Fish diversity and invasive species detection in the Perak River, Malaysia, through eDNA metabarcoding

Authors

• Ghazanfer Ali, Institute of Biological Sciences
• Subha Bhassu, Institute of Biological Sciences
• Jiao Yang, Institute of Biological Sciences
• Thenmoli AP Govindasamy, Institute of Biological Sciences
• Norhafiza Mohd Arshad, Universiti Malaya
• Lavanya Vythalingam, Heriot-Watt University
• Satoshi Nagai, Japan Fisheries Research and Education Agency

Document Type

Article

Publication Date

4-1-2026

Abstract

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.

Keywords

Biodiversity conservation, Environmental DNA (eDNA), Freshwater fish diversity, Invasive species detection, Perak River

Publication Title

Global Ecology and Conservation

ISSN

2351-9894

DOI

10.1016/j.gecco.2026.e04070

Recommended Citation

Ali, Ghazanfer; Bhassu, Subha; Yang, Jiao; AP Govindasamy, Thenmoli; Arshad, Norhafiza Mohd; Vythalingam, Lavanya; and Nagai, Satoshi, "Fish diversity and invasive species detection in the Perak River, Malaysia, through eDNA metabarcoding" (2026). Research Publications (2026 to 2030). 863.
https://knova.um.edu.my/research_publications_2026_2030/863

Funders

Kementerian Tenaga dan Sumber Asli

Volume

66

Publisher

Elsevier B.V.