Next-Generation Sequencing Identification Tools for Nee Soon freshwater swamp forest, Singapore

Abstract

Many invertebrate and plant species are difficult to identify even by taxonomic experts. This has created a major obstacle for understanding the ecology of tropical environments. Here we explore the use of new large-scale, cost-effective approaches to species identification using Next-Generation Sequencing (“DNA barcodes”). Due to the rapid drop in sequencing cost, such barcodes have the potential to help with many identification tasks and they will facilitate regular monitoring of habitats. We use this approach to explore the species diversity of Nee Soon freshwater swamp forest and provide taxonomic identification tools for the fauna and flora of the forest. DNA-barcode libraries were generated for the flora (>1000 barcodes; 170 chloroplast genomes) and fauna (ca. 3000 barcodes). In addition, highresolution images of 502 animal and 200 plant species were placed on an online image database (“Biodiversity of Singapore”). These images are available to help experts and non-experts alike to identify and appreciate these species. The new databases document Nee Soon’s impressive diversity, but they are also important for in-depth studies of fauna-floral species interactions. For example, the plant barcodes were used to reconstruct the diet of Raffles’ banded langur based on faecal samples. Overall, we find that the fauna in Nee Soon freshwater swamp forest is very diverse and includes many rare species, and that the species composition is very distinct from those living in surrounding habitats. Animal specimens are readily sequenced, while plant specimens (especially those represented by sapwood samples) remain a challenge. However, newer techniques (e.g. based on genome skimming) are starting to help with obtaining plant DNA-barcodes.