Case Study
Submitted By
| Name: | Michael Mincarone |
| Institution: | Universidade do Vale do Itajaí |
| Country: | Brazil |
| Email: | mincarone@univali.br |
Title & Categories
| Case Study Title: | Confluence of capabilities: DNA Barcoding the Marine Fishes of Brazil |
| Focus Theme: | Biotic inventory of multiple taxa in a region or habitat |
| Geographic Region: | Atlantic Ocean |
| Habitat Type: | Marine open ocean water column, Marine nearshore benthos, Marine deep ocean benthos, Marine continental slope benthos, Marine continental shelf water column, Marine continental shelf benthos |
| Taxonomic Group: | f: Osteichthyes, f: Chondrichthyes |
| Project Duration: | 4/2007 to 12/2007 |
Scope
To completely process (collect, identify, tissue sample, digital photograph, GPS, voucher, and DNA Barcode sequences) several hundred samples of marine fishes from the fisheries of Brazil’s largest port, Itajai. (FAO area 41) and contribute to FISH-BOL.
Purpose
- Collect and voucher – The catch (and almost more importantly, the by-catch) of the commercial fisheries can be obtained at no cost for the collections per se. The cost per specimen will be absorbed by the Museu Oceanografico and Universidade do Vale do Itajai.
- Training, part I – The Brazilian team will be trained in tissue sampling compatible with the high-throughput lab automation, and in gathering all associated metadata. - OnBoard Observer Program – Funding will be obtained for reinstatement of the proven program of placing recent marine biology graduates on commercial fishing vessels with the added purpose of taking tissue samples from voucher specimens for DNA Barcoding. - Training, part II – subsequent trip(s) to the LAB will provide hands-on training in the processing (lab and IT) of a DNA barcoding project to member(s) of the Brazilian team. CBOL funding requested. - DNA Barcoding. The SI/LAB team will produce high-quality DNA extractions & COI barcodes for all barcode compliant specimens (maximum 5 per species). - All data to be injected into FISH-BOL and BOLD as fully barcode compliant records, with release to GenBank within 1 calendar year from date of upload into BOLD.Background
- Brazil: The Oceanographic Museum at the Vale do Itajai University has made a commitment to growing it’s fish collection, and in the past 10 years, that collection has grown to include more than 11,300 specimens representing 725 species. In 2002, 2003, and 2005 an “OnBoard Observer Program” enlisted recent marine biology graduates to accompany commercial fishing vessels and this resulted in 4-5 fold increases in samples for the collection (see Figure 1). The Museum maintains a strong interest in growing the collection, and would like to see the value of that collection increase by having A) validation of the identification of the specimens via DNA Barcoding and B) Tissues available for other molecular studies. Additionally, they are eager to participate in the FISH-BOL and DNA Barcoding efforts for their region.
- LAB (NMNH): with the infrastructure in place to 1) collect, 2) identify, 3) photograph, 4) GPS, 5) tissue sample and most importantly 6) transfer and 7) voucher these valuable specimens, the only costs to the lab are for high quality DNA extractions, PCR and sequencing of the COI barcode region, and archiving of the DNA. - Sample movement: One of the most compelling features of this collaboration is the pre-existing MTA (Materials Transfer Agreement) between the University and the Smithsonian Institution’s NMNH. This removes one of the greatest barriers to transporting the genetic resources from the bio-resource rich country to the laboratories capable of and interested in doing both the training and workflow.Logistics
- Mincarone goes to NMNH for training (with Lee Weigt) in tissue sampling;
- Training observers at MOVI (Mincarone and two selected observers);
- Observers go collect/tissue samples from marine fishes off southern Brazil;
- The voucher specimens are curated at MOVI;
- Mincarone brings tissue samples to LAB (NMNH) for Barcoding and training on data;
- All data are injected into FISH-BOL and BOLD.