1. DNA Barcoding Amy Driskell Laboratories of Analytical Biology
National Museum of Natural History
Smithsonian Institution, Wash. DC

2. Outline Barcoding in general Uses & Examples Barcoding Bocas Algae
Data, Analysis, etc.

3. What is a DNA barcode? A fingerprint for identification of everything
A short, easily and universally amplifiable, and reasonably variable piece of DNA

4. Requirements For “Barcode” label in GenBank, for “Reference” in BOLD
Sequence is from a vouchered specimen - Re-identify
Voucher meta-information required: GPS coordinates, photographs (in situ, in some cases), collector and identifier data - Re-collect
DNA sequence is high quality (minimum length, minimum coverage, minimum “quality scores” - Compare
Raw data (chromatograms) publicly available - Re-analyze

5. Organizations
Consortium for the Barcode of Life (CBOL) (
Barcode of Life Database (BOLD) (
International Barcode of Life (iBOL) (
FishBOL, All Birds Barcoding Initiative, MarBOL, etc. etc.

6. Barcode “Markers”
Animals: Mitochondrial cytochrome oxidase subunit I (CO1/COX1) ~ 650 bp
BUT, not variable in cnidarians, 16S rDNA historically more informative in many groups (e.g. frogs, some crustaceans). Second marker possible.
Fungi: Nuclear internal transcribed spacer (ITS)
Non-coding gene and difficult to align. But long history in fungal studies, large existing databases, CO1 contains introns.

7. Barcode “Markers” Red & Brown Algae: CO1 Green Plants: Not decided
Not nearly as “universally” amplifiable as in animals, requires many different primers
Green Plants: Not decided
SI botanists promote rBCL and the trnH-psbB spacer
Others prefer for rBCL and matK
All are chloroplast genes
Green algae? Still not clear

8. DNA Barcoding is an imperfect science
Evolutionary History:
Hybridization (plastid genomes)
Pseudogenes
Heteroplasmy or multiple copies (nuclear markers)
Lineage sorting, recent speciation
Slow rates of sequence divergence
Practical Difficulties
Lack of universality
Co-amplification
Incomplete sampling
Lack of taxonomic experts

9. Barcode of Life Database (BOLD)

10. Today’s Statistics BOLD GenBank Total: 570,000 Species: 62,000
“Reference”: 234,000
“Ref” species: 13,774
GenBank
“Barcode” keyword: 37,000

11. Algal Barcodes in BOLD

12. SI’s Barcoding Philosophy
Collaborate - taxonomic experts, students
Train - students, interns, other researchers
Assist - lab setup, protocol development, collecting
Archive - a “lending library” of high quality, well-vouchered DNAs
Explore biodiversity in collaboration with taxonomists and phylogeneticists.

13. Biologically Interesting Uses
Biodiversity Exploration
Discovery of sibling species
Quick assessment of local diversity
“DNA assisted alpha taxonomy”
Ecological & Behavioral Studies
Habitat assessment
Stomach content analysis

14. L.A.B. Examples LAB & Bocas taxonomic workshops
CeDAMAR Antarctic deep sea surveys
Caribbean Fish
Central American Frogs
Biocode Moorea

15. Practical, Fundable Uses
Method of identification, particularly useful to non-experts
Import/export and pest control
Fisheries management
Water and habitat quality assessment
Partial or fragmentary sample analysis
Associating different life stages

16. L.A.B. Examples USAF/FAA “Bird Strike” Project Larval Fish ID
US Food & Drug Agency
US Enviromental Protection Agency

17. Barcoding Bocas Algae Collections 2007, 2008, 2009 ~1000 specimens
Red Algae: ~250 specimens sequenced
Lab protocol and primer development

18. The Process of Barcoding
Extraction: methods, machines, timing

19. The Process of Barcoding
2. Amplification - Polymerase Chain Reaction
-Primers

20. The Process of Barcoding
3. Sequencing

21. The Process of Barcoding
Submission and organization of metadata
Quality control, data processing
Accuracy checking

22. Nov. 9-13, 2009
Website: dnabarcodes2009.org