Exploring the biodiversity of the lakes of the Malay Archipelago using environmental DNA metabarcoding

The freshwater ecosystems of Southeast Asia are some of the most highly threatened in the world, due to anthropogenic impact from climate change, deforestation, the creation of hydropower dams and over-harvesting. Rapid, cost-effective and reliable monitoring of biodiversity is essential for the conservation of the exceptional biotic richness within this region. The emerging field of environmental DNA (eDNA) monitoring, using trace cells or fragments of DNA released into an environment to assign species to locations has potential toprovide this type of information. In this thesis, I explore the use of eDNA metabarcoding for monitoring freshwater aquatic biodiversity within Southeast Asia, focusing on fishes within the lakes of the Malay Archipelago. Firstly, I contributed to a published review of the field of eDNA in which we discuss how the field has developed, address current challenges, and predict future developments. Secondly, I conducted sampling of lakes across the Malaysian Peninsula as an initial exploration into the use of eDNA in tropical freshwaters using the ethanol precipitation method of environmental DNA collection, as well as conducted a mesocosm experiment to test eDNA degradation. Although this work did not produce reliable results, and therefore is not included in this thesis, it provided important experience in implementing eDNA sampling in the tropics. Thirdly, after initial trouble shooting, I tested options for isolation and storage of aquatic eDNA to inform best practice solutions for eDNA field researchers, and found that the use of an enclosed filter system combined with a preservation buffer was the best approach. Fourthly, I conducted intensive sampling of a lake in Indonesia to investigate the dynamics of eDNA information within a tropical lentic environment, and found heterogenous detection of extant biodiversity. Finally, I undertook a large-scale biogeography study of the lakes of the Malay Archipelago, sampling from western Sumatra across to eastern Sulawesi using a filter approach for environmental DNA collection. Metabarcoding of aquatic eDNAsamples was then employed for all samples, with a combination of primers targeting differen t mitochondrial regions to achieve a broad scope of biodiversity information. From the data, I recovered native, endemic and rare species, as well as introduced and invasive species linked to fisheries, aquaculture, the ornamental trade and pest-control. Overall, aquatic eDNA metabarcoding demonstrated great potential, allowing ecosystem level species detection, but further work on eDNA distribution, improving to barcoding capabilities and the reliability of quantification from eDNA will greatly deepen the possibilities presented by aquatic eDNA metabarcoding in advancing wildlife and biodiversity monitoring in Southeast Asia.