An overview of molecular identification of insect fauna with special emphasis on chalcid wasps (Hymenoptera: Chalcidoidea) of India

Ajaz RASOOL, Tariq AHMAD, Bashir Ahmad GANAI, Shaziya GULL

Abstract


Identifying organisms has grown in importance as we monitor the biological effects of global climate change and attempt to preserve species diversity in the face of accelerating habitat destruction. Classical taxonomy falls short in this race to catalogue biological diversity before it disappears. Differentiating subtle anatomical differences between closely related species requires the subjective judgment of highly trained specialists – and few are being trained in institutes today. DNA barcodes allow non-experts to objectively identify species – from small, damaged, or even industrially processed material. The aim of DNA barcoding is to establish a shared community resource of DNA sequences commonly used for identification, discrimination or taxonomic classification of organisms. It is a method that uses a short genetic marker in an organism's DNA to identify and distinguish its belonging from particular species, varieties or inter varieties. This simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant-quarantine officers and studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made them a major target of DNA barcoding. In this review, we present an overview of DNA barcoding of insects with emphasis on Chalcid wasps of India.

Keywords


biological diversity; catalogue; chalcid wasps; classical taxonomy, DNA barcode; DNA sequence, genetic marker

Full Text:

PDF

References


Altschul, S.F., Gish, W., Miller, W.E., Myers, W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

Axel, J., Seraina, K., Lars, V., Heraty, J.M., Sharkey, M., & Fredrik, R. (2013). "The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data". PLoS ONE, 8(8), e69344. https://doi.org/10.1371/journal.pone.0069344

Bensasson, D., Zhang, D. X., & Hewitt, G. M. (2000). Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Molecular Biology and Evolution, 17(3), 406-415. https://doi.org/10.1093/oxfordjournals.molbev.a026320

Beutel, R.G., & Pohl, H. (2006). Endopterygote systematic- where do we stand and what is the goal(Hexapoda: Arthropoda). Systematic Entomology, 31, 202–219. https://doi.org/10.1111/j.1365-3113.2006.00341.x

Blaxter, M.L. (2004). The promise of DNA taxonomy. Philosophical Transactions of the Royal Society London B, 359, 669-679. https://doi.org/10.1098/rstb.2003.1447

Brower, A. V. (2006). Problems with DNA barcodes for species delimitation:‘ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Systematics and Biodiversity, 4(2), 127-132. https://doi.org/10.1017/S147720000500191X

Busse, H.J., Denner, E.B.M., & Lubitz, W. (1996). “Classification and identification of bacteria: Current approaches to an old problem. Overview of methods used in bacterial systematic.” Journal of Biotechnology, 47, 3-38. https://doi.org/10.1016/0168-1656(96)01379-X

Chase, M.W., Salamin, N., Wilkinson, M., Dunwell, J.M., Kesanakurthi, R.P., Haidar, N., & Savolainen, V. (2005). Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B. Biological Sciences, 360, 1889–1895. https://doi.org/10.1098/rstb.2005.1720

Clare, E.L., Lim, B.K., Engstrom, M.D., Eger, J.L., & Hebert, P.D.N. (2007). DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes, 7, 184–190. https://doi.org/10.1111/j.1471-8286.2006.01657.x

Clare, E.L., Fraser, E.E., Braid, H.E., Fenton, M.B., & Hebert, P.D.N. (2009). Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis) - using a molecular approach to detect arthropod prey. Molecular Ecology, 18, 2532-2542. https://doi.org/10.1111/j.1365-294X.2009.04184.x

Craft, K.J., Pauls, S.U., Darrow, K., Miller, S.E., Hebert, P.D.N., Helgen, L. E., Novotny, V., & Weiblen, G.D. (2010). Population genetics of ecological communities with DNA barcodes: an example from New Guinea Lepidoptera. Proceedings of the National Academy of Science, 11, 5041-5046. https://doi.org/10.1073/pnas.0913084107

Dasmahapatra, K.K., Elias, M., Hill, R.I., Hoffman, J.I., & Mallet, J. (2010) Mitochondrial DNA barcoding detects some species that are real, and some that are not. Molecular Ecology Resources, 10, 264-273. https://doi.org/10.1111/j.1755-0998.2009.02763.x

Decaëns, T., & Rougerie, R. (2008). Descriptions of two new species of Hemileucinae (Lepidoptera: Saturniidae) from the region of Muzo in Colombia - evidence from morphology and DNA barcodes. Zootaxa, 1944, 34-52.

Ekrem, T., Willassen, E., & Stur, E. (2007). A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution, 43, 530-542. https://doi.org/10.1016/j.ympev.2006.11.021

ENVIS (2011) - Centre on Floral Diversity, Ministry of Environment, Forest & Climate Change, Governement of India, (accessed on 30 July 2017).

Floyd, R., Abebe, E., Papert, A., & Blaxter, M. (2002). Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839–850. https://doi.org/10.1046/j.1365-294X.2002.01485.x

Foottit, R.G., Maw, H.E.L., Havill, N.P., Ahern, R.G., & Montgomery, E. (2009). DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea). Molecular Ecology Resource, 9, 188-195. https://doi.org/10.1111/j.1755-0998.2009.02644.x

Frézal, L., & Leblois, R. (2009). Four years of DNA barcoding: Current advances and prospects. Infection, Genetics and Evolution, 8, 727-736. https://doi.org/10.1016/j.meegid.2008.05.005

Gaikward, S. (2014). DNA Barcoding: The Indian Scenario. Barcode Bulletin, International Barcode of life, 5(4). Available from http://ibol.org/

Gellissen, G., & Michaelis, G. (1987). Gene Transfer. Annals of the New York Academy of Sciences, 503(1), 391-401. https://doi.org/10.1111/j.1749-6632.1987.tb40625.x

Geraci, C.J., Mohammed, A.A., & Zhou, X. (2011). DNA barcoding facilitates description of unknown faunas: a case study on Trichoptera in the headwaters of the Tigris River, Iraq. Journal of the North American Benthological Society, 30, 163- 173. https://doi.org/10.1899/10-011.1

Greenstone, M.H. (2006). Molecular methods for assessing insect parasitism. Bulletin of entomological research, 96, 1-13. Available from https://doi.org/10.1079/BER2005402

Greenstone, M.H., Rowley, D.L., Heimbach, U., Lundgren, G., Pfannenstiel, R.S., & Rehner, S.A. (2005). Barcoding generalist predators by polymerase chain reaction: carabids and spiders. Molecular Ecology, 14, 3247-3266. https://doi.org/10.1111/j.1365-294X.2005.02628.x

Greenstone, M.H., Vandenberg, N.J., & Hu, J.H. (2011). Barcode haplotype variation in north American agroecosystem lady beetles (Coleoptera: Coccinellidae). Molecular Ecological Resources, 11, 629-637. https://doi.org/10.1111/j.1755-0998.2011.03007.x

Grimaldi, D.A., & Engel M.S. (2005). Evolution of the Insects. Cambridge University Press, Cambridge.

Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W., & Hebert, P.D.N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, USA, 103, 968-971. https://doi.org/10.1073/pnas.0510466103

Hajibabaei, M., Singer, G.A.C., Hebert, P.D.N., & Hickey, D.A. (2007). DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. TRENDS in Genetics, 23, 167-172. https://doi.org/10.1016/j.tig.2007.02.001

Hausmann, A., Haszprunar, G., & Hebert, P.D.N. (2011). DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions. PLoS ONE, 6, e17134. https://doi.org/10.1371/journal.pone.0017134

Hebert, P.D.N., Cywinska, A., Ball, S.L., & DeWaard, J.R. (2003). Biological Identification through DNABarcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270, 313-321. https://doi.org/10.1098/rspb.2002.2218

Hebert, P.D.N., Penton, E.H., Burns, J.M., Janzen, D.H., & Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, USA, 101, 14812-14817. https://doi.org/10.1073/pnas.0406166101

Hlaing, T., Tun-lin, W., Somboon, P., Socheat, D., Setha, T., Min, S., Chang, M.S., & Walton, C. (2009). Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies. BMC Genetics, 10, 11. https://doi.org/10.1186/1471-2156-10-11

Hrcek, J., Miller, S.E., Quicke, D.L.J., & Smith, M.A. (2011). Molecular detection of trophic links in a complex insect host-parasitoid food web. Molecular Ecological Resources, 11(5), 786-94. https://doi.org/10.1111/j.1755-0998.2011.03016.x

Insect Barcode Informatica (IBIn). – Indian council of Agricultural Research, National Bureau of Agricultural Insect Resources. Available from http://www.cib.res.in/ibin/index.php (accessed on 30 July 2017)

Ivanova, N.V., Borisenko, A.V., & Hebert, P.D.N. (2009). Express barcodes: racing from specimen to identification. Molecular Ecological Resources, 9, 35- 41. https://doi.org/10.1111/j.1755-0998.2009.02630.x

Jalali, S.K., Ojha, R., Venkatesan, T., & Chakravarthy, A.K. (2015). DNA Barcoding for Identification of Agriculturally Important Insects. New Horizons in Insect Science: Towards Sustainable Pest Management: Springer, India, pp. 13-23. https://doi.org/10.1007/978-81-322-2089-3_2

Jarman, S.N. & Elliott, N.G. (2000). DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, ‘living fossils' from the Triassic. Journal of Evolution Biology, 1(3), 624-633. https://doi.org/10.1046/j.1420-9101.2000.00207.x

Jinbo U., Kato T., & Ito M. (2011). Current progress in DNA barcoding and future implications for entomology. Entomological Science, 14, 107–124. https://doi.org/10.1111/j.1479-8298.2011.00449.x

Jurado-Rivera, J.A., Vogler, A.P., Reid, C.A.M., Petitpierre, E., & Gomez-Zurita, J. (2009). DNA barcoding insect-host plant associations. Proceedings of the Royal Society of London B: Biological Sciences, 276, 639-648. https://doi.org/10.1098/rspb.2008.1264

Kerr, K.C.R., Stoeckle, M.Y., Dove, C.J., Weigt, L.A., Francis, C.M., & Hebert, P.D.N. (2007). Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes, 7, 535–543. https://doi.org/10.1111/j.1471-8286.2007.01670.x

Kumara, G.A., Venkatesana Stouthamerb, R., Niranjanaa, P., Lalithaa, Y., & Jalalia, S.K. (2009). Internal transcribed spacer-2 restriction fragment length polymorphism (ITS-2-RFLP) tool to differentiate some exotic and indigenous trichogrammatid egg parasitoids in India. Biological Control, 49 (3), 207-213. https://doi.org/10.1016/j.biocontrol.2009.02.010

Lee, W., Kim, H., Lim, J., Choi, H.R., Kim, Y., Kim, Y.S., Ji, J.Y., Foottit, R.G., & Lee, S. (2010). Barcoding aphids (Hemiptera:Aphididae) of the Korean Peninsula: updating the global data set. Molecular Ecological Resources, 11 (1), 32-7. https://doi.org/10.1111/j.1755-0998.2010.02877.x

Lukhtanov, V.A., Sourakov, A., Zakharov, E.V., & Hebert, P.D.N. (2009). DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification. Molecular Ecological. Resources, 9, 1302-1310. https://doi.org/10.1111/j.1755-0998.2009.02577.x

Mayhew, P.J. (2007.). “Why there are so many insect species? Perspectives from fossils and Phylogenies”. Biological Reviews, 82 (3), 425-454. https://doi.org/10.1111/j.1469-185X.2007.00018.x

Miller, K.B., Alarie, Y., Wolfe, G.W., & Whiting, M.F. (2005). Association of insect life stages using DNA sequences: the larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytiscidae). Systematic Entomology, 30, 499-509. https://doi.org/10.1111/j.1365-3113.2005.00320.x

Munro, J.B., Heraty, J.M., Burks, R.A., Hawks, D., Mottern, J., Cruaud, A., Rasplus, J.Y., & Jansta, P. (2011). A Molecular Phylogeny of the Chalcidoidea (Hymenoptera), PLoS One, 6 (11), e27023. https://doi.org/10.1371/journal.pone.0027023

Padial, J.M., & Riva, I.D.L. (2007). Integrative taxonomists should use and produce DNA barcodes. Magnolia Press Zootaxa, 1586, 67–68.

Pfenninger, M., Nowak, C., Kley, C., Steinke, D., & Streit, B. (2007). Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Molecular Ecology, 16 (9), 1957-68. https://doi.org/10.1111/j.1365-294X.2006.03136.x

Pinzon-Navarro, S., Jurado-Rivera, J.A., Gomez-Zurita, J., Lyal, C.H.C., & Vogler, A.P. (2010). DNA profiling of host–herbivore interactions in tropical forests. Systematic Entomology, 35 (Suppl 1), 18–32.

Pires, A.C., & Marinoni, L. (2010). DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies. Biota Neotropica, 10 (2), 339-346. https://doi.org/10.1590/S1676-06032010000200035

Plaisance, L., Caley, M. J., Borisenko, A.V., Sones, J.E., & Hebert, P.D.N. (2009). The front-end logistics of DNA barcoding: challenges and prospects. Molecular Ecological Resources, 9, 27-34. https://doi.org/10.1111/j.1755-0998.2009.02629.x

Pratheepa, M., Jalali, S.K., Arokiaraj, R.S., Venkatesan, T., Panda, M.N.M., & Pattar, S. (2014). Insect Barcode Information System Volume: Bioinformation, 10(2), 98-100. https://doi.org/10.6026/97320630010098

Preethi, N., Lakshmi, P., & Menon, D. (2016). Diversity and Distribution of Chalcid Wasps in Kerala: Key Biological Control Agents in Cultivated Ecosystems. Arthropod Diversity and Conservation in the Tropics and Sub-tropics, Springer Singapore, pp. 213-226. https://doi.org/10.1007/978-981-10-1518-2_13

Ratnasingham, S., & Hebert, P.D.N. (2007). BOLD: The Barcode of Life Data System. Molecular Ecological Notes, 7, 355-64. Available from (http://www.barcodinglife.org). https://doi.org/10.1111/j.1471-8286.2007.01678.x

Raupach, M.J., Astrin, J.J., Hanning, K., Peters, M.K., Stoeckle, M.Y., & Wägele, J.W. (2010). Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Frontiers in Zoology, 7(1), 26. https://doi.org/10.1186/1742-9994-7-26

Rivera, J., & Currie, D.C. (2009). Identification of Nearctic black flies using DNA Barcodes (Diptera: Simuliidae). Molecular Ecological Resources, 9, 224 236. https://doi.org/10.1111/j.1755-0998.2009.02648.x

Rubinoff, D., Cameron, S., & Will, K. (2006). A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. Journal of Heredity, 97(6), 581-594. https://doi.org/10.1093/jhered/esl036

Salokannel, J., Rantala, M.J., & Whalberg, N. (2010). DNA-barcoding clarifies species definitions of Finnish Apatania (Trichoptera: Apataniidae). Entomologica Fennica, 21, 1-11.

Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., & Lane, R. (2005). Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B. Biological Sciences, 360, 1805–1811. https://doi.org/10.1098/rstb.2005.1730

Sheffield, K.A., Hebert, P.D.N., Kevan, P.G., & Packer, L. (2009). DNA Barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies. Molecular Ecological Resources, 9, 196-207. https://doi.org/10.1111/j.1755-0998.2009.02645.x

Shufran, K.A., & Puterka, G.J. (2011). DNA Barcoding to Identify All Life Stages of Holocyclic Cereal Aphids (Hemiptera: Aphididae) on Wheat and Other Poaceae. Annals of the Entomological Society of America, 104, 39-42. https://doi.org/10.1603/AN10129

Sithanantham, S., Chandish, R.B., Jalali, S.K., & Bakthavatsalam, N. Molecular Taxonomy of Trichogammatids . Biological control of insect pests using egg parasitoids., 1, 39-66.

Smith, M.A, Fernandez-Triana, J., Roughley, R., & Hebert, P.D.N. (2009). DNA barcode accumulation curves for understudied taxa and areas. Molecular Ecological Resources, 9, 208-216. https://doi.org/10.1111/j.1755-0998.2009.02646.x

Smith, M.A., Fisher, B.L., & Hebert, P.D.N. (2005). DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philosophical Transactions of the Royal Society B. Biological Sciences, 360, 1825-1834. https://doi.org/10.1098/rstb.2005.1714

Smith, M.A., Woodley, N.E., Janzen, D.H., Hallwachs, W., & Hebert, P.D.N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Acadamy of Sciences, USA, 103, 3657-3662. https://doi.org/10.1073/pnas.0511318103

Song, H., Buhay, J. E., Whiting, M. F., & Crandall, K. A. (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the national academy of sciences, 105(36), 13486-13491. https://doi.org/10.1073/pnas.0803076105

Strutzenberger, P., Brehm, G., & Fiedler, K. (2010). DNA barcoding-based species delimitation increases species count of Eois (Geometridae) moths in a well-studied tropical mountain forest by up to 50 %. Insect Science, 18, 349-362. https://doi.org/10.1111/j.1744-7917.2010.01366.x

Tautz, D., Arctander P., Minelli, A., Thomas, R.H., & Vogler, A.P. (2003). A plea for DNA taxonomy. Trends in Ecology and Evolution, 18, 70–74. https://doi.org/10.1016/S0169-5347(02)00041-1

Theron, J., & Cloete, T.E. (2000). Molecular techniques for determining microbial diversity and community structure in natural environments. Critical Reviews in Microbiology, 26, 37–57. https://doi.org/10.1080/10408410091154174

Vaglia, T., Haxaire, J., Kitching, I.J., Meusnier, I., & Rougerie, R. (2008). Morphology and DNA barcoding reveal three cryptic species within the Xylophanes neoptolemus and loelia species-groups (Lepidoptera: Sphingidae). Zootaxa, 1923, 18-36.

Venkatesan, T., Prabhakar, R., Baskar, R., Jalalia, S.K., & Lalitha, C.R. (2016). Differentiation of some indigenous and exotic trichogrammatids (Hymenoptera: Trichogrammatidae) from India based on Internal transcribed spacer-2 and cytochrome oxidase-I markers and their phylogenetic relationship. Biological Control, 101, 130-137. https://doi.org/10.1016/j.biocontrol.2016.07.005

Ward, R.D., Zemlak, T.S., Innes, B.H., Last P.R., & Hebert, P.D.N. (2005). DNA barcoding of Australia’s fish species. Philosophical Transactions of the Royal Society B. Biological Sciences, 360, 1847–1857. https://doi.org/10.1098/rstb.2005.1716

Wheat, C.W., & Watt, W.B. (2008). A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera: Pieridae). Molecular Phylogenetics and Evolution, 47, 893-902. https://doi.org/10.1016/j.ympev.2008.03.013

Wiemers, M., & Fiedler, K. (2007). Does the DNA barcoding gap exist?–a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in zoology, 4(1), 8. https://doi.org/10.1186/1742-9994-4-8

Williams, S.T., & Knowlton, N. (2001). Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp Genus Alpheus. Molecular Biology and Evolution, 18, 1484-1493. https://doi.org/10.1093/oxfordjournals.molbev.a003934

Yoshitake, H., Kato, T., Jinbo, U., & Ito, M. (2008). A new Wagnerinus (Coleoptera: Curculionidae) from northern Japan: description including a DNA barcode. Zootaxa, 1740, 15-27.

Zhang, D. X., & Hewitt, G. M. (1996). Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution, 11(6), 247-251. https://doi.org/10.1016/0169-5347(96)10031-8

Zhou, X., Robinson, J.L., Geraci, C.J., Parker, C.R., Flint, J.R.O.S., Etnier, D.A., Ruiter, D., Dewalt, R.E., Jacobus, L.M., & Hebert, P.D.N. (2011). Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the great smoky mountains national park. Journal of the North American Benthological Society, 30, 131-162. https://doi.org/10.1899/10-010.1




DOI: http://dx.doi.org/10.14720/aas.2018.111.1.22

Refbacks

  • There are currently no refbacks.


Copyright (c) 2018 Ajaz RASOOL, Tariq AHMAD, Bashir Ahmad GANAI, Shaziya GULL

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

 

Acta agriculturae Slovenica is an Open Access journal published under the terms of the Creative Commons CC BY License.

                           


eISSN 1854-1941