Efficiency of DNA Barcodes for Identification and Documenting Aquatic Insect Diversity in Rice Fields
Keywords:
biodiversity, COI, rice field, species delimitationAbstract
Rapid and accurate identifications are crucial for biodiversity assessment. Yet, traditional methods for species identification have some limitations. In this study, we tested the efficiency of mitochondrial cytochrome c oxidase I barcoding sequences for species identification and documenting diversity of aquatic insects in the rice fields of Thailand. Considerable success rate (80%) for species identification was found among the species of the order Odonata. Unidentifiable specimens of immatures were successfully associated with conspecific adults or by matching with reference sequences in the public DNA barcoding library. However, some specimens were ambiguous, possibly due to incomplete lineage sorting of closely related species or erroneous identification of the sequences in the public database. The technique was less successful for other insect orders because a lack of reference sequences in the DNA barcode library limits the utility of DNA barcoding. The Poisson tree process and Automatic Barcode Gap Discovery species delimitations revealed that the number of species recognized is more than twice that based on morphological identification. Therefore, DNA barcoding has potential for use in species identification and biodiversity assessment of the aquatic insects in the rice field ecosystem.
References
Anisimova, M. and Gascuel, O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Systematic Biology, 55: 539-552.
Bambaradeniya, C.N.B. and Amerasinghe, F.P. 2003. Biodiversity associated with the rice field agroecosystem in Asian countries: a brief review. Working Paper 63, International Water Management Institute, Colombo, Sri Lanka. 24 pp.
Bambaradeniya, C.N.B., Edirisinghe, J.P., De Silva, D.N., Gunatilleke, C.V.S., Ranawana, K.B. and Wijekoon, S. 2004. Biodiversity associated with an irrigated rice agro-ecosystem in Sri Lanka. Biodiversity and Conservation, 13(9): 1715-1753.
Boonsoong, B. 2014. Field guide to larvae of mayflies, stoneflies and caddisflies in Thailand. Kasetsart University Press, Bangkok, Thailand. 78 pp.
Damm, S., Schierwater, B. and Hadrys, H. 2010. An integrative approach to species discovery in odonates: from character‐based DNA barcoding to ecology. Molecular Ecology, 19(18): 3881-3893.
Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8): 772-772.
Edirisinghe, J.P. and Bambaradeniya, C.N. 2010. Rice fields: an ecosystem rich in biodiversity. Journal of the National Science Foundation of Sri Lanka, 34(2): 57-59.
Elias, M., Hill, R.I., Willmott, K.R., Dasmahapatra, K.K., Brower, A.V., Mallet, J. and Jiggins, C.D. 2007. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal Society of London. Series B, Biological sciences, 274(1627): 2881-2889.
Federico Rizo-Patrón, V., Kumar, A., Colton, M.B.M., Springer, M. and Trama, F.A. 2013. Macroinvertebrate communities as bioindicators of water quality in conventional and organic irrigated rice fields in Guanacaste, Costa Rica. Ecological Indicators, 29: 68-78.
Folmer, O., Hoeh, W.R., Black, M.B. and Vrijenhoek, R.C. 1994. Conserved primers for PCR amplification of mitochondrial DNA from different invertebrate phyla. Molecular Marine Biology and Biotechnology, 3: 294-299.
Frézal, L. and Leblois, R. 2008. Four years of DNA barcoding: current advances and prospects. Infection, Genetics and Evolution, 8(5): 727-736.
Funk, D.J. and Omland, K.E. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology and Systematics, 34(1): 397-423.
Gattolliat, J.L. and Monaghan, M.T. 2010. DNA-based association of adults and larvae in Baetidae (Ephemeroptera) with the description of a new genus Adnoptilum inMadagascar. Journal of the North American Benthological Society, 29: 1042-1057.
Gill, B.A., Harrington, R.A., Kondratieff, B.C., Zamudio, K.R., Poff, L.N. and Funk, C.W. 2013. Morphological taxonomy, DNA barcoding, and species diversity in southern Rocky Mountain headwater streams. Freshwater Science, 33(1): 288-301.
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. 2010.New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59: 307-321.
Huelsenbeck, J.P. and Ronquist, F.R. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics, 17: 754-755.
Jackson, J.K., Battle, J.M., White, B.P., Pilgrim, E.M., Stein, E.D., Miller, P.E. and Sweeney, B.W. 2014. Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications. Freshwater Science, 33(1): 312-324.
Jinbo, U., Kato, T. and Ito, M. 2011. Current progress in DNA barcoding and future implications for entomology. Entomological Science, 14(2): 107-124.
Lawler, S.P. 2001. Rice fields as temporary wetlands: a review. Israel Journal of Zoology, 47(4): 513-528.
Miller, K.B., Alarie, Y., Wolfe, G.W. and 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.
Nilsson, R.H., Ryberg, M., Kristiansson, E., Abarenkov, K., Larsson, K.H. and Kõljalg, U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS One, 1(1): e59.
O'Grady, E.W. and May, M.L. 2003. A phylogenetic reassessment of the subfamilies of Coenagrionidae (Odonata: Zygoptera). Journal of Natural History, 37(23): 2807-2834.
Puillandre, N., Lambert, A., Brouillet, S., Achaz, G. 2012. ABGD, Automatic Barcode GapDiscovery for primary species delimitation. Molecular Ecology, 21: 1864-1877.
Pramual, P. and Adler, P.H. 2014. DNA barcoding of tropical black flies (Diptera: Simuliidae) of Thailand. Molecular Ecology Resources, 14: 262-271.
Pramual, P., Simwisat, K. and Martin, J. 2016. Identification and reassessment of the specific status of some tropical freshwater midges (Diptera: Chironomidae) using DNA barcode data. Zootaxa, 4072(1): 39-60.
Pramual, P. and Wongpakam, K. 2014. Association of black fly (Diptera: Simuliidae) life stages using DNA barcode. Journal of Asia-Pacific Entomology, 17: 549-554.
Rach, J., DeSalle, R., Sarkar, I.N., Schierwater, B. and Hadrys, H. 2008. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society of London. Series B, Biological sciences, 275(1632): 237-247.
Rivera, J. and Currie, D.C. 2009. Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae). Molecular Ecology Resources, 9: 224-236.
Roger, P.A., Heong, K.L. and Teng, P.S. 1991. Biodiversity and sustainability of wetland rice production: role and potential of microorganisms and invertebrates. In: Hawksworth, D.L. (ed) The Biodiversity of Microorganisms and Invertebrates: Its Role in Sustainable Agriculture. CAB International, Wallingford, UK, pp 117-136.
Sangpradub, N. 2016. Common aquatic insects of Sakaerat Environmental Research Station. Center of Excellence on Biodiversity, Chulalongkorn University, Bangkok, Thailand. 130 pp.
Sangpradub, N. and Boonsoong, B. 2006. Identification of freshwater invertebrates of the Mekong River and tributaries. Vientiane: Mekong River Commission. 274 pp.
Shen, Y.Y., Chen, X. and Murphy, R.W. 2013. Assessing DNA barcoding as a tool for species identification and data quality control. PLoS One, 8(2): e57125.
Scherr, S.J. and McNeely, J.A. 2008. Biodiversity conservation and agricultural sustainability: towards a new paradigm of ‘ecoagriculture’ landscapes. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 363(1491): 477-494.
Stamatakis, A., Hoover, P. and Rougemont, J. 2008. A rapid bootstrap algorithm for the RAxML web-servers. Systematic Biology, 75: 758-771.
Sweeney, B.W., Battle, J.M., Jackson, J.K. and Dapkey, T. 2011. Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? Journal of the North American Benthological Society, 30(1): 195-216.
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30 (12): 2725-2729.
Tscharntke, T., Clough, Y., Wanger, T.C., Jackson, L., Motzke, I., Perfecto, I., Vandermeer, J. and Whitbread, A. 2012. Global food security, biodiversity conservation and the future of agricultural intensification. Biological Conservation, 151(1): 53-59.
Watanabe, K., Koji, S., Hidaka, K. and Nakamura, K. 2013. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management. Environmental Entomology, 42(5): 841-850.
Wilson, A.L., Watts, R.J. and Stevens, M.M. 2008. Effects of different management regimes on aquatic macroinvertebrate diversity in Australian rice fields. Ecological Research, 23(3): 565-572.
Zhang, J., Kapli, P., Pavlidis, P. and Stamatakis, A. 2013. A general species delimitation method with applications of phylogenetic placements. Bioinformatics, 29: 2869-2876.
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