DNA BARCODING: FOUNDATIONS AND APPLICATIONS FOR SOUTHEAST ASIAN FRESHWATER FISHES

Hadi Dahruddin, Renny Kurnia Hadiaty, Nicolas Hubert
10.14203/treubia.v43i0.2968
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Abstract

Identifying and delineating species are the primary tasks of taxonomy. Owing to the decreasing interest of the nations for taxonomy and the inventory of living beings, funds have been drastically decreasing during the last two decades for taxonomic studies. As a consequence, the worldwide pool of taxonomists has dramatically decreased. DNA barcoding, as an automated tool for species delineation and identification, proved to rejuvenate the field of taxonomy and open new perspectives in ecology and conservation. In the present review, we will discuss how DNA barcoding established as a new paradigm in taxonomy and how DNA barcoding has been recently integrated in taxonomic studies. We will further detail the potential applications for species identifications and discuss how DNA barcoding may positively impact the inventory and conservation of living beings, particularly in biodiversity hotspots. We emphasise the benefit of DNA barcoding for the conservation of Southeast Asian freshwater fishes.

Keywords

biodiversity hotspots; DNA barcoding; integrative taxonomy; species delineation, species identification

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References

Agnarsson, I. & M. Kuntner 2007. Taxonomy in a changing world: seeking solutions for a science in crisis. Systematic Biology 56 (3):531–539.

April, J., R.L. Mayden, R.H. Hanner & L. Bernatcheza 2011. Genetic calibration of species diversity among North America’s freshwater fishes. Proceedings of the National Academy of Sciences 108 (26):10602–10607.

Ardura, A., A.R. Linde, J.C. Moreira & E.G. Vazquez 2010. DNA barcoding for conservation and management of Amazonian commercial fish. Biological Conservation 143: 1438-1443.

Armstrong, K.F. & S.L. Ball 2005. DNA barcodes for biosecurity: invasive species identification. Philosophical Transactions of the Royal Society B 360:1813-1823.

Barber P. & S.L. Boyce 2006. Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proceedings of the Royal Society London B 273: 2053-2061

Blaxter, M. 2003. Counting Angels with DNA. Nature 421: 122-124.

Butcher, B. A., M. A. Smith, M. J. Sharkey, D. L. J. Quicke 2012. A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadiniae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species. Zootaxa 3457:1-232.

Caterino, M.S. & A.K. Tishechkin 2006. DNA identification and morphological description of the first confirmed larvae of Hetaeriinae (Coleoptera: Histeridae). Systematic Entomology 31: 405–418.

Clare, E.L., B.K. Lim, M.D. Engstrom, J.L. Eger & P.D.N. Hebert 2007. DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes 7: 184-190.

Collins, R.A., K.F. Armstrong, R. Meier, Y. Yiz, S.D.J. Brown, R. Cruickshanks, S. Keeling & C. Jonston 2012. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. Plos One 7 (1): e28381. doi: 10.1371/journal.pone.0028381.

Cutarelli, A., M.G. Amoroso, A. De-Roma, S. Girardi, G. Galiero, A. Guarino & F. Corrado 2014. Italian market and commercial fish species identification by DNA sequencing revealing frauds. Food Control 37: 46-50.

Dayrat, B. 2005. Toward integrative taxonomy. Biological Journal of the Linnean Society 85: 407–415.

De-Carvalho, M.R., F.A. Bockmann, D.S. Amorim, M. Devivo, M.D.T. Piza, N.A. Menezes, J.L. De-Figueiredo, R.M.C. Castro, A.C. Gill & J.D. Mc-Eachran et al. 2005. Revisiting the taxonomic impediment. Science 307 (5708): 353pp. doi: 10.1126/science.307.5708.353b.

De-Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56 (6): 879–886.

Floyd, R., J. Lima, J. De-Waard, L. Humble & R. Hanner 2010. Common goals: policy implications of DNA barcoding as a protocol for identification of arthropod pests. Biological Invasions 12:2947-2954.

Forest, F., R. Grenyer, M. Rouget, T.J. Davies, R.M. Cowling, D.P. Faith, A. Balmford, J.C. Manning, S. Proches, M. VanDer-Bank, G. Reeves, T.A.J. Hedderson & V. Savolainen 2007. Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445:757-760.

Fouquet, A., A. Gilles, M. Vences, C. Marty, M. Blanc & N.J. Gemmell 2007. Underestimation of species richness in Neotropical frogs revealed by mtDNA analyses. Plos One 2 (10):e1109.

Froese, R. & D. Pauly 2014. Fishbase world wide web electronic publication. [Online] [accessed 30 October 2014].

Funk, D.J. & K.E. Omland 2003. Species-level paraphyly and polyphyly: frequency, causes and consequences, with insights from animal mitonchondria DNA. Annual Review of Ecology, Evolution and Systematics 34: 397-423.

Gemeinholzer , B., I. Rey, K. Weising, M. Grundmann, A.N. Muellner, H. Zetzsche, G. Droege, O. Seberg, G. Petersen, D. Rawson et al. 2010. Organizing specimen and tissue preservation in the field for subsequent molecular analyses. In: J. Eymann, J. Degreef, C. Häuser, J.C. Monje, Y. Samyn, D. Vanden-Spiegel (eds.), Manual on field recording techniques and protocols for All Taxa Biodiversity Inventories and Monitoring. The Belgian National Focal Point to the Global Taxonomy Initiative Press, Belgium, 8 (1): pp. 129–157.

Godfray, H.C.J. 2002. Challenges for taxonomy. Nature 417: 17-19.

Godfray, H.C.J. 2006. To boldy sequence. TRENDS in Ecology and Evolution 21:503-504.

Godfray, H.C.J. 2007. Linnaeus in the information age. Nature 446: 259-260.

Godfray, H.C.J. & S. Knapp 2004. Introduction of taxonomy for the twentyfirst century. Philosophical Transactions of the Royal Society B 359: 559–569.

Haye, P.A., N.I. Segovia, R. Vera, M.D.L.A Gallardo & C.G. Escarate 2012. Authentication of crab-meat commercialized in Chile using DNA barcoding. Food Control 25: 239-244.

Hebert, P.D.N., A. Cywinska, S.L. Ball & J.R. De-Waard 2003. Biological identifications through DNA barcoding. Proceedings of the Royal Society London B 270: 313-321.

Hebert, P.D.N. & T.R. Gregory 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54 (5):852–859.

Hebert, P.D.N., E.H. Penton, J.M. Burns, D.H. Janzen & W. Hallwachs 2004a. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences 101: 14812–14817.

Hebert, P.D.N., M.Y. Stoeckle, T.S. Zemlak & C.M. Francis. 2004b. Identification of birds through DNA Barcodes. Plos Biology 2 (10): 1657-1663.

Hoffman, M., C. Hilton-Taylor, A. Angulo, M. Böhm, T.M. Brooks, S.H.M. Butchart, K.E. Carpenter, J. Chanson, B. Collen, N.A. Cox et al. 2010. The impact of Conservation on the status of the world's vertebrates. Science 330:1503-1509.

Holmes, B.H., D. Steinke & R.D. Ward 2009. Identification of shark and ray fins using DNA barcoding. Fisheries Research 95:280-288.

Hubert, N., B. Espiau, C. Meyer & S. Planes 2015. Identifying the ichthyoplankton of a coral reef using DNA barcodes. Molecular Ecology Resources 15: 57-67.

Hubert, N., R. Hanner, E. Holm, N.E. Mandrak, E. Taylor, M. Burridge, D. Watkinson, P. Dumont, A. Curry, P. Bentzen et al. 2008. Identifying Canadian freshwater fishes through DNA barcodings. PLoS One 3 (6): E2490. doi: 10.1371/journal.pone.0002490.

Hubert, N., C.P. Meyer, H.J. Bruggemann, F. Guerin, R.J.L. Komeno, B. Espiau, R. Causse, J.T. Williams & S. Planes 2012. Cryptic diversity in Indo-Pacific coral reef fishes revealed by DNA barcoding provides new support to the centre of overlap hypothesis. PLoS One 7 (3): e28987. doi:10.1371/journal.pone.0028987.

Hubert, N., E.D. Trottin, J.O. Irisson, C. Meyer & S. Planes 2010. Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Molecular Phylogenetics and Evolution 55: 1195-1203.

Ivanova, N.V., T.S. Zemlak, R.H. Hanner & P.D.N. Hebert 2007. Universal primers cocktails for fish DNA barcoding. Molecular Ecology Notes 7:544-548.

Jaafar, T.N.A.M., M.I. Taylor, S.A.M. Nor, M. De-Bruyn & G.R. Carvalho 2012. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). Plos One 7 (11): e49623. doi:10.1371/journal.pone.0049623.

Kadarusman, N. Hubert, R.K. Hadiaty, Sudarto, E. Paradis & L. Pouyaud 2012. Cryptic diversity in Indo-Australian Rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate. PLoS One 7 (7): e40627. doi: 10.1371/journal.pone.0040627.

Kerr, K.C.R., M.Y. Stoeckle, C.J. Dove, L.A. Weigt, C.M. Francis & P.D.N. Hebert 2007. Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes 7 (4): 535-543.

Ko, H.L., Y.T. Wang, T.S. Chiu, M.A. Lee, M.Y. Leus, K.J. Chang, W.Y. Chen & K.T. Shao 2013. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. Plos One 8 (1): e53451. doi:10.1371/journal.pone.0053451.

Kottelat, M., A.J. Whitten, S.N. Kartikasari & S. Wirjoatmodjo 1993. Freshwater fishes of Western Indonesia and Sulawesi. Periplus Editions Limited, Jakarta, 79 pp.

Kottelat, M. & T. Whitten 1996. Freshwater biodiversity in asia (with special reference to fish). The Word Bank, Washington, 59 pp.

Lamoureux, J.F., J.C. Morrison, T.H. Ricketts, D.M. Olson, E. Dinerstein, M.W. McKnight & H.H. Shugart 2006. Global tests of biodiversity concordance and the importance of endemism. Nature 440:212-214.

Mallet, J. & K. Willmott 2003. Taxonomy: renaissance or tower of babel?. TRENDS in Ecology and Evolution 18 (2): 57-59.

Maralit, B.A., R.D. Aguila, M.F.H. Ventolero, S.K.L. Perez, D.A. Willette & M.D. Santos 2013. Detection ofmislabeled commercial fishery by-products in the Philippines using Barcodings DNA and its implications to food traceability and safety. Food Control 33: 119-125.

Matsui, M., Mumpuni & A. Hamidy 2012. Description of a new species of Hylarana from Sumatra (Amphibia, Anura). Current Herpetology 31 (1): 38-46.

Miller, S.E. 2007. DNA barcoding and the renaissance of taxonomy. Proceedings of the National Academy of Sciences 104 (12): 4775-4776.

Myers, N., R.A. Mittermeier, C.G. Mittermeier, G.A.B. Da-Fonseca & J. Kent 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.

Nelson, J.S. 2006. Fishes of the word. John Wiley & Sons, New Jersey, 601 pp.

Nishikawa, K., M. Matsui, H.S. Yong, N. Ahmad, P. Yambun, D.M. Belabut, A. Sudin, A. Hamidy, N.L. Orlov, H. Ota et al. 2012. Molecular phylogeny and biogeography of Southeast Asia from the caecilians (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland. Molecular Phylogenetics and Evolution 63: 714-723.

Orme, C.D.L., R.G. Davies, M. Burgess, F. Eigenbrod, N. Pickup, V.A. Olson, A.J. Webster, T.S. Ding et al. 2005. Global hotspots of species richness are not congruent with endemism or threat. Nature 436:1016-1019.

Pamilo, P. & M. Nei 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568-581.

Pante, E., N. Puillandre, A. Viricel, S. Arnaud-Haond, D. Aurelle, M. Castelin, A. Chenuil, C. Destombe, D. Forcioli, M. Valero, F. Viard, S. Samadi 2015. Species are hypotheses: avoid connectivity assessment based on pillars of sand. Molecular Ecology 24: 525-544.

Paz, F.D.C., J.d.S. Batista & J.I.R. Porto 2014. DNA barcodes of Rosy Tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon Basin. Plos One 9 (5): e98603. doi: 10.1371/journal.pone.0098603.

Pegg, C.G., B. Sinclair, L. Briskey & W.J. Aspden 2006. MtDNA barcode identification of fish larvae in the southern great barrier reef, Australia. Scientia Marina 70: 7–12.

Pereira, L.H.G., R. Hanner, F. Foresti & C. Oliveira 2013. Can DNA barcoding accurately discriminate megadiverse neotropical freshwater fish fauna?. BMC Genetics 14:20.

Pfenninger, M., M. Cordellier & B. Streit 2006. Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata). BMC Evolutionary Biology 6: 100.

Puckridge, M., N. Andreakis, S.A. Appleyard & R.D. Ward 2013. Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Molecular Ecology Resources 13: 32-42.

Radulovici, A.E., P. Archambault & F. Dufresne 2010. DNA barcodings for marine biodiversity: moving fast forward?. Diversity 2: 450-472.

Raghavan, R., N. Dahanukar, M.F. Tlusty, A.L. Rhyne, K.K. Kumar, S. Molur & A.M. Rosser 2013. Uncovering an obscure trade: threatened freshwater fishes and the aquarium pet markets. Biological Conservation 164: 158-169.

Ratnasingham, S. & P.D.N. Hebert 2007. BOLD: the barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes 7 (3): 355-364.

Riedel, A., K. Sagata, Y. R. Suhardjono, R. Tänzler, M. Balke 2013. Integrative taxonomy on the fast track - towards more sustainability in biodiversity research. Frontiers in Ecology 10:15.

Seberg, O., C.J. Humphries, S. Knapp, D.W. Stevenson, G. Petersen, N. Scharff & N.M. Andersen 2003. Shortcuts in systematics? a commentary on DNA-based taxonomy. TRENDS in Ecology and Evolution 18 (2): 63-65.

Sechrest, W., T.M. Brooks, G.A.B. da Fonseca, W.R. Konstant, R.A. Mittermeier, A. Purvis, A.B. Rylands & J.L. Gittleman. 2002. "Hotspots and the conservation of evolutionary history." Proceedings of the National Academy of Sciences 99 (4): 2067-2071.

Smith, M.A., B.L. Fisher & P.D.N. Hebert 2005. DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philosophical Transactions of the Royal Society B 360: 1825–1834.

Smith, M.A., J.J. Rodriguez, J.B. Whitfield, A.R. Deans, D.H. Jansen, W. Hallwachs & P.D.N. Hebert 2008. Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections. Proceedings of the National Academy of Sciences 105 (34): 12359-12364.

Smith, M.A., D.M. Wood, D.H. Janzen, W. Hallwachs & P.D.N. Hebert 2007. DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists. Proceedings of the National Academy of Sciences 104: 4967–4972.

Steinke, D., T.S. Zemlak & P.D.N. Hebert 2009. Barcoding nemo: DNA-based identifications for the ornamental fish trade. Plos One 4 (7): e6300. doi: 10.1371/journal.pone.0006300.

Stribling, J.B. 2006. Environmental protection using DNA barcodes or taxa? Bioscience 56: 878-879.

Sutrisno, H., M.S.A. Zein & S. Sulandari 2013. DNA barcoding. In: Zein MSA, Prawiradilaga DM (eds.), DNA barcoding Fauna Indonesia. Kencana Press, Jakarta, pp. 9-21.

Tautz, D., P. Arctander, A. Minelli, R.H. Thomas & A.P. Vogler. 2002. DNA points the way ahead in taxonomy. Nature 418: 479.

Tautz, D., P. Arctander, A. Minelli, R.H. Thomas & A.P. Vogler. 2003. A plea for DNA taxonomy. TRENDS in Ecology and Evolution 18 (2): 70-74.

Ubaidillah, R. & H. Sutrisno 2009. Introduction to biosystematics: theory and practice. LIPI Press, Jakarta, 198 pp.

Veiga, A.M., O.D. Dominguez, J.E. Alacid & J. Lyons 2014. The aquarium hobby: can sinners become saints in freshwater fish conservation?. Fish and Fisheries. doi: 10.1111/faf.12097.

Vernooy, R., E. Haribabu, M.R. Muller, J.H. Vogel, P.D.N. Hebert, D.E. Schindel, J. Shimura & G.A.C. Singer 2010. Barcoding life to conserve biological diversity: beyond the taxonomic imperative. PLoS Biology 8 (7): e1000417. doi: 10.1371 / journal.pbio.1000417.

Victor, B.C., R. Hanner, M. Shivji, J. Hyde & C. Caldow 2009. Identification of the larval and juvenile stages of the Cubera Snapper, Lutjanus cyanopterus, using DNA barcoding. Zootaxa 2215: 24-36

Ward, R.D., T.S. Zemlak, B.H. Innes, P.R. Last, P.D.N. Hebert 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B 360:1847-1857.

Weigt, L.A., A.C. Driskell, C.C. Baldwin & A. Ormos 2012. DNA barcoding fishes. In: Kress WJ, Erickson DL (eds.), DNA barcodes: Methods and Protocols. Humana Press, Washington, pp. 109-126.

Winterbottom, R., R.H. Hanner, M. Burridge & M. Zur 2014. A cornucopia of cryptic species - a DNA barcoding analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes). ZooKeys 381: 79-111.

Witt, J., D.S. Threloff, L. Doug & P.D.N. Hebert 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology 15: 3073–3082.

Wong, E.H.K. & R.H. Hanner 2008. DNA barcoding detects market substitution in North American seafood. Food Research International 41: 828-837.

Zhang, D.X. & G.M. Hewitt 1996. Nuclear integrations: challenge for mitochondria DNA markers. TRENDS in Ecology and Evolution 11: 247-251.

DOI: https://doi.org/10.14203/treubia.v43i0.2968
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