Marine Fisheries Management Research Articles

Planning for climate change resilience—Collation, update and assessment of Mozambique’s marine fisheries data and management

Planning for climate change resilience—Collation, update and assessment of Mozambique’s marine fisheries data and management

Community structure and environmental drivers of offshore hard-bottom reef fishes in the northern Gulf of Mexico

Abstract Understanding patterns in community structure in large marine ecosystems is necessary for advancing community- and ecosystem-based approaches to marine fisheries management. We analyzed data from a large-scale, fishery-independent video survey to quantify the structure of reef fish communities on offshore hard-bottom reef habitats in the northern Gulf of Mexico (nGOM). A novel aspect of this work is that all species visualized on videos were identified and enumerated over a 13-year period, which allowed for a comprehensive analysis of fish community structure. We observed a total of 243 fish species from 54 families and 14 orders. Species richness and biodiversity varied considerably across the nGOM and were highest in regions that harbor extensive coral reef habitat (south Florida, Louisiana-Texas shelf). Multivariate analyses identified 12 species assemblages, with important fishery species and species of concern (i.e. IUCN-listed) occurring in the largest identified assemblages. One assemblage composed mostly of large-bodied fishery species accounted for 45% by number and 89% by weight of all fish observed. Species assemblages were most strongly associated with depth, temperature, and substrate composition, with weaker associations with the amount of attached algae and vertical relief, while species richness was positively correlated with bottom water temperature. In general, large-scale bathymetric and hydrographic factors (e.g. depth, temperature) were more important than local topographic structure and biogenic habitat in structuring reef fish communities at the spatial scales (i.e.1000 km) considered here. Our results advance ecosystem-based approaches to fisheries management by providing a basis for incorporating multispecies spatial dynamics into the monitoring and assessment of hard-bottom reef fish communities in the nGOM.

Charting sustainable waters: Governance challenges and opportunities for fisheries and coastal beach resources in a West African country

Marine fisheries and beaches (i.e., backshore, foreshore and shoreface) are essential for providing ecosystem services globally, with coastal states being at the forefront of this benefit. Consequently, several policies, legislations, and governance processes must be formulated to ensure their sustainable use due to the impact of anthropogenic and natural pressures. This study aims to analyse the legal and institutional frameworks for the management of marine fisheries and beach resources (such as flora (coconut), fauna (ghost crabs), dunes, and rocky components) under key international laws and conventions, using Ghana as a case study. The study identifies the strengths, weaknesses, opportunities, and threats (SWOT) within resource management, as well as their impact on the country’s progress in the attainment of the Sustainable Development Goals (SDGs) and Africa Union Agenda 2063. Data was collected through interviews with fishers, coastal residents, and other relevant stakeholders, as well as a review of secondary data. The results unveil a distinctive contrast in the regulatory landscape between fisheries and beach resources. While numerous policies have been formulated to ensure the sustainable management of fisheries, the same level of attention and commitment has not been extended to beach resources. The SWOT analysis revealed that some of the strengths in the governance of marine fisheries and beach resources rest on the availability of institutions and laws. The weakness lies in inadequate enforcement and data gathering and analyses to inform decision making. This study provides as an illuminating exploration into the legal and institutional underpinnings of marine fisheries and beach resource management in Ghana, shedding light on the critical junctures where improvements are needed.

Application of Measured Fishing Method in Kei Islands, Maluku Province

As an implementation of Government Regulation of the Republic of Indonesia Number 11 of 2023 concerning Measured Fishing in Indonesian waters, the Ministry of Marine Affairs and Fisheries is implementing a priority program agenda by implementing the measured fishing method (Penangkapan Ikan Terukur/PIT) in a number of waters in Indonesia in zone classification. Measured Fishing is a controlled and proportional fishing practice, carried out in special zones with certain quotas to maintain the sustainability of fish resources and their ecosystems. The implementation of this PIT method has been carried out in the province of Maluku, Kei Islands which are included in zone 3. This policy is a response to the serious challenges faced in marine fisheries management, including overfishing and ecosystem degradation. With clear regulations, it is hoped that it can reduce pressure on fish populations and support sustainable economic growth for coastal communities. The implementation of this policy requires support and collaboration between the government, fisheries business actors, academics, and the community to ensure its success. Evaluation and scientific research will be key in measuring the impact and effectiveness of this policy, as well as in identifying areas of improvement needed to improve the sustainability of the fisheries sector in Indonesia for a better future.

On the development of criteria for determining the effectiveness of technical working groups: A case study about information processes in marine conservation and fisheries management in Belize

Use of scientific information in evidence-based decision-making is critically important in addressing coastal and ocean management concerns. In an ecosystem-based management context, ensuring that the “right” information (reliable) is available can be particularly challenging as the information often resides in different organizations with different management mandates. Many governmental and intergovernmental organizations have used a range of approaches, including technical advisory committees and working groups, to facilitate multidisciplinary input into the development of appropriate policies and management practices. This study examined the roles of multiple stakeholders participating in technical working groups that assist in decision-making for marine fisheries management in Belize, a coastal country in Central America. Through interviews with members of three working groups – the Spawning Aggregation Working Group, the Managed Access Working Group, and the National Hicatee Conservation and Monitoring Network – and decision-makers in the Belize Fisheries Department, information production processes and pathways for information uptake into policy were investigated. Major characteristics of communication at the science-policy interface associated with each working group were revealed. Important communication enablers and barriers were identified related to the operation of the working groups, such as membership commitment and resource availability, which influenced knowledge exchange within and outside the groups. Based on the results, a set of requirements for the creation and operation of effective working groups was formulated with regard to requisite inputs, the operational processes, and the types and uses of the information outputs of the groups. These requirements serve as a foundation for development of indicators of the effectiveness of working groups in environmental management contexts that support communication and decision-making at science-policy interfaces.

Unraveling dispersal of a coastal fish species in the juvenile life stage in the Yellow Sea using otolith chemistry

Dispersal is a critical process in marine ecology, with profound implications for population conservation and fisheries management. Previous research has predominantly focused on reef-associated species, but studying the dispersal of more mobile fish species in nearshore environments is exceptionally challenging due to the complex coastal hydrography similar to reefs, and therefore dispersal knowledge of some coastal migratory behavior fish remains preliminary. In this study, we investigated the dispersal of a coastal fish species (small yellow croaker Larimichthys polyactis) in its juvenile life stage using otolith elemental fingerprints. We aimed to investigate the dispersal patterns of juveniles with otolith chemistry and identify potential natal sources. Results indicated that (1) significant geographical variations in the otolith elemental signatures can be considered as natural markers for assessing fish dispersal; (2) although small yellow croakers in the juvenile life stage are capable of settlement, a significant proportion of individuals continue subsequent passive dispersal; (3) juveniles may have originated from 2 natal sources in the sampling areas based on the differences in the near-core chemistry fingerprints. Results demonstrate the applicability of otolith chemistry fingerprints as natural tags in coastal waters and suggest that juveniles with the ability to settle will still employ dispersal strategies. This study contributes to research on fish dispersal in the early life stage and has significant implications for the marine fishery management of small yellow croaker.

A hotspot and mechanism of enhanced bottom intrusion on the southern New England shelf

Understanding the occurrence of the intrusion of open ocean water onto continental shelves has scientific significance and societal relevance as the intrusion can significantly disrupt the marine ecosystem and fisheries. High-resolution numerical modeling is used to investigate the spatiotemporal occurrence and mechanisms of highly anomalous bottom intrusions on the southern New England shelf. Based on multi-year numerical simulations, this study reveals a hotspot of cross-isobath bottom-intensified intrusions at a topographic trough. Examination of multiple events portrays a robust mechanism of locally enhanced bottom intrusions. Persistent upwelling-favorable winds set up an enhanced pressure gradient field at the topographic trough and drive the intrusion a large-distance onshore. Numerical experiments with and without the topographic trough show that the localized pressure gradient results from a combination of the shelf orientation and local bathymetry. Although highly anomalous waters on the shelf relate to wind forcing, correlations between the wind stress anomaly and bottom salinity anomaly at the location of the enhanced intrusion is modest, implying the need to incorporate other environmental factors to develop more deterministic prediction models for subsurface conditions on the shelf. The results have important implications for marine environment and fisheries management.

Social sustainability in Bangladesh marine fisheries management: A case from Hatiya fishing community

Social sustainability in fisheries focuses on retaining or improving societal welfare in the fishery system without threatening its long-term financial benefits and socio-cultural welfare. However, often social sustainability issues are ignored while implementing any fisheries management actions rather than only focusing on economic and environmental sustainability issues. This study assesses the social sustainability in Bangladesh marine fisheries management gaining insights from the coastal and marine fisheries-dependent communities of Hatiya Upazila in 2021–2022 using a mixed method approach especially focusing on the social issues during the marine fishing ban. Results have shown positive effects on fish production but negative implications on the socio-economic circumstances of the reliant households after the implementation of the marine fishing ban. During the ban, the ability of around 33 % of fisher households to have 3 meals a day has drastically reduced to 2 or 1 meal per day. Households' average fish intake has reduced from 7 kg to 4 kg per week during the ban. Similarly, there have been detrimental effects on family relationships, healthcare access and children's education during the ban. Moreover, pregnant women and children have suffered greatly from protein deficiencies as fishers could not buy protein-rich foods for their families during the ban. Due to the shortage of alternate income-generating activities (AIGAs), almost 71 % of fishers became indebted during the ban. To assist the fishers during the ban, the government has implemented several measures, such as offering incentives (40 kg of rice per registered fisherman per month) and/or AIGA but those are too scant to recompense for the loss that is incurred due to the fishing ban. Finally, this study provides some way forward to bring social sustainability that is affected due to the marine fishing ban as well as to partly meet the targets of Sustainable Development Goals 1, 2, 14 and 15.

Interannual variability of the East African Coastal Current associated with the El Niño-Southern Oscillation

Abstract The East African Coastal Current (EACC) is an important western boundary current of the tropical South Indian Ocean and plays an important role in the ocean circulation and biogeochemical cycles in the Indian Ocean. This study investigates the interannual variability of the EACC and its dynamical mechanisms. The result shows that the EACC has interannual variability associated with the El Niño-Southern Oscillation (ENSO) during 1993-2017. The EACC shows a significantly positive correlation with the Niño3.4 index with a correlation coefficient of 0.65, lagging the Niño3.4 index by 18 months. During the decaying phases of El Niño (La Niña) events, the negative (positive) sea level anomaly (SLA) propagates westward as upwelling (downwelling) Rossby waves from the southeast Indian Ocean to the southwest Indian Ocean, and then strengthens (weakens) the EACC due to zonal SLA gradient off the East African coast under geostrophic equilibrium. The SLA gradually weakens in the southeast Indian Ocean during its westward propagation but strengthens in the southwest Indian Ocean promoted by local wind stress curl anomaly. This study can improve our understanding of the relationship between the western boundary current of the tropical South Indian Ocean and large-scale ENSO air-sea processes, and is important for managing marine fisheries and ecosystems on the East African coast.

Underwater Fish Object Detection with Degraded Prior Knowledge

Understanding fish distribution, behavior, and abundance is crucial for marine ecological research, fishery management, and environmental monitoring. However, the distinctive features of the underwater environment, including low visibility, light attenuation, water turbidity, and strong currents, significantly impact the quality of data gathered by underwater imaging systems, posing considerable challenges in accurately detecting fish objects. To address this challenge, our study proposes an innovative fish detection network based on prior knowledge of image degradation. In our research process, we first delved into the intrinsic relationship between visual image quality restoration and detection outcomes, elucidating the obstacles the underwater environment poses to object detection. Subsequently, we constructed a dataset optimized for object detection using image quality evaluation metrics. Building upon this foundation, we designed a fish object detection network that integrates a prompt-based degradation feature learning module and a two-stage training scheme, effectively incorporating prior knowledge of image degradation. To validate the efficacy of our approach, we develop a multi-scene Underwater Fish image Dataset (UFD2022). The experimental results demonstrate significant improvements of 2.4% and 2.5%, respectively, in the mAP index compared to the baseline methods ResNet50 and ResNetXT101. This outcome robustly confirms the effectiveness and superiority of our process in addressing the challenge of fish object detection in underwater environments.

Sonar Fish School Detection and Counting Method Based on Improved YOLOv8 and BoT-SORT

Fish object detection and counting in pelagic fisheries face many challenges in complex environments. Sonar imaging technology offers a solution because it generates high-resolution images underwater. In this paper, we propose a sonar-based fish object detection and counting method using an improved YOLOv8 combined with BoT-SORT to address issues such as missed detection, false detection, and low accuracy caused by complex factors such as equipment motion, light changes, and background noise in pelagic environments. The algorithm utilizes the techniques of lightweight upsampling operator CARAFE, generalized feature pyramid network GFPN, and partial convolution. It integrates with the BoT-SORT tracking algorithm to propose a new region detection method that detects and tracks the schools of fish, providing stable real-time fish counts in the designated area. The experimental results indicate that while focusing on maintaining a lightweight design, the improved algorithm achieved a 3.8% increase in recall and a 2.4% increase in mAP0.5 compared to the original algorithm. This significantly impacts scientific and rational fishery planning, marine resource protection, and improved productivity. At the same time, it provides important data support for marine ecological monitoring, environmental protection, and fishery management, contributing to sustainable fishery development and marine ecology preservation.

M-fisheries prototype: Innovating towards evidence-based planning and decision-making in marine fisheries management

Kenya’s marine fisheries sector has the potential for increased growth. However, fisheries managers in Kenya currently face the challenge of poor, missing or aggregated catch data. This paper explores Information and Communication Technology (ICT)-based solutions in the fisheries sector. The study adopts exploratory research design. It reports a review and analysis of two ICT-based solutions in the fisheries sector, conducted in the year 2020. From the analysis, the study proposes the development of M-Fisheries Prototype, as an answer to the challenges of the two reviewed solutions. The prototype introduces an SMS/USSD app for data collection. The SMS/USSD app aligns to the mobile-rich but internet-poor context of the fish landing sites, as it addresses the challenges of the other mobile-based systems that only require the use of smartphones. These challenges include infrastructural accessibility, technical usability and internet data costs.

Exploring tradeoffs in southeast United States marine fisheries management using management strategy evaluation

Recreational fishing is the fastest growing sector in industrialized nations and can have substantial impacts on marine fish populations and ecosystems. Commercial objectives are typically characterized by maximizing yield and fishery stability whereas recreational anglers generally prefer sustained access to fishing and the availability of larger fish. Achieving these objectives while balancing tradeoffs between recreational and commercial fishing is essential to effective recreational and mixed-use fisheries management. Balancing multiple sector objectives is of particular concern in the southeast United States (US), where recreational fishing is the dominant source of mortality for marine fish stocks. We developed and applied a size-structured management strategy evaluation (MSE) tool, individually, to two stocks in southeast US Atlantic waters, black sea bass (Centropristis striata), a sedentary reef fish in overfished condition, and cobia (Rachycentron canadum), a migratory coastal pelagic fish, to evaluate the performance and tradeoffs of mixed management procedures against a variety of objectives. Several recreational and commercial objectives were aligned: fishers sought to conserve the stock and maximize catch, which simplified the evaluation of tradeoffs. We tested management procedures over alternate states of recruitment for black sea bass, and natural mortality for cobia. Management procedures that allowed harvest for black sea bass resulted in or risked an overfished status if the current weak recruitment regime continues, but could rebuild with no fishing regardless of recruitment state. Although results were sensitive to uncertainty in recruitment, no management procedures could achieve historic landings for either sector, and only management procedures that reduced effort consistently resulted in a reduced number of dead discards. No management procedures resulted in an overfished status for cobia. Management procedures for cobia generally achieved objectives and were robust to uncertainty in natural mortality. In both case studies, tradeoffs occurred between maximizing catch and season length and maintaining a stronger size structure in the population. This study resulted in a flexible MSE tool with strong potential utility for scoping management procedures that explicitly consider recreational fishing objectives.

Artificial structure selection by economically important reef fishes at North Carolina artificial reefs

Artificial reefs can play an important role in marine fisheries management by supplementing or enhancing natural habitats. Despite their increased use in recent years, the choice of structures used at artificial reefs remains largely haphazard due to the lack of information on reef structure performance. Few studies have examined the use of different artificial reef structures by individual fish. From 2021-2022, we acoustically tagged 72 black sea bass (Centropristis striata), 34 gag (Mycteroperca mircrolepis), 27 greater amberjack (Seriola dumerili), nine almaco jack (S. rivoliana), and eight red snapper (Lutjanus campechanus) on four artificial reef complexes near Cape Lookout, North Carolina, U.S. Available artificial reef structures consisted of materials of various sizes and heights made of concrete and metal. We tracked tagged fish using a fine-scale positioning system for ~100 days. Black sea bass exhibited high site fidelity to the artificial structure where we caught them, rarely moving away from that structure. The limited movement resulted in low transition probabilities; we conclude that black sea bass do not select for particular artificial structures. Gag and red snapper moved greater distances away from artificial structures and routinely moved between them. Greater amberjack and almaco jack moved the most within the complexes displaying circling behavior around individual structures and were the only species that regularly moved off the artificial reef complexes. Greater amberjack movements away from artificial sites were most commonly directed to surrounding shipwrecks. Whereas gag, red snapper, almaco jack, and greater amberjack used all available structures, they consistently selected for high relief structures, such as vessels, more than other structures. These results will be useful to managers charged with decisions on what types of structures to place at artificial reef complexes to supplement or enhance habitat for economically important fishes.

Integration of spatial justice into navigating the combat on illegal, unreported and unregulated fishing in ocean and coastal areas

As a geographical dimension of justice, spatial justice is characterized by the interplay of social justice and heterogeneous spaces, including the ocean. Despite the generous contribution of ocean to humankind, concerns over aquatic spatial justice are disproportionately lacking. Among the core disruptors of ocean justice, illegal, unreported and unregulated (IUU) fishing imposes a major threat to global fisheries governance. The synthesis of spatial analysis and justice perspective can generate new insights to help understand and potentially address IUU fishing. To examine the spatial (in)justices concerning IUU fishing, we first propose a novel tripartite framework that envisions space as a form of opportunity, society and rights to externalize its socio-environmental implications. Then we integrate productive, distributive and consumptive justices to examine the spatial variations of IUU stakeholders along the fish value chain, and use stakeholder analysis to investigate spatial powers and conflicts regarding both a micro scale of fish communities, and a macro scale of states (coastal state, flag state, port state and market state) and supernational players (regional fisheries management organizations and marine protected areas). It is discovered that certain regions provide greater spatial benefits that stimulate IUU behaviors; IUU misconducts cause spatial differentiation and spatial deprivation that disrupt social orders in fish communities; space can empower stakeholders’ inclusive and proper engagement into the place-based management process against IUU fishing. Since the spatialized vision has been increasingly highlighted in marine fisheries management, it is suggested to intervene in the world ocean by leveraging spatial knowledge, managing spatial conflicts and facilitating spatial action, in order to promote spatial justice and better combat IUU fishing globally.

Ecosystem‐level reference points: Moving toward ecosystem‐based fisheries management

AbstractObjectiveTo support the movement in marine fisheries management toward ecosystem‐based fisheries management by exploring ecosystem‐level reference points (ELRPs) as an option for managing fisheries at the ecosystem level. An ELRP is an ecosystem harvest level or indicator with one or more associated benchmarks or thresholds (i.e., targets, limits) to identify, monitor, or maintain desirable ecosystem conditions and functions.MethodsThis paper explores the development and implementation of ELRPs in fisheries management to support ecosystem and fisheries sustainability, help identify when ecosystem changes that impact fisheries resources occur, and foster discussions of trade‐offs in management decisions.ResultWe organize existing and potential ELRPs into five categories (statistical analysis of nonlinear dynamics and tipping points, ecosystem productivity, ecosystem trophic information, biodiversity, and human dimensions), provide an overview of analytical methods that can estimate ELRP benchmarks, provide examples of where ELRP benchmarks are being used today, and evaluate pros and cons of the different ELRP categories. We also attempt to identify potential next steps for fisheries scientists and managers to further the science, development, and application of ELRPs.ConclusionEcosystem‐level reference points can be used as a proactive accountability mechanism to achieve ecosystem objectives and maintain the ecosystem in a preferred operating space or as an early warning that ecosystem‐level changes (e.g., tipping points) could be imminent if current biological and ecological trends in the system continue.

Tide impacts the dispersion of eDNA from nearshore net pens in a dynamic high‐latitude marine environment

AbstractEnvironmental DNA (eDNA) is increasingly used to detect animals in aquatic habitats, but uncertainty remains about the relationship between the present location of an animal relative to eDNA detections. In marine environments, physical characteristics—such as tides and currents—can influence the distribution of eDNA. In this study, we make use of hatchery net pens containing >46 million juvenile chum salmon (Oncorhynchus keta) in nearshore Southeast Alaska to test for dispersion of eDNA and the effects of tide. Initially, we collected and filtered surface water every 80 m along a 2 km transect to test eDNA attenuation over surface distance during incoming and outgoing tides on a single day. The following year, we sampled at three depths (0 m, 5 m, and 10 m) every 500 m along the same transect as well as along a perpendicular transect, to understand dispersion by depth and in additional directions. Chum salmon eDNA was quantified using species‐specific qPCR. We found that surface samples showed a consistent signal of decreasing chum salmon eDNA across the 2 km transect (R2 = 0.665), with the majority of eDNA detections within 1.5 km of the net pens. Tide had a significant effect, resulting in higher concentrations of chum DNA throughout the transect during incoming tide and a steeper decline in eDNA over distance during outgoing tide (R2 = 0.759). Depth affected chum salmon DNA concentration, with the majority of eDNA at the surface and a decreasing amount of DNA with increasing depth. This study addresses one of the critical knowledge gaps in applying eDNA to marine fisheries management by providing empirical evidence of eDNA dispersion and demonstrating that most eDNA detections are likely from nearby individuals that are either currently or recently present. Yet even at close proximity, eDNA signal strength fluctuates and depends on the physical environmental variables during a given sampling event.

Identifying the key factors influencing spatial and temporal variations of regional coastal fishing activities

Fishing is one of the most pervasive human activities for harvesting natural resources. Accurate understanding of the dynamic variations of regional fishing activities and their influence mechanisms is crucial for marine conservation and fisheries management. Previous studies have described the spatio-temporal distribution of fishing operations. However, there is still a need for a comprehensive interpretation of why and how these variations occur, especially in regional coastal waters. In this study, taking the Bohai Sea and its adjacent waters as an example, the correlation between regional fishing activities and multiple factors, including the marine environment, geographical position, socio-economic conditions, and marine management policies, was investigated from the perspective of human geography. Automatic Identification System (AIS) data for fishing vessels were used, combining remote sensing, geographic information system (GIS), and statistical models. The results indicated that the spatio-temporal variations of regional coastal fishing activities were driven by complex interactions among these factors. Overall, the average explanatory power of socio-economic and geographical position factors on fishing activities was higher than that of marine environmental factors. The importance of the marine environment and geographical position for fishing activities varied throughout different seasons. The sensitivity of fishing activities to geographical position was relatively high, with the explained deviance exceeding 62% of the total explained deviance. Intensive fishing was primarily observed within a particular range of the sea surface temperature frontal gradient (0.20–0.60 °C/km) or sea surface chlorophyll-a frontal gradient (1.06–1.25). The spatial distribution of fishing activities is effectively constrained by implemented marine management policies. This study sheds new light on the key factors influencing regional fishing activities in coastal waters and highlights the complexity of their interaction effects. These findings can provide a theoretical basis for the restoration of fishery resources and marine fishing management.

Performance Comparison ConvDeconvNet Algorithm Vs. UNET for Fish Object Detection

The precise identification and localization of fish entities within visual data is essential in diverse domains, such as marine biology and fisheries management, within computer vision. This study provides a thorough performance evaluation of two prominent deep learning algorithms, ConvDeconvNet and UNET, in the context of fish object detection. Both models are assessed using a dataset comprising a wide range of fish species, considering various factors, including accuracy of detection, speed of processing, and complexity of the model. The findings demonstrate that ConvDeconvNet exhibits superior performance in terms of detection accuracy, attaining a noteworthy degree of precision and recall in identifying fish entities. In contrast, the UNET model displays a notable advantage in terms of processing speed owing to its distinctive architectural design, rendering it a viable option for applications requiring real-time performance. The discourse surrounding the trade-off between accuracy and speed is examined, offering valuable perspectives for algorithm selection following specific criteria. Furthermore, this study highlights the significance of incorporating a diverse range of datasets for training and testing purposes when utilizing these models, as it significantly influences their overall performance. This study makes a valuable contribution to the continuous endeavors to improve the detection of fish objects in underwater images. It provides a thorough evaluation and comparison of ConvDeconvNet and UNET, thereby assisting researchers and practitioners in making well-informed decisions regarding selecting these models for their specific applications.

Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra

The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.