References
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 , 134-147.
Antich, A., Palacin, C., Wangensteen, O. S., & Turon, X. (2021). To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics,22 , 177.
Baamrane, M. A. A., Shehzad, W., Ouhammou, A., Abbad, A., Naimi, M., Coissac, E., … Znari, M. (2012). Assessment of the food habits of the Moroccan dorcas gazelle in M’Sabih Talaa, West Central Morocco, using the trnL approach. PLoS ONE , 7 , e35643.
Bálint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, J. A., Lindahl, B., … Tedersoo, L. (2016). Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiology Reviews, 40 , 686-700.
Bhat, A. H., Prabhu, P., & Balakrishnan, K. (2019). A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.Journal of Biosciences, 44 , 9.
Bidartondo, M. I. (2008). Preserving accuracy in GenBank. Science, 319, 1616.
Bienert, F., De Danieli, S., Miquel, C., Coissac, E., Poillot, C., Brun, J. J., & Taberlet, P. (2012). Tracking earthworm communities from soil DNA. Molecular Ecology, 21 , 2017-2030.
Bohmann, K., Elbrecht ,V., Carøe, C., Bista, L., Leese, F., Bunce, M., Yu, D. W., … Creer, S. (in press). Strategies for sample labelling and library preparation in DNA metabarcoding studies.Molecular Ecology Resources .
Botnen, S. S., Davey, M. L., Halvorsen, R., & Kauserud, H. (2018). Sequence clustering threshold has little effect on the recovery of microbial community structure. Molecular Ecology Resources, 18 , 1064-1076.
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, 176-182.
Bridge, P. D., Roberts, P. J., Spooner, B. M., & Panchal, G. (2003). On the unreliability of published DNA sequences. New Phytologist, 160 , 43-48.
Brown, E. A., Chain, F. J. J., Crease, T. J., MacIsaac, H. J., & Cristescu, M. E. (2015). Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecology and Evolution, 5 , 2234-2251.
Calderón-Sanou, I., Münkemüller, T., Boyer, F., Zinger, L., & Thuiller, W. (2020). From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? Journal of Biogeography, 47 , 193–206.
Capo, E., Giguet-Covex, C., Rouillard, A., Nota, K., Heintzman, P., Vuillemin, A. …Parducci, L. (2021). Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations. Quaternary 4, 6.
Chen, W., & Ficetola, G. F. (2020). Statistical and numerical methods for Sedimentary-ancient-DNA-based study on past biodiversity and ecosystem functioning. Environmental DNA, 2 , 115–129.
Clare, E. L., Chain, F. J. J., Littlefair, J. E., & Cristescu, M. E. (2016). The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data. Genome, 59 , 981-990.
Couton, M., Baud, A., Daguin-Thiébaut, C., Corre, E., Comtet, T., & Viard, F. (2021). High-throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally. Ecology and Evolution, 11 , 5533-5546.
Dickie, I. A., Boyer, S., Buckley, H. L., Duncan, R. P., Gardner, P. P., Hogg, I. D., … Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA‐based studies. Molecular Ecology Resources, 18 , 940-952.
Eichmiller, J. J., Miller L. M., & Sorensen, P.W. (2016). Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Molecular Ecology Resources, 16 , 56-68.
Elbrecht, V., Taberlet, P., Dejean, T., Valentini, A., Usseglio-Polatera, P., Beisel, J. N., … Leese, F. (2016). Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ, 4 , 12.
Epp, L. S., Boessenkool, S., Bellemain, E. P., Haile, J., Esposito, A., Riaz, T., … Brochmann, C. (2012). New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology, 21, 1821-1833.
Fahner, N. A., Shokralla, S., Baird, D. J., & Hajibabaei, M. (2016). Large-scale monitoring of plants through environmental DNA metabarcoding of soil: Recovery, resolution, and annotation of four DNA markers.PLoS ONE, 11 , e0157505.
Federhen, S. (2015). Type material in the NCBI Taxonomy Database.Nucleic Acids Research, 43 , D1086-D1098.
Ficetola, G. F., Boyer, F, Valentini, A. Bonin, Meyer, A., Dejean, T., … Taberlet, P. (2021). Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding.Molecular Ecology, 30 , 3189–3202.
Ficetola, G. F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessière, J., … Pompanon, F. (2010). An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11 , 434.
Froslev, T. G., Kjoller, R., Bruun, H. H., Ejrnaes, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates.Nature Communications, 8 , 11.
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 , e0139633.
Guerrieri, A., Bonin, A., Münkemüller, T., Gielly, L., Thuiller, W., & Ficetola, G. F. (2021). Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology, 30 , 3313-3325.
Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B-Biological Sciences, 270, S96-S99.
Jackson, M. A., Bell, J. T., Spector, T. D., & Steves, C. J. (2016). A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units. PeerJ, 4 , 19.
Janssen, P., Bec, S., Fuhr, M., Taberlet, P., Brun, J.-J., & Bouget, C. (2018). Present conditions may mediate the legacy effect of past land-use changes on species richness and composition of above- and below-ground assemblages. Journal of Ecology, 106 , 306-318.
Kopylova, E., Navas-Molina, J. A., Mercier, C., Xu, Z. Z., Mahe, F., He, Y., … Knight, R. (2016). Open-source sequence clustering methods improve the state of the art. mSystems, 1 , 16.
Kunin, V., Engelbrektson, A., Ochman, H., & Hugenholtz, P. (2010). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12 , 118-123.
Lear, G., Dickie, I., Banks, J., Boyer, S., Buckley, H. L., Buckley, T. R., … Holdaway, R. (2018). Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples.New Zealand Journal of Ecology, 42 , 10.
Leray, M., Knowlton, N., Ho, S. L., Nguyen, B. N., & Machida, R. J. (2019). GenBank is a reliable resource for 21stcentury biodiversity research. Proceedings of the National Academy of Sciences of the United States of America, 116 , 22651-22656.
Lopes, C. M., Baêta, D., Valentini, A., Lyra, M. L., Sabbag, A. F., Gasparini, J. L., … Zamudio, R. K. (2021). Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA.Molecular Ecology, 30 , 3289-3298.
Macher, T.-H., Beermann, A. J., & Leese, F. (2021). TaxonTableTools: A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data. Molecular Ecology Resources, 21 , 1705-1714.
Mächler, E., Walser, J.-C., & Altermatt, F. (2021). Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers. Molecular Ecology, 30 , 3326-3339.
Mercier, C., Boyer, F., Bonin, A., & Coissac, E. (2013). SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.Programs and Abstracts of the SeqBio 2013 Workshop , 27-29.
Meyer, C. P., & Paulay, G. (2005). DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology, 3 , 2229-2238.
Mioduchowska, M., Czyz, M. J., Goldyn, B., Kur, J., & Sell, J. (2018). Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too ”universal” ? PLoS ONE, 13 , e0199609.
Nichols, R. V., Vollmers, C., Newsom, L. A., Wang, Y., Heintzman, P. D., Leighton, M., … Shapiro, B. (2018). Minimizing polymerase biases in metabarcoding. Molecular Ecology Resources, 18 , 927-939.
Paliy, O., & Shankar, V. (2016). Application of multivariate statistical techniques in microbial ecology. Molecular Ecology, 25 , 1032-1057.
Porco, D., Bedos, A., Penelope, G., Janion, C., Skarżyński, D., Stevens, M. I., … Deharveng, L. (2012). Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding. Invertebrate Systematics, 26 , 470-477.
R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
Roy, J., Mazel, F., Sosa-Hernández, M. A., Dueñas, J. F., Hempel, S., Zinger, L., & Rillig, M. C. (2019). The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution. New Phytologist, 224,936-948.
Schloss, P. D. (2021). Amplicon sequence variants artificially split bacterial genomes into separate clusters. mSphere, 6 , e00191-00121.
Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA for biodiversity research and monitoring. Oxford University Press, Oxford.
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., … Willerslev, E. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.Nucleic Acids Research, 35 , e14.
Taberlet, P., Prud’homme, S. M., Campione, E., Roy, J., Miquel, C., Shehzad, W., … Coissac, E. (2012). Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology, 21 , 1816-1820.
Tatangelo, V., Franzetti, A., Gandolfi, I., Bestetti, G., & Ambrosini, R. (2014). Effect of preservation method on the assessment of bacterial community structure in soil and water samples. FEMS Microbiology Letters , 356 , 32-38.
Valkiūnas, G., Atkinson, C. T., Bensch, S., Sehgal, R. N., & Ricklefs, R. E. (2008). Parasite misidentifications in GenBank: how to minimize their number? Trends in Parasitology , 24 , 247-248.
Venables, W. N., & Ripley, B. D. (2002). Modern applied statistics with S. Fourth Edition. Springer, New York.
Wei, Z.-G., Zhang, X.-D., Cao, M., Liu, F., Qian, Y., & Zhang, S.-W. (2021). Comparison of methods for picking the operational taxonomic units from amplicon sequences. Frontiers in Microbiology ,12 , 644012.
Zinger, L., Bonin, A., Alsos, I., Bálint, M., Bik, H., Boyer, F., … Taberlet, P. (2019). DNA metabarcoding - need for robust experimental designs to draw sound ecological conclusions.Molecular Ecology, 28 , 1857-1862.
Zinger, L., Chave, J., Coissac, E., Iribar, A., Louisanna, E., Manzi, S., … Taberlet, P. (2016). Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. Soil Biology & Biochemistry , 96 , 16-19.