DNA Barcodes: Methods and Protocols

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 the Tree of Life - A. Animals - Insects

John James Wilson and Scott E. Miller

4. Barcoding Methods for Invertebrates

Nathaniel Evans & Gustav Paulay

5. DNA Barcoding of Amphibians and Reptiles

Miguel Vences, Zoltán 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

Darío 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, Neil1; 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 Stöger

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 Mariño-Ramírez

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