Gardens’ Bulletin Singapore 70 (Suppl. 1): 155-173. 2018 
doi: 10.26492/gbs70(suppl.l). 2018-08 
155 
Next-Generation identification tools for Nee Soon 
freshwater swamp forest, Singapore 
S.N. Kutty 1 , W. Wang 2 , Y. Ang 2 , Y.C. Tay 1 , J.K.I. Ho 1 & R. Meier 1 - 2 
Evolutionary Biology Laboratory, Department of Biological Sciences, 
National University of Singapore, 
14 Science Drive 4, 117543 Singapore 
meier@nus.edu.sg 
2 Lee Kong Chian Natural History Museum, National University of Singapore, 
2 Conservatory Drive, 117377 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, high- 
resolution 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. 
Keywords. DNA-barcoding, Next-Generation sequencing, online image database, species 
discovery 
Introduction 
One of the most irritating and fascinating properties of tropical environments is that 
they are species-rich (0degaard, 2000). The large number of species means that there 
are potentially a large number of important biological players in a system. This makes 
it very difficult to understand critical interactions that sustain the environment. This 
problem is exacerbated by the fact that the identification of biological specimens to 
species level is far from straightforward and yet important, because species have 
