Site-based integrative analysis of biodiversity in tropical rainforests
- Focus: To unearth the biodiversity of tropical rainforests in a site-based approach, using both DNA and traditional sampling methods
- Funding: The Museum
- Start date: 2013
- End date: 2016
We are assessing the complex biodiversity of tropical rainforests using innovative sequencing methods to increase the ease and rate of species identification.
Our in-depth assessment of spatially defined plots in the rainforest will also include standardised sampling methods.
Site-based analysis will enable us to compare total biodiversity and turnover in the same sites and in different locations.
By integrating the analysis of genetic and species levels, we expect to discover new emerging patterns that will help us understand the processes that drive biodiversity.
In addition, in most parts of the world the remaining primary forest sites are adjacent to areas in various states of disturbance and secondary regrowth. Studying the dynamics of change and its
We are following a site-based approach, carrying out in-depth assessment of diversity at specific localities in tropical rainforests of Borneo and Latin America.
We will be comparing total diversity and turnover at study sites and using this information to establish general patterns of biodiversity.
Site-based studies have the advantage of
- simplified logistics
- repeat visits to
- conduct long-term trapping
- study seasonal change
We are sampling at the site using standardized protocols for
- arthropod sampling
- spatially explicit sampling
- calibrating short sampling against permanent series
- generate DNA grade specimen
Arthropod samples obtained with standard trapping methods (Malaise, flight-interception, pitfall) usually produce thousands of specimens from a complex mixture of species (‘biodiversity soup’”).
Specimen sorting and species-level identification is extremely time consuming and requires specialist expertise.
Collection and storage
Dry and frozen collection workflow (unifying existing Museum collections and databases, linked to KEmu collection management system).
We have adapted the metagenomics procedures used to study complex mixtures of samples in microbial communities to use mitochondrial (mt) genomes.
Only mitochondrial DNA is targeted for sequence analysis, after further enrichment with various procedures that exploit the greater AT content of mtDNA compared to nuclear DNA in insects.
Technology produces huge numbers of sequence reads, which permits the cost effective analysis of mtDNA even if they constitute only a small fraction of the total.
Our general model of biodiversity for interpreting site-based sequence data is based on stochastic (random) dispersal.
Species-genetic diversity correlation (SGDC)
When analysing a single site, neutral processes predict that total species diversity at a site (as a function of size, connectivity and age of a habitat patch) is positively correlated to the genetic diversity of each local species (as a function of population size and age).
SGDC provides a framework for testing diversity patterns at multiple hierarchical levels.
Would you like to get involved?
We are interested in collaborations with researchers involved in studying:
- tropical ecosystems of arthropods worldwide
- agroecosystems and environmental monitoring
- application of site-based approaches of mitogenomes to non-arthropods.