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This book presents a comprehensive overview of DNA barcoding and molecular phylogeny, along with a number of case studies. It discusses a number of areas where DNA barcoding can be applied, such as clinical microbiology, especially in relation to infection management; DNA database management; and plant -animal interactions, and also presents valuable information on the DNA barcoding and molecular phylogeny of microbes, algae, elasmobranchs, fishes, birds and ruminant mammals. Furthermore it features unique case studies describing DNA barcoding of reptiles dwelling in Saudi Arabian deserts, genetic variation studies in both wild and hatchery populations of Anabas testudineus, DNA barcoding and molecular phylogeny of Ichthyoplankton and juvenile fishes of Kuantan River in Malaysia, and barcoding and molecular phylogenetic analysis of indigenous bacteria from fishes dwelling in a tropical tidal river. Moreover, since prompt identification and management of invasive species is vital to prevent economic and ecological loss, the book includes a chapter on DNA barcoding of invasive species. Given its scope, this book will appeal not only to researchers, teachers and students around the globe, but also to general readers.
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 BiologyTM 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.
DNA barcoding has become a well-accepted and popular tool for the identification of species and the detection of cryptic taxonomic diversity. As such, it has a tremendous potential for a wide variety of applications in taxonomy, agronomy, conservation biology, forensics etc. Therefore, several countries, institutions and organizations have launched DNA barcoding projects in the context of the international ?Consortium for the Barcode of Life? (CBOL) initiative. Also Belgium has done so with the establishment of the FWO research community ?Belgian Network for DNA barcoding?. In 2012, this network organized the ?Third European Conference for the Barcode of Life? (ECBOL3) in Brussels. During this event a call was made to publish a collection of papers under the thematic title ?DNA barcoding: a practical tool for fundamental and applied biodiversity research?. With the financial support of the EC project ?ViBRANT? (Virtual Biodiversity Research and Access Network for Taxonomy), 21 papers were bundled to form this special ?ZooKeys? issue with the aim to present various applications, advantages and limitations of DNA barcoding. Hence, it is the editors? hope that this issue provides a modest, but timely, contribution to the already vast literature on DNA barcoding.
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 successfulDNA 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.
More than two third of the surface area of our planet is covered by oceans and assessment of the marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine recourses for food, energy and other requirements. This puts pressure on the fragile marine environment and needs sustainable conservation efforts. Marine species identification using traditional taxonomical methods are often burdened with taxonomic controversies. Here in this book we will discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be helpful in the assessment of cryptic species which are widespread in marine environment, and can also be used to link the different life cycle stages to the adult which is difficult to accomplish in marine ecosystems. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. DNA barcoding of different marine groups ranging from the microbes to mammals is to be revealed. In conjugation with newer and faster techniques like high throughput sequencing, DNA barcoding is serving as an effective modern tool in marine biodiversity assessment and conservation.
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.
DNA Barcoding has been promoted since 2003 as a new, fast, digital genomics-based means of identifying natural species based on the idea that a small standard fragment of any organism's genome (a so-called "micro-genome") can faithfully identify and help to classify every species on the planet. The fear that species are becoming extinct before they have ever been known fuels barcoders, and the speed, scope, economy and "user-friendliness" claimed for DNA barcoding, as part of the larger ferment around the "genomics revolution", has also encouraged promises that it could inspire humanity to reverse its biodiversity-destructive habits. This book is based on six years of ethnographic research on changing practices in the identification and classification of natural species. Informed both by Science and Technology Studies (STS) and the anthropology of science, the authors analyse DNA barcoding in the context of a sense of crisis concerning global biodiversity loss, but also the felt inadequacy of taxonomic science to address such loss. The authors chart the specific changes that this innovation is propelling in the collecting, organizing, analyzing, and archiving of biological specimens and biodiversity data. As they do so they highlight the many questions, ambiguities and contradictions that accompany the quest to create a genomics-based environmental technoscience dedicated to biodiversity protection. They ask what it might mean to recognise ambiguity, contradiction, and excess more publicly as a constitutive part of this and other genomic technosciences. Barcoding Nature will be of interest to students and scholars of sociology of science, science and technology studies, politics of the environment, genomics and post-genomics, philosophy and history of biology, and the anthropology of science.
Up-to-date information on methods is crucial in this rapidly advancing field. This compendium includes the latest information on generating, applying and analyzing DNA as well as step-by-step detail and troubleshooting tips and advice from experts.