately depends on their incorporation into concrete assessment schemes, it is crucial to consider how they could be embedded in existing policy instruments. The incorporation of epigenetic biomarkers into regulatory monitoring frameworks has become an increasingly relevant topic, particularly within the context of the European Union Water Framework Directive (WFD) (Table 3), which establishes ecological status assessments that integrate chemical, biological and functional indicators of ecosystem health. We focus on the WFD here because it is one of the most influential and widely adopted regulatory models for aquatic ecosystems and explicitly calls for effect-based indicators that can act as early-warning tools in water-quality assessment. The WFD explicitly encourages the development of effect-based monitoring tools capable of detecting early biological impairment, a need that motivated the publication of the European technical report by Wernersson and colleagues, which highlights the limitations of traditional monitoring approaches that rely heavily on chemical concentrations and late-stage physiological endpoints, recommending instead the implementation of sensitive molecular biomarkers able to signal sublethal stress before community-level deterioration becomes evident (Wernersson et al., 2015).

Although this foundational report primarily focuses on biochemical and cellular-level endpoints, its framework is fully compatible with the integration of epigenetic markers, particularly those that capture environmentally induced modifications in DNA methylation, histone states and small RNA profiles. Within coastal and estuarine environments, bivalves such as Mytilus and Crassostrea already serve as sentinel organisms in WFD monitoring programs, and their suitability for molecular biomonitoring is well documented through omics-based approaches that have been used to detect harmful compounds, classify pollution gradients and uncover molecular signatures associated with chronic exposure (Suárez-Ulloa et al., 2013).

The addition of DNA methylation and chromatin-level indicators would substantially strengthen this framework because epigenetic marks respond rapidly to environmental variation and can reveal biological stress long before population declines or shifts in species composition occur. Recent studies integrating genetic and epigenetic datasets reinforce that environmentally driven molecular changes—including methylation alterations and chromatin remodeling—are key components of rapid adaptation to multiple stressors, such as acidification, thermal anomalies and hypoxia, demonstrating that complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global-change stressors (Brennan et al., 2025).

Incorporating such markers into WFD assessments would allow regulators to quantify biological impairment in a mechanistic and temporally sensitive manner, particularly in regions where chemical concentrations fluctuate or where complex mixture effects make single-compound assessments insufficient. Advances in omics-enabled monitoring demonstrate that large-scale molecular datasets can be used to evaluate ecological status and resilience in ways aligned with the WFD’s mandate for integrative assessment, with genomic and transcriptomic tools contributing substantially to the design and evaluation of marine protected areas and illustrating how molecular indicators can be embedded into regulatory frameworks and management plans (Jeffery et al., 2022).

The same logic applies to epigenetic indicators: by revealing how environmental gradients shape gene regulation across populations and habitats, they can help identify water bodies transitioning from “good” to “moderate” ecological status before macroscopic deterioration occurs. Moreover, epigenetically responsive loci associated with acidification or thermal stress—such as those identified in corals under altered pH and temperature regimes, where hypomethylation of metabolic genes such as PDK4 has been observed in response to prolonged acidification, modulating phenotypic plasticity and favoring local adaptation (Putnam et al., 2016)—could serve as diagnostic molecular endpoints particularly relevant to climate-sensitive ecoregions. Nevertheless, the integration of epigenetic biomarkers into the WFD presents challenges that parallel those noted in the technical report. The absence of baseline epigenomes for many European marine species complicates the establishment of reference conditions, an essential requirement for WFD status classification (Andersen et al., 2004). Unlike genomic resources, which are rapidly expanding through large consortia, dedicated epigenetic databases for marine taxa are still scarce and fragmented, meaning that most comparative analyses rely on project-specific datasets rather than standardized repositories (Balard et al., 2024; Sawh et al., 2025).

Spatial variability in epigenetic baselines—driven by genetic structure, local adaptation and seasonality—must also be addressed to avoid misinterpretation of natural variation as anthropogenic stress. These limitations, however, are increasingly mitigated by the expanding availability of reference genomes, improved comparative bioinformatic pipelines and population-wide molecular surveys across marine taxa (Catarino et al., 2025; Petrocheilou et al., 2026). Taken together, these developments suggest that epigenetic biomarkers offer substantial promise within the WFD structure, particularly as early-warning indicators that complement traditional chemical analyses and ecological indices (Oros et al., 2025). By integrating effect-based molecular diagnostics with broader ecological assessments, regulatory agencies can improve the sensitivity, specificity and predictive power of coastal water evaluations. This approach aligns directly with the WFD’s long-term goal of achieving good ecological status through proactive, mechanism-informed monitoring capable of responding to accelerating environmental change (Smith et al., 2025).

Severe environmental changes result in large-scale biodiversity loss, and currently one million species are at risk of extinction (Díaz et al., 2019). Individual species and species composition provide essential contributions to ecosystem functioning and human health (Cardinale et al., 2012; Díaz et al., 2018, 2019; Duffy et al., 2017), such that biodiversity loss can directly reduce ecosystem health and the contributions of nature to human well-being (Brauman et al., 2020; Cardinale et al., 2012; Le Provost et al., 2023). In light of this problem, one of the central objectives of conservation and biological management strategies is to mitigate and anticipate the impacts of environmental changes (Carvalho et al., 2019).

Most of these efforts still focus primarily on species diversity itself, as well as on phylogenetic diversity among species, even though biodiversity varies across multiple hierarchical scales (Des Roches et al., 2021; Laikre et al., 2020). Therefore, existing approaches tend to overlook the importance of diversity within species—i.e. intraspecific diversity—which can rapidly decline under environmental change, as documented by Exposito-Alonso et al. (2022); Leigh et al. (2019) and Millette et al. (2020) in studies of genetic diversity. Concomitantly, it is well established that interspecific diversity shapes community structure and ecosystem functioning (Raffard et al., 2021).

Numerous studies across distinct taxonomic groups have demonstrated that variation among ecotypes, populations and genotypes can substantially influence population growth rates, community-level diversity—including both species richness and evenness—and key ecosystem functions such as primary productivity, nutrient cycling and decomposition (Govaert et al., 2024; Matthews et al., 2016; Pantel et al., 2015). Although the materials identified in the recent search do not directly address these specific studies, some works conceptually align with the broader theme that ecological and evolutionary processes jointly structure biodiversity and ecosystem functioning, particularly those exploring the mechanisms connecting ecological communities and genetic diversity (Overcast et al., 2021) or discussing the population–species continuum in the context of conservation genomics (Coates et al., 2018). These sources emphasize the interplay between ecological interactions and evolutionary divergence, which indirectly resonates with the patterns highlighted in our synthesis.

It is important to note that interspecific and intraspecific diversity are not independent of one another. These two levels of biodiversity often exhibit positive correlations in natural communities (Vellend et al., 2014), and the effects of one level of diversity on ecosystem functioning may depend on variation at the other level. In Crawford and Rudgers (2010), for example, the relationship between interspecific diversity and whole-community plant biomass depended on the degree of intraspecific diversity within the dominant plant species. Recent work continues to reinforce this integrative perspective, showing that both intra- and interspecific variation can jointly mediate ecosystem processes and that their contributions may be comparable in magnitude (Govaert et al., 2024), while large-scale manipulative experiments in tropical systems demonstrate that changes in both forms of diversity can influence herbivory and other ecosystem-level responses (Grele et al., 2024). Although these newer studies do not examine the same mechanisms reported by Crawford and Rudgers (2010), they reaffirm that interactions between the two biodiversity levels are central to understanding ecosystem functioning.

When ecosystem functioning is understood as the sum of the functional contributions of individuals within a community, its value may change due to an increase or decrease in interspecific and/or intraspecific diversity. This increase or decrease may be driven by changes in the abundance—including gains or losses—of interspecific groups (that is, species) or intraspecific groups (that is, phenotypic groups within species), as well as by changes in the functional contributions of specific interspecific and intraspecific groups (Govaert et al., 2024). In this framework, ecosystem functioning becomes contingent not only on which species are present and how abundant they are, but also on the phenotypic and genetic structure within those species, such that both levels of diversity jointly determine the overall functional output of the community (de Bello et al., 2021; Whitlock, 2014).

Against this backdrop, epigenetic variation adds an additional, conservation-relevant layer to biodiversity because it can modulate phenotypes and functional traits without changes in DNA sequence and can, in some cases, be transmitted across generations. By shaping intraspecific phenotypic diversity and influencing how populations respond to environmental stress on ecological time scales, epigenetic mechanisms have direct implications for the capacity of species and communities to maintain ecosystem functioning under rapid change (Balard et al., 2024; Lamka et al., 2022). From a conservation perspective, this suggests that epigenetic diversity—captured by environmentally responsive DNA methylation, histone modifications and regulatory RNA profiles—may complement traditional genetic and species-level metrics as a proxy for adaptive potential and resilience in changing marine environments (Cao et al., 2023; Li and Tollefsbol, 2011).