Environmental DNA and Conventional Sampling Capture Complementary Patterns of Ichthyofaunal Diversity in the Selangor River Estuary, Malaysia

ABSTRACT

Mangroves are a key ecosystem for coastal fishery resources, hence understanding the spatial distribution of fish communities is crucial for sustainable management, especially given that conventional net fishing can be ecologically destructive and taxonomically selective. The present research aims to (1) assess and compare the total fish diversity from both environmental DNA (eDNA) metabarcoding and fish catch, (2) analyze the influence of physicochemical parameters on the distribution of fishes and (3) evaluate the complementarity between these two methods. We conducted fish sampling (using drift and trammel nets) and eDNA metabarcoding (using the 12S rRNA MiFish primers) along a salinity gradient in Selangor River, a key mangrove estuary and major fishery ground in Peninsular Malaysia. We detected 89 taxa (68 species) from the eDNA dataset, and 16 taxa (10 species) from the conventional catch. The dominant mangrove fish families found in the eDNA dataset (Gobiidae, Leiognathidae and Lutjanidae) and fish catch (Ariidae, Ambassidae and Sciaenidae) could be confidently matched to known habitat preference in coastal areas. Our data highlighted that water temperature, salinity, pH and wave height is strongly associated with fish community patterns. We infer that eDNA accumulates at the river mouth, particularly under low‐tide conditions. Although eDNA metabarcoding detected thrice as many species as compared to conventional catch, the results from these methods are complementary, as each contributed unique detections with some overlap. Our combined approach contributed a preliminary inventory of fish species to support the biodiversity management of Kuala Selangor and highlighted the importance of integrating eDNA metabarcoding as a biomonitoring tool for ichthyofaunal surveys. Beyond this local context, our findings serve as a scalable framework, for integrating methods to improve regional assessments of fish diversity across Southeast Asia.