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 biologicalcommunities 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 DNAare 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.
1: Introduction to environmental DNA (eDNA) 2: DNA metabarcode choice and design 3: Reference databases 4: Sampling 5: DNA extraction 6: DNA amplification and multiplexing 7: DNA sequencing 8: DNA metabarcoding data analysis 9: Single-species detection 10: Environmental DNA for functional diversity 11: Some early landmark studies 12: Freshwater ecosystems 13: Marine environments 14: Terrestrial ecosystems 15: Palaeoenvironments 16: Host-associated microbiota 17: Diet analysis 18: Analysis of bulk samples 19: The future of eDNA metabarcoding
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