Environmental DNA: For Biodiversity Research and MonitoringThe objective of this practical handbook is to provide ecologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practice studies and analyses based on environmental DNA. |
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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