References
Aizpurua, O., Budinski, I., Georgiakakis, P., Gopalakrishnan, S.,
Ibañez, C., Mata, V., … Alberdi, A. (2018). Agriculture shapes
the trophic niche of a bat preying on multiple pest arthropods across
Europe: Evidence from DNA metabarcoding. Molecular Ecology ,27 (3), 815–825. doi: 10.1111/mec.14474
Alberdi, A., Aizpurua, O., Bohmann, K., Gopalakrishnan, S., Lynggaard,
C., Nielsen, M., & Gilbert, M. T. P. (2019). Promises and pitfalls of
using high‐throughput sequencing for diet analysis. Molecular
Ecology Resources , 19 (2), 327–348. doi: 10.1111/1755-0998.12960
Alberdi, A., Aizpurua, O., Gilbert, M. T. P., & Bohmann, K. (2018).
Scrutinizing key steps for reliable metabarcoding of environmental
samples. Methods in Ecology and Evolution , 9 (1), 134–147.
doi: 10.1111/2041-210X.12849
Altschul, Stephen F., Gish, Warren, Miller, W., Myers, Eugene W., &
Lipman, David J. (1990). Basic Local Alignment Search Tool.Journal of Molecular Biology , 215 (3), 403–410.
Berry, T. E., Osterrieder, S. K., Murray, D. C., Coghlan, M. L.,
Richardson, A. J., Grealy, A. K., … Bunce, M. (2017). DNA
metabarcoding for diet analysis and biodiversity: A case study using the
endangered Australian sea lion (Neophoca cinerea). Ecology and
Evolution , 7 (14), 5435–5453. doi: 10.1002/ece3.3123
Bohmann, K., Mirarab, S., Bafna, V., & Gilbert, M. T. P. (2020). Beyond
DNA barcoding: The unrealized potential of genome skim data in sample
identification. Molecular Ecology , 29 (14), 2521–2534.
doi: 10.1111/mec.15507
Boussarie, G., Bakker, J., Wangensteen, O. S., Mariani, S., Bonnin, L.,
Juhel, J.-B., … Mouillot, D. (2018). Environmental DNA
illuminates the dark diversity of sharks. Science Advances ,4 (5), eaap9661. doi: 10.1126/sciadv.aap9661
Callahan, B. J., McMurdie, P. J., & Holmes, S. P. (2017). Exact
sequence variants should replace operational taxonomic units in
marker-gene data analysis. The ISME Journal , 11 (12),
2639–2643. doi: 10.1038/ismej.2017.119
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A.
J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference
from Illumina amplicon data. Nature Methods , 13 (7),
581–583. doi: 10.1038/nmeth.3869
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J.,
Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and
applications. BMC Bioinformatics , 10 (1), 421. doi:
10.1186/1471-2105-10-421
Cardeñosa, D., Fields, A., Abercrombie, D., Feldheim, K., Shea, S. K.
H., & Chapman, D. D. (2017). A multiplex PCR mini-barcode assay to
identify processed shark products in the global trade. PLOS ONE ,12 (10), e0185368. doi: 10.1371/journal.pone.0185368
Carøe, C., & Bohmann, K. (2020). Tagsteady: A metabarcoding
library preparation protocol to avoid false assignment of sequences to
samples [Preprint]. Molecular Biology. doi:
10.1101/2020.01.22.915009
Carroll, E. L., Gallego, R., Sewell, M. A., Zeldis, J., Ranjard, L.,
Ross, H. A., … Constantine, R. (2019). Multi-locus DNA
metabarcoding of zooplankton communities and scat reveal trophic
interactions of a generalist predator. Scientific Reports ,9 (1), 281. doi: 10.1038/s41598-018-36478-x
Chua, P. Y. S., Crampton‐Platt, A., Lammers, Y., Alsos, I. G.,
Boessenkool, S., & Bohmann, K. (2021). Metagenomics: A viable tool for
reconstructing herbivore diet. Molecular Ecology Resources ,21 (7), 2249–2263. doi: 10.1111/1755-0998.13425
Coghlan, S. A., Shafer, A. B. A., & Freeland, J. R. (2020). Development
of an environmental DNA metabarcoding assay for aquatic vascular plant
communities. Environmental DNA , edn3.120. doi: 10.1002/edn3.120
Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan,
L., Sims, D. W., … Mariani, S. (2019). Non‐specific amplification
compromises environmental DNA metabarcoding with COI. Methods in
Ecology and Evolution , 10 (11), 1985–2001. doi:
10.1111/2041-210X.13276
Corse, E., Tougard, C., Archambaud‐Suard, G., Agnèse, J., Messu Mandeng,
F. D., Bilong Bilong, C. F., … Dubut, V. (2019).
One‐locus‐several‐primers: A strategy to improve the taxonomic and
haplotypic coverage in diet metabarcoding studies. Ecology and
Evolution , 9 (8), 4603–4620. doi: 10.1002/ece3.5063
D’Aloia, C. C., Bogdanowicz, S. M., Harrison, R. G., & Buston, P. M.
(2017). Cryptic genetic diversity and spatial patterns of admixture
within Belizean marine reserves. Conservation Genetics ,18 (1), 211–223. doi: 10.1007/s10592-016-0895-5
De Barba, M., Miquel, C., Boyer, F., Mercier, C., Rioux, D., Coissac,
E., & Taberlet, P. (2014). DNA metabarcoding multiplexing and
validation of data accuracy for diet assessment: Application to
omnivorous diet. Molecular Ecology Resources , 14 (2),
306–323. doi: 10.1111/1755-0998.12188
Deagle, B. E., Jarman, S. N., Coissac, E., Pompanon, F., & Taberlet, P.
(2014). DNA metabarcoding and the cytochrome oxidase subunit I marker:
Not a perfect match. Biology Letters , 10 (9), 20140562.
doi: 10.1098/rsbl.2014.0562
Deagle, B. E., Thomas, A. C., McInnes, J. C., Clarke, L. J., Vesterinen,
E. J., Clare, E. L., … Eveson, J. P. (2019). Counting with
DNA in metabarcoding studies: How should we convert sequence
reads to dietary data? Molecular Ecology , 28 (2), 391–406.
doi: 10.1111/mec.14734
Devloo-Delva, F., Huerlimann, R., Chua, G., Matley, J. K., Heupel, M.
R., Simpfendorfer, C. A., & Maes, G. E. (2019). How does marker choice
affect your diet analysis: Comparing genetic markers and digestion
levels for diet metabarcoding of tropical-reef piscivores. Marine
and Freshwater Research , 70 (1), 8. doi: 10.1071/MF17209
Djurhuus, A., Closek, C. J., Kelly, R. P., Pitz, K. J., Michisaki, R.
P., Starks, H. A., … Breitbart, M. (2020). Environmental DNA
reveals seasonal shifts and potential interactions in a marine
community. Nature Communications , 11 (1), 254. doi:
10.1038/s41467-019-14105-1
Djurhuus, A., Pitz, K., Sawaya, N. A., Rojas-Márquez, J., Michaud, B.,
Montes, E., … Breitbart, M. (2018). Evaluation of marine
zooplankton community structure through environmental DNA metabarcoding:
Metabarcoding zooplankton from eDNA. Limnology and Oceanography:
Methods , 16 (4), 209–221. doi: 10.1002/lom3.10237
Edgar, R. C. (2018). Updating the 97% identity threshold for 16S
ribosomal RNA OTUs. Bioinformatics , 34 (14), 2371–2375.
doi: 10.1093/bioinformatics/bty113
Elbrecht, V., Braukmann, T. W. A., Ivanova, N. V., Prosser, S. W. J.,
Hajibabaei, M., Wright, M., … Steinke, D. (2019). Validation of
COI metabarcoding primers for terrestrial arthropods. PeerJ ,7 , e7745. doi: 10.7717/peerj.7745
Elbrecht, V., & Leese, F. (2015). Can DNA-Based Ecosystem Assessments
Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence
Relationships with an Innovative Metabarcoding Protocol. PLOS
ONE , 10 (7), e0130324. doi: 10.1371/journal.pone.0130324
Evans, N. T., Olds, B. P., Renshaw, M. A., Turner, C. R., Li, Y., Jerde,
C. L., … Lodge, D. M. (2016). Quantification of mesocosm fish and
amphibian species diversity via environmental DNA metabarcoding.Molecular Ecology Resources , 16 (1), 29–41. doi:
10.1111/1755-0998.12433
Fernandes, T. J. R., Silva, C. R., Costa, J., Oliveira, M. B. P. P., &
Mafra, I. (2017). High resolution melting analysis of a COI mini-barcode
as a new approach for Penaeidae shrimp species discrimination.Food Control , 82 , 8–17. doi:
10.1016/j.foodcont.2017.06.016
Fields, A. T., Abercrombie, D. L., Eng, R., Feldheim, K., & Chapman, D.
D. (2015). A Novel Mini-DNA Barcoding Assay to Identify Processed Fins
from Internationally Protected Shark Species. PLOS ONE ,10 (2), e0114844. doi: 10.1371/journal.pone.0114844
Günther, B., Knebelsberger, T., Neumann, H., Laakmann, S., & Martínez
Arbizu, P. (2018). Metabarcoding of marine environmental DNA based on
mitochondrial and nuclear genes. Scientific Reports , 8 (1),
14822. doi: 10.1038/s41598-018-32917-x
Haiminen, N., Edlund, S., Chambliss, D., Kunitomi, M., Weimer, B. C.,
Ganesan, B., … Beck, K. L. (2019). Food authentication from
shotgun sequencing reads with an application on high protein powders.Npj Science of Food , 3 (1), 24. doi:
10.1038/s41538-019-0056-6
Hajibabaei, M., Smith, M. A., Janzen, D. H., Rodriguez, J. J.,
Whitfield, J. B., & Hebert, P. D. N. (2006). A minimalist barcode can
identify a specimen whose DNA is degraded: BARCODING. Molecular
Ecology Notes , 6 (4), 959–964. doi:
10.1111/j.1471-8286.2006.01470.x
Haynes, E., Jimenez, E., Pardo, M. A., & Helyar, S. J. (2019). The
future of NGS (Next Generation Sequencing) analysis in testing food
authenticity. Food Control , 101 , 134–143. doi:
10.1016/j.foodcont.2019.02.010
Horreo, J. L., Ardura, A., Pola, I. G., Martinez, J. L., &
Garcia-Vazquez, E. (2013). Universal primers for species authentication
of animal foodstuff in a single polymerase chain reaction: Universal
primers for species authentication. Journal of the Science of Food
and Agriculture , 93 (2), 354–361. doi: 10.1002/jsfa.5766
Jeunen, G., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R.,
Stat, M., … Gemmell, N. J. (2019). Environmental DNA (eDNA)
metabarcoding reveals strong discrimination among diverse marine
habitats connected by water movement. Molecular Ecology
Resources , 19 (2), 426–438. doi: 10.1111/1755-0998.12982
Kitano, T., Umetsu, K., Tian, W., & Osawa, M. (2007). Two universal
primer sets for species identification among vertebrates.International Journal of Legal Medicine , 121 (5), 423–427.
doi: 10.1007/s00414-006-0113-y
Kobus, R., Abuín, J. M., Müller, A., Hellmann, S. L., Pichel, J. C.,
Pena, T. F., … Schmidt, B. (2020). A big data approach to
metagenomics for all-food-sequencing. BMC Bioinformatics ,21 (1), 102. doi: 10.1186/s12859-020-3429-6
Koziol, A., Stat, M., Simpson, T., Jarman, S., DiBattista, J. D.,
Harvey, E. S., … Bunce, M. (2019). Environmental DNA
metabarcoding studies are critically affected by substrate selection.Molecular Ecology Resources , 19 (2), 366–376. doi:
10.1111/1755-0998.12971
Lahoz-Monfort, J. J., Guillera-Arroita, G., & Tingley, R. (2016).
Statistical approaches to account for false-positive errors in
environmental DNA samples. Molecular Ecology Resources ,16 (3), 673–685. doi: 10.1111/1755-0998.12486
Lee, P. N., McFall-Ngai, M. J., Callaerts, P., & de Couet, H. G.
(2009). Preparation of genomic DNA from Hawaiian bobtail squid (Euprymna
scolopes) tissue by cesium chloride gradient centrifugation. Cold
Spring Harbor Protocols , 2009 (11), doi: 10.1101/pdb.prot5319
Leray, M., & Knowlton, N. (2015). DNA barcoding and metabarcoding of
standardized samples reveal patterns of marine benthic diversity.Proceedings of the National Academy of Sciences , 112 (7),
2076–2081. doi: 10.1073/pnas.1424997112
Leray, M., Knowlton, N., Ho, S.-L., Nguyen, B. N., & Machida, R. J.
(2019). GenBank is a reliable resource for 21st century biodiversity
research. Proceedings of the National Academy of Sciences ,116 (45), 22651–22656. doi: 10.1073/pnas.1911714116
Locatelli, N. S., McIntyre, P. B., Therkildsen, N. O., & Baetscher, D.
S. (2020). GenBank’s reliability is uncertain for biodiversity
researchers seeking species-level assignment for eDNA. Proceedings
of the National Academy of Sciences , 117 (51), 32211–32212. doi:
10.1073/pnas.2007421117
Machida, R. J., & Knowlton, N. (2012). PCR primers for metazoan nuclear
18S and 28S ribosomal DNA sequences. PLoS ONE , 7 (9),
e46180. doi: 10.1371/journal.pone.0046180
Mariac, C., Vigouroux, Y., Duponchelle, F., García-Dávila, C., Nunez,
J., Desmarais, E., & Renno, J. F. (2018). Metabarcoding by capture
using a single COI probe (MCSP) to identify and quantify fish species in
ichthyoplankton swarms. PLOS ONE , 13 (9), e0202976. doi:
10.1371/journal.pone.0202976
Marín, A., Serna, J., Robles, C., Ramírez, B., Reyes-Flores, L. E.,
Zelada-Mázmela, E., … Alfaro, R. (2018). A glimpse into the
genetic diversity of the Peruvian seafood sector: Unveiling species
substitution, mislabeling and trade of threatened species. PLOS
ONE , 13 (11), e0206596. doi: 10.1371/journal.pone.0206596
Martin, M. (2011). Cutadapt removes adapter sequences from
high-throughput sequencing reads. EMBnet.Journal , 17 (1).
doi: https://doi.org/10.14806/ej.17.1.200
McInnes, J. C., Alderman, R., Deagle, B. E., Lea, M., Raymond, B., &
Jarman, S. N. (2017). Optimised scat collection protocols for dietary
DNA metabarcoding in vertebrates. Methods in Ecology and
Evolution , 8 (2), 192–202. doi: 10.1111/2041-210X.12677
McInnes, J. C., Jarman, S. N., Lea, M.-A., Raymond, B., Deagle, B. E.,
Phillips, R. A., … Alderman, R. (2017). DNA Metabarcoding as a
Marine Conservation and Management Tool: A Circumpolar Examination of
Fishery Discards in the Diet of Threatened Albatrosses. Frontiers
in Marine Science , 4 , 277. doi: 10.3389/fmars.2017.00277
McKnight, D. T., Huerlimann, R., Bower, D. S., Schwarzkopf, L., Alford,
R. A., & Zenger, K. R. (2019). microDecon: A highly accurate
read‐subtraction tool for the post‐sequencing removal of contamination
in metabarcoding studies. Environmental DNA , 1 (1), 14–25.
doi: 10.1002/edn3.11
Meusnier, I., Singer, G. A., Landry, J.-F., Hickey, D. A., Hebert, P.
D., & Hajibabaei, M. (2008). A universal DNA mini-barcode for
biodiversity analysis. BMC Genomics , 9 (1), 214. doi:
10.1186/1471-2164-9-214
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K.,
… Iwasaki, W. (2015). MiFish, a set of universal PCR primers for
metabarcoding environmental DNA from fishes: Detection of more than 230
subtropical marine species. Royal Society Open Science ,2 (7), 150088. doi: 10.1098/rsos.150088
Miya, Masaki, Gotoh, R. O., & Sado, T. (2020). MiFish metabarcoding: A
high-throughput approach for simultaneous detection of multiple fish
species from environmental DNA and other samples. Fisheries
Science . doi: 10.1007/s12562-020-01461-x
Mo, W. Y., Man, Y. B., & Wong, M. H. (2018). Use of food waste, fish
waste and food processing waste for China’s aquaculture industry: Needs
and challenge. Science of The Total Environment , 613–614 ,
635–643. doi: 10.1016/j.scitotenv.2017.08.321
Oksanen, J., F. Guillaume Blanchet, Friendly, M., Roeland Kindt, Pierre
Legendre, Dan McGlinn, … Wagner, H. (2019). Vegan: Community
Ecology Package. R package version 2.5-6 (Version 2.5-6).
R Core Team. (2019). R: A language and environment for statistical
computing . Vienna, Austria: R Foundation for Statistical Computing.
Retrieved from https://www.R-project.org/
Ratnasingham, S., & Hebert, P. D. N. (2007). BARCODING: Bold: The
Barcode of Life Data System (http://www.barcodinglife.org): BARCODING.Molecular Ecology Notes , 7 (3), 355–364. doi:
10.1111/j.1471-8286.2007.01678.x
Ripp, F., Krombholz, C., Liu, Y., Weber, M., Schäfer, A., Schmidt, B.,
… Hankeln, T. (2014). All-Food-Seq (AFS): A quantifiable screen
for species in biological samples by deep DNA sequencing. BMC
Genomics , 15 (1), 639. doi: 10.1186/1471-2164-15-639
Salter, I., Joensen, M., Kristiansen, R., Steingrund, P., &
Vestergaard, P. (2019). Environmental DNA concentrations are correlated
with regional biomass of Atlantic cod in oceanic waters.Communications Biology , 2 (1), 461. doi:
10.1038/s42003-019-0696-8
Schnell, I. B., Bohmann, K., & Gilbert, M. T. P. (2015). Tag jumps
illuminated—Reducing sequence-to-sample misidentifications in
metabarcoding studies. Molecular Ecology Resources , 15 (6),
1289–1303. doi: 10.1111/1755-0998.12402
Shaw, J. L. A., Clarke, L. J., Wedderburn, S. D., Barnes, T. C.,
Weyrich, L. S., & Cooper, A. (2016). Comparison of environmental DNA
metabarcoding and conventional fish survey methods in a river system.Biological Conservation , 197 , 131–138. doi:
10.1016/j.biocon.2016.03.010
Shen, W., & Xiong, J. (2019). TaxonKit: A cross-platform and efficient
NCBI taxonomy toolkit. BioRxiv . doi: 10.1101/513523
Shokralla, S., Hellberg, R. S., Handy, S. M., King, I., & Hajibabaei,
M. (2015). A DNA mini-barcoding system for authentication of processed
fish products. Scientific Reports , 5 (1), 15894. doi:
10.1038/srep15894
Shokralla, S., Porter, T. M., Gibson, J. F., Dobosz, R., Janzen, D. H.,
Hallwachs, W., … Hajibabaei, M. (2015). Massively parallel
multiplex DNA sequencing for specimen identification using an Illumina
MiSeq platform. Scientific Reports , 5 (1), 9687. doi:
10.1038/srep09687
Silva, L. P., Mata, V. A., Lopes, P. B., Pereira, P., Jarman, S. N.,
Lopes, R. J., & Beja, P. (2019). Advancing the integration of
multi‐marker metabarcoding data in dietary analysis of trophic
generalists. Molecular Ecology Resources , 19 (6),
1420–1432. doi: 10.1111/1755-0998.13060
Singer, G. A. C., Fahner, N. A., Barnes, J. G., McCarthy, A., &
Hajibabaei, M. (2019). Comprehensive biodiversity analysis via
ultra-deep patterned flow cell technology: A case study of eDNA
metabarcoding seawater. Scientific Reports , 9 (1), 5991.
doi: 10.1038/s41598-019-42455-9
Smith, D. P., & Peay, K. G. (2014). Sequence depth, not PCR
replication, improves ecological inference from next generation DNA
sequencing. PLoS ONE , 9 (2), e90234. doi:
10.1371/journal.pone.0090234
Staats, M., Arulandhu, A. J., Gravendeel, B., Holst-Jensen, A.,
Scholtens, I., Peelen, T., … Kok, E. (2016). Advances in DNA
metabarcoding for food and wildlife forensic species identification.Analytical and Bioanalytical Chemistry , 408 (17),
4615–4630. doi: 10.1007/s00216-016-9595-8
Stampar, S. N., Broe, M. B., Macrander, J., Reitzel, A. M., Brugler, M.
R., & Daly, M. (2019). Linear Mitochondrial Genome in Anthozoa
(Cnidaria): A Case Study in Ceriantharia. Scientific Reports ,9 (1), 6094. doi: 10.1038/s41598-019-42621-z
Tacon, A. G. J., & Metian, M. (2008). Global overview on the use of
fish meal and fish oil in industrially compounded aquafeeds: Trends and
future prospects. Aquaculture , 285 (1–4), 146–158. doi:
10.1016/j.aquaculture.2008.08.015
Tange, O. (2011). GNU Parallel: The Command-Line Power Tool. The
USENIX Magazine , 63 (1), 42–47.
Thomsen, P. F., Kielgast, J., Iversen, L. L., Møller, P. R., Rasmussen,
M., & Willerslev, E. (2012). Detection of a Diverse Marine Fish Fauna
Using Environmental DNA from Seawater Samples. PLoS ONE ,7 (8), e41732. doi: 10.1371/journal.pone.0041732
Valdez-Moreno, M., Ivanova, N. V., Elías-Gutiérrez, M., Pedersen, S. L.,
Bessonov, K., & Hebert, P. D. N. (2019). Using eDNA to biomonitor the
fish community in a tropical oligotrophic lake. PLOS ONE ,14 (4), e0215505. doi: 10.1371/journal.pone.0215505
Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen,
P. F., … Dejean, T. (2016). Next-generation monitoring of aquatic
biodiversity using environmental DNA metabarcoding. Molecular
Ecology , 25 (4), 929–942. doi: 10.1111/mec.13428
Yeo, D., Srivathsan, A., & Meier, R. (2020a). Longer is Not Always
Better: Optimizing Barcode Length for Large-Scale Species Discovery and
Identification. Systematic Biology , syaa014. doi:
10.1093/sysbio/syaa014
Yeo, D., Srivathsan, A., & Meier, R. (2020b). Longer is Not Always
Better: Optimizing Barcode Length for Large-Scale Species Discovery and
Identification. Systematic Biology , 69 (5), 999–1015. doi:
10.1093/sysbio/syaa014
Zhang, S., Zhao, J., & Yao, M. (2020). A comprehensive and comparative
evaluation of primers for metabarcoding eDNA from fish. Methods in
Ecology and Evolution , 2041-210X.13485. doi: 10.1111/2041-210X.13485
Zinger, L., Bonin, A., Alsos, I. G., Bálint, M., Bik, H., Boyer, F.,
… Taberlet, P. (2019). DNA metabarcoding—Need for robust
experimental designs to draw sound ecological conclusions.Molecular Ecology , 28 (8), 1857–1862. doi:
10.1111/mec.15060