DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Jordan M. Casey; Emma Ransome; Allen G. Collins; Angka Mahardini; Eka M. Kurniasih; Andrianus Sembiring; Nina M. D. Schiettekatte; Ni Kadek Dita Cahyani; Aji Wahyu Anggoro; Mikaela Moore; Abby Uehling; Mahdi Belcaid; Paul H. Barber; Jonathan B. Geller; Christopher P. Meyer

doi:10.1002/edn3.245

journal article Open Access Aug 10, 2021

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Jordan M. Casey

Emma Ransome Allen G. Collins Angka Mahardini Eka M. Kurniasih Andrianus Sembiring Nina M. D. Schiettekatte

Ni Kadek Dita Cahyani

Aji Wahyu Anggoro

Mikaela Moore Abby Uehling Mahdi Belcaid Paul H. Barber

Jonathan B. Geller Christopher P. Meyer

Environmental DNA Vol. 3 No. 6 pp. 1229-1246 · Wiley

View at Publisher Save 10.1002/edn3.245

Abstract

AbstractDNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macroeukaryotes, we use standardized sampling from autonomous reef monitoring structures (ARMS) deployed in the world's most biodiverse marine ecosystem, the Coral Triangle, to compare the performance of COI and 18S markers. We then compared metabarcoding data to image‐based annotations of ARMS plates. Although both markers provided similar estimates of taxonomic richness and total sequence reads, marker choice skewed estimates of eukaryotic diversity. The COI marker recovered relative abundances of the dominant sessile phyla consistent with image annotations. Both COI and the image annotations provided higher relative abundance estimates of Bryozoa and Porifera and lower estimates of Chordata as compared to 18S, but 18S recovered 25% more phyla than COI. Thus, while COI more reliably reflects the occurrence of dominant sessile phyla, 18S provides a more holistic representation of overall taxonomic diversity. Ideal marker choice is, therefore, contingent on study system and research question, especially in relation to desired taxonomic resolution, and a multimarker approach provides the greatest application across a broad range of research objectives. As metabarcoding becomes an essential tool to monitor biodiversity in our changing world, it is critical to evaluate biases associated with marker choice.

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Details

Published: Aug 10, 2021
Vol/Issue: 3(6)
Pages: 1229-1246
License: View

Authors

J

Jordan M. Casey

Department of Marine Science Marine Science Institute University of Texas at Austin Port Aransas Texas USA; Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA

E

Emma Ransome

Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA; Department of Life Sciences Imperial College London UK

A

Allen G. Collins

Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA; National Systematics Laboratory NOAA Fisheries Washington District of Columbia USA

A

Angka Mahardini

Jeju Marine Research Center Korea Institute of Ocean Science and Technology Jeju Republic of Korea; Indonesian Biodiversity Research Center Denpasar Bali Indonesia

E

Eka M. Kurniasih

Yayasan Biodiversitas Indonesia Denpasar Bali Indonesia

A

Andrianus Sembiring

Yayasan Biodiversitas Indonesia Denpasar Bali Indonesia

N

Nina M. D. Schiettekatte

PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan France; Laboratoire d’Excellence “CORAIL” Perpignan France

N

Ni Kadek Dita Cahyani

Indonesian Biodiversity Research Center Denpasar Bali Indonesia; Yayasan Biodiversitas Indonesia Denpasar Bali Indonesia; Department of Ecology and Evolutionary Biology University of California – Los Angeles Los Angeles California USA

A

Aji Wahyu Anggoro

Yayasan Biodiversitas Indonesia Denpasar Bali Indonesia; Department of Ecology and Evolutionary Biology University of California – Los Angeles Los Angeles California USA

M

Mikaela Moore

Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA; Department of Geological Sciences and Geological Engineering Queen’s University Kingston ON Canada

A

Abby Uehling

Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA

M

Mahdi Belcaid

Department of Information and Computer Sciences University of Hawaii at Mānoa Honolulu Hawaii USA

P

Paul H. Barber

Department of Ecology and Evolutionary Biology University of California – Los Angeles Los Angeles California USA

J

Jonathan B. Geller

Moss Landing Marine Laboratories San José State University Moss Landing California USA

C

Christopher P. Meyer

Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA

Funding

National Science Foundation Award: OISE 1243541

United States Agency for International Development Award: 497‐A‐00‐10‐00008‐00

Cite This Article

Jordan M. Casey, Emma Ransome, Allen G. Collins, et al. (2021). DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity. Environmental DNA, 3(6), 1229-1246. https://doi.org/10.1002/edn3.245

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

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