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