KSEF R&D: Applying next generation sequencing technology to estimate biodiversity: A new tool to accurately, rapidly and efficiently solve an old problem

The number of species on Earth has been a subject of debate for centuries and current estimates range over an order of magnitude. Even rather low estimates of ~6.1 million arthropod species imply that over 250 years of Linnaean-based taxonomy has only described ~1/5 of the Earth’s diversity. With the current rate of biodiversity loss, it is a certainty that many arthropod species will become extinct before they are known to science. It is therefore of interest to document biodiversity now and advanced DNA sequencing techniques can provide a means to do so. The proposed research will apply next generation sequencing technology to record the genetic diversity of an experimental forest in Kentucky. Bulk arthropod samples will be extracted and a diagnostic mitochondrial DNA region (COI) will be amplified with newly-developed universal primers. Illumina sequencing will then sequence millions of amplified fragments in a matter of days. Bioinformatics software (QIIME, MACSE) will compute the number of unique sequences present, calculate observed species, identify species by querying the sequences in the Barcode of Life Database, and compute diversity rarefaction curves and various diversity metrics. This methodology is a vast improvement over those of a recent multi-million dollar study which took over 100 taxonomists and a decade to arrive at an approximation with wide variance. By relying on sequence data alone it will be possible to design a repeatable protocol that can be used anywhere on Earth by just a few researchers. The results of this study will create a new standard in biodiversity measurement that can be used to create an accurate estimate of global arthropod diversity. The methods can be applied to track environmental impacts of global climate change or human-induced landscape changes over time and may revolutionize the bio-consulting industry.