Introduced species dominate DNA-based surveys of Southeast Asian lakes

Alice Evans^1,2, Simon Creer¹, Gary R. Carvalho¹, M. Thomas P. Gilbert², Mohd Nor Siti Azizah³, Gusti Ngurah Kade Mahardika⁴, Paul Barber⁵, Mark de Bruyn^1,6

¹School of Biological Sciences, Bangor University, Bangor, UK

²Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

³Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia

⁴Faculty of Veterinary Medicine, Udayana University, Bali, Indonesia

⁵Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095, USA

⁶Australian Research Centre for Human Evolution, School of Environment and Science, Griffith University, Brisbane 4111, Australia

Southeast Asia is a biologically ‘megadiverse’ region with high species richness and endemicity. Indonesia, for example, has an estimated four thousand fish species, with at least one thousand of these being restricted to fresh waters. The main threats to freshwater biodiversity in Southeast Asia include water pollution, flow modification, habitat degradation, over exploitation, environmental change, and non-native species introductions. In recent IUCN assessments, 16 of the 31 globally extinct freshwater fish species are endemic to SE Asia. To assess the extent of non-native freshwater species introductions in this region, we used environmental DNA metabarcoding to survey eleven lakes across Peninsular Malaysia, Sumatra, Java, Bali, Borneo (Kalimantan), and Sulawesi. Here, we show that non-native species dominated environmental DNA assays from these lakes. Across the large geographic range that we sampled, native species are being replaced by species introduced from other areas of Southeast Asia, Latin America, or Africa, for fisheries, aquaculture, sport fishing, ornamental, or pest-control purposes. We anticipate that environmental DNA metabarcoding will provide a rapid, cost-effective toolkit for broadscale monitoring of non-native species, including in other megadiverse regions such as Africa and Latin America.