Environmental DNA: For Biodiversity Research and Monitoring

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Oxford University Press, 2018 - 253页
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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 functionalgenes 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 nowa 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 adiversity 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 environmentalDNA.
 

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目录

CHAPTER 1 Introduction to environmental DNA eDNA
1
CHAPTER 2 DNA metabarcode choice and design
7
CHAPTER 3 Reference databases
21
CHAPTER 4 Sampling
28
CHAPTER 5 DNA extraction
35
CHAPTER 6 DNA amplification and multiplexing
41
CHAPTER 7 DNA sequencing
58
CHAPTER 8 DNA metabarcoding data analysis
65
CHAPTER 14 Terrestrial ecosystems
114
CHAPTER 15 Paleoenvironments
121
CHAPTER 16 Hostassociated microbiota
127
CHAPTER 17 Diet analysis
131
CHAPTER 18 Analysis of bulk samples
140
CHAPTER 19 The future of eDNA metabarcoding
144
Appendix 1 Examples of primer pairs available for DNA metabarcoding
151
Appendix 2 Threehundred and eightyfour 384 tags of eight nucleotides with at least three differences among them
217

CHAPTER 9 Singlespecies detection
85
CHAPTER 10 Environmental DNA for functional diversity
90
CHAPTER 11 Some early landmark studies
99
CHAPTER 12 Freshwater ecosystems
104
CHAPTER 13 Marine environments
110
Appendix 3 Checklist when designing a PCRbased DNA metabarcoding experiment
220
References
223
Index
247
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作者简介 (2018)

After teaching biology in high school for 10 years, Pierre Taberlet obtained his PhD in ecology in 1992 at the Universite Grenoble Alpes. He is currently senior CNRS scientist in Laboratoire d'Ecologie Alpine at the Universite Grenoble Alpes. He has been heavily involved in developinginnovative molecular tools for tackling ecological questions. He was the recipient of the Molecular Ecology Prize in 2007 and is a member of the Norwegian Academy of Sciences and Letters (2005) and of Academia Europaea (2014).Aurelie Bonin obtained her PhD in genomics of local adaption in 2006. After various postdoctoral positions in population genomics and ecology, she is now a DNA metabarcoding project leader for the French AnaEE (Analysis and Experimentation on Ecosystems) https://www.anaee-france.fr/.Lucie Zinger obtained her PhD in microbial ecology in 2009. She is currently assistant professor at the Institut de Biologie de l'Ecole Normale Superieure in Paris. She is interested in the fields of biogeography, macroecology, community ecology, and microbial ecology, as well as eDNA-basedtechniques to uncover the diversity of elusive organisms. Her current work focuses on the distribution and assembly mechanisms of microorganisms in soils, oceans, plant leaves, and insects.Geneticist and bioinformatician, Eric Coissac obtained his PhD in genetics and genomics in 1996 at the Universite Pierre et Marie Curie in Paris. He is currently associate professor at Universite Grenoble Alpes in Laboratoire d'Ecologie Alpine.

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