DNA Barcoding: A simple way of identifying species by DNA

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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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  • 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”
  • DNA Barcoding: A simple way of identifying species by DNA

    1. 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. 2. DNA barcode: a short, standardized gene region for identifying animal, plant, and fungal species WHAT, WHY, WHERE
    3. 3. Why DNA to ID species? • Bits and Pieces • Immature Forms • Multitude of Species
    4. 4. Where Apply DNA ID? • Human Health • Environment • Scientific Discovery
    5. 5. ? FOR EXAMPLE: FOOD SAFETY, ACCURACY
    6. 6. DISEASE VECTORS Culex pipiens WEST NILE VIRUS Culicens incidens NON-VECTOR Egg raft ? ?
    7. 7. ? TRADE IN ENDANGERED SPECIES NYC 2012 CHINA 2013 BRAZIL 2012
    8. 8. Google Impact Award 2012 $3M BARCODE OF WILDLIFE PROJECT Aim: Establishing legal DNA barcode standards for endangered and threatened species
    9. 9. Banbury Center, Cold Spring Harbor March 2003, September 2003  Proc Royal Soc London B 2003
    10. 10. 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)
    11. 11. 5’ COI • 5’ cytochrome c oxidase subunit I • distinguishes 95% species Standard DNA barcode for animals (648 bp) mitochondrion mitochondrial genome
    12. 12. BIG challenge: 1.9M species 1 square = 10,000 species Other plants
    13. 13. THREE STUDENT DISCOVERIES HMS Beagle in Galapagos by John Chancellor
    14. 14. Can we identify sushi with DNA barcoding? Kate Stoeckle Louisa Strauss 11th grade Trinity School, NYC
    15. 15. 1. Shop (and eat) 2. Sample 3. Document What they did
    16. 16. 4. Sequence 5. Match to database
    17. 17. 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
    18. 18. For example
    19. 19. Story attracted wide interest Korean Daily NewsCBS Early Show Page 1
    20. 20. Kate Stoeckle and Louisa Strauss August 22, 2008
    21. 21. Textbooks McGraw-Hill,2012Pearson, 2013
    22. 22. Brenda Tan, Matt Cost NPR Science Friday interview
    23. 23. New York Post
    24. 24. 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
    25. 25. TeaBOL “DIY” DNA lab (~$5K equipment)
    26. 26. Student investigations inspired… 2011-12: 75 teams, 218 students, 30 high schools
    27. 27. LARGE SCALE PATTERNS? Cameron Coffran, Mark Y. Stoeckle Rockefeller University SCIENTIFIC INVESTIGATION
    28. 28. LARGE TREES HARD TO “READ” For example:
    29. 29. “boxes” = species; size reflects # seqs/species Species are species, whether butterflies or birds KLEE DIAGRAM (after artist Paul Klee)
    30. 30. KLEE REVEALS HIGHER-LEVEL CLUSTERS Suggests evolution proceeds by bursts (punctuated equilibrium) 704 BIRD SPECIES (songbirds) (songbirds) Q q
    31. 31. 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?
    32. 32. 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
    33. 33. NCP specimens by mail, local collecting 26july2013 68th/York,NYC
    34. 34. NCP so far ~100 specimens 37 contributors 38 locations
    35. 35. z NCP so far: 3 genetic types in NYC, 1 per building; different species? A. NJ tree B. 35 NCP 23 GenBank
    36. 36. Acknowledgments

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