Next-Generation 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.

Integrated research, conservation and management of Nee Soon freshwater swamp forest, Singapore: hydrology and biodiversity

“…Lim et al (2018) list the molluscs of Nee Soon, and Cai et al (2018a) the odonates, in the terrestrial and aquatic domains. Kutty et al (2018) describe the use of next generation sequencing to forge the links between field identifications and image databases of the freshwater swamp forest flora and fauna. Sun et al (2018) use numerical modelling to describe some of the projected impacts of climate change on stream flow and groundwater conditions.…”

Diversity, distribution and habitat characteristics of dragonflies in Nee Soon freshwater swamp forest, Singapore

“…They recommended that evidence of breeding, especially the presence of tenerals or exuviae, be used to outline ecological requirements when questions of conservation or population monitoring arise. Hence, future studies should dedicate more effort towards the collection and identification of larvae, including barcoding and environmental DNA (Kutty et al, 2018), to complement the adult surveys thus presenting a more representative odonate community in Nee Soon freshwater swamp forest.…”

Conservation outputs and recommendations for Nee Soon freshwater swamp forest, Singapore

“…However, getting these identifications is particularly challenging in tropical environments. Fortunately, a number of new tools promise to make this task less daunting (Kutty et al, 2018). New imaging techniques help with illustrating relevant characters and new and cheaper DNA barcoding techniques will allow for the generation of databases that can be used by many researchers.…”

“…Another eight papers have been accepted for publication Chong et al, 2018;Clews et al, 2018;Ho et al, 2018;Kutty et al, 2018;Lim et al, 2018;Nguyen et al, 2018;Sun et al, 2018). used for editing and data management.…”

“…Literature Review of freshwater swamp forest literature and research on the Nee Soon freshwater swamp forest updated (Tan et al, 2013;Clews et al, 2018); new results derived from this project presented on vegetation (Chong et al, 2018), fauna Li et al, 2016;Ho et al, 2018;Lim et al, 2018) and cryogenics (Kutty et al, 2018).…”