9 | 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
Arranz, V., Pearman, W. S., Aguirre, J. D., & Liggins, L. (2020).
MARES, a replicable pipeline and curated reference database for marine
eukaryote metabarcoding. Scientific Data , 7 (1), 1–8.
Ávila-Arcos, M. C., Cappellini, E., Romero-Navarro, J. A., Wales, N.,
Moreno-Mayar, J. V., Rasmussen, M., Fordyce, S. L., Montiel, R.,
Vielle-Calzada, J.-P., Willerslev, E., & Gilbert, M. T. P. (2011).
Application and comparison of large-scale solution-based DNA
capture-enrichment methods on ancient DNA. Scientific Reports ,1 (1), 74. https://doi.org/10.1038/srep00074
Banchi, E., Ametrano, C. G., Greco, S., Stanković, D., Muggia, L., &
Pallavicini, A. (2020). PLANiTS: a curated sequence reference dataset
for plant ITS DNA metabarcoding. Database , 2020 .
Banos, S., Lentendu, G., Kopf, A., Wubet, T., Glöckner, F. O., & Reich,
M. (2018). A comprehensive fungi-specific 18S rRNA gene sequence primer
toolkit suited for diverse research issues and sequencing platforms.BMC Microbiology , 18 (1), 190.
https://doi.org/10.1186/s12866-018-1331-4
Barbera, P., Kozlov, A. M., Czech, L., Morel, B., Darriba, D., Flouri,
T., & Stamatakis, A. (2019). EPA-ng: massively parallel evolutionary
placement of genetic sequences. Systematic Biology , 68 (2),
365–369.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C.
C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar,
F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C.
J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase,
J., … Caporaso, J. G. (2019). Reproducible, interactive, scalable
and extensible microbiome data science using QIIME 2. Nature
Biotechnology , 37 (8), 852–857.
https://doi.org/10.1038/s41587-019-0209-9
Bovo, S., Utzeri, V. J., Ribani, A., Cabbri, R., & Fontanesi, L.
(2020). Shotgun sequencing of honey DNA can describe honey bee derived
environmental signatures and the honey bee hologenome complexity.Scientific Reports , 10 (1), 9279.
https://doi.org/10.1038/s41598-020-66127-1
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/doi:10.1111/1755-0998.12428
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.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman,
F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K.,
Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J.
E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung,
M., … Knight, R. (2010). QIIME allows analysis of high-throughput
community sequencing data. Nature Methods , 7 (5), 335–336.
https://doi.org/10.1038/nmeth.f.303
Chave, J. (2013). The problem of pattern and scale in ecology: what have
we learned in 20 years? Ecology Letters , 16 , 4–16.
Collins, R. A., Trauzzi, G., Maltby, K. M., Gibson, T. I., Ratcliffe, F.
C., Hallam, J., Rainbird, S., Maclaine, J., Henderson, P. A., & Sims,
D. W. (2021). Meta‐Fish‐Lib: a generalised, dynamic DNA reference
library pipeline for metabarcoding of fishes. Journal of Fish
Biology , 99 (4), 1446–1454.
Cowart, D. A., Murphy, K. R., & Cheng, C.-H. C. H. C. (2018).
Metagenomic sequencing of environmental DNA reveals marine faunal
assemblages from the West Antarctic Peninsula. Marine Genomics ,37 (September 2017), 148–160.
https://doi.org/https://doi.org/10.1016/j.margen.2017.11.003
Cross, H., Sønstebø, J. H., Nagy, N. E., Timmermann, V., Solheim, H.,
Børja, I., Kauserud, H., Carlsen, T., Rzepka, B., Wasak, K.,
Vivian-Smith, A., & Hietala, A. M. (2017). Fungal diversity and
seasonal succession in ash leaves infected by the invasive ascomycete
Hymenoscyphus fraxineus. New Phytologist , 213 (3),
1405–1417. https://doi.org/https://doi.org/10.1111/nph.14204
Dave, R. N. (1991). Characterization and detection of noise in
clustering. Pattern Recognition Letters , 12 (11), 657–664.
Edgar, R. C. (2010). Search and clustering orders of magnitude faster
than BLAST. Bioinformatics (Oxford, England) , 26 (19),
2460–2461. https://doi.org/10.1093/bioinformatics/btq461
Edgar, R. C. (2016). SINTAX: a simple non-Bayesian taxonomy classifier
for 16S and ITS sequences. BioRxiv , 74161.
https://doi.org/10.1101/074161
Federhen, S. (2012). The NCBI Taxonomy database. Nucleic Acids
Research , 40 (D1), D136–D143.
https://doi.org/10.1093/nar/gkr1178
Ficetola, G. F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W.,
Bessière, J., Taberlet, P., & Pompanon, F. (2010). An In silico
approach for the evaluation of DNA barcodes. BMC Genomics ,11 (1), 434. https://doi.org/10.1186/1471-2164-11-434
Gold, Z., Curd, E., Goodwin, K., Choi, E., Frable, B., Thompson, A., Jr,
H. J. W., Burton, R., Kacev, D., & Barber, P. (2021). Improving
Metabarcoding Taxonomic Assignment: A Case Study of Fishes in a Large
Marine Ecosystem . https://doi.org/10.22541/au.161407483.33882798/v1
Hagelberg, E., Hofreiter, M., & Keyser, C. (2015). Ancient DNA: the
first three decades. Philosophical Transactions of the Royal
Society B: Biological Sciences , 370 (1660), 20130371.
https://doi.org/10.1098/rstb.2013.0371
Hebert, P. D. N., & Gregory, T. R. (2005). The Promise of DNA Barcoding
for Taxonomy. Systematic Biology , 54 (5), 852–859.
https://doi.org/10.1080/10635150500354886
Hleap, J. S., Littlefair, J. E., Steinke, D., Hebert, P. D. N., &
Cristescu, M. E. (2021). Assessment of current taxonomic assignment
strategies for metabarcoding eukaryotes. Molecular Ecology
Resources , 21 (7), 2190–2203.
Hugenholtz, P., & Tyson, G. W. (2008). Metagenomics. Nature ,455 (7212), 481–483. https://doi.org/10.1038/455481a
Ihrmark, K., Bödeker, I., Cruz-Martinez, K., Friberg, H., Kubartova, A.,
Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., &
Clemmensen, K. E. (2012). New primers to amplify the fungal ITS2
region–evaluation by 454-sequencing of artificial and natural
communities. FEMS Microbiology Ecology , 82 (3), 666–677.
Iwasaki, W., Fukunaga, T., Isagozawa, R., Yamada, K., Maeda, Y., Satoh,
T. P., Sado, T., Mabuchi, K., Takeshima, H., & Miya, M. (2013).
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with
an accurate and automatic annotation pipeline. Molecular Biology
and Evolution , 30 (11), 2531–2540.
Jeunen, G.-J., Urban, L., Lewis, R., Knapp, M., Lamare, M., Rayment, W.,
Dawson, S., & Gemmell, N. (2020). Marine environmental DNA (eDNA)
for biodiversity assessments: a one-to-one comparison between eDNA and
baited remote underwater video (BRUV) surveys.https://doi.org/10.22541/au.160278512.26241559/v1
Jeunen, G. J., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R.,
Stat, M., Bunce, 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.
https://doi.org/10.1111/1755-0998.12982
Johnson, J. S., Spakowicz, D. J., Hong, B.-Y., Petersen, L. M.,
Demkowicz, P., Chen, L., Leopold, S. R., Hanson, B. M., Agresta, H. O.,
Gerstein, M., Sodergren, E., & Weinstock, G. M. (2019). Evaluation of
16S rRNA gene sequencing for species and strain-level microbiome
analysis. Nature Communications , 10 (1), 5029.
https://doi.org/10.1038/s41467-019-13036-1
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S.,
& Madden, T. L. (2008). NCBI BLAST: a better web interface.Nucleic Acids Research , 36 (suppl_2), W5–W9.
Kanz, C., Aldebert, P., Althorpe, N., Baker, W., Baldwin, A., Bates, K.,
Browne, P., van den Broek, A., Castro, M., & Cochrane, G. (2005). The
EMBL nucleotide sequence database. Nucleic Acids Research ,33 (suppl_1), D29–D33.
Key, F. M., Posth, C., Krause, J., Herbig, A., & Bos, K. I. (2017).
Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for
Authentication. Trends in Genetics , 33 (8), 508–520.
https://doi.org/https://doi.org/10.1016/j.tig.2017.05.005
Kõljalg, U., Larsson, K., Abarenkov, K., Nilsson, R. H., Alexander, I.
J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., & Larsson, E.
(2005). UNITE: a database providing web‐based methods for the molecular
identification of ectomycorrhizal fungi. New Phytologist ,166 (3), 1063–1068.
Kovalenko, K. E., Thomaz, S. M., & Warfe, D. M. (2012). Habitat
complexity: approaches and future directions. Hydrobiologia ,685 (1), 1–17. https://doi.org/10.1007/s10750-011-0974-z
Leray, M., Ho, S.-L., Lin, I.-J., & Machida, R. J. (2018). MIDORI
server: a webserver for taxonomic assignment of unknown metazoan
mitochondrial-encoded sequences using a curated database.Bioinformatics , 34 (21), 3753–3754.
Leray, M., Knowlton, N., & Machida, R. J. (2022). MIDORI2: A collection
of quality controlled, preformatted, and regularly updated reference
databases for taxonomic assignment of eukaryotic mitochondrial
sequences. Environmental DNA , n/a (n/a).
https://doi.org/https://doi.org/10.1002/edn3.303
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez,
V., Boehm, J. T., & Machida, R. J. (2013). A new versatile primer set
targeting a short fragment of the mitochondrial COI region for
metabarcoding metazoan diversity: Application for characterizing coral
reef fish gut contents. Frontiers in Zoology , 10 (1),
1–14. https://doi.org/10.1186/1742-9994-10-34
Martin, M. (2011). Cutadapt removes adapter sequences from
high-throughput sequencing reads. EMBnet. Journal , 17 (1),
10–12.
Matsen, F. A., Kodner, R. B., & Armbrust, E. V. (2010). pplacer: linear
time maximum-likelihood and Bayesian phylogenetic placement of sequences
onto a fixed reference tree. BMC Bioinformatics , 11 (1),
1–16.
Meiklejohn, K. A., Damaso, N., & Robertson, J. M. (2019). Assessment of
BOLD and GenBank - Their accuracy and reliability for the identification
of biological materials. PloS One , 14 (6),
e0217084–e0217084. https://doi.org/10.1371/journal.pone.0217084
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K.,
Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H., Kondoh, M., &
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. https://doi.org/10.1098/rsos.150088
Murali, A., Bhargava, A., & Wright, E. S. (2018). IDTAXA: a novel
approach for accurate taxonomic classification of microbiome sequences.Microbiome , 6 (1), 1–14.
Porter, T. M., & Hajibabaei, M. (2018). Over 2.5 million COI sequences
in GenBank and growing. PLOS ONE , 13 (9), e0200177.
https://doi.org/10.1371/journal.pone.0200177
Porter, T. M., & Hajibabaei, M. (2020). Putting COI Metabarcoding in
Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity
Analysis . In Frontiers in Ecology and Evolution (Vol. 8).
https://www.frontiersin.org/article/10.3389/fevo.2020.00248
Qiong, W., M., G. G., M., T. J., & R., C. J. (2007). Naïve Bayesian
Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial
Taxonomy. Applied and Environmental Microbiology , 73 (16),
5261–5267. https://doi.org/10.1128/AEM.00062-07
Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The Barcode of Life
Data System (http://www. barcodinglife. org). Molecular Ecology
Notes , 7 (3), 355–364.
Richardson, R. T., Sponsler, D. B., McMinn‐Sauder, H., & Johnson, R. M.
(2020). MetaCurator: A hidden Markov model‐based toolkit for extracting
and curating sequences from taxonomically‐informative genetic markers.Methods in Ecology and Evolution , 11 (1), 181–186.
Robeson, M. S., O’Rourke, D. R., Kaehler, B. D., Ziemski, M., Dillon, M.
R., Foster, J. T., & Bokulich, N. A. (2020). RESCRIPt: Reproducible
sequence taxonomy reference database management for the masses.Biorxiv .
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016).
VSEARCH: a versatile open source tool for metagenomics. PeerJ ,4 , e2584.
Schoch, C. L., Ciufo, S., Domrachev, M., Hotton, C. L., Kannan, S.,
Khovanskaya, R., Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B.,
Sharma, S., Soussov, V., Sullivan, J. P., Sun, L., Turner, S., &
Karsch-Mizrachi, I. (2020). NCBI Taxonomy: a comprehensive update on
curation, resources and tools. Database , 2020 , baaa062.
https://doi.org/10.1093/database/baaa062
Scott, H., L., K. J., & B., F. P. (2021). Toward a genome sequence for
every animal: Where are we now? Proceedings of the National
Academy of Sciences , 118 (52), e2109019118.
https://doi.org/10.1073/pnas.2109019118
Seeber, P. A., McEwen, G. K., Löber, U., Förster, D. W., East, M. L.,
Melzheimer, J., & Greenwood, A. D. (2019). Terrestrial mammal
surveillance using hybridization capture of environmental DNA from
African waterholes. Molecular Ecology Resources , 19 (6),
1486–1496. https://doi.org/https://doi.org/10.1111/1755-0998.13069
Seersholm, F. V, Cole, T. L., Grealy, A., Rawlence, N. J., Greig, K.,
Knapp, M., Stat, M., Hansen, A. J., Easton, L. J., Shepherd, L.,
Tennyson, A. J. D., Scofield, R. P., Walter, R., & Bunce, M. (2018).
Subsistence practices, past biodiversity, and anthropogenic impacts
revealed by New Zealand-wide ancient DNA survey. Proceedings of
the National Academy of Sciences , 115 (30), 7771 LP – 7776.
https://doi.org/10.1073/pnas.1803573115
Somervuo, P., Koskela, S., Pennanen, J., Henrik Nilsson, R., &
Ovaskainen, O. (2016). Unbiased probabilistic taxonomic classification
for DNA barcoding. Bioinformatics , 32 (19), 2920–2927.
https://doi.org/10.1093/bioinformatics/btw346
Soulé, M. E. (1985). What is conservation biology? BioScience ,35 (11), 727–734.
Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T.
E., Newman, S. J., Harvey, E. S., & Bunce, M. (2017). Ecosystem
biomonitoring with eDNA: metabarcoding across the tree of life in a
tropical marine environment. Scientific Reports , 7 (1),
12240. https://doi.org/10.1038/s41598-017-12501-5
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev,
E. (2012). Towards next-generation biodiversity assessment using DNA
metabarcoding. Molecular Ecology , 21 (8), 2045–2050.
https://doi.org/10.1111/j.1365-294X.2012.05470.x
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C.,
Valentini, A., Vermat, T., Corthier, G., Brochmann, C., & Willerslev,
E. (2007). Power and limitations of the chloroplast trn L (UAA) intron
for plant DNA barcoding . Nucleic Acids Research , 35 (3),
e14–e14. https://doi.org/10.1093/nar/gkl938
Taberlet, P., Gielly, L., Pautou, G., & Bouvet, J. (1991). Universal
primers for amplification of three non-coding regions of chloroplast
DNA. Plant Molecular Biology , 17 (5), 1105–1109.
White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification
and direct sequencing of fungal ribosomal RNA genes for phylogenetics.PCR Protocols: A Guide to Methods and Applications , 18 (1),
315–322.
Wood, D. E., & Salzberg, S. L. (2014). Kraken: ultrafast metagenomic
sequence classification using exact alignments. Genome Biology ,15 (3), 1–12.
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., &
Madden, T. L. (2012). Primer-BLAST: A tool to design target-specific
primers for polymerase chain reaction. BMC Bioinformatics ,13 (1), 134. https://doi.org/10.1186/1471-2105-13-134
Zhang, S., Zhao, J., & Yao, M. (2020). A comprehensive and comparative
evaluation of primers for metabarcoding eDNA from fish. Methods in
Ecology and Evolution , 11 (12), 1609–1625.
https://doi.org/https://doi.org/10.1111/2041-210X.13485