DNA barcoding makes it easier for experts and non- experts to identify species including from bits and pieces, immature forms, and those with many close look-alikes. Applications include health, environment, and education. High school students are using DNA barcoding to explore the world around them and make scientific discoveries. Like a giant Wikipedia entry, the multitude of researchers depositing DNA barcodes in GenBank are creating the first large-scale maps of the genetic structure of biodiversity.
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DNA Barcoding: A simple way of identifying species by DNA
1. DNA Barcoding:
A simple way of identifying
species by DNA
Mark Y. Stoeckle, M.D.
Program for the Human Environment
The Rockefeller University
• What, Why, Where
• Student Discoveries
• Large-scale Patterns
2. DNA barcode: a
short, standardized gene
region for identifying
animal, plant, and fungal
species
WHAT, WHY, WHERE
3. Why DNA to ID species?
• Bits and Pieces
• Immature Forms
• Multitude of Species
4. Where Apply DNA ID?
• Human Health
• Environment
• Scientific Discovery
8. Google Impact Award 2012 $3M
BARCODE OF
WILDLIFE
PROJECT
Aim: Establishing legal DNA barcode standards for
endangered and threatened species
9. Banbury Center, Cold Spring Harbor
March 2003, September 2003
Proc Royal Soc London B 2003
10.
11. 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)
12. 5’ COI
• 5’ cytochrome c oxidase subunit I
• distinguishes 95% species
Standard DNA barcode for animals
(648 bp)
mitochondrion
mitochondrial
genome
18. 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
25. 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
33. 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
34. NCP specimens by mail, local collecting
26july2013
68th/York,NYC
Why use DNA to identify species? First, lots of the things we want to identify are in bits and pieces. For instance, this is a photomicrograph of bat guano and is filled with undigested bits of insects from what the bat ate. An expert might be able to pick out a few pieces as being from a beetle or a moth for instance. But all the pieces have DNA. The DNA may be damaged but it is intact enough to recover the short DNA barcode segment. So DNA barcoding can be really helpful for food webs. Second, lots of things are immature forms that look more or less alike even though they are different species. By appearance it’s hard or sometimes impossible to tell one fish egg from another, or larval forms of insects, or non-flowering parts of plants such as leaves or roots. Third, there are just a lot of species. This are moths attracted to a light in Costa Rica. There are 160,000 species of moths in the world. Even an expert can identify only a few thousand. If you wanted to use experts to identify these, you’d first have to sort them out and send to specialists who were expert in particular groups. This would be slow and expensive. DNA testing can help anyone match the insects to their names.
We can apply this to look at groups of species. We see the same pattern of blocks of highly-correlated sequences.
What’s next? This summer we started a “National Cockroach Project”