Biodiversity and Distribution of Marine Fishes in Indonesia inferred by Environmental DNA

Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring. This study investigates the effectiveness of environmental DNA (eDNA) to capture fish biodiversity across a pronounced biodiversity gradient in Indonesia. A total of 15,219,431 sequence reads of 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed 774 Amplified Sequence Variants (ASVs). Patterns of fish diversity based on eDNA partially conformed to expectations based on traditional biodiversity survey methods, with highest fish biodiversity in Raja Ampat, with generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site by site comparisons, both in terms of total number of taxa recovered and ablity to assign species names to ASVs. This result stands in a stark contrast to eDNA studies temperate and tropical ecosystems with lower diversity. Analysis showed that while sequencing depth was sufficient to capture all fish diversity within individual samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Results of this study highlight two major challenge of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient to attach species names to ASVs. Second, sampling design based on studies from lower diversity temperate ecosystems may be inadequate to capture the diversity of high diversity ecosystems