Ecological Biomonitoring

In: Advances in Ecological Research Ser v.Volume 59

In: Issn Ser. v.Volume 59

Abstract

Front Cover -- Next Generation Biomonitoring: Part 2 -- Copyright -- Contents -- Contributors -- Preface -- References -- Acknowledgements -- Chapter One: Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencin ... -- 1. Introduction -- 2. Materials and Methods -- 2.1. Mock Communities -- 2.2. Library Preparation for Roche 454 -- 2.3. Library Preparation for Illumina MiSeq -- 2.4. Bioinformatics and Data Analysis -- 2.5. Assigning Taxonomy to OTUs and Dereplicated Sequences -- 3. Results -- 3.1. Sequence and Read Depth -- 3.2. OTU Clustering and the Effect of Singletons -- 3.3. Species Detection -- 3.4. OTU Precision -- 3.5. Impact of Merging and Appending MiSeq Reads on Species Detection and OTU Estimates -- 4. Discussion -- 4.1. Read Depth and Singletons -- 4.2. OTU Clustering -- 4.3. Experimental Design -- 4.4. Implications for Biomonitoring -- 5. Conclusions -- Acknowledgements -- References -- Chapter Two: Linking DNA Metabarcoding and Text Mining to Create Network-Based Biomonitoring Tools: A Case Study on Borea ... -- 1. Introduction -- 1.1. Ecological Networks as Biomonitoring Tools -- 1.2. New Tools to Rapidly Assess Biodiversity and Annotate It With Ecological Information -- 1.3. Freshwater Biodiversity Hotspots as Candidates for Exploring Novel Approaches for Biodiversity Assessment -- 1.4. Exploring the Generation of DNA Ecological Networks for Aquatic Biomonitoring -- 2. Building Heuristic Food Webs for Wetland Biomonitoring: A Case Study -- 2.1. DNA Sample Collection, Metabarcoding, and Bioinformatics Pipeline -- 2.2. Development of Text-Mining Pipeline for Traits of Freshwater Organisms -- 2.3. Evaluation, and Iterative Refinements to Text-Mining Pipeline for Body Size -- 2.4. Rule-Based Procedure for Retrieving Trait Information for Heuristic Food Web Construction