Environmental DNA: For Biodiversity Research and MonitoringEnvironmental 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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4 Sampling 4.1 4.2 4.3 The cycle of edNA in the environment 4.1.1 State and origin 4.1.2 Fate 4.1.3 Transport Sampling design 4.2.1 Focusing on the appropriate dNA population 4.2.2 defining the sampling strategy Sample preservation 5 ...
4 Sampling 4.1 4.2 4.3 The cycle of edNA in the environment 4.1.1 State and origin 4.1.2 Fate 4.1.3 Transport Sampling design 4.2.1 Focusing on the appropriate dNA population 4.2.2 defining the sampling strategy Sample preservation 5 ...
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... analyses 8.4.1 Sampling effort and representativeness 8.4.1.1 Evaluating representativeness of the sequencing per pCR 8.4.1.2 Evaluating representativeness at the sampling unit or site level 8.4.2 Handling samples with varying ...
... analyses 8.4.1 Sampling effort and representativeness 8.4.1.1 Evaluating representativeness of the sequencing per pCR 8.4.1.2 Evaluating representativeness at the sampling unit or site level 8.4.2 Handling samples with varying ...
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11 12 13 14 10.2 Metagenomics and metatranscriptomics: sequencing more than a barcode 10.2.1 General sampling constraints 10.2.1.1 Optimization of the number of samples 10.2.1.2 Enrichment in target organisms 10.2.1.3 Enrichment in ...
11 12 13 14 10.2 Metagenomics and metatranscriptomics: sequencing more than a barcode 10.2.1 General sampling constraints 10.2.1.1 Optimization of the number of samples 10.2.1.2 Enrichment in target organisms 10.2.1.3 Enrichment in ...
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... permafrost 15.2.1 Overview of the emergence of permafrost as a source of edNA 15.2.2 Large-scale analysis of permafrost samples for reconstructing past plant communities 15.3 Archaeological midden material 15.3.1 Bulk archaeological ...
... permafrost 15.2.1 Overview of the emergence of permafrost as a source of edNA 15.2.2 Large-scale analysis of permafrost samples for reconstructing past plant communities 15.3 Archaeological midden material 15.3.1 Bulk archaeological ...
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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 |
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常见术语和短语
abundance allows amplified analysis approach assess Bacteria barcode biodiversity Chapter collected Comments communities compared considered contain controls corresponding Coverage cycles database detection diet diversity dNA extraction dNA metabarcoding Ecology ecosystems edNA environment Environmental DNA estimated et al example experiment filtering forward primer fragment functional gene genomic Genus Family Order highly identified implemented important length length in bp limited marker metagenomics methods microbial mismatches with forward molecular MOTUs NCBI taxid nucleotides Number of mismatches obtained organisms plant polymerase positive possible potential protocol rdNA reads Recommended annealing temperature Reference reference database region relative represent Research Reverse primer rRNA samples sediments sequencing silico similar single soil species Species Genus Family standard step strategy studies Taberlet Target gene target group Target taxonomic group taxa tion Zinger
书目信息
| 名称 | Environmental DNA: For Biodiversity Research and Monitoring |
| 作者 | Pierre Taberlet, Aurélie Bonin, Lucie Zinger, Eric Coissac |
| 版本 | 插图版 |
| 出版商 | Oxford University Press, 2018 |
| ISBN | 0198767226, 9780198767220 |
| 页数 | 253页 |
| 导出参考文献 | BiBTeX EndNote RefMan |