DNA Barcodes Methods and Protocols

About this book

A DNA barcode in its simplest definition is one or more short gene sequences taken from a standardized portion of the genome that is used to identify species through reference to DNA sequence libraries or databases. In DNA Barcodes: Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used with DNA barcodes. These methods include the latest information on techniques for generating, applying, and analyzing DNA barcodes across the Tree of Life including animals, fungi, protists, algae, and plants. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Barcodes: Methods and Protocols aids scientists in continuing to study methods from wet-lab protocols, statistical, and ecological analyses along with guides to future, large-scale collections campaigns.

Contents

I. Introduction
1. Introduction (W. John Kress & David L. Erickson, Smithsonian, USA)

II. DNA Barcodes for the Tree of Life
2. Introduction to Animal DNA Barcoding Protocols Lee A. Weigt, Amy Driskell, Andrea Ormos, Chris Meyer, and Allen Collins
3. DNA Barcodes for Insects John James Wilson
4. Barcoding Methods for Invertebrates Nathaniel Evans & Gustav Paulay
5. DNA Barcoding of Amphibians and Reptiles Miguel Vences, Zoltan T. Nagy, Gontran Sonet, Erik Verheyen
6. DNA Barcoding Fishes Lee A. Weigt, Amy Driskell, Andrea Ormos
7. DNA Barcoding Birds: from Field Collection to Data Analysis Dario A. Lijtmaer, Kevin C. R. Kerr, Mark Y. Stoeckle and Pablo L.Tubaro
8. DNA Barcoding in Mammals Natalia V. Ivanova, Elizabeth L. Clare, Alex V. Borisenko
9. Methods for DNA Barcoding of Fungi Ursula Eberhardt
10. Methods for DNA Barcoding Photosynthetic Protists Emphasizing the Macroalgae and Diatoms Gary W. Saunders and Daniel C. McDevit
11. DNA Barcoding Methods for Land Plants Aron J. Fazekas, Maria L. Kuzmina, Steven G. Newmaster, and Peter M. Hollingsworth

III. Generating DNA Barcode Data
12. Field Information Management Systems (FIMS) for DNA Barcoding Deck, John; Gross, Joyce; Stones-Havas, Steven; Davies, Neil; Shapley, Rebecca & Meyer, Christopher
13. Laboratory Information Management Systems (LIMS) for DNA Barcoding Meaghan Parker; Steven Stones-Havas, Craig Starger and Chris Meyer
14. DNA Extraction, Preservation and Amplification Thomas Knebelsberger and Isabella Stoger
15. DNA Mini-barcodes Mehrdad Hajibabaei and Charly McKenna
16. Next Generation Sequencing: Multiplexing Multiple Barcode Amplicons into Single 454 Run Ryuji Machida and Nancy Knowlton

IV. Applications of DNA Barcode Data
17. The Practical Evaluation of Barcode Efficacy John L. Spougeand Leonardo Marino-Ramirez
18. Plant DNA Barcodes, Taxonomic Management and Species Discovery in Tropical Forests Christopher W. Dick and Campbell O. Webb
19. Construction and Analysis of Phylogenetic Trees using DNA Barcode Data David L. Erickson and Amy C. Driskell
20. Phylogenetic Analyses of Ecological Communities Using Barcode Data Nathan G. Swenson

V. Case Studies on DNA Barcodes
21. DNA Barcodes: FISH-BOL, a Case Study Robert D. Ward
22. Generating Plant DNA Barcodes for Trees in Long-term Forest Dynamics Plots W. John Kress, Ida C. Lopez, David L. Erickson
23. Future Directions David L. Erickson and W. John Kress

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