All Bocas Barcoding Alliance
DNA Barcoding in the Southern Caribbean.
The All Bocas Barcoding Alliance (ABBA) is the ongoing effort to develop an exhaustive DNA barcode reference database of the fauna and flora of Bocas del Toro, Panama. This joint Smithsonian Institution project between the Natural History Museum's Laboratory of Analytical Biology and the Smithsonian Tropical Research Institute's Bocas Research Station aims to create a database of DNA barcodes for over 95% of the organisms in Bocas del Toro.
The first phase of this project is focused on the marine organisms. Work on the sponges, hydroids, and tunicates is already well underway and we anticipate that we will have DNA barcodes of 85% of the macroscopic marine fauna of Bocas del Toro by 2010 and 90% of the macroscopic marine flora by 2011.
Well documented DNA barcodes are useful tools for identifying samples where the morphological features have not been preserved. Barcodes can be used to identify stomach contents for diet analyses, the source of poached meat and seafood, and to match unidentified larvae with known adults. We think the data we produce will be a useful tool for other researchers working in the Caribbean.
Why Bocas del Toro?
Bocas del Toro is a biologically rich region of Panama with complex habitats ranging from highland cloud forest to Caribbean mangroves and reefs. Coordinated efforts are already underway at the Smithsonian Tropical Research Institute (STRI) for taxonomic experts to survey and inventory the marine fauna and flora of the archipelago (http://striweb.si.edu/bocas_database).
Preliminary results from these efforts show that the area around the Bocas Research Station are particularly rich in marine life. After only 10 days of sampling there were more tunicate species recorded for Bocas del Toro than any other site in the Caribbean except for Guadalupe. Sponge diversity is the third highest in the Caribbean and representatives of 90% of Caribbean corals and soft corals can be found easily throughout the region.
Long-term monitoring of the physical environment and the development of a GIS system for the region adds to the value of the data.
Who We Are
ABBA Team Leaders:
Such a large effort requires coordination of priorities, funding, field collections and laboratory work as well as hands-on interaction at all stages of the collecting, processing, and sequencing efforts. Team leaders, Drs. Rachel Collin and Amy Driskell lead the field and laboratory components respectively.
- Dr. Rachel Collin - Rachel.firstname.lastname@example.org
Rachel, the Director of STRI's Bocas Research Station since 2002, coordinates the taxonomic experts and their field collections. Her group surveys of the marine life of the region has resulted in a special issue of the Caribbean Journal of Science documenting the biodiversity of the region as well as the Bocas del Toro Species Database
- Dr. Amy Driskell -
DNA barcodes are only as good as the identifications of the reference samples. ABBA relies on the participation of an international group of dedicated taxonomic experts to collect and identify each gold-standard barcode voucher. Please contact Dr. Rachel Collin (Rachel.email@example.com) if you are interested in participating in ABBA as a taxonomist on any group of organisms.
Contributing Taxonomists include:
- Dr. Robert Thacker - Porifera
- Dr. Cristina Diaz - Porifera
- Dr. Rosana Rocha - Tunicates
- Dr. Gretchen Lambert - Tunicates
- Dr. Maria-Pia Miglietta - Hydroids
Any large-scale DNA barcoding effort hinges on the careful and efficient processing of thousands of samples. The Laboratory of Analytical Biology (LAB: http://lab.si.edu/) uses a Qiagen BioSprint magnetic bead extractor to extract the DNA on-site in Bocas del Toro. Sequences are generated with high-throughput sequencing in the LAB in Washington DC. Data are entered into the Barcode database.
- Lee Weigt -
- Dr. Amy Driskell -
- Jeff Hunt -
Progress to Date
During the summer of 2006 we collected and identified xx samples of tunicates, sponges and hydroids. Xx have been sequenced successfully for COI and we anticipate that xx sequences from these organisms will be in the Barcode of Life database by the end of 2007.
Collin, R; Weigt, L; Driskell, A; Rocha, R., Miglietta, M-P., and R. W. Thacker. 2007. All Bocas Barcoding Alliance. Part 1: DNA barcoding of the marine organisms of Bocas del Toro, Panama. Integrative and Comparative Biology.
The collection, vouchering and DNA barcoding of sponges, hydroids and tunicates launched the All Bocas Barcoding Alliance's (ABBA) effort to exhaustively barcode the fauna and flora of Bocas del Toro, Panama. The first phase of this project is focused on the marine organisms. This joint Smithsonian project between the Natural History Museum's Laboratory of Analytical Biology (LAB) and the Smithsonian Tropical Research Institute's Bocas Research Station aims to create a database of DNA barcodes for over 90% of the macroscopic marine fauna of Bocas del Toro by 2010 and macroscopic marine flora by 2011. During 2006, experts collected and identified 100 known species of sponges, 60 tunicates and 60 hydroids with a total of 1,500 tissue samples. This accounts for a total of 66%, 84% and 90% of the species officially reported for these taxa in Bocas del Toro. A Qiagen BioSprint magnetic bead extractor was used to extract the DNA on-site and COI sequences were generated from these extractions at the LAB in Washington DC. This experience provided proof of concept for rapidly and efficiently generating high quality DNA extractions for DNA barcoding from taxa as they are identified by experts at the point of collection. Efforts are underway to obtain funding to census and barcode the marine algae and microscopic fauna.