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

  1. Douglas W. Yu1,2,†,*,
  2. Yinqiu Ji1,†,
  3. Brent C. Emerson2,‡,
  4. Xiaoyang Wang1,
  5. Chengxi Ye1,
  6. Chunyan Yang1,
  7. Zhaoli Ding3

Article first published online: 3 MAY 2012

DOI: 10.1111/j.2041-210X.2012.00198.x

Issue

Methods in Ecology and Evolution

Methods in Ecology and Evolution

Volume 3, Issue 4, pages 613–623, August 2012

Additional Information

How to Cite

Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C. and Ding, Z. (2012), Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3: 613–623. doi: 10.1111/j.2041-210X.2012.00198.x

Author Information

  1. 1

    Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd., Kunming, Yunnan 650223, China

  2. 2

    School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK

  3. 3

    Kunming Biodiversity Large-Apparatus Regional Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

  1. †

    Joint first authors.

  2. ‡

    Present address: Island Ecology and Evolution Research Group, IPNA-CSIC, C/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain.

* Correspondence author. E-mail: dougwyu@gmail.com

  1. Correspondence site: http://www.respond2articles.com/MEE/

  2. †

    Joint first authors.

  3. ‡

    Present address: Island Ecology and Evolution Research Group, IPNA-CSIC, C/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain.

  4. Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms

Publication History

  1. Issue published online: 30 JUL 2012
  2. Article first published online: 3 MAY 2012
  3. Received 3 January 2012; accepted 26 February 2012 Handling Editor: Robert Freckleton

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Keywords:

  • 454 Genome Sequencer FLX System;
  • DNA barcoding;
  • high-throughput sequencing;
  • metagenetics;
  • metagenomics;
  • OTU picking;
  • phylogenetic diversity

Summary

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.

2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’.

3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding.

4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

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