DNA Barcodes, 2012
Methods and Protocols
Methods in Molecular Biology Series, Vol. 858

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.

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

A compendium of the latest information on generating, applying, and analyzing DNA

Provides step-by-step detail essential for reproducible results

Contatins key notes and implementation advice from the experts