Andújar, C, Arribas, P, Ruzicka, F, Crampton-Platt, A, Timmermans, MJTN & Vogler, AP 2015. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol Ecol. 24:3603–3617.
Andújar, C, Arribas, P, Yu, DW, Vogler, AP & Emerson, BC 2018. Why the COI barcode should be the community DNA metabarcode for the metazoa. Mol Ecol. 27:3968–3975.
Ansorge, WJ 2009. Next-generation DNA sequencing techniques. N Biotechnol. 25:195–203.
Appeltans, W, Ahyong, ST, Anderson, G, Angel, MV, Artois, T, Bailly, N, Bamber, R, Barber, A, Bartsch, I, Berta, A, Błażewicz-Paszkowycz, M, Bock, P, Boxshall, G, Boyko, CB, Brandāo, SN, Bray, RA, Bruce, NL, Cairns, SD, Chan, T-Y, Cheng, L, Collins, AG, Cribb, T, Curini-Galletti, M, Dahdouh-Guebas, F, Davie, PJF, Dawson, MN, De Clerck, O, Decock, W, De Grave, S, de Voogd, NJ, Domning, DP, Emig, CC, Erséus, C, Eschmeyer, W, Fauchald, K, Fautin, DG, Feist, SW, Fransen, CHJM, Furuya, H, Garcia-Alvarez, O, Gerken, S, Gibson, D, Gittenberger, A, Gofas, S, Gómez-Daglio, L, Gordon, DP, Guiry, MD, Hernandez, F, Hoeksema, BW, Hopcroft, RR, Jaume, D, Kirk, P, Koedam, N, Koenemann, S, Kolb, JB, Kristensen, RM, Kroh, A, Lambert, G, Lazarus, DB, Lemaitre, R, Longshaw, M, Lowry, J, Macpherson, E, Madin, LP, Mah, C, Mapstone, G, McLaughlin, PA, Mees, J, Meland, K, Messing, CG, Mills, CE, Molodtsova, TN, Mooi, R, Neuhaus, B, Ng, PKL, Nielsen, C, Norenburg, J, Opresko, DM, Osawa, M, Paulay, G, Perrin, W, Pilger, JF, Poore, GCB, Pugh, P, Read, GB, Reimer, JD, Rius, M, Rocha, RM, Saiz-Salinas, JI, Scarabino, V, Schierwater, B, Schmidt-Rhaesa, A, Schnabel, KE, Schotte, M, Schuchert, P, Schwabe, E, Segers, H, Self-Sullivan, C, Shenkar, N, Siegel, V, Sterrer, W, Stöhr, S, Swalla, B, Tasker, ML, Thuesen, EV, Timm, T, Todaro, MA, Turon, X, Tyler, S, Uetz, P, van der Land, J, Vanhoorne, B, van Ofwegen, LP, van Soest, RWM, Vanaverbeke, J, Walker-Smith, G, Walter, TC, Warren, A, Williams, GC, Wilson, SP & Costello, MJ 2012. The magnitude of global marine species diversity. Curr Biol. 22:2189–2202.
Bellemain, E, Carlsen, T, Brochmann, C, Coissac, E, Taberlet, P & Kauserud, H 2010. ITS as an environmental DNA barcode for fungi: an
in silico approach reveals potential PCR biases. BMC Microbiol. 10:189 pp.
Caporaso, JG, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK, Fierer, N, Peña, AG, Goodrich, JK, Gordon, JI, Huttley, GA, Kelley, ST, Knights, D, Koenig, JE, Ley, RE, Lozupone, CA, McDonald, D, Muegge, BD, Pirrung, M, Reeder, J, Sevinsky, JR, Turnbaugh, PJ, Walters, WA, Widmann, J, Yatsunenko, T, Zaneveld, J & Knight, R 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 7:335–336.
Cha, RS & Thilly, WG 1993. Specificity, efficiency, and fidelity of PCR. PCR Methods Appl. 3:S18–S29.
Crampton-Platt, A, Timmermans, MJ, Gimmel, ML, Kutty, SN, Cockerill, TD, Vun Khen, C & Vogler, AP 2015. Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Mol Biol Evol. 32:2302–2316.
Davenport, CF & Tümmler, B 2013. Advances in computational analysis of metagenome sequences. Environ Microbiol. 15:1–5.
Decelle, J, Probert, I, Bittner, L, Desdevises, Y, Colin, S, de Vargas, C, Galí, M, Simó, R & Not, F 2012. An original mode of symbiosis in open ocean plankton. Proc Natl Acad Sci U S A. 109:18000–18005.
Dodsworth, S 2015. Genome skimming for next-generation biodiversity analysis. Trends Plant Sci. 20:525–527.
Drummond, AJ, Newcomb, RD, Buckley, TR, Xie, D, Dopheide, A, Potter, BCM, Heled, J, Ross, HA, Tooman, L, Grosser, S, Park, D, Demetras, NJ, Stevens, MI, Russell, JC, Anderson, SH, Carter, A & Nelson, N 2015. Evaluating a multigene environmental DNA approach for biodiversity assessment. Gigascience. 4:46 pp.
Eberhardt, U 2012. Methods for DNA barcoding of fungi. Methods Mol Biol. 858:183–205.
Edgar, RC 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 10:996–998.
Federhen, S 2012. The NCBI Taxonomy database. Nucleic Acids Res. 40(Database issue):D136–D143.
Fenchel, T 1988. Marine plankton food chains. Annu Rev Ecol Syst. 19:19–38.
Fontaneto, D, Kaya, M, Herniou, EA & Barraclough, TG 2009. Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy. Mol Phylogenet Evol. 53:182–189.
Greshake, B, Zehr, S, Dal Grande, F, Meiser, A, Schmitt, I & Ebersberger, I 2016. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol Ecol Resour. 16:511–523.
Haider, B, Ahn, TH, Bushnell, B, Chai, J, Copeland, A & Pan, C 2014. Omega: an overlap-graph
de novo assembler for metagenomics. Bioinformatics. 30:2717–2722.
Hays, GC, Richardson, AJ & Robinson, C 2005. Climate change and marine plankton. Trends Ecol Evol. 20:337–344.
Hebert, PDN, Cywinska, A, Ball, SL & deWaard, JR 2003a. Biological identifications through DNA barcodes. Proc Biol Sci. 270:313–321.
Hebert, PDN, Penton, EH, Burns, JM, Janzen, DH & Hallwachs, W 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly
Astraptes fulgerator
. Proc Natl Acad Sci U S A. 101:14812–14817.
Hebert, PDN, Ratnasingham, S & deWaard, JR 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci. 270(Suppl 1):S96–S99.
Hillmann, B, Al-Ghalith, GA, Shields-Cutler, RR, Zhu, Q, Gohl, DM, Beckman, KB, Knight, R & Knights, D 2018. Evaluating the information content of shallow shotgun metagenomics. mSystems. 3:e00069–18.
Krehenwinkel, H, Wolf, M, Lim, JY, Rominger, AJ, Simison, WB & Gillespie, RG 2017. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding. Sci Rep. 7:17668 pp.
Kress, WJ, Garcia-Robledo, C, Uriarte, M & Erickson, DL 2015. DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol. 30:25–35.
Kröger, N & Poulsen, N 2008. Diatoms-from cell wall biogenesis to nanotechnology. Annu Rev Genet. 42:83–107.
Leasi, F & Todaro, MA 2009. Meiofaunal cryptic species revealed by confocal microscopy: the case of
Xenotrichula intermedia (Gastrotricha). Mar Biol. 156:1335–1346.
Lee, HG, Kim, HM, Min, J, Kim, K, Park, MG, Jeong, HJ & Kim, KY 2017. An advanced tool, droplet digital PCR (ddPCR), for absolute quantification of the red-tide dinoflagellate,
Cochlodinium polykrikoides Margalef (Dinophyceae). Algae. 32:189–197.
Liu, S, Wang, X, Xie, L, Tan, M, Li, Z, Su, X, Zhang, H, Misof, B, Kjer, KM, Tang, M, Niehuis, O, Jiang, H & Zhou, X 2016. Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. Mol Ecol Resour. 16:470–479.
Losos, JB 2010. Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E. O. Wilson award address. Am Nat. 175:623–639.
Luo, R, Liu, B, Xie, Y, Li, Z, Huang, W, Yuan, J, He, G, Chen, Y, Pan, Q, Liu, Y, Tang, J, Wu, G, Zhang, H, Shi, Y, Liu, Y, Yu, C, Wang, B, Lu, Y, Han, C, Cheung, DW, Yiu, SM, Peng, S, Xiaoqian, Z, Liu, G, Liao, X, Li, Y, Yang, H, Wang, J, Lam, T-W & Wang, J 2012. SOAPdenovo2: an empirically improved memory-efficient short-read
de novo assembler. GigaScience. 1:18 pp.
Martin, M 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17:10–12.
McManus, GB & Katz, LA 2009. Molecular and morphological methods for identifying plankton: what makes a successful marriage? J Plankton Res. 31:1119–1129.
Pawlowski, J, Audic, S, Adl, S, Bass, D, Belbahri, L, Berney, C, Bowser, SS, Cepicka, I, Decelle, J, Dunthorn, M, Fiore-Donno, AM, Gile, GH, Holzmann, M, Jahn, R, Jirků, M, Keeling, PJ, Kostka, M, Kudryavtsev, A, Lara, E, Lukeš, J, Mann, DG, Mitchell, EAD, Nitsche, F, Romeralo, M, Saunders, GW, Simpson, AGB, Smirnov, AV, Spouge, JL, Stern, RF, Stoeck, T, Zimmermann, J, Schindel, D & de Vargas, C 2012. CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10:e1001419 pp.
Pawluczyk, M, Weiss, J, Links, MG, Egaña Aranguren, M, Wilkinson, MD & Egea-Cortines, M 2015. Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples. Anal Bioanal Chem. 407:1841–1848.
Peng, Y, Leung, HC, Yiu, SM & Chin, FY 2012. IDBA-UD: a
de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 28:1420–1428.
Porazinska, DL, Giblin-Davis, RM, Faller, L, Farmerie, W, Kanzaki, N, Morris, K, Powers, TO, Tucker, AE, Sung, W & Thomas, WK 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol Ecol Resour. 9:1439–1450.
Porter, TM & Hajibabaei, M 2018. Scaling up: a guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol. 27:313–338.
Quast, C, Pruesse, E, Yilmaz, P, Gerken, J, Schweer, T, Yarza, P, Peplies, J & Glöckner, FO 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41(Database issue):D590–D596.
Roy, K & Foote, M 1997. Morphological approaches to measuring biodiversity. Trends Ecol Evol. 12:277–281.
Saunders, GW & McDevit, DC 2012. Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms. Methods Mol Biol. 858:207–222.
Schloss, PD, Westcott, SL, Ryabin, T, Hall, JR, Hartmann, M, Hollister, EB, Lesniewski, RA, Oakley, BB, Parks, DH, Robinson, CJ, Sahl, JW, Stres, B, Thallinger, GG, Van Horn, DJ & Weber, CF 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 75:7537–7541.
Schuster, SC 2007. Next-generation sequencing transforms today’s biology. Nat Methods. 5:16–18.
Scotland, RW, Olmstead, RG & Bennett, JR 2003. Phylogeny reconstruction: the role of morphology. Syst Biol. 52:539–548.
Straub, SC, Parks, M, Weitemier, K, Fishbein, M, Cronn, RC & Liston, A 2012. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot. 99:349–364.
Taberlet, P, Coissac, E, Pompanon, F, Brochmann, C & Willerslev, E 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol. 21:2045–2050.
Tang, M, Tan, M, Meng, G, Yang, S, Su, X, Liu, S, Song, W, Li, Y, Wu, Q, Zhang, A & Zhou, X 2014. Multiplex sequencing of pooled mitochondrial genomes: a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res. 42:e166 pp.
Walker, BH 1992. Biodiversity and ecological redundancy. Conserv Biol. 6:18–23.
Zhang, J, Kobert, K, Flouri, T & Stamatakis, A 2014. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 30:614–620.
Zhou, J, Bruns, MA & Tiedje, JM 1996. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 62:316–322.
Zhou, X, Adamowicz, SJ, Jacobus, LM, Dewalt, RE & Hebert, PDN 2009. Towards a comprehensive barcode library for arctic life: Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Front Zool. 6:30 pp.
Zhou, X, Li, Y, Liu, S, Yang, Q, Su, X, Zhou, L, Tang, M, Fu, R, Li, J & Huang, Q 2013. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience. 2:4 pp.