Rapid DNA/eDNA-Based ID Tools for Improved Chondrichthyan Monitoring and Management

Abstract

Rapid DNA/eDNA-based ID tools, which detect specific genetic patterns without requiring sequencing, are essential for biodiversity and wildlife trade monitoring, particularly for species of conservation concern. However, the practical application of these methods remains limited by the availability of standardised protocols, accessibility of resources, and coverage across diverse taxa. This challenge is especially pronounced for Chondrichthyes, a group heavily overexploited due to fishing and illegal trade, and with data scarcity for conservation assessments. Despite their ecological and economic importance, many species lack reference sequences in databases, as well as other molecular data and tools, hindering the development of molecular tools for species identification and trade regulation. This review synthesises the current state of rapid DNA/eDNA-based ID tools for the detection of chondrichthyan species, including established and emerging methods. It also compiles available taxon-specific primers to facilitate efficient species identification and recommends the most suitable methods. We identify key gaps in taxonomic and geographic coverage, emphasising the need for further research to expand these tools to under-represented species and regions. Additionally, we highlight the importance of integrating genetic approaches into enforcement frameworks to enhance conservation strategies and regulatory compliance. By providing an accessible reference for time- and cost-effective genetic monitoring, this work will support evidence-based decision-making and improve the practical application of rapid DNA/eDNA-based ID tools in the conservation and management of Chondrichthyes species worldwide.

Keywords: LAMP; Multiplex PCR; conservation genetics; ddPCR; elasmobranch; environmental DNA; fisheries management; qPCR; sharks and rays; species identification.

FIGURE 1

Overview of studies employing rapid DNA/eDNA‐based ID tools for Chondrichthyes identification in tissue and environmental DNA (eDNA) applications. (A) Global distribution of studies, mapped by the locations of first and last authors. Note that author locations do not necessarily reflect the geographic areas where samples were collected. Pie charts indicate the proportional use of tissue DNA and eDNA applications. (B) Temporal distribution of studies for each application. (C) Comparative distribution of studies employing different rapid DNA/eDNA‐based ID tools across both tissue DNA and eDNA applications. Tools categorised as “on‐site identification” include LAMP and FASTFISH‐ID. For more details on each tool, see Box 2.

FIGURE 2

Overview of taxon‐specific primers designed for Chondrichthyes detection. (A) Total number of primers developed across the eight molecular markers identified for tissue DNA and eDNA applications. (B) Proportion of taxon‐specific primers between sharks, rays and chimaeras. (C) Heatmap organised by family illustrating the abundance of taxon‐specific primers across the eight molecular markers.