DNA Barcoding From DNA to ID Inspiring Excellence

ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG What is DNA Barcoding? = ? Inspiring Excellence

What DNA Barcoding Works On matK rbcL CHLOROPLASTMITOCHONDRION CO1

Fail: Sequence is completely conserved, good for PCR, but uninformative as barcode Fail: Sequence shows no conservation, impossible for PCR, but good as barcode Win: Sequence shows ~70% conservation, good for PCR, good as barcode Why DNA Barcoding Works

matK rbcL CHLOROPLASTMITOCHONDRION CO1

ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG 1. Sample Organism 4. Sequence DNA 2. Extract DNA 3. Amplify “Barcode” DNA 5. Compare sequence against database How DNA Barcoding Works

ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG Why is DNA Barcoding Important? Inspiring Excellence

Issue #1: No one knows how many species there are.

How Many Species Can You Name? How many Animals did you name? How many mammals? How many plants? How many insects? “Cat” Felis catus “Dog” Canis lupus familiaris “Oak Tree” Quercus alba “Shark” Ginglymostoma cirratum “Beetle” Popillia japonica

Currently between 1.5 and 2 million species are described/known This number may represent as little as half of the true number of species Perhaps more than 1/3 of all species are threatened (IUCN Red list version ) VertebratesSpecies Mammals5,490 Birds9,998 Reptiles9,084 Amphibians6,433 Fishes31,300 Total62,305 Invertebrate s Species Insects1,000,000 Mollusks85,00 Crustaceans47,000 Corals2,175 Arachnids102,248 Total (+others) 1,305,250 PlantsSpecies Angiosperms281,821 Gymnosperms1,021 Ferns and Allies 12,000 Mosses16,236 Algae10,134 Total321,212

Issue #2: There is a lack of agreement of what “species” means.

Canis lupusCanis lupus (familiaris) Anas platyrhynchos Defining “species” is complex and depends on many factors: Interbreeding capabilities Morphological variation Ecological context Genetic similarities

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Issue #3: Traditional taxonomic identification methods may be inadequate and too slow to capture vanishing biodiversity

Classical taxonomy is difficult for non-experts to understand Leaves alternate proximally, opposite and ultimately decussate distally, 6–16 × 4–13 cm; petiole ca. as long as blade, winged, base clasping, basal lobes stipulate, growing as extensions of wings, less than 1 mm wide; blade 5–7-veined, ovate, glabrous, base typically sagittate, margins entire, apex acute to acuminate. Staminate inflorescences axillary, 1–2 per axil, paniculate, fasciculate; panicles bearing flowers singly,bracteolate, in a zigzag pattern along rachis, internodes less than 2 mm; rachis to 25 cm, secondary axes 1–3(–6), fasciculate, less than 3 cm, each subtended by deltate-ovate bracteole shorter than 1 mm. Pistillate inflorescences solitary, 4– 8(–20)-flowered, 6–35 cm, internodes ca. 1 cm. Adding to the complexity: immature, damaged or incomplete specimen may make identification impossible.

Issue #4: DNA Barcoding provides opportunities to investigate things

DNA Barcoding Engages and Transforms Curiosity Into Practical Inquiry

Kate Stoeckle August 23, 2008

Research questions can be about any living thing or about non-living things (foods or other products) that have DNA. Are there invasive (non-native) plants in my local park? What are the most popular types of flowers in my city? Do the teas I buy at my supermarket really contain the ingredients on the package? How many different living organisms can I find in an office building? Whose droppings are these? What research questions could you ask? Examples: Inspiring Excellence

DNA extraction Kit PCR machine and reagents DNA sequencing (Genewiz, other) Bioinformatic tools (analysis of DNA sequence) Materials & Equipment for DNA Barcoding Inspiring Excellence

Sequence Prepare Compare Identify Share DNA Barcoding Analysis Inspiring Excellence

Contributing to big science Inspiring Excellence GenBank BOLD

ACGAGTCGGTAGCTGCCCTCTGACTGCA TCGAATTGCTCCCCTACTACGTGCTATA TGCGCTTACGATCGTACGAAGATTTAT AGAATGCTGCTAGCTGCTCCCTTATTCG ATAACTAGCTCGATTATAGCTACGATG 1. Sample Organism 4. Sequence DNA 2. Extract DNA 3. Amplify “Barcode” DNA 5. Compare sequence against database How DNA Barcoding Works

Find NCBI’s MapViewer; identify difference between human and chimpanzee genome; check situation in all 4 other primate genomes provided Make sea shell phylogenetic tree, work through hhmi.org/biointeractive/activities/shells/online/index.html hhmi.org/biointeractive/activities/shells/online/index.html Review users.ugent.be/~avierstr/principles/phylogeny.html *users.ugent.be/~avierstr/principles/phylogeny.html Review _TUTORIAL/Tree-tutorial.html * _TUTORIAL/Tree-tutorial.html Review Constructing an Evolutionary Tree (Binder) Review Stockle paper on DNA, Taxonomy & Barcode of Life (pre-Readings) * Links worked on ; if they fail, find the 2 sites through Google Assignments

Questions? Inspiring Excellence