10.5061/DRYAD.RR4XGXD8R
Casey, Jordan M
0000-0002-2434-7207
The University of Texas at Austin
Ransome, Emma
Imperial College London
Collins, Allen G
Smithsonian Institution
Mahardini, Angka
Korea Institute of Ocean Science and Technology
Kurniasih, Eka M
Yayasan Biodiversitas Indonesia
Sembiring, Andrianus
Yayasan Biodiversitas Indonesia
Schiettekatte, Nina M D
PSL Research University
Cahyani, Ni Kadek Dita
0000-0003-4484-6414
University of California Los Angeles
Wahyu Anggoro, Aji
University of California Los Angeles
Moore, Mikaela
Queen's University
Uehling, Abby
Smithsonian Institution
Belcaid, Mahdi
University of Hawaii at Manoa
Barber, Paul H
University of California Los Angeles
Geller, Jonathan B
Moss Landing Marine Laboratories
Meyer, Christopher P
Smithsonian Institution
DNA metabarcoding marker choice skews perception of marine eukaryotic
biodiversity
Dryad
dataset
2021
FOS: Biological sciences
National Science Foundation
https://ror.org/021nxhr62
OISE 1243541
2021-07-29T00:00:00Z
2021-07-29T00:00:00Z
en
https://doi.org/10.5281/zenodo.5140458
5655222 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
DNA 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
macro-eukaryotes, 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 multi-marker 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.
All methods are available in the associated manuscript in Environmental DNA.
This submission is connected to the manuscript entitled, "DNA
metabarcoding marker choice skews perception of marine eukaryotic
biodiversity" published in Environmental DNA. Files include the
metadata ("Bali_Metadata.csv"), final COI OTU table
("COI_OTU_Taxonomy.csv"), final 18S data OTU table
("18S_OTU_Taxonomy.csv"), CoralNet image analysis data
("coralnet.csv"), the R script (COIv18S.R) used for all analyses
in the manuscript, and a README file that defines variables and describes
data files (CASEY_README.txt).