Skip to main content Skip to main navigation menu Skip to site footer
Type: Articles
Published: 2011-06-29
Page range: 46-54
Abstract views: 50
PDF downloaded: 3

Barcoding without DNA? Species identification using near infrared spectroscopy

Departamento de Zoologia, Universidade Federal do Paraná, UFPR, Curitiba, Paraná, 81531- 980, Brazil Instituto de Ecologia. La Paz, Bolivia
Departamento de Zoologia, Universidade Federal do Paraná, UFPR, Curitiba, Paraná, 81531- 980, Brazil
Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Campinas, São Paulo, 13084-971, Brazil
Departamento de Química, Universidade Federal do Rio Grande do Norte, Lagoa Nova, Natal 59072-970, Brazil
Departamento de Zoologia, Universidade Federal do Paraná, UFPR, Curitiba, Paraná, 81531- 980, Brazil
Centro de nanociencias y nanotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado postal 356. Ensenada, B. C. México
General metabolomics Neodexiopsis DNA barcoding near infrared spectroscopy

Abstract

Hennig's holomorphology concept defines taxonomy as a process that synthesizes evidence from all relevant comparative sources. One possible source is metabolomics, in which the global metabolic profile is analyzed. An integral metabolic profile can be quickly obtained, nondestructively, through spectroscopy in the near infrared region. Here we use near infrared spectroscopy and chemometry to identify nine species of flies in the genus Neodexiopsis Malloch (Muscidae, Diptera). This genus is the most species-rich of the Muscoidea in the Neotropical region. Identification success demonstrates that near infrared spectroscopy may provide a new source of data to test and organize hypotheses of species delimitation. Comparing near infrared spectroscopy with DNA barcoding, spectroscopy may have even greater conceptual merit as a true barcode of life.

References

  1. Albuquerque, D. de O. (1956a) Duas espécies novas de “Neodexiopsis” Mall., 1920 (Diptera, Muscidae). Revista Brasileira de Biologia, 16, 195–200.

    Albuquerque, D. de O. (1956b) Novas espécies de Coenosiinae (Diptera-Muscidae). Boletim do Museu Nacional. Nova série, Zoologia, 146, 1–23.

    Aldrich, B.T., Maghirang, E.B., Dowell, F.E. & Kambhampati, S. (2007) Identification of termite species and subspecies of the genus Zootermopsis using near-infrared reflectance spectroscopy. Journal of Insect Science, 7, 1–18.

    Ami, D., Natalello, A., Zullini, A. & Dogli, S.M. (2007) Fourier transform infrared microspectroscopy as a new tool for nematode studies. FEBS letters, 576, 297–300.

    Antonialli Junior, W.F., Lima, S.M., Andrade, L.H.C. & Súarez, Y.R. (2007) Comparative study of the cuticular hydrocarbon in queens, workers and males of Ectatomma vizottoi (Hymenoptera, Formicidae) by Fourier transform-infrared photoacoustic spectroscopy. Genetics and Molecular Research 6, 492–499.

    Antonialli Junior, W.F., Súarez, Y.R., Izida, T., Andrade, L.H.C. & Lima, S.M. (2008) Intra-and interspecifc variation of cuticular hydrocarbon composition in two Ectatomma species (Hymenoptera: Formicidae) based on Fourier transform infrared photoacoustic spectroscopy. Genetics and Molecular Research, 7, 559–566.

    Benedict, A.A. (1955) Group classification of virus preparations by infrared spectroscopy. Journal of Bacteriology, 69, 264–269.

    CAMO Software AS. The Unscrambler™. Complete software package for Multivariate Data Analysis and Experimental Design. Version 6. 0.

    CBOL (2008) Consortium for the barcoding of the life. Washington, DC. Available from http://barcoding.si.edu/DNAbarcoding.htm (Accessed 13 november 2009).

    Chopin, T., Kerin, B.F. & Mazerolle, R. (1999) Phycocolloid chemistry as a taxonomic indicator of phylogeny in the Gigartinales, Rhodophyceae: a review and current developments using Fourier transform infrared diffuse reflectance spectroscopy. Phycological Research, 47, 167–188.

    Cole, T.J., Ram, M.S., Dowell, F.E., Omwega, C.O., Overholt, W.A. & Ramaswamy, S.B. (2003) Near-infrared spectroscopic method to identify Cotesia flavipes and Cotesia sesamiae (Hymenoptera: Braconidae). Annals of the Entomological Society of America, 96, 865–869.

    Costacurta, N.C., Marinoni, R.C. & Carvalho, C.J.B. de. (2003) Fauna de Muscidae (Diptera) em três localidades do Estado de Paraná, capturada com armadilha Malaise. Revista Brasileira de Entomologia, 47, 389–397.

    Costacurta, N.C., Couri, M.S. & Carvalho, C.J.B. de. (2005) Descriptions of new species with a key to identification of the genus Neodexiopsis Malloch (Diptera, Muscidae) in Brazil. Revista Brasileira de Entomologia, 49, 353–366.

    Couri, M.S. & Albuquerque, D. de O. (1979) Estudos sobre Neodexiopsis Malloch, 1920 com notas nomenclaturais sobre Coenosiinae (Diptera, Muscidae). Revista Brasileira de Biologia, 39, 499–517.

    Cvacka, J., Jiros, P., Obotnik, J., Hanus, R. & Svatos, A. (2006) Analysis of insect cuticular hydrocarbons using matrix-assisted laser desorption/ionization mass spectrometry. Journal of Chemical Ecology, 32, 409–434.

    Dayrat, B. (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society, 85, 407–415.

    Dharmaraj, S., Suhaimi Jamaludin, A., Mohammad Razak, H., Valliappan, R., Atinah Ahmad, N., Lay Harn, G. & Ismail, Z. (2006) The classification of Phyllanthus niruri Linn. according to location by infrared spectroscopy. Vibrational Spectroscopy, 41, 68–72.

    Dowell, F.E., Throne, J.E., Wang, D. & Baker, J.E. (1999) Identifying stored-grain insects using near-infrared spectroscopy. Journal of Economical Entomology, 92, 165–169.

    Dowell, F.E., Parker, A.G., Benedict, M.Q., Robinson, A.S., Broce, A.B. & Wirtz, R.A. (2005) Sex separation of tsetse fly pupae using near-infrared spectroscopy. Bulletin of Entomological Research, 95, 249–57.

    Downey, G., McElhinney, J. & Fearn, T. (2000) Species identification in selected raw homogenized meats by reflectance spectroscopy in the mid-infrared, near-infrared, and visible ranges. Applied Spectroscopy, 54, 894–899.

    Eriksson, L., Antti, H., Gottfries, J., Holmes, E., Johansson, E., Lindgran, F., Long, I., Lundstedt, T., Trygg, J. & Wold, S. (2004) Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabolomics (gpm). Analytical and Bioanalytical Chemistry, 380, 419–429.

    Fiehn, O., Kristal, B., Ommen, B.V., Summer, L.V., Sansone, S. & Taylor, C. (2006) Establishing Reporting Standards for Metabolomic and Metabonomic Studies: A Call for Participation. OMICS A Journal of Integrative Biology, 10, 158–163.

    Girija, K.R., Sasikala, Ch., Ramana, CH.V. Spröer, C., Takaichi, S., Thiel, V. & Imhoff, J.F. (2010) Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils, International Journal of Systematic and Evolutionary Microbiology, 60, 2099–2107.

    Hall, M.H., Dutro, S.M. & Klowed, M.J. (1990) Determination by near-Infrared reflectance spectroscopy of mosquito (Diptera: Culicidae) bIoodmeal size. Journal of Medical Entomology, 27, 76–79.

    Hennig, W. (1966) Phylogenetic Systematics. University of Illinois Press, Urbana, pp. 1–514.

    Hubert, M. & Engelen, S. (2007) Fast cross-validation of high-breakdown resampling methods for PCA. Computational Statistics & Data Analysis, 51, 5013–5024.

    Himmelreich, U., Somorjai, R.L., Dolenko, B., Ok, C.L., Daniel, H., Ronan, R.M., Mountford, C.E. & Sorrell, T.C. (2003) Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy. Applied and Environmental Microbiology, 69, 4566–4574.

    Kim, S.W., Ban, S.H., Chung, H., Cho, S., Chung, H.J., Choi, P.S., Yoo, O.J. & Liu, J.R. (2004) Taxonomic discrimination of flowering plants by multivariate analysis of Fourier transform infrared spectroscopy data. Plant Cell Reports, 23, 246–250.

    Klarica, J. Bittner, L., Pallua, J., Pezzei, C., Huck-Pezzei, V., Dowell, F., Schied, J., Bonn, G.K., Huck, C., Schlick-Steiner, B.C. & Steiner, F.M. (2011) Near-Infrared Imaging Spectroscopy as a Tool to Discriminate Two Cryptic Tetramorium Ant Species. Journal of Chemical Ecology. Available from http://www.springerlink.com/content/m768755n0p341114/ (Accessed 1 june 2011)

    Klaus, A. & Schawaroch, V. (2006) New methodology utilizing confocal laser scanning microscopy for systematic analysis in arthropods (Insecta). Integrative and Comparative Biology, 46, 207–214.

    Kron, P., Suda, J. & Husband, B.C. (2007) Applications of flow cytometry to evolutionary and population biology. Annual Review of Ecology Evolution and Systematics, 38, 847–76.

    Lai, S., Goodacre, R. & Manchester, L.N. (2004) Whole-organism fingerprinting of the Genus Carnobacterium using fourier transform infrared spectroscopy (FT-IR). Systematic and Applied Microbiology, 27, 186–191.

    Landis, J.R. & Koch, G.G. (1977) The measurement of observer agreement for categorical data. Biometrics, 33, 159–74.

    Lazzari, S.M.N., Ceruti, F.C., Rodriguez-Fernandez, J.I., Opit, G. & Lazzari, F.A. (2010) Intra and interspecific variation assessment in Psocoptera using near spectroscopy. Julius-Kühn-Archiv, 425, 139–144.

    Malloch, J.R. (1934) Muscidae. In: Diptera of Patagonia and South Chile, 7, 171–346.

    Marinoni, R.C. & Dutra, R.R.C. (1991) Levantamento da fauna entomológica no estado de Paraná. Introdução. Situações climática e florística de oito pontos de coleta. Dados faunísticos de agosto de 1986 a julho de 1987. Revista Brasileira de Zoologia, 8, 31–73.

    Mayagaya, V.S., Michel, K., Benedict, M.Q., Killeen,G.F. Wirtz, R.A. Ferguson, H.M. & Dowell, F.E. (2009) Non-destructive determination of age and species of Anopheles gambiae s.l. using near-infrared spectroscopy. American Journal of Tropical. Medicine and Hygiene, 81, 622–630.

    MetabolomicsSociety (2009) Information about metabolomics in the life sciences. Ardmore, Oklahoma. Available from http://129.128.185.121/metabolomics_society/ (Accessed 9 march 2009).

    Micks, D.W. & Benedict, A.A. (1953) Infrared spectrophotometry as a means for identification of mosquitoes. Proceedings of the Society of Experimental Biology and Medicine, 84, 12–14.

    Micks, D.W. & Scrollini, F. (1954) An infrared spectrometric study of the Culex pipiens complex. Rivista di Parasitologia, 15, 161–165.

    Mullen, S.P., Mendelson, T.C., Schal, C. & Shaw, K.L. (2007) Rapid evolution of cuticular hydrocarbons in a species radiation of acoustically diverse Hawaiian crickets (Gryllidae: Trigonidae: Laupala). Evolution, 61, 223–231.

    Munck, L. (2007) A new holistic exploratory approach to systems biology by near infrared spectroscopy evaluated by chemometrics and data inspection. Journal of Chemometrics, 21, 406–426.

    Naumann, D. (2000) Infrared spectroscopy in microbiology. in: R. A. Meyers (ed.) "Encyclopedia of Analytical Chemistry", John Wiley & Sons, Ltd., Chichester, pp. 102–131.

    Newey, P.S., Robson, S.K.A. & Crozier, R.H. (2008) Near-infrared spectroscopy identifies the colony and nest of origin of weaver ants, Oecophylla smaragdina. Insectes Sociaux, 55, 171–175.

    Norgaard, L., Saudland, A., Wagner, J., Nielsen, J.P., Munck, L. & Engelsen, S.B. (2000) Interval Partial Least-Squares Regression (iPLS): A comparative chemometric study with an example from Near-Infrared Spectroscopy. Applied Spectroscopy, 54, 413–419.

    Oberreuter, H., Seiler, H. & Scherer, S. (2002) Identification of coryneform bacteria and related taxa by Fourier-transform infrare d (FT-IR) spectroscopy. International Journal of Systematic and Evolutionary Microbiology, 52, 91–100.

    Paliwal, J., Wang, W., Symons, S.J. & Karunakaran, C. (2004) Insect species and infestation level determination in stored wheat using near-infrared spectroscopy. Canadian Biosystems Engineering, 46, 717–724.

    Pasquini, C. (2003) Near infrared spectroscopy: fundamentals practical aspects and analytical applications. Journal of the Brazilian Chemical Society, 14, 138–219.

    Penney, D., Dierick, M., Cnudde, V., Asschaele, B., Vlassenbroeck, J., Hoorebeke, L.V. & Jacobs, P. (2007) First fossil Micropholcommatidae (Araneae), imaged in Eocene using X-Ray computed tomography. Zootaxa, 1623, 47–53

    Perez-Mendoza, J., Dowell, F.E., Broce, A.B., Throne, J.E., Wirtz, R.A., Feng, X., Fabrick, J.A. & Baker, J.E. (2002) Chronological age-grading of house flies by using near-infrared spectroscopy. Journal of Medical Entomology, 39, 499–508 .

    Perez-Mendoza, J., Throne, J.E., Dowell, F.E. & Baker, J.E. (2003) Detection of insect fragments in wheat flour by near-infrared spectroscopy. Journal of Stored Products Research, 39, 305–312.

    Perez-Mendoza, J., Throne, J.E., Dowell, F.E. & Baker, J.E. (2004) Chronological age-grading of three species of stored-product beetles by using near-infrared spectroscopy. Journal of Economic Entomology, 97, 1159–1167.

    Puskar, L., Tuckermann, R., Frosch, T., Popp, J., Ly, V., McNaughton, D. & Wood, B.R. (2007) Raman acoustic levitation spectroscopy of red blood cells and Plasmodium falciparum trophozoites. Lab on a Chip, 7, 1125–1131.

    Ratnasingham, S. & Hebert, P. (2007) The Barcode of Life Database. Molecular Ecology Notes, 7, 355–364.

    Raxworthy, C.J., Ingram, C.M., Rabibisoa, N. & Pearson, R.G. (2008) Applications of ecological niche modeling for species delimitation: A review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Systematic Biology. 56, 907–923.

    Rodríguez-Fernández, J.I., de Carvalho, C.J.B. & Moura, M.O. (2006) Estrutura de assembléias de Muscidae (Diptera) no Paraná: uma análise por modelos nulos. Revista Brasileira de Entomologia, 50, 93–100.

    Séné, C.F.B., McCann, M.C., Wilson, R.H. & Crinter, R. (1994) Fourier-transform raman and fourier-transform infrared spectroscopy. An investigation of five higher plant cell walls and their components. Plant Physiology, 106, 1623–1631.

    SAS Institute Inc. JMP™. statistical package. Version 3. 1.

    Shevtsova, E., Hansson, C., Janzen, D.H. & Kjærandsen, J. (2011) Stable structural color patterns displayed on transparent insect wings Proceedings of the National Academy of Science Early Edition, DOI: 10.1073/pnas.1017393108, available from: www.pnas.org/cgi/doi/10.1073/pnas.1017393108.

    Snyder, F.M. (1957b) Notes and descriptions of some Neotropical Muscidae (Diptera). Bulletin of the American Museum of Natural History, 113, 437–490. [Note correction on p. viii of the journal.]

    Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A.D., Kämpfer, P., Maiden, M.C.J., Nesme, X., Rosselló-Mora, R., Swings, J., Truper, H.G., Vauterin, L., Ward, A.C. & Whitman, W.B. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology, 52, 1043–1047.

    Timmins, E.M., Howell, S.A. , Alsberg, B.K., Noble, W.C. & Goodacre, R. (1998) Rapid differentiation of closely related Candida species and strains by pyrolysis-mass spectrometry and fourier transform-infrared spectroscopy. Journal of Clinical Microbiology, 36, 367–374.

    Tolleson, D.R., Randel, R.D., Stuth, J.W. & Neuendorff, D.A. (2005) Determination of sex and species in red and fallow deer by near infrared reflectance spectroscopy of the faeces. Small Ruminant Research, 57, 141–150.

    Wenning, M., Seiler, H. & Scherer, S. (2002) Fourier-Transform Infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Applied and Environmental Microbiology, 10, 4717–4721.

    Wenning, M., Theilmann, V. & Scherer, S. (2006) Rapid analysis of two food-borne microbial communities at the species level by Fourier-transform infrared microspectroscopy. Environmental Microbiology, 5, 848–857.

    Wheeler, Q.D. (2008) Undisciplined thinking: morphology and Hennig’s unfinished revolution. Systematic Entomology, 33, 2–7.

    Winder, C.L., Carr, E., Goodacre, R. & Seviour, R. (2004) The rapid identification of Acinetobacter species using Fourier transform infrared spectroscopy. Journal of Applied Microbiology, 96, 328–339.

    Zhao, H., Parry, R.L., Ellis, D.I., Griffith, G.W. & Goodacre, R. (2006) The rapid differentiation of Streptomyces isolates using Fourier transform infrared spectroscopy. Vibrational Spectroscopy, 40, 213–218.