Fish Diversity and Invasive Species Detection in the Perak River, Malaysia, Through eDNA Metabarcoding

Freshwater ecosystems are among the most threatened globally, facing rapid biodiversity declines due to habitat degradation, pollution, overexploitation, and invasive species introductions. Southeast Asia, recognized as a global freshwater biodiversity hotspot, is experiencing some of the highest extinction risks. The Perak River, Malaysia’s second-longest river, supports diverse fish communities critical for regional ecological stability and food security, but comprehensive biodiversity assessments have been lacking. This study used environmental DNA (eDNA) metabarcoding targeting the 12S rRNA gene to comprehensively assess fish diversity and detect invasive species across the Perak River. Water samples from five locations were analyzed using high-throughput sequencing on the Illumina MiSeq platform. We identified 16 orders, 32 families, 51 genera, and 57 species, with Cyprinidae being the dominant family (15.78% of species). Invasive species such as Micropterus salmoides, Oreochromis spp., and Gambusia affinis recognised as invasive either globally or in Malaysia were also detected, raising ecological concerns. Our results highlight the efficiency of eDNA metabarcoding for non-invasive biodiversity monitoring in tropical river systems and demonstrate its potential for early detection of invasive species. This pioneering baseline study provides essential data to guide conservation strategies, inform management policies, and contribute to broader efforts addressing freshwater biodiversity loss in Southeast Asia.