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  • 1
    Call number: 9780191079993 (e-book)
    Type of Medium: 12
    Pages: 1 online resource (254 pages)
    Edition: First edition
    ISBN: 9780191079993 (e-book)
    Language: English
    Note: Contents Acknowledgments 1 Introduction to environmental DNA (eDNA) 1.1 Definitions 1.2 A brief history of eDNA analysis 1.3 Constraints when working with eDNA 1.4 Workflow in eDNA studies and main methods used 1.5 Environmental DNA as a monitoring tool 2 DNA metabarcode choice and design 2.1 Which DNA metabarcode? 2.2 Properties of the ideal DNA metabarcode 2.3 In silica primer design and testing 2.3.1 Prerequisites 2.3.2 Reference sequences: description, filtering, and formatting for ecoPrimers 2.3.3 In silica primer design with ecoPrimers 'Ihe ecoPrimers output 2.3.4 In silica primer testing with ecoPCR The ecoPCR output Filtering of the ecoPCR output Evaluation of primer conservation Taxonomic resolution and Bs index 2.4 Examples of primer pairs available for DNA metabarcoding 3 Reference databases 3.1 Extracting reference databases from EMBL/GenBank/DDBJ 3.1.1 Downloading a local copy of EMBL 3.1.2 Identifying sequences corresponding to the relevant metabarcode 3.2 Marker-specific reference databases 3.2.1 Nuclear rRNA gene reference databases 3.2.2 Eukaryote-specific databases 3.3 Building a local reference database 3.3.1 PCR-based local reference database 3.3.2 Shotgun-based local reference database 3.4 Current challenges and future directions 4 Sampling 4.1 The cycle of eDNA in the environment 4.1.1 State and origin 4.1.2 Fate 4.1.3 Transport 4.2 Sampling design 4.2.1 Focusing on the appropriate DNA population 4.2.2 Defining the sampling strategy 4.3 Sample preservation 5 DNA extraction 5.1 From soil samples 5.2 From sediment 5.3 From litter 5.4 From fecal samples 5.5 From water samples 6 DNA amplification and multiplexing 6.1 Principle of the PCR 6.2 Which polymerase to choose? 6.3 The standard PCR reaction 6.4 The importance of including appropriate controls 6.4.1 Extraction negative controls 6.4.2 PCR negative controls 6.4.3 PCR positive controls 6.4.4 Tagging system controls 6.4.5 Internal controls 6.5 PCR optimization 6.6 How to limit the risk of contamination? 6.7 Blocking oligonucleotides for reducing the amplification of undesirable sequences 6.8 How many PCR replicates? 6.9 Multiplexing several metabarcodes within the same PCR 6.10 Multiplexing many samples on the same sequencing lane 6.10.1 Overview of the problem 6.10.2 Strategy 1: single-step PCR with Illumina adapters 6.10.3 Strategy 2: two-step PCR with Illumina adapters 6.10.4 Strategy 3: single-step PCR with tagged primers 7 DNA sequencing 7.1 Overview of the first, second, and third generations of sequencing technologies 7.2 The Illumina technology 7.2.1 Library preparation 7.2.2 Flow cell, bridge PCR, and clusters 7.2.3 Sequencing by synthesis 7.2.4 Quality scores of the sequence reads 8 DNA metabarcoding data analysis 8.1 Basic sequence handling and curation 8.1.1 Sequencing quality The pros and cons of read quality-based filtering Quality trimming software 8.1.2 Paired-end read pairing 8.1.3 Sequence demultiplexing 8.1.4 Sequence dereplication 8.1.5 Rough sequence curation 8.2 Sequence classification 8.2.1 Taxonomic classification 8.2.2 Unsupervised classification 8.2.3 Chimera identification 8.3 Taking advantages of experimental controls 8.3.1 Filtering out potential contaminants 8.3.2 Removing dysfunctional PCRs 8.4 General considerations on ecological analyses 8.4.1 Sampling effort and representativeness Evaluating representativeness of the sequencing per PCR Evaluating representativeness at the sampling unit or site level 8.4.2 Handling samples with varying sequencing depth 8.4.3 Going further and adapting the ecological models to metabarcoding 9 Single-species detection 9.1 Principle of the quantitative PCR (qPCR) 9.1.1 Recording amplicon accumulation in real time via fluorescence measurement 9.1.2 The typical amplification curve 9.1.3 Quantification of target sequences with the Ct method 9.2 Design and testing of qPCR barcodes targeting a single species 9.2.1 1he problem of specificity 9.2.2 qPCR primers and probe 9.2.3 Candidate qPCR barcodes 9.3 Additional experimental considerations 9.3.1 General issues associated with sampling, extraction, and PCR amplification 9.3.2 The particular concerns of contamination and inhibition 10 Environmental DNA for functional diversity 10.1 Functional diversity from DNA metabarcoding 10.1.1 Functional inferences 10.1.2 Targeting active populations 10.2 Metagenomics and metatranscriptomics: sequencing more than a barcode 10.2.1 General sampling constraints Optimization of the number of samples Enrichment in target organisms Enrichment in functional information 10.2.2 General molecular constraints 10.2.3 From sequences to functions Assembling (or not) a metagenome Sorting contigs or reads in broad categories Extracting functional information via taxonomic inferences Functional annotation of metagenomes 11 Some early landmark studies 11.1 Emergence of the concept of eDNA and first results on microorganisms 11.2 Examining metagenomes to explore the functional information carried by eDNA 11.3 Extension to macroorganisms 12 Freshwater ecosystems 12.1 Production, persistence, transport, and delectability of eDNA in freshwater ecosystems 12.1.1 Production 12.1.2 Persistence 12.1.3 Transport/ diffusion distance 12.1.4 Detectability 12.2 Macroinvertebrates 12.3 Diatoms and microeukaryotes 12.4 Aquatic plants 12.5 Fish, amphibians, and other vertebrates 12.5.1 Species detection 12.5.2 Biomass estimates 12.6 Are rivers conveyer belts of biodiversity information? 13 Marine environments 13.1 Environmental DNA cycle and transport in marine ecosystems 13.2 Marine microbial diversity 13.3 Environmental DNA for marine macroorganisms 14 Terrestrial ecosystems 14.1 Delectability, persistence, and mobility of eDNA in soil 14.2 Plant community characterization 14.3 Earthworm community characterization 14.4 Bacterial community or metagenome characterization 14.5 Multitaxa diversity surveys 1 5 Paleoenvironments 15.1 Lake sediments 15.1.1 Pollen, macrofossils, and DNA metabarcoding 15.1.2 Plants and mammals from Lake Anteme 15.1.3 Viability in the ice-free corridor in North America 15.2 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 fish bones from Madagascar 15.3.2 Midden from Greenland to assess past human diet 16 Host-associated microbiota 16.1 DNA dynamics 16.2 Early molecular-based works 16.3 Post-holobiont works 17 Diet analysis 17.1 Some seminal diet studies 17.1.1 Proof of concept-analyzing herbivore diet using next-generation sequencing 17.1.2 Assessing the efficiency of conservation actions in Bialowieza forest 17.1.3 Characterizing carnivore diet, or how to disentangle predator and prey eDNA 17.1.4 Analyzing an omnivorous diet, or integrating several diets in a single one 17.2 Methodological and experimental specificities of eDNA diet analyses 17.2.1 eDNAsources Feces Gut content Whole body 17.2.2 Quantitative aspects Relationship between the amount of ingested food and DNA quantity in the sample Quantifying DNA with PCR and next-generation sequencing Empirical correction of abundances 17.2.3 Diet as a sample of the existing biodiversity 17.2.4 Problematic diets 18 Analysis of bulk samples 18.1 What is a bulk sample? 18.2 Case studies 18.2.1 Bulk insect samples for biodiversity monitoring 18.2.2 Nematode diversity in tropical rainforest 18.2.3 Marine metawan diversity in benthic ecosystems 18.3 Metabarcoding markers for bulk samples 18.4 Alternative strategies 19 The future of eDNA metabarcoding 19.1 PCR-based approaches 19.1.1 Singl
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    In:  Supplement to: Bajard, Manon; Poulenard, Jérôme; Sabatier, Pierre; Etienne, David; Ficetola, Francesco; Chen, Wentao; Gielly, Ludovic; Taberlet, Pierre; Rioux, Delphine; Develle, Anne-Lise; Rey, Pierre-Jérôme; Moulin, Bernard; de Beaulieu, Jacques-Louis; Arnaud, Fabien (in press): Long-term changes in alpine pedogenetic processes: effect of millennial agro-pastoralism activities (French-Italian Alps). Geoderma
    Publication Date: 2020-01-17
    Description: Human activities are known to modify soil properties; however, the associated modifications to soil processes are poorly documented, as they must be studied over long time scales. Lake Verney, which is on the Italian side of the Petit Saint-Bernard Pass in the French-Italian Alps (2188 m a.s.l) provides a sediment record of the last 11 000 cal. yrs BP. Analysis of multiple proxies within this sediment sequence, including sedimentological characteristics, mineral geochemistry (as determined using XRF and extractable Fe fractions), pollen and non-pollen palynomorphs (NPPs) and sediment DNA (sedDNA) analysis, is compared with analyses of current soils and paleosols within this mountain ecosystem in order to understand the main drivers of long-term pedogenesis. We performed principle component analysis on both the sediment proxies and the soil geochemical properties to identify different sediment endmembers that reflect different types of soil horizons, mainly stagnic and spodic. These horizons are characteristic of specific soil processes and their associated land uses. During the first part of the Holocene, a decrease in the carbonate fraction in the sediment reflects the loss of carbonate material from soils that occurred as early as postglacial vegetation became established . The migration of Fe-complexes until 6000 cal. yrs BP indicates the development of Podzols in the catchment. The first signs of human land use are detected at 4300 cal. yrs BP according to analyses of sedDNA and NPPs. Increases in the input of terrestrial organic matter, associated with forest clearance suggests degradation of the surface horizons of the Podzols. Erosion increased during the Roman Period due to sheep grazing. Then, while erosion was still increasing, Podzols developed into Stagnosols after the Middle Ages with cow grazing which is consistent with the current functioning of the soils. The history of the paleosols and archaeological stratigraphy within the study area confirm the model of soil evolution inferred from the lake sediments and allow us to characterize the human-induced "metapedogenetic phase" of the evolution of the soil cycle. Anthropo-pedogenesis may define the development of soils during the Anthropocene. The main consequence of this change in the functioning of the soils is a reduced sequestration of soil carbon.
    Type: Dataset
    Format: application/zip, 6 datasets
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  • 7
    ISSN: 1432-0762
    Keywords: Key words Paternity exclusion ; Extra-pair copulation ; Monogamy ; Hair ; Marmota marmota
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genetic parentage and pedigrees of 35 litters from 12 family groups of monogamous Alpine marmot (Marmota marmota) in the French Alps were analyzed using six hypervariable sequence repeat nuclear loci (microsatellites). All of the members of these family groups were sampled during a 5-year period. Hairs taken directly from animals served as a source of DNA for amplification of the loci. Our results indicate that the genetic mating system of the Alpine marmot is quite different from a strictly monogamous breeding system. Extra-pair paternity occurred in 11 of the 35 litters (31.4%). Of the 134 juveniles typed, 26 (19.4%) could be attributed to extra-pair copulation (EPC). We examine hypotheses which could explain the evolution of EPC and discuss the different patterns of extra-pair mating.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1573-5028
    Keywords: chloroplast DNA ; non-coding region ; polymerase chain reaction ; primer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 358 (1992), S. 197-197 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] SIR - We wish to report that hairs collected in the field are a potentially valuable source of DNA for genetic studies that may help in the management of the endangered Pyrenean brown bear (Ursus arctos) without disturbing the animals themselves. Recent estimates suggest that the Pyrenean ...
    Type of Medium: Electronic Resource
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