DNA Barcoding and Community Structure Assessment of a Tropical Forest

Tropical forests are one of the world`s largest carbon sinks, yet they have been lost at high rates due to agriculture, logging, grazing, construction of dams, and other infrastructural development. Brunei Darussalam offers the richest ecosystems on earth; the dipterocarp rainforests offers a home for 3,500 species of vascular plants. The forest type takes its name from the economically important plant family, Dipterocarpaceae that dominates. The angiosperm classification based on molecular data (APG III) makes possible the construction of a reasonable hypothesis for the expected phylogenetic patterns present in all angiosperm plant communities including forest composition. Here, we aim to answer the question "what is the phylogenetic structure within the subplots of the 25 ha plot of Dipterocarp forest at Kuala Belalong?" To answer this question, we will use DNA barcoding to identify the species in a 25 ha forest plot comprising 100 subplots each of 10x10 m 2 . Subplots will be taken randomly, considering the different ecological niches of this forest. This larger plot is already tagged by the CTFS (Centre for Tropical Forest Science), which co-ordinates 48 plots in 22 countries. For barcoding, we will sequence plastid regions rbcL and matK, as recommended by Consortium for the Barcode of Life (CBOL), including all individuals >1cm dbh. These barcode sequences will be used to reconstruct a robust phylogenetic tree using Bayesian inference and maximum parsimony. Trees will be compared with expected phylogenetic patterns (APG III) to confirm the presence of phylogenetic clustering or over-dispersion. Barcoded species of well represented Angiosperm families of these plots will be incorporated into the available rbcL and matK sequence matrices to get the molecular phylogeny of the family concerned. Phylocom will be used to analyze the phylogenetic community structure and quantify community indices such as net relatedness index (NRI) and the nearest taxon index (NTI) for each subplot. A positive NRI and NTI will confirm the phylogenetic relatedness of the vegetation in the community and negative will indicate randomness. Correlation between community indices and ecological parameters will be examined to determine the influence of abiotic parameters on the community structure of the plots. A second-generation sequencing technique (RAD - restriction site associated DNA) offers a high-throughput method of sampling loci across multiple entire genomes for phylogeny reconstruction. We will apply RAD-seq to get well resolved phylogeny of the dipterocarps in subplot as well as in other plots across Batu Apoi in Kuala Belalong to evaluate community structure of the co-occurring species. Dipterocarps from Danum (Malaysia) and Thailand will be included for RAD analyses to understand ecological and evolutionary processes that influence community assembly at local and regional level.

Barcode helped to identify plants growing in a tropical Southeast forest. It is not easy to identify plants in a rich tropical forest. Barcode also helps one to identify the plants even young stages, even when there is no flowers or fruits to identify them. In the case of classical taxonomy one need proper vegetative and reproductive parts to identify the plants.