DNA Barcoding, 1st ed. 2024 Methods and Protocols Methods in Molecular Biology Series, Vol. 2744

This volume covers the latest advancements and methods used to study DNA barcoding. The chapters in this book are organized into six parts: theory, DNA manipulation, specialized barcoding methods, analysis of DNA barcodes, completing a successful DNA barcode project, and barcoding as citizen science. Part One looks at several theoretical issues in DNA barcoding concerned with DNA barcodes that can and should be used. Part Two discusses protocols for processing samples into DNA barcodes, including DNA isolation, sequencing and managing samples, and the resulting DNA barcodes. Part Three explores the next generation of DNA barcoding such as FRET-based detection, dual nanopore detection, skimming, and closed-tube methods. Part Four addresses programs and websites that handle DNA barcoding data, and includes character-based approaches, barcode gap methods, integrated approaches, and Barcode of Life Database. Part Five offers protocols for producing a successful DNA barcoding project including plant and animal examples and protocols for generating a DNA Barcode Reference Library. Lastly, Part Six talks about several novel protocols for setting up an educational program using DNA barcodes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, DNA Barcoding: Methods and Protocols encompasses a wide range of techniques and will be a useful reference tool for both scientist and student.

Preface…
Table of Contents…
Contributing Authors…

Part IDNA Barcoding Theory and Practice
Rob DeSalle

1.  Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy
David E. Schindel and Roderic M. P. Page

2. Species Diagnosis and DNA Taxonomy
Dirk Ahrens

3. Delimiting Species with Single-Locus DNA Sequences
Nicolas Hubert, Jarrett D. Phillips, and Robert H. Hanner

4. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy
Aurélien Miralles, Nicolas Puillandre, and Miguel Vences

5. DNA Barcodes in Taxonomic Descriptions
Andrew V.Z. Brower and Rob DeSalle

Part II DNA Manipulation and Sequencing
Rob DeSalle

6. Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification
Jennifer Hackett, Sharon Pepenella, Cristina Fernandez Marco, Louise Bodt, Lina Ruiz Grajales, Jeffrey Petracca, Justin Burke, Bruce Nash, and David Andrew Micklos

7. Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Sample
Oliver Hyman, Amanda Cass, Ray Enke, Amanda Storm, and Bruce Nash

8. DNA Sequencing Technologies and DNA Barcoding
Anisha David, Deepa Arul Priya J., and Akash Gautam

9. DNA Barcoding and Metabarcoding Protocols for Species Identification
Kyleen E. Elwick, Natalie Damaso, and James M. Robertson

10. Environmental DNA Isolation, Validation, and Preservation Methods
Seth W. Cunningham, Michael Tessler, Jicayla Johnson-Rosemond, Iesha S. Whittaker, and Mercer R. Brugler

Part III Specialized DNA Barcoding Methods
Rob DeSalle

11. Single-Molecule FRET-Based Multiplexed Detection
Srishty Gulati, Kalani M. Wijesinghe, and Soma Dhakal

12. DNA Barcodes using a Dual Nanopore Device
Swarnadeep Seth and Aniket Bhattacharya

13. ddRAD Sequencing and DNA Barcoding
Vladislav Ivanov, Kyung Min Lee, and Marko Mutanen

14. Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing
Amrita Srivathsan and Rudolf Meier

15. Generating 2D Barcode for DNA Barcode Sequences
Rui Liu, Yujun Wang, Xinjing Yao, and Chang Liu

16. Analyses of Nuclear Reads Obtained using Genome Skimming
Siavash Mirarab and Vineet Bafna

17. Recent Advances in Closed-Tube Barcoding for FastFish-ID
J. Aquiles Sanchez, John E. Rice, and Lawrence J. Wangh

Part IV Analyzing DNA Barcode Data
Rob DeSalle

18. iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2
Miguel Vences, Stefanos Patmanidis, Alexander Fedosov, Aurélien Miralles, and Nicolas Puillandre

19. DNA Barcode-Based Species Diagnosis with MolD
Alexander Fedosov, Nicolas Puillandre, Frank Fischell, Stefanos Patmanidis, Aurélien Miralles, and Miguel Vences

20. Species Delimitation and Exploration of Species Partitions with ASAP and LIMES
Nicolas Puillandre, Aurélien Miralles, Sophie Brouillet, Alexander Fedosov, Frank Fischell, Stefanos Patmanidis, and Miguel Vences

21. Characteristic Attribute Organization System (CAOS):Identifying Classification Rules Based on Phylogenetically Organized Sequences
Vivek Ramanan and Indra Neil Sarkar

22. CAOS-R: Character-Based Barcoding
Tjard Bergmann

23. Classification of DNA Sequence Based on a Non-Gradient Algorithm: Pseudoinverse Learners
Mohammed A. B. Mahmoud

24. A Measure of the DNA Barcode Gap for Applied and Basic Research
Jarrett D. Phillips, Cortland K. Griswold, Robert G. Young, Nicolas Hubert, and Robert H. Hanner

25. Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases
Natalie Damaso, Kyleen E. Elwick, and James M. Robertson

26. BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data
Sujeevan Ratnasingham, Catherine Wei, Dean Chan, Jireh Agda, Josh Agda, Liliana Ballesteros-Mejia, Hamza Ait Boutou, Zak Mohammad El Bastami, Eddie Ma, Ramya Manjunath, Dana Rea, Chris Ho, Angela Telfer, Jaclyn McKeowan, Miduna Rahulan, Claudia Steinke, Justin Dorsheimer­, Megan Milton, and Paul D.N. Hebert

Part V Generating a Successful DNA Barcode Project
Rob DeSalle

27. Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants
Brandon S. Whitley, Zhao Li, Laura Jones, and Natasha de Vere

28. MetaZooGene Atlas and Database:  Reference Sequences for Marine Ecosystems
Todd D. O’Brien, Leocadio Blanco-Bercial, Jennifer M. Questel, Paola G. Batta-Lona, and Ann Bucklin

29. Principles for Constructing DNA Barcode Reference Libraries
Rodger Gwiazdowski

30. Recent Applications of FastFish-ID
Lawrence J. Wangh, John E. Rice, and J. Aquiles Sanchez

Part VI DNA Barcoding, Teaching, and Citizen Science
Rob DeSalle

31. A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding
Sharon Pepenella, Jennifer Hackett, Cristina Fernandez-Marco, Jeffry Petracca, Christine Marizzi, David A. Micklos, and Bruce Nash

32. Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives
Latasha Wright, Jeanne Garbarino, and Christine Marizzi

33. DNA Barcoding for an Undergraduate Class
Maria Shumskaya

34. Analysis of DNA Barcodes Using DNA Subway
Jason Williams, Bruce Nash, Cornel Ghiban, Mohammed Khalfan, Uwe Hilgert, Susan Lauter, Chun-hua Yang, and David Micklos

35. A Glossary of DNA Barcoding Terms
Miguel Vences, Aurélien Miralles, and Rob DeSalle

Subject Index List…

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts