Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding.

By Yinqiu Ji, L. Ashton, S. Pedley, D. Edwards, Yong Tang, A. Nakamura, R. Kitching, P. Dolman, P. Woodcock, Felicity A. Edwards and 11 more. Ecology Letters, 2013

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To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3d030286482f637302212fe70c3469da95a028ab

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Citations in the corpus

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, background): “…of known taxonomic composition, we show that an alternative barcode that targets a shorter region of the COI gene outperforms the 658 bp region that is commonly used for metabarcoding metazoans (Carew et al., 2013; Ji et al., 2013; Dowle et al., 2015; Elbrecht and Leese, 2015; Zaiko et al., 2015).”
A practical guide to DNA metabarcoding for entomological ecologists (2020, methodology): “3), which generally improves taxon recovery (Ji et al., 2013; Clarke et al., 2017; Elbrecht & Leese, 2017).”
Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil (2016, methodology): “Only recently HTS approaches were extended to the analysis of macroscopic diversity (e.g. Ji et al. 2013), and metabarcoding of soil mesofauna has been performed using universal primers for Metazoa (e.g. Wu et al. 2011; Yang et al. 2013, 2014) or targeting particular lineages, such as nematodes…”
The ecologist's field guide to sequence‐based identification of biodiversity (2016, methodology): “2015) and terrestrial (Ji et al. 2013) ecosystems for identifying macroinvertebrates.”
How will the ‘molecular revolution’ contribute to biological recording? (2015, background): “…assembled samples of known composition (e.g. Hiiesalu et al., 2012; Yu et al., 2012) and several studies have demonstrated that metabarcoding generates reliable qualitative estimates of diversity (Fonseca et al., 2010; Hiiesalu et al., 2012; Yu et al., 2012; Yoccoz et al., 2012; Ji et al., 2013).”
Assessing the cost‐efficiency of environmental DNA sampling (2016, methodology): “Secondly, using eDNA sampling in a multispecies framework (e.g. metabarcoding: Thomsen et al. 2012a; Ji et al. 2013) could further increase the cost-efficiency of the eDNA approach, especially when sampling multiple taxonomic groups that require different survey methods.”
Metabarcoding of marine zooplankton: prospects, progress and pitfalls (2016, background): “In recent years, high-throughput DNA sequencing (HTS) technologies have resulted in dramatic advances in practical, cost-effective molecular approaches to the analysis of environmental samples (Bourlat et al., 2013; Ji et al., 2013).”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, background): “…sushi meals (Vandamme et al., 2016), deep sea sediments (Guardiola et al., 2015), permafrost ice cores (Willerslev et al., 2003), terrestrial insect collections (Ji et al., 2013), animal faeces (Kartzinel et al., 2015) and seawater samples (Thomsen, Kielgast, Iversen, Møller, et al., 2012a).”
Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes (2014, background): “, 2014) and the expanding field of environmental DNA analysis (Hajibabaei et al., 2011; Taberlet et al., 2012; Thomsen et al., 2012; Ji et al., 2013).”
Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring (2017, background): “All laboratory steps from DNA extraction to library preparation currently accumulate to 70€ per sample, leading to a total cost of 180€ per sample in this study, similar to previous estimates (Ji et al. 2013; Stein et al. 2014).”