References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J.
(1990). Basic local alignment search tool. Journal of Molecular
Biology , 215 (3), 403–410.
https://doi.org/10.1016/S0022-2836(05)80360-2
Bass, D., Rueckert, S., Stern, R., Cleary, A. C., Taylor, J. D., Ward,
G. M., & Huys, R. (2021). Parasites, pathogens, and other symbionts of
copepods. Trends in Parasitology , 37 (10), 875–889.
https://doi.org/10.1016/j.pt.2021.05.006
Berg, J. (1979). Discussion of methods of investigating the food of
fishes, with reference to a preliminary study of the prey ofGobiusculus flavescens (Gobiidae). Marine Biology ,50 (3), 263–273. https://doi.org/10.1007/BF00394208
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., &
Coissac, E. (2016). obitools: a unix-inspired software package for DNA
metabarcoding. Molecular Ecology Resources , 16 (1),
176–182. https://doi.org/10.1111/1755-0998.12428
Bray, J. R., & Curtis, J. T. (1957). An Ordination of the Upland Forest
Communities of Southern Wisconsin. Ecological Monographs ,27 (4), 325–349. https://doi.org/10.2307/1942268
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.
https://doi.org/10.1186/1471-2105-10-421
Casper, R. M., Jarman, S. N., Deagle, B. E., Gales, N. J., & Hindell,
M. A. (2007). Detecting prey from DNA in predator scats: A comparison
with morphological analysis, using Arctocephalus seals fed a known diet.Journal of Experimental Marine Biology and Ecology ,347 (1–2), 144–154. https://doi.org/10.1016/j.jembe.2007.04.002
Cleary, A. C., & Durbin, E. G. (2016). Unexpected prevalence of
parasite 18S rDNA sequences in winter among Antarctic marine protists.Journal of Plankton Research , 38 (3), 401–417.
https://doi.org/10.1093/plankt/fbw005
Cleary, A. C., Durbin, E. G., Rynearson, T. A., & Bailey, J. (2016).
Feeding by Pseudocalanus copepods in the Bering Sea: Trophic
linkages and a potential mechanism of niche partitioning. Deep-Sea
Research Part II: Topical Studies in Oceanography , 134 ,
181–189. https://doi.org/10.1016/j.dsr2.2015.04.001
Cleary, A. C., Søreide, J. E., Freese, D., Niehoff, B., & Gabrielsen,
T. M. (2017). Feeding by Calanus glacialis in a high arctic
fjord: Potential seasonal importance of alternative prey. ICES
Journal of Marine Science , 74 (7), 1937–1946.
https://doi.org/10.1093/icesjms/fsx106
Conover, R. J. (1988). Comparative life histories in the generaCalanus and Neocalanus in high latitudes of the northern
hemisphere. Hydrobiologia , 167 (1), 127–142.
https://doi.org/10.1007/BF00026299
Conover, R. J., & Huntley, M. (1991). Copepods in ice-covered
seas—Distribution, adaptations to seasonally limited food, metabolism,
growth patterns and life cycle strategies in polar seas. Journal
of Marine Systems , 2 (1), 1–41.
https://doi.org/10.1016/0924-7963(91)90011-I
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan,
B. J. (2018). Simple statistical identification and removal of
contaminant sequences in marker-gene and metagenomics data.Microbiome , 6 (1), 226.
https://doi.org/10.1186/s40168-018-0605-2
Deagle, B. E., Kirkwood, R., & Jarman, S. N. (2009). Analysis of
Australian fur seal diet by pyrosequencing prey DNA in faeces.Molecular Ecology , 18 (9), 2022–2038.
https://doi.org/10.1111/j.1365-294X.2009.04158.x
Durbin, E. G., & Casas, M. C. (2014). Early reproduction byCalanus glacialis in the Northern Bering Sea: The role of ice
algae as revealed by molecular analysis. Journal of Plankton
Research , 36 (2), 523–541. https://doi.org/10.1093/plankt/fbt121
Edgar, R. (2016). UNOISE2: improved error-correction for Illumina 16S
and ITS amplicon sequencing. BioRxiv , 081257.
https://doi.org/10.1101/081257
Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S. M.,
Driver, D. A., Berg, R. H., Kim, S. K., Norden, B., & Nielsen, P. E.
(1993). PNA hybridizes to complementary oligonucleotides obeying the
Watson–Crick hydrogen-bonding rules. Nature , 365 (6446),
566–568. https://doi.org/10.1038/365566a0
Eisenhauer, N., & Hines, J. (2021). Invertebrate biodiversity and
conservation. Current Biology , 31 (19), R1214–R1218.
https://doi.org/10.1016/j.cub.2021.06.058
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.
https://doi.org/10.1371/journal.pone.0130324
Gast, R. J., Dennett, M. R., & Caron, D. A. (2004). Characterization of
Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing
Gradient Gel Electrophoresis. Applied and Environmental
Microbiology , 70 (4), 2028 LP – 2037.
https://doi.org/10.1128/AEM.70.4.2028-2037.2004
Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O.
S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding
Extracellular DNA from Sediments of Marine Canyons. PLOS ONE ,10 (10), e0139633. https://doi.org/10.1371/journal.pone.0139633
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L.,
Boutte, C., Burgaud, G., De Vargas, C., Decelle, J., Del Campo, J.,
Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H.
C. F., Lara, E., Le Bescot, N., Logares, R., … Christen, R.
(2013). The Protist Ribosomal Reference database (PR2): A catalog of
unicellular eukaryote Small Sub-Unit rRNA sequences with curated
taxonomy. Nucleic Acids Research , 41 (D1), D597–D604.
https://doi.org/10.1093/nar/gks1160
Hirai, J., Hamamoto, Y., Honda, D., & Hidaka, K. (2018). Possible
aplanochytrid (Labyrinthulea) prey detected using 18S metagenetic diet
analysis in the key copepod species Calanus sinicus in the
coastal waters of the subtropical western North Pacific. Plankton
and Benthos Research , 13 (2), 75–82.
https://doi.org/10.3800/pbr.13.75
Ho, T. W., Hwang, J. S., Cheung, M. K., Kwan, H. S., & Wong, C. K.
(2017). DNA-based study of the diet of the marine calanoid copepod
Calanus sinicus. Journal of Experimental Marine Biology and
Ecology , 494 , 1–9. https://doi.org/10.1016/j.jembe.2017.04.004
Jaccard, P. (1901). Étude comparative de la distribution florale dans
une portion des Alpes et des Jura. Bulletin de La Société Vaudoise
Des Sciences Naturelles , 37 , 547–579.
Kamenova, S., Mayer, R., Rubbmark, O. R., Coissac, E., Plantegenest, M.,
& Traugott, M. (2018). Comparing three types of dietary samples for
prey DNA decay in an insect generalist predator. Molecular Ecology
Resources , 18 (5), 966–973.
https://doi.org/10.1111/1755-0998.12775
Kellert, S. R. (1993). Values and Perceptions of Invertebrates.Conservation Biology , 7 (4), 845–855.
https://doi.org/10.1046/j.1523-1739.1993.740845.x
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn,
M., & Glöckner, F. O. (2013). Evaluation of general 16S ribosomal RNA
gene PCR primers for classical and next-generation sequencing-based
diversity studies. Nucleic Acids Research , 41 (1), e1–e1.
https://doi.org/10.1093/nar/gks808
Kohn, M. H., & Wayne, R. K. (1997). Facts from feces revisited.Trends in Ecology & Evolution , 12 (6), 223–227.
https://doi.org/10.1016/S0169-5347(97)01050-1
Leray, M., & Knowlton, N. (2017). Random sampling causes the low
reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding.PeerJ , 2017 (3). https://doi.org/10.7717/peerj.3006
Lightbody, G., Haberland, V., Browne, F., Taggart, L., Zheng, H.,
Parkes, E., & Blayney, J. K. (2019). Review of applications of
high-throughput sequencing in personalized medicine: barriers and
facilitators of future progress in research and clinical application.Briefings in Bioinformatics , 20 (5), 1795–1811.
https://doi.org/10.1093/bib/bby051
McMurdie, P. J., & Holmes, S. (2013). phyloseq: An R Package for
Reproducible Interactive Analysis and Graphics of Microbiome Census
Data. PLOS ONE , 8 (4), e61217.
https://doi.org/10.1371/journal.pone.0061217
Miller-ter Kuile, A., Apigo, A., & Young, H. S. (2021). Effects of
consumer surface sterilization on diet DNA metabarcoding data of
terrestrial invertebrates in natural environments and feeding trials.Ecology and Evolution , 11 (17), 12025–12034.
https://doi.org/10.1002/ece3.7968
Morrill, A., Kaunisto, K. M., Mlynarek, J. J., Sippola, E., Vesterinen,
E. J., & Forbes, M. R. (2021). Metabarcoding prey DNA from fecal
samples of adult dragonflies shows no predicted sex differences, and
substantial inter-individual variation, in diets. PeerJ ,9 . https://doi.org/10.7717/peerj.12634
Nielsen, P. E., Egholm, M., Berg, R. H., & Buchardt, O. (1991).
Sequence-selective recognition of DNA by strand displacement with a
thymine-substituted polyamide. Science , 254 (5037),
1497–1500. https://doi.org/10.1126/science.1962210
Novotny, A., Zamora-Terol, S., & Winder, M. (2021). DNA metabarcoding
reveals trophic niche diversity of micro and mesozooplankton species.Proceedings of the Royal Society B: Biological Sciences ,288 (1953). https://doi.org/10.1098/rspb.2021.0908
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P.,
McGlinn, D., Minchin, P. R., O’Hara, R. B., Simpson, G. L., Solymos, P.,
Stevens, M. H. H., Szoecs, E., & Wagner, H. (2019). Vegan: community
ecology package. Ordination methods, diversity analysis and other
functions for community and vegetation ecologists. R package ver, 2-3.Cran R .
Orum, H., Nielsen, P. E., Egholm, M., Berg, R. H., Buchardt, O., &
Stanley, C. (1993). Single base pair mutation analysis by PNA directed
PCR clamping. Nucleic Acids Research , 21 (23), 5332–5336.
https://doi.org/10.1093/nar/21.23.5332
Piñol, J., Mir, G., Gomez-Polo, P., & Agustí, N. (2015). Universal and
blocking primer mismatches limit the use of high-throughput DNA
sequencing for the quantitative metabarcoding of arthropods.Molecular Ecology Resources , 15 (4), 819–830.
https://doi.org/10.1111/1755-0998.12355
Piñol, J., San Andrés, V., Clare, E. L., Mir, G., & Symondson, W. O. C.
(2014). A pragmatic approach to the analysis of diets of generalist
predators: The use of next-generation sequencing with no blocking
probes. Molecular Ecology Resources , 14 (1), 18–26.
https://doi.org/10.1111/1755-0998.12156
Piñol, J., Senar, M. A., & Symondson, W. O. C. (2019). The choice of
universal primers and the characteristics of the species mixture
determine when DNA metabarcoding can be quantitative. Molecular
Ecology , 28 (2), 407–419. https://doi.org/10.1111/mec.14776
Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman,
S. N., & Taberlet, P. (2012). Who is eating what: Diet assessment using
next generation sequencing. Molecular Ecology , 21 (8),
1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Ray, J. L., Althammer, J., Skaar, K. S., Simonelli, P., Larsen, A.,
Stoecker, D., Sazhin, A., Ijaz, U. Z., Quince, C., Nejstgaard, J. C.,
Frischer, M., Pohnert, G., & Troedsson, C. (2016). Metabarcoding and
metabolome analyses of copepod grazing reveal feeding preference and
linkage to metabolite classes in dynamic microbial plankton communities.Molecular Ecology , 25 (21), 5585–5602.
https://doi.org/10.1111/mec.13844
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016).
VSEARCH: A versatile open source tool for metagenomics. PeerJ ,2016 (10). https://doi.org/10.7717/peerj.2584
Santoferrara, L. F. (2019). Current practice in plankton metabarcoding:
optimization and error management. Journal of Plankton Research .
https://doi.org/10.1093/plankt/fbz041
Shi, Y., Hoareau, Y., Reese, E. M., & Wasser, S. K. (2021). Prey
partitioning between sympatric wild carnivores revealed by DNA
metabarcoding: a case study on wolf (Canis lupus ) and coyote
(Canis latrans ) in northeastern Washington. Conservation
Genetics , 22 (2), 293–305.
https://doi.org/10.1007/s10592-021-01337-2
Sipos, R., Székely, A. J., Palatinszky, M., Révész, S., Márialigeti, K.,
& Nikolausz, M. (2007). Effect of primer mismatch, annealing
temperature and PCR cycle number on 16S rRNA gene-targetting bacterial
community analysis. FEMS Microbiology Ecology , 60 (2),
341–350. https://doi.org/10.1111/j.1574-6941.2007.00283.x
Sousa, L. L., Silva, S. M., & Xavier, R. (2019). DNA metabarcoding in
diet studies: Unveiling ecological aspects in aquatic and terrestrial
ecosystems. Environmental DNA , 1 (3), 199–214.
https://doi.org/10.1002/edn3.27
Symondson, W. O. C. (2002). Molecular identification of prey in predator
diets. Molecular Ecology , 11 (4), 627–641.
https://doi.org/10.1046/j.1365-294X.2002.01471.x
Troedsson, C., Lee, R. F., Walters, T., Stokes, V., Brinkley, K.,
Naegele, V., & Frischer, M. E. (2008). Detection and discovery of
crustacean parasites in blue crabs (Callinectes sapidus ) by using
18S rRNA gene-targeted denaturing high-performance liquid
chromatography. Applied and Environmental Microbiology ,74 (14), 4346–4353. https://doi.org/10.1128/AEM.02132-07
Urban, P., Præbel, K., Bhat, S., Dierking, J., & Wangensteen, O. S.
(2022). DNA metabarcoding reveals the importance of gelatinous
zooplankton in the diet of Pandalus borealis , a keystone species
in the Arctic. Molecular Ecology , 31 (5), 1562–1576.
https://doi.org/10.1111/mec.16332
Vestheim, H., & Jarman, S. N. (2008). Blocking primers to enhance PCR
amplification of rare sequences in mixed samples - A case study on prey
DNA in Antarctic krill stomachs. Frontiers in Zoology ,5 (1), 12. https://doi.org/10.1186/1742-9994-5-12
Wangensteen, O. S., Palacín, C., Guardiola, M., & Turon, X. (2018). DNA
metabarcoding of littoral hard-bottom communities: high diversity and
database gaps revealed by two molecular markers. PeerJ , 6 ,
e4705–e4705. https://doi.org/10.7717/peerj.4705
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D.,
Francois, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhm, M.,
Pedersen, T. L., Miller, E., Bache, S. M., Muller, K., Ooms, J.,
Robinson, D., Seidel, D. P., Spinu, V., … Yutani, H. (2019).
Welcome to the tidyverse. Journal of Open Source Software ,4 (43), 1686. https://www.r-project.org/
Yeh, H. D., Questel, J. M., Maas, K. R., & Bucklin, A. (2020).
Metabarcoding analysis of regional variation in gut contents of the
copepod Calanus finmarchicus in the North Atlantic Ocean.Deep-Sea Research Part II: Topical Studies in Oceanography .
https://doi.org/10.1016/j.dsr2.2020.104738
Zamora-Terol, S., Novotny, A., & Winder, M. (2020). Reconstructing
marine plankton food web interactions using DNA metabarcoding.Molecular Ecology , 29 (17), 3380–3395.
https://doi.org/10.1111/mec.15555
Zamora-Terol, S., Novotny, A., & Winder, M. (2021). Molecular evidence
of host-parasite interactions between zooplankton and Syndiniales.Aquatic Ecology , 55 (1), 125–134.
https://doi.org/10.1007/s10452-020-09816-3