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