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Frontiers in Ocean Sustainability ·

Volume 4 - 2026 | https://doi.org/10.3389/focsu.2026.1820724

Integrating molecular taxonomy and genomics to strengthen marine biosecurity: a Mediterranean perspective

  • Noel Vella1*corresponding author
  • Adriana Vella1*corresponding author
  1. Conservation Biology Research Group, Department of Biology, Faculty of Science, University of Malta, Msida, Malta
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Abstract

The introduction of non-indigenous species (NIS) threatens marine biodiversity, ecosystem services and biosecurity worldwide. Rapid and accurate NIS identification is a fundamental first step in understanding biological introductions and managing invasive species. While traditional taxonomy remains invaluable, its reliance on morphological traits and taxon-specific expertise can significantly hinder the identification of cryptic species and early life stages. Molecular approaches, particularly DNA barcoding and eDNA metabarcoding, overcome these limitations by enabling reliable detection across diverse taxa and life stages, complementing classical methods. However, accurate molecular identification relies heavily on the integrity of curated reference databases, ideally sourced from native populations. Recent large-scale initiatives focusing on standardized genetic and genomic approaches are critical for establishing the reference libraries required for regulatory confidence. Furthermore, population-level genomic analyses are increasingly necessary to capture the complexity of marine introductions. These tools detect multiple introductions, population-level admixture and enhanced adaptive potential in novel environments. Genomic approaches also reveal complex dynamics, including intraspecific introgression between introduced populations, hybridization between closely related species and cryptic invasion of introduced alleles into native populations. This manuscript emphasizes the need for frameworks that integrate rigorous, standardized molecular taxonomy and population genomics into biosecurity frameworks providing practitioners with clear methodological guidance to enable well-informed management strategies.

Keywords

1 Introduction

Globally the acceleration of marine non-indigenous species (NIS) introductions and biological invasions are reshaping biological communities at an unprecedented rate (Seebens et al., 2025), driven by the synergistic pressures of intensifying maritime traffic, climatic shifts modifying environmental suitability and dispersal dynamics, and expanding artificial coastal infrastructure (Seebens et al., 2017, 2018; Sardain et al., 2019; Bereza et al., 2020; Katsanevakis et al., 2025; Seebens et al., 2025). As a densely populated, semi-enclosed sea hosting major shipping routes, the Mediterranean is a hotspot for NIS (Zenetos et al., 2022a,b). Its ports and marinas amplify opportunities for introductions and secondary dispersals, compounded by recurrent introductions via the Suez Canal (Galil et al., 2015). This intense anthropogenic pressure, maritime connectivity, climatic warming and pronounced biogeographical heterogeneity (Occhipinti-Ambrogi and Galil, 2010; Zenetos and Galanidi, 2020; Katsanevakis et al., 2025) make this basin an ideal model for understanding the complex interplay of anthropogenic and environmental drivers related to NIS biology (Lejeusne et al., 2010).

Over the past few decades, established NIS populations in the Mediterranean have increased significantly (Zenetos and Galanidi, 2020; Zenetos et al., 2022a) driving biodiversity loss and ecosystem degradation and threatening ecosystem services (Kourantidou et al., 2021; Tsirintanis et al., 2022; Zenetos et al., 2022b; Gjedde et al., 2024; Bodey et al., 2025). This basin's ongoing “tropicalization” is characterized by an influx of thermophilic species from the Red Sea and the Atlantic Ocean, continuously yielding new records of NIS (Zenetos et al., 2022b; Ragkousis et al., 2023), especially within the warmer eastern basin where the ratio of alien to native species is highest (Katsanevakis et al., 2014, 2025; Galil et al., 2018).

While NIS governance frameworks expanded significantly to address these threats, they frequently lag behind the extensive scientific knowledge and technological advances accumulated in NIS invasion biology (Faulkner et al., 2020; Seebens et al., 2025). This mismatch between rigid governance and dynamic biological reality risks creating blind spots in marine biosecurity. Traditional visual monitoring struggles to identify cryptic taxa, small-bodied individuals, early life stages (Briski et al., 2011; Vella et al., 2017; Bezeng and Van Der Bank, 2019) and low-abundance populations (Fediajevaite et al., 2021; Fonseca et al., 2023). By the time populations become visually conspicuous, eradication is usually logistically and economically unfeasible (Cuthbert et al., 2021). Therefore, integrating high-resolution molecular tools, ranging from DNA barcoding to eDNA metabarcoding and population genomics, is fundamentally necessary. This perspective article highlights how the currently established scientific capability can translate into practical, standardized tools for management and policy implementation.

2 Current governance frameworks for marine biosecurity

Globally, the Convention on Biological Diversity, through the Kunming–Montreal Global Biodiversity Framework, commits Parties under Target 6 to reduce the impacts of NIS by managing introduction pathways, preventing the establishment of priority species and at least halving introductions by 2030 (CBD, 2022; CBD and IUCN, 2024). These commitments are reinforced under United Nations Sustainable Development Target 15.8 (UN, 2026). In the marine environment, these objectives are also supported by the Ballast Water Management Convention, which regulates ballast water discharge to reduce transboundary transfers of viable organisms (IMO, 2026), and by the International Maritime Organization's Biofouling Guidelines, addressing hull-mediated dispersal (MEPC, 2023). However, compliance monitoring predominantly relies on visual inspections and typically focuses on indicator taxa, utilizing traditional methods that lack the diagnostic sensitivity of modern molecular techniques currently available to accurately detect early NIS introductions and track invasion dynamics.

Within the European Union, governance relies on the EU Invasive Alien Species Regulation, which targets the prevention, early detection, rapid eradication and management of invasive species of EU concern (European Commission, 2026b). This is complemented by the Marine Strategy Framework Directive (MSFD), which under Descriptor 2 of Good Environmental Status, requires EU Member States to ensure that NIS introductions do not adversely alter the structure, functioning and resilience of marine ecosystems (European Commission, 2026a). Regionally, coordination in the Mediterranean is provided by the Barcelona Convention and its Action Plan on Introductions of Non-Indigenous Species (UN Environment/MAP, 2017), focusing on pathway management, monitoring and adaptive response strategies, adjusting global measures to region-specific contexts.

Although there have been advancements in NIS governance frameworks aiming to harmonize actions by interrupting key stages of the invasion process, primarily focusing on pathway regulation, their reporting protocols remain predominantly based on species presence-absence records. This treats NIS introductions and invasions as discrete events rather than ongoing demographic and evolutionary processes. The species-based approach, typically adopted by these frameworks, poses a significant operational vulnerability. The legislative process to formally evaluate and list a new species of concern often takes years. In a rapidly changing Mediterranean Sea, a newly introduced thermophilic species can establish reproducing populations, disperse via secondary pathways and expand its geographic range far faster than the centralized policy can be updated to regulate it (Occhipinti-Ambrogi and Galil, 2010; Seebens et al., 2017).

The successful implementation of these regulatory instruments depends upon the early and accurate identification of NIS. Although conventional morphological taxonomy remains methodologically indispensable, its limitations are particularly pronounced in marine systems and uneven regional capacity further exacerbates identification bottlenecks. NIS often display morphologies that may be unfamiliar to local experts, and identification is frequently confounded by phenotypic plasticity, cryptic species complexes and taxonomic ambiguities in early life-stages (Vella et al., 2017; Zenetos et al., 2017). The latter often lack reliable identification keys (Ko et al., 2013) despite being the primary dispersal phase during range expansion for many NIS. These constraints not only hinder accurate detection but also delay management responses, allowing invasions to proceed undetected during their early establishment phases.

Additionally, persistent taxonomic and biogeographical biases further weaken biosecurity systems with conspicuous organisms, namely vertebrates and macrofauna, dominating both scientific research and regulatory attention (Seebens et al., 2018, 2025; Gjedde et al., 2024). Conversely, small-bodied organisms, including plankton, meiofauna and early life stages, remain underrepresented despite their critical role in marine dispersal. Such biases risk underestimating the role of founding populations in establishing NIS populations and possible subsequent invasions while leaving key introduction pathways widely unmonitored.

3 Discussion: the role of molecular tools in marine biosecurity

3.1 Enhancing species identification and detection capabilities

To overcome the limitations of traditional morphological identification, molecular approaches such as DNA barcoding and eDNA metabarcoding, are increasingly utilized to enhance the speed, scale, and accuracy of NIS detection. Case studies from the Mediterranean clearly demonstrate how DNA barcoding resolves cryptic taxa and corrects historical misidentifications (Bariche et al., 2015; Vella et al., 2017). For instance, morphological similarities previously led to the misidentification of the toxic pufferfish Lagocephalus guentheri. Correcting such taxonomic errors is critical not only for filling knowledge gaps in ecological monitoring but also for safeguarding public health (Vella et al., 2017; Giusti et al., 2019). Similar molecular interventions have proven essential for taxa exhibiting high levels of cryptic diversity, such as damselfish (family Pomacentridae), where morphological similarities and variable intraspecific colorations make visual surveys difficult (Tsadok et al., 2015; Vella et al., 2015a, 2016a,b; Osca et al., 2020). While not very sensitive compared to genomic markers, DNA barcoding has also led to the identification of possible regions for source populations (Vella et al., 2015b; Schubart et al., 2023; Vella et al., 2023).

Furthermore, eDNA surveillance acts as an effective, non-invasive early warning system capable of detecting low-abundance species that evade visual surveys. Current research indicates that eDNA metabarcoding typically identifies more species than traditional underwater visual assessments (Roblet et al., 2024). This sensitivity is particularly critical for detecting rare or elusive taxa during the early phases of an invasion, when population densities are too low for conventional detection. Studies such as Varrella et al. (2025) and Vella et al. (2025) have successfully identified the eDNA of NIS in high-risk introduction hubs including ports and marinas, reporting the genetic signatures of NIS never before recorded in their respective countries. Such monitoring provides biosecurity managers with the data needed to implement early mitigation measures. Additionally, recent eDNA analyses of ballast water, both within the Mediterranean and globally, have identified genetic signatures of NIS (Li et al., 2025a,b; Rani et al., 2026). Applying these techniques across broad spatial and temporal scales requires a paradigm shift in biodiversity monitoring, transitioning from direct observation, which relies on physical capture or visual census, to indirect molecular detection (Blancher et al., 2022; Zhang et al., 2023).

Despite offering unprecedented detection capabilities, the efficacy of these molecular tools relies inherently on the quality of the data available in genetic databases (e.g., GenBank, BOLD). These databases suffer from some unverified sequences that are not backed by scientific publications, taxonomic misidentifications and missing metadata (Collins and Cruickshank, 2013; Leray et al., 2019; Pentinsaari et al., 2020). These flaws can cause inaccurate species identifications or false positives during automated eDNA assignments (Carlton and Schwindt, 2024), potentially misdirecting mitigation measures while eroding policymakers' and managers' trust in these technologies (Sepulveda et al., 2020). Consequently, rigorous database curation is essential (Radulovici et al., 2021). Nonetheless, it must be stressed that conventional morphological techniques also suffer from high rates of misidentifications (Vella et al., 2017; Zenetos et al., 2017). Thus, the fundamental issue is not the molecular technique itself, but the robustness of its application, highlighting that standardized complementary methods remain essential to maximize diagnostic assurance.

To embed molecular tools into statutory frameworks, researchers must provide practitioners with clearer methodological guidance and standardized protocols. This necessity is driving major initiatives to enhance databases with reference sequences of well-documented and curated specimens, ideally sourced from native populations. The recently launched pan-European Biodiversity Genomics Europe (BGE) project represents such an effort by bringing together the European Reference Genome Atlas (ERGA) and International Barcode of Life in Europe (iBOL Europe), with the latter focusing on standardizing DNA barcoding methodologies for rapid, scientifically reliable molecular species identification (McCartney et al., 2024; iBOL Europe, 2026; Koureas et al., 2026). At the global level, to ensure regulatory confidence and minimize database-driven errors, platforms such as the Barcode of Life Data System (BOLD) have established strict minimum requirements. In the case of BOLD these include the use of universally accepted loci, a minimum sequence length and curated voucher metadata including geospatial collection details (Ratnasingham et al., 2024).

Molecular techniques should be regarded as a component of integrated taxonomy (Tancoigne and Ollivier, 2017; Sandall et al., 2023) and therefore to minimize inaccuracies, it is crucial that rigorous standard methodological pipelines of specimen and DNA curation are followed both when building DNA barcode reference libraries and also during routine molecular taxonomy analyses (Rimet et al., 2021). Whenever possible, specimens must be collected and recorded with well-documented metadata, morphological details and photographic evidence, while laboratory analyses and reporting should follow standardized protocols (Fediajevaite et al., 2021; Ratnasingham et al., 2024; Rani et al., 2026). Additionally, for eDNA monitoring, metabarcoding approaches should be complemented by parallel morphological and visual sampling (Xanthopoulou et al., 2025), especially when an eDNA signal detects a high-risk invasive species. In such cases, targeted physical surveys must be deployed to visually confirm the presence of the organism, validate the molecular hit and assess the population status of the NIS. The formalization of these validation steps enables molecular taxonomy to provide the highly reproducible, legally defensible data required to enforce modern marine biosecurity and trigger faster eradication responses.

3.2 Understanding the biology of NIS and associated biological invasions

While species identification and detection through DNA barcoding and metabarcoding is a critical first step, this does not fully capture the complexity of ongoing population-level processes (Rius and Darling, 2014; McGaughran et al., 2024), and therefore, the integration of population genetic and genomic tools (e.g. WGS and RADseq) is essential. The latter tools provide a deeper understanding of the mechanisms underpinning a species' biology (Formenti et al., 2022; Theissinger et al., 2023), improve the identification of source populations (Vella et al., 2015b, 2023; Schubart et al., 2023) and the evolutionary drivers that lead to invasion success (Kołodziejczyk et al., 2025).

Marine invasions are not shaped by isolated first records but by population-level processes operating across interconnected biological communities, with multiple independent introductions now recognized as the norm (Brown and Barney, 2021; Kołodziejczyk et al., 2025). Repeated introductions from genetically distinct sources generate population admixture, restoring genetic diversity lost through initial founder effects and enabling previously distinct populations to interbreed, thereby producing novel genotypes with enhanced adaptive potential. Within this context, genomic approaches can reveal complex dynamics such as hybridization between closely related species and intraspecific introgression between distinct populations of an introduced species, processes that are frequently exacerbated by secondary dispersal via maritime transportation and natural range expansion of the various introduced populations.

This mixture resolves the “genetic paradox” of invasion biology, explaining how small, newly established populations maintain high adaptive potential in new environments (Kołodziejczyk et al., 2025). In the Mediterranean, this is particularly exemplified by Lessepsian migration via the Suez Canal, which allows recurrent gene flow from the Indo-Pacific into the eastern Mediterranean basin. This biological corridor continuously enriches the NIS gene pool, enhancing their resilience to environmental stressors.

While this admixture drives the success of NIS populations, a different form of genetic exchange poses a direct threat to native biodiversity, namely when local populations introgress with non-native lineages of the same species, introducing non-native alleles into the local gene pool. The Mediterranean is rich in diversity with approximately 20% of the species considered as endemic (Coll et al., 2010) and has various native species with distinct genetic signatures, both between different ecoregions within the basin and even between the Mediterranean and the adjacent Atlantic Ocean (Patarnello et al., 2007; Pascual et al., 2017; Ragionieri et al., 2024). Consequently, the introduction of non-native lineages that can interbreed with native conspecifics leads to cryptic invasions (Morais and Reichard, 2018; Rusterholz and Baur, 2025). This is typically an underreported threat because it involves species that are already native to the region, so it easily goes unnoticed unless species-specific population studies are carried out. In this regard, nuclear markers are required to detect such cryptic invasions and subsequent intraspecific introgression by monitoring the genetic diversity of native populations alongside the spread of introduced alleles. While the introduction of novel alleles may increase overall genetic diversity and potentially enhance the adaptive capacity of native populations, this genetic admixture comes at a cost. These introduced genotypes can lead to an irreversible loss of unique, locally adapted genetic traits that native populations rely on for survival in specific habitats (Todesco et al., 2016; Quilodrán et al., 2018).

Consequently, genetic and genomic data allow researchers to reconstruct complex invasion routes, differentiate natural dispersal from anthropogenic transfers, and track rapid adaptive evolution, while simultaneously enabling the inference of effective population sizes and gene flow (Mable, 2019; Theissinger et al., 2023). However, to fully benefit from these capabilities, there is the need for well-curated, high-quality reference genomes (Formenti et al., 2022). These reference genomes lay the foundations for assessing the adaptation and selection in both NIS and native species.

To translate these genomic advancements into actionable policy, risk assessment frameworks must expand beyond simply tracking introduction frequencies to include monitoring of genetic diversity within introduced populations. Integrating genomic data into these frameworks reframes invasions as dynamic evolutionary processes rather than static events, enabling biosecurity managers to improve their projections of adaptive trajectories and deploy more effective mitigation strategies (Carroll et al., 2014).

3.3 Operational priorities for process-based invasion governance

Despite significant scientific advances, these advanced techniques and the requisite expertise frequently remain confined to academia (Taylor et al., 2017) rather than being accessible to biosecurity practitioners. This creates a disconnect between technological capabilities and applied biosecurity governance (Shafer et al., 2015). Bridging this gap is imperative and requires overcoming institutional skepticism toward molecular tools. In the Mediterranean, as globally, current frameworks often underestimate the evolutionary complexities of NIS. Most regulatory bodies rely on species-level blacklists, morphological presence-absence reporting and initial pathway restrictions (Tollington et al., 2017). These approaches frequently fail to address taxonomic shortcomings, ongoing population admixture and the secondary dispersal of invasive species across the basin. Moreover, static species lists lack the flexibility to accommodate the taxonomic revisions, cryptic diversity and genetic variation routinely revealed by molecular tools.

Aligning monitoring frameworks with contemporary biological understanding requires a conceptual transition from event-based to process-based invasion governance (Table 1; Figure 1), systematically integrating molecular tools into risk assessments and early warning systems (Makiola et al., 2020; Sepulveda et al., 2020). This transition also requires institutional adaptations, including specialized training and the formal regulatory acceptance of molecular evidence. Even under current instruments, implementation remains uneven across regions due to disparities in surveillance capacity, baseline knowledge and enforcement mechanisms (Early et al., 2016). Therefore, the integration of advanced molecular tools risks further widening the gaps in technical capacity and financial resources across jurisdictions. These risks must be mitigated through better-coordinated capacity-building, shared reference libraries, technology transfer and harmonized data-sharing frameworks.

Table 1. Advancing marine biosecurity frameworks from event-based monitoring to dynamic, process-based governance driven by integrated taxonomy and genomics.

FeatureEvent-based governance (traditional)Process-based governance (proposed)
Primary toolMorphological taxonomyIntegrated taxonomy (morphological and molecular) and genomics
Detection targetConspicuous adult life stagesAll life stages (including eggs and larvae) and eDNA traces
Invasion modelDiscrete introduction eventsContinuous demographic and evolutionary processes
Monitoring objectiveSpecies presence/absenceSpecies diversity, genetic diversity, admixture and adaptive potential
Policy triggerStatic species inventories and blacklistsDynamic risk assessments and genomic indicators
Operational workflow linking biological sampling and environmental DNA collection to genetic and genomic outputs that inform species detection, population-level inference, and management decisions. The diagram highlights the iterative feedback between evidence generation and sampling design within an adaptive, process-based governance framework.
Figure 1. Operational workflow linking biological sampling and environmental DNA collection to genetic and genomic outputs that inform species detection, population-level inference, and management decisions. The diagram highlights the iterative feedback between evidence generation and sampling design within an adaptive, process-based governance framework.

To effectively translate this scientific knowledge into practical management tools, the following operational priorities must be adopted by Mediterranean jurisdictions:

  • Standardizing reference libraries: Biosecurity frameworks must actively support platforms that generate open-access, fully curated and voucher-backed DNA barcoding and genomic reference data. Prioritizing data collection from high-risk ports and introduction hubs is critical to build robust baselines for source attribution and to strengthen the application of these databases in biosecurity.
  • Routine molecular identification: While eDNA is crucial for broad environmental screening, biosecurity protocols must also integrate targeted molecular taxonomy for the accurate identification of collected organisms. This ensures rapid confirmation even when morphological identification is difficult.
  • Implementing integrative early warning systems: Routine biosecurity surveillance, including port monitoring and ballast water checks, should embed eDNA metabarcoding as a primary screening tool. However, this must be cross-validated with parallel morphological sampling and integrative taxonomic workflows to ensure high-confidence reporting that managers can legally act upon.
  • Monitoring evolutionary dynamics and hybrids: Regional frameworks (e.g., MSFD, Barcelona Convention) must incorporate genetic and genomic indicators. Monitoring must build upon accurate integrative taxonomy, utilizing genomic data to track the population structure, adaptive potential, hybridization and the cryptic introgression of both NIS and native stocks.
  • Capacity building and knowledge transfer: To operate these tools without exacerbating regional disparities, significant investment is required in training biosecurity practitioners. Clear methodological guidelines are necessary to ensure the reproducible and standardized application of these tools across the diverse jurisdictions of the Mediterranean basin.

4 Conclusion

Marine biosecurity frameworks must evolve beyond traditional, event-based monitoring. Understanding the ongoing complexities of non-indigenous species introductions and population expansions requires a decisive shift toward dynamic, process-based governance driven by integrated taxonomy and genomics. The resulting management and operational benefits for early warning systems and risk assessments are critical. Ultimately, a transition toward genetically and genomically informed governance is urgently required if policy is to reflect the true dynamics of NIS and associated invasion processes while protecting the ecological and evolutionary resilience of native biodiversity.

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Footnotes

Edited by: Ishtiyaq Ahmad, University of Kashmir, India

Reviewed by: Natalia Petit-Marty, Institute of Marine Research, Spanish National Research Council (CSIC), Spain

Lapo Ragionieri, Free University of Bozen-Bolzano, Italy

Statements

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding

The author(s) declared that financial support was received for this work and/or its publication. The authors declare that this work received open access publication funding from the Environment and Resources Authority (ERA) Malta, Malta Enterprise and the Parliamentary Secretariat for Youth, Research and innovation of the Government of Malta as support to promote the outputs of the University of Malta UMP's international conference on Marine and Maritime Sustainable Developments: Research and Applications.

Data availability

The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding authors.

Author contributions

NV: Conceptualization, Investigation, Visualization, Writing – original draft, Writing – review & editing. AV: Conceptualization, Funding acquisition, Investigation, Visualization, Writing – original draft, Writing – review & editing.

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Citation

Vella, N. & Vella, A. (2026). Integrating molecular taxonomy and genomics to strengthen marine biosecurity: a Mediterranean perspective. Frontiers in Ocean Sustainability, Volume 4. https://doi.org/
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*Correspondence: Noel Vella; Adriana Vella

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