GENETIC SEQUENCING FOR MEASURING BIODIVERSITY IN RECENT AND ANCIENT MARINE SEDIMENTS

Taxonomic biodiversity, measured by counting the number of species present in a given area, is the most common method of capturing ecosystem biodiversity in recent and ancient environments. While this method is widely accepted, it is limited by poor preservation and identification of many individuals, making it impossible to include every species within an ecosystem and resulting in loss of some diversity information. To address this issue, we measured the genetic biodiversity (in which species are determined based on sequencing of their DNA) of shallow marine ecosystems by extracting and sequencing the 18S ribosomal gene from bulk carbonate sediment samples taken from several locations around the Caribbean island of Grand Cayman. By comparing genetic and taxonomic biodiversity, we hope to provide a more reliable, or at least a supplementary, measure of molluscan biodiversity in this ecosystem.

Sediment samples were collected from three shallow (~8-10-ft depth) marine locations around Grand Cayman. These sediments were mostly composed of calcium carbonate from shell fragments of bivalves, gastropods, and other calcareous macroorganisms. Molluscan taxonomic diversity was measured by identifying individual shells. DNA was extracted using the QIAquick PCR Purification kit by QIAgen, and a hypervariable ~110 basepair fragment of the 18S rRNA gene was amplified using a high-fidelity PCR master mix. While results are forthcoming, we hypothesize that genetic sequencing will show higher species richness than traditional taxonomic biodiversity measures, as DNA can be collected from specimens too small or damaged to identify. However, if DNA is degraded or our amplification procedures are biased, genetic biodiversity could be misrepresented. We will compare our genetic and manual methods to determine if the genetic method is a less expensive and less time intensive method of accurately representing biodiversity.