DNA Barcoding: A simple way of identifying
species by DNA
Mark Y. Stoeckle, M.D.
Program for the Human EnvironmentThe Rockefeller University
• What, Why, Where• Student Discoveries• Large-scale Patterns
DNA barcode: a short, standardized gene region for identifying animal, plant, and fungal species
WHAT, WHY, WHERE
Why DNA to ID species?
• Bits and Pieces
• Immature Forms
• Multitude of Species
Where Apply DNA ID? • Human Health
• Environment
• Scientific Discovery
?
FOR EXAMPLE: FOOD SAFETY, ACCURACY
DISEASE VECTORS
Culex pipiensWEST NILE VIRUS
Culicens incidensNON-VECTOR
Egg raft
?
?
?
TRADE IN ENDANGERED SPECIES
NYC 2012
CHINA 2013
BRAZIL 2012
Google Impact Award 2012 $3M
BARCODE OF WILDLIFE PROJECT
Aim: Establishing legal DNA barcode standards forendangered and threatened species
Banbury Center, Cold Spring HarborMarch 2003, September 2003
Proc Royal Soc London B 2003
Ideal DNA barcode• Present in all organisms• Distinguishes all species• Easy to amplify and sequence
Agreed-upon standards• Animals: COI (mitochondrial)• Plants: matK+rbcL (chloroplast)• Fungi: ITS (nuclear)
5’ COI
• 5’ cytochrome c oxidase subunit I• distinguishes 95% species
Standard DNA barcode for animals
(648 bp)mitochondrion
mitochondrialgenome
BIG challenge: 1.9M species
1 square = 10,000 species Other plants
THREE STUDENT DISCOVERIES
HMS Beagle in Galapagos by John Chancellor
Can we identify sushi with
DNA barcoding?
Kate StoeckleLouisa Strauss
11th grade Trinity School, NYC
1. Shop (and eat) 2. Sample
3. Document
What they did
4. Sequence
5. Match to database
What they found
-One-quarter samples mislabeled, all as more expensive or more desirable fish-Mislabeling in 6/10 groceries/fish markets and 2/3 restaurants
For example
Story attracted wide interest
Korean Daily NewsCBS Early Show
Page 1
Kate Stoeckle andLouisa Strauss
August 22, 2008
Textbooks
McGraw-Hill,2012Pearson, 2013
Brenda Tan, Matt CostNPR Science Friday interview
New York Post
Stoeckle MY, Gamble CC, Kirpekar R, Young G, Ahmed S, Little DP (2011) Commercial teas highlight plant DNA barcode identification successes and challenges. Nature Sci Report 1:42.
Tea Barcode of Life Project (TeaBOL)
Social media metrics: 98th percentile “Online Attention”
• 1/3 of herbal teas had unlisted ingredients• incl chamomile, lawn grass, weeds
TeaBOL “DIY” DNA lab(~$5K equipment)
Student investigations inspired…
2011-12: 75 teams, 218 students, 30 high schools
LARGE SCALE PATTERNS?
Cameron Coffran, Mark Y. StoeckleRockefeller University
SCIENTIFIC INVESTIGATION
LARGE TREES HARD TO “READ”For example:
“boxes” = species; size reflects # seqs/species
Species are species, whether butterflies or birds
KLEE DIAGRAM (after artist Paul Klee)
KLEE REVEALS HIGHER-LEVEL CLUSTERS
Suggests evolution proceeds by bursts (punctuated equilibrium)
704 BIRD SPECIES
(songbirds) (songbirds)Q
q
WHAT’S NEXT?
http://phe.rockefeller.edu/barcode/cockroachproject.html
What Students and other citizen scientists collect American cockroaches and analyze their genetic diversity
Why• Are there different genetic types?• Do they differ between buildings, cities?• Are there undiscovered species?
NCP Researchers
FIELD WORK• NCP field collectors (37 individuals so far) (http://phe.rockefeller.edu/barcode/blog/national-cockroach-project-contributors/
LABORATORY ANALYSIS• Joyce Xia, Class of 2014,
Hunter High School, NYC
SUPERVISORS• Daniel Kronauer, Laboratory of Insect Social Evolution, The
Rockefeller University• Christoph von Beeren, Laboratory of Insect Social Evolution• Mark Stoeckle, Program for the Human Environment, The
Rockefeller University
NCP specimens by mail, local collecting
26july201368th/York,NYC
NCP so far
~100 specimens 37 contributors 38 locations
z
NCP so far: 3 genetic types in NYC, 1 per building; different species?
A. NJ tree B. 35 NCP23 GenBank
Acknowledgments