High-resolution community analysis of deep-sea copepods using MALDI-TOF protein fingerprinting

Abe, 2012, Short-term changes in population structure and vertical distribution of mesopelagic copepods during the spring bloom in the Oyashio region, Deep-Sea Res. I, 65, 100, 10.1016/j.dsr.2012.02.009 Ahdesmaki, M., Zuber, V., Gibb, S., Strimmer, K., 2015. sda: Shrinkage discriminant analysis and CAT score variable selection. R package version 1.3.6. 〈http://CRAN.R-project.org/package=sda〉. Ambler, 1987, Vertical habitat-partitioning by copepodites and adults of subtropical oceanic copepods, Mar. Biol., 94, 561, 10.1007/BF00431403 Anderson, 2001, Zooplankton community during the transition from spring bloom to oligotrophy in the open NW Mediterranean and effects of wind events. 2. Vertical distribution and migrations, J. Plankton Res., 23, 243, 10.1093/plankt/23.3.243 Arnold, 1998, Fingerprint matching of E. coli strains with matrix-assisted laser desorption ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach, Rapid Commun. Mass Spectrom., 12, 630, 10.1002/(SICI)1097-0231(19980529)12:10<630::AID-RCM206>3.0.CO;2-0 Auel, 1999, The ecology of Arctic deep-sea copepods (Euchaetidae and Aetideidae). Aspects of their distribution, trophodynamics and effect on the carbon flux, Rep. Polar Res., 319, 1 Beaugrand, 2002, Diversity of calanoid copepods in the North Atlantic and adjacent seas: species association and biogeography, Mar. Ecol. Prog. Ser., 232, 179, 10.3354/meps232179 Bickford, 2006, Cryptic species as a window on diversity and conservation, Trends Ecol. Evol., 22, 148, 10.1016/j.tree.2006.11.004 Blanco-Bercial, 2007, RFLP procedure to discriminate between Clausocalanus Giesbrecht, 1888 (Copepoda, Calanoida) species in the central Cantabrian Sea, J. Exp. Mar. Biol. Ecol., 344, 73, 10.1016/j.jembe.2006.12.016 Bode, 2017, Unravelling diversity of deep-sea copepods using integrated morphological and molecular techniques, J. Plankton Res., 39, 600, 10.1093/plankt/fbx031 Bucklin, 1996, Molecular diversity of the copepod, Nannocalanus minor: genetic evidence of species and population structure in the North Atlantic Ocean, J. Mar. Res., 54, 285, 10.1357/0022240963213385 Bucklin, 2003, Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausoalanidae, Mar. Biol., 142, 333, 10.1007/s00227-002-0943-1 Bucklin, 2010, DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition, Deep-Sea Res. II, 57, 40, 10.1016/j.dsr2.2009.08.005 Campbell, 2005, Species differentiation of insects and other multicellular organisms using matrix-assisted laser desorption/ionization time of flight mass spectrometry protein profiling, Syst. Entomol., 30, 186, 10.1111/j.1365-3113.2004.00279.x Clarke, K.R., Gorley, R.N., 2006. PRIMER v6: User manual tutorial. PRIMER-E, Plymouth. Cornils, 2014, Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida), Front. Zool., 11, 19, 10.1186/1742-9994-11-19 Damkaer, D.M., 1975. Calanoid copepods of the genera Spinocalanus and Mimocalanus from the central Arctic Ocean, with a review of the Spinocalanidae. Seattle, NOAA Technical Reports NMFS CIRC-391. De Meester, 2016, Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition, Oecologia, 182, 559, 10.1007/s00442-016-3677-3 Derycke, 2016, Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct mircobiomes with intraspecific variability, Mol. Ecol., 25, 2093, 10.1111/mec.13597 Diekmann, 2008, Rapid classification and identification of salmonellae at the species and subspecies levels by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry, Appl. Environ. Microbiol., 74, 7767, 10.1128/AEM.01402-08 Dieme, 2014, Accurate identification of Culicidae at aquatic developmental stages by MALDI-TOF MS profiling, Parasit. Vectors, 7, 544, 10.1186/s13071-014-0544-0 Feltens, 2010, Discrimination of different species from the genus Drosophila by intact protein profiling using matrix-assisted laser desorption ionization mass spectrometry, BMC Evol. Biol., 10, 95, 10.1186/1471-2148-10-95 Fenselau, 2001, Characterization of intact microorganisms by MALDI mass spectrometry, Mass Spectrom. Rev., 20, 157, 10.1002/mas.10004 Fišer, 2018, Cryptic species as a window into the paradigm shift of the species concept, Mol. Ecol., 27, 613, 10.1111/mec.14486 Gibb, S., 2014. MALDIquantForeign: Import/Export routines for MALDIquant. R pack. ver. 0.9. 〈http://CRAN.R-project.org/package=MALDIquantForeign〉. Gibb, 2012, MALDIquant: a versatile R package for the analysis of mass spectrometry data, Bioinform., 28, 2270, 10.1093/bioinformatics/bts447 Goetze, 2003, Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae, Proc. R. Soc. Lond. B, 270, 2321, 10.1098/rspb.2003.2505 Grice, 1971, Deep water calanoid copepods from the Mediterranean Sea. Family Spinocalanidae, Cah. Biol. Mar., 12, 273 Hebert, 2003, Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc. R. Soc. Lond. B, 270, 96, 10.1098/rsbl.2003.0025 Holland, 1996, Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom., 10, 1227, 10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6 Hoof, 2006, Copepod biodiversity as an indicator of changes in ocean and climate conditions of the northern California current ecosystem, Limnol. Oceanogr., 51, 2607, 10.4319/lo.2006.51.6.2607 Jarman, 1999, Extracting and visualizing matrix-assisted laser desorption/ionization time-of-flight mass spectral fingerprints, Rapid Commun. Mass Spectrom., 13, 1586, 10.1002/(SICI)1097-0231(19990815)13:15<1586::AID-RCM680>3.0.CO;2-2 Kaufmann, 2011, Evaluation of matrix-assisted laser desorption/ionization time of flight mass spectrometry for characterization of Culicoides nubeculosus biting midges, Med. Vet. Entomol., 25, 32, 10.1111/j.1365-2915.2010.00927.x Karger, 2012, Species determination and characterization of developmental stages of ticks by whole-animal matrix-assisted laser desorption/ionization mass spectrometry, Ticks Tick.-borne Dis., 3, 78, 10.1016/j.ttbdis.2011.11.002 Knowlton, 1993, Sibling species in the sea, Annu. Rev. Ecol. Syst., 24, 189, 10.1146/annurev.es.24.110193.001201 Kosobokova, 2011, Patterns of zooplankton diversity through the depths of the Arctic's central basins, Mar. Biodiv., 41, 29, 10.1007/s12526-010-0057-9 Krishnamurthy, 1996, Detection of pathogenic and nonpathogenic bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom., 10, 883, 10.1002/(SICI)1097-0231(19960610)10:8<883::AID-RCM594>3.0.CO;2-V Kuriyama, 2006, Species diversity and niche-partitioning in the pelagic copepods of the family Scolecitrichidae (Calanoida), Crustaceana, 79, 293, 10.1163/156854006776759554 Laakmann, 2012, Evolution in the deep sea: biological traits, ecological and phylogenetics of pelagic copepods, Mol. Phylogenet. Evol., 65, 535, 10.1016/j.ympev.2012.07.007 Laakmann, 2013, Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences, Mol. Ecol. Res., 13, 862, 10.1111/1755-0998.12139 Lee, 2002, Morphological stasis in the Eurytemora affinis species complex (Copepoda: Temoridae), Hydrobiologia, 480, 111, 10.1023/A:1021293203512 Levitan, 2004, Mechanisms of reproductive isolation among sympatric broadcast-spawning corals of the Montastraea annularis species complex, Evol., 58, 308, 10.1111/j.0014-3820.2004.tb01647.x Li, 2000, Characterization of Aspergillus spores by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom., 14, 2392, 10.1002/1097-0231(20001230)14:24<2393::AID-RCM178>3.0.CO;2-9 Longhurst, 1985, Relationship between diversity and the vertical structure of the upper ocean, Deep-Sea Res., 32, 1535, 10.1016/0198-0149(85)90102-5 Mathis, 2015, Identification of phlebotomine sand flies using one MALDI-TOF MS reference database and two mass spectrometer systems, Parasit. Vectors, 8, 266, 10.1186/s13071-015-0878-2 Matsuura, 2010, Species diversity and vertical distribution of the deep-sea copepods of the genus Euaugaptilus in the Sulu and Celebes Sea, Deep-Sea Res II, 57, 2098, 10.1016/j.dsr2.2010.09.013 Mazzeo, 2008, Fish authentication by MALDI-TOF mass spectrometry, J. Agric. Food Chem., 56, 11071, 10.1021/jf8021783 McManus, 2009, Molecular and morphological methods for identifying plankton: what makes a successful marriage?, J. Plankton Res., 31, 1119, 10.1093/plankt/fbp061 Müller, 2013, Identification of cryptic Anopheles mosquito species by molecular protein profiling, PLoS ONE, 8, e57486, 10.1371/journal.pone.0057486 Palumbi, 1994, Genetic divergence, reproductive isolation, and marine speciation, Annu. Rev. Ecol. Syst., 25, 547, 10.1146/annurev.es.25.110194.002555 Pappin, 1993, Rapid identification of proteins by peptide-mass fingerprinting, Curr. Biol., 3, 327, 10.1016/0960-9822(93)90195-T R Development Core Team, 2015 Razouls, C., de Bovée, F., Kouwenberg, J., Desreumaux, N., 2005-2017. Diversity and Geographic Distribution of Marine Planktonic Copepods. http://copepodes.obs-banyuls.fr/en. Riccardi, 2012, Potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of freshwater zooplankton: a pilot study with three Eudiaptomus (Copepoda: Diaptomidae) species, J. Plankton Res., 34, 484, 10.1093/plankt/fbs022 Rocha-Olivares, 2001, Decoupling of molecular and morphological evolution in deep lineages of a meiobenthic harpacticoid copepod, Mol. Biol. Evol., 18, 1088, 10.1093/oxfordjournals.molbev.a003880 Rossel, 2018, Automatic specimen identification of harpacticoids (Crustacea:Copepoda) using Random Forest and MALDI-TOF mass spectra, including a post hoc test for false positive discovery, Methods Ecol. Evol., 1 Rossel, 2018, Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF), Front. Mar. Sci., 5, 149, 10.3389/fmars.2018.00149 Ryzhov, 2001, Characterization of the protein subset desorbed by MALDI from whole bacterial cells, Anal. Chem., 73, 746, 10.1021/ac0008791 Salla, 2013, Matrix-assisted laser desorption ionization mass spectrometry for identification of shrimp, Anal. Chim. Acta, 794, 55, 10.1016/j.aca.2013.07.014 Sandrin, 2013, MALDI TOF MS profiling of bacteria at the strain level: a review, Mass Spectrom. Rev., 32, 188, 10.1002/mas.21359 Sano, 2013, Feeding habits of mesopelagic copepods in Sagami Bay: insights from integrative analysis, Prog. Oceanogr., 110, 11, 10.1016/j.pocean.2013.01.004 Schukat, 2014, Complex trophic interactions of calanoid copepods in the Benguela upwelling system, J. Sea Res., 85, 186, 10.1016/j.seares.2013.04.018 Scriven, 2016, Niche partitioning in a sympatric cryptic species complex, Ecol. Evol., 6, 1328, 10.1002/ece3.1965 Seng, 2010, MALDI-TOF-mass spectrometry applications in clinical microbiology, Future Microbiol., 5, 1733, 10.2217/fmb.10.127 Shimode, 2009, Life history and ontogenetic vertical migration of Neocalanus gracilis in the western North Pacific Ocean, Aquat. Biol., 7, 295, 10.3354/ab00201 Steinmann, 2013, Evaluation of matrix-assisted laser desorption/ionization time of flight mass spectrometry for the identification of ceratopogonid and culicid larvae, Parasitology, 140, 318, 10.1017/S0031182012001618 Strimmer, K., 2014. crossval: Generic functions for cross validation. R package version 1.0.2. 〈http://CRAN.R-project.org/package=crossval〉. Thum, 2009, Deep genetic divergence among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diatomidae) challenge the hypothesis of Pleistocene speciation, Biol. J. Linn. Soc., 96, 150, 10.1111/j.1095-8312.2008.01105.x Turner, 2004, The importance of small planktonic copepods and their roles in pelagic marine food webs, Zool. Stud., 43, 255 Turner, 2015, Zooplankton fecal pellets, marine snow, phytodetritus and the ocean's biological pump, Prog. Oceanogr., 130, 205, 10.1016/j.pocean.2014.08.005 Verheye, 1992, Vertical distribution and diel vertical migration of Calanoides carinatus (Krøyer, 1849) developmental stages in the southern Benguela upwelling region, J. Exp. Mar. Biol. Ecol., 158, 123, 10.1016/0022-0981(92)90312-X Volta, 2012, Discrimination of freshwater fish species by matrix-assisted desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS): a pilot study, J. Limnol., 71, 164, 10.4081/jlimnol.2012.e17 Warnes, G.R., Bolker, B., Bonebakker, L., Gentleman, R., Huber, W., Liaw, A., Lumley, T., Maechler, M., Magnusson, A., Moeller, S., Schwartz, M., Venables, B., 2015. gplots: Various R programming tools for plotting data. R package version 2.17.0. 〈http://CRAN.R-project.org/package=gplots〉. Weissburg, 1998, Following the invisible trail: Kinematic analysis of mate-tracking in the copepod Temora longicornis, Philos. Trans. R. Soc. Lond. B, 353, 701, 10.1098/rstb.1998.0236 Wieser, 2012, MALDI-TOF MS in microbiological diagnostics – identification of microorganisms and beyond (mini review), Appl. Microbiol. Biotechnol., 93, 965, 10.1007/s00253-011-3783-4 Yamaguchi, 2004, Vertical distribution patterns of pelagic copepods as viewed from the predation pressure hypothesis, Zool. Stud., 43, 475 Yamaguchi, 2007, Vertical distribution and feeding ecology of a copepod Gaetanus variabilis in the southern Japan Sea during winter, La Mer, 45, 47 Yssouf, 2013, Matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identifications of tick vectors, J. Clin. Microbiol., 51, 522, 10.1128/JCM.02665-12 Yssouf, 2013, Matrix-assisted laser desorption ionization – time of flight mass spectrometry: an emerging tool for the rapid identification of mosquito vectors, PLoS One, 8, e72380, 10.1371/journal.pone.0072380