Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

By Douglas W. Yu, Yinqiu Ji, Brent C. Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang, Zhaoli Ding. 2012

653 citations recorded by the source corpus.

1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d1b10095ad18c56611eb559f9b0b14f70889409e

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Citations in the corpus

How will the ‘molecular revolution’ contribute to biological recording? (2015, methodology): “This high throughput approach, known as “DNA metabarcoding”, is particularly powerful for revealing cryptic biodiversity (Creer et al., 2010; Bik et al., 2012; Yu et al., 2012).”
The ecologist's field guide to sequence‐based identification of biodiversity (2016, background): “For larger organisms (e.g. macroinvertebrates), bulk communities can be homogenized or ‘souped’ (Yu et al. 2012) either with or without subsampling body parts from larger organisms that would otherwise swamp sequencing runs with excessive amounts of biomass and therefore genomic information.”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “The 454 pyrosequencing platform was used with increasing frequency prior to 2013 but declined in popularity after this date (e.g. Stoeck et al. 2010; Pawlowski et al. 2011; Yu et al. 2012; Parducci et al. 2013; Pochon et al. 2013; Yang et al. 2014; Zimmermann et al. 2015), coinciding with a rise in ”
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities (2013, background): “Recent empirical studies have demonstrated that 454 pyrosequencing is a powerful discovery tool for the ‘rare biosphere’ (e.g. Fonseca et al. 2010; Behnke et al. 2011; Thomsen et al. 2011; Yu et al. 2012).”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, methodology): “The term ‘DNA metabarcoding’ encompasses two distinct methodologies: (a) bulk sample metabarcoding, which is the direct amplification of a concentrated mixture of organisms, from for example, plankton (Clarke, Beard, Swadling, & Deagle, 2017), arthropods (Yu et al., 2012) or gut material (Leray et a”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, background): “…Illumina MiSeq, COI barcodes, extracellular DNA, AMBI, biotic indices, macroinvertebrates INTRODUCTION Environmental biomonitoring in coastal and marine ecosystems often relies on comprehensively, accurately, and repeatedly characterizing the benthic macroinvertebrate community (Yu et al., 2012).”
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents (2013, background): “Nevertheless, metabarcoding is still a relatively new approach, and both methodological and analytical improvements are necessary to further expand its range of applications [7,14].”
Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports (2016, background): “When coupled with high-throughput sequencing, barcoding of bulk samples – metabarcoding – enables rapid screening of taxonomically complex communities (Taberlet et al., 2012; Yu et al., 2012) with the sensitivity to detect rare organisms such as endangered species and early invaders.”
A general species delimitation method with applications to phylogenetic placements (2013, background): “The estimated number of putative species for the genus as inferred by GMYC was 48 (with confidence limits ranging between 46 and 52 species).”
Insights into global diatom distribution and diversity in the world’s ocean (2016, methodology): “With the advent of high-throughput DNA sequencing, DNA metabarcoding has now emerged as a rapid and effective method to develop a global inventory of biodiversity that cannot be detected using classical microscopic methods (27, 28).”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “…samples by comparing samples with a wide set of multivariate statistical procedures (e.g. ANOSIM, PERMANOVA) and visualization tools e.g. Principal Component Analysis (PCA), Principal Coordinates Analysis (PCoA), Non-metric multidimensional scaling (NMDS) (Thomas et al., 2012; Yu et al., 2012).”
Utility of Environmental DNA for Monitoring Rare and Indicator Macroinvertebrate Species (2014, background): “© 2014 by The Society for Freshwater Science. investigators have shown that DNA sequence-based approaches in combination with next generation sequencing can be used to assess biodiversity from arthropod bulk samples (Hajibabaei et al. 2011, Yu et al. 2012).”