Non-homologous COI barcode regions: a serious concern in decapod molecular taxonomy

References

• Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–65.
   PubMed Web of Science ®Google Scholar
• Batista AC, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL. (2014). Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: Implications for fishery management. ZooKeys 457:271–88.
   PubMed Web of Science ®Google Scholar
• Buhay JE. (2009). “COI-like” sequences are becoming problematic in molecular systematics and DNA barcoding studies. J Crust Biol 20:96–110.
   Web of Science ®Google Scholar
• Collins RA, Cruickshank RH. (2013). The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–75.
   PubMed Web of Science ®Google Scholar
• Costa FO, de Waard JR, Boutillier J, Ratnasingham S, Dooh R, Hajibabaei M, Hebert PDN. (2007). Biological identifications through DNA barcodes: The case of the Crustacea. Can J Fish Aquat Sci 64:272–95.
   Web of Science ®Google Scholar
• De Bruyn M, Nugroho E, Hossain MM, Wilson JC, Mather PB. (2005). Phylogeographic evidence for the existence of an ancient biogeographic barrier: The Isthmus of Kra Seaway. Heredity 94:370–8.
   PubMed Web of Science ®Google Scholar
• De Bruyn M, Wilson JA, Mather PB. (2004a). Huxleys line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Mol Phylogenet E 30:251–7.
   PubMed Web of Science ®Google Scholar
• De Bruyn M, Wilson JC, Mather PB. (2004b). Reconciling geography and genealogy: Phylogeography of giant freshwater prawns from the Lake Carpentaria region. Mol Ecol 13:3515–26.
   PubMed Web of Science ®Google Scholar
• De Man JG. (1879). On some species of the genus Palaemon Fabr. With descriptions of two new forms. Notes Leyden Museum 1:165–84.
   Google Scholar
• Deepak J, Anilkumar KP, Nidhin B, Saswata M, Harikrishnan M. (Submitted for publication). Molecular marker (mtCOI) reveals the trade of non-indigenous species Macrobrachium malcolmsonii (Milne Edwards) in Kerala. Submitted for publication.
   Google Scholar
• Deshmukh VD. (2013). Principles of Crustacean Taxonomy. Manual on taxonomy and identification of commercially important crustaceans of India. 28–39. http://eprints.cmfri.org.in/9645/.
   Google Scholar
• Excoffier L, Laval G, Schneider S. (2005). Arlequin(version 3.0): An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50.
   PubMed Web of Science ®Google Scholar
• Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessiere J, Taberlet Pompanon F. (2010). An In silico approach for the evaluation of DNA barcodes. BMC Genomics 11:434.
   PubMed Web of Science ®Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–9.
   PubMedGoogle Scholar
• Goswami M, Lakra WS, Rajaswaminathan T, Rathore G. (2010). Development of cell culture system from the giant freshwater prawn Macrobrachium rosenbergii (de Man). Mol Biol Rep 37:2043–8.
   PubMed Web of Science ®Google Scholar
• Hall TA. (1999). Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp Ser 41:95–8.
   Google Scholar
• Hebert PDN, Cywinska A, Ball SL, de Waard JR. (2003a). Biological identifications through DNA barcodes. Proc Biol Sci 270:313–21.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Gregory TR. (2005). The promise of DNA barcoding for taxonomy. Syst Biol 54:852–9.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–17.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Ratnasingham S, De Waard JR. (2003b). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc R. Soc Lond B 270:596–9.
   Web of Science ®Google Scholar
• Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. (2004b). Identification of birds through DNA barcodes. PLoS Biol 2:1657–63.
   Web of Science ®Google Scholar
• Hedgecock D, Stelmach DJ, Nelson K, Lindenfelser NE, Malecha SR. (1979). Genetic divergence and biogeography of natural populations of Macrobrachium rosenbergii. Proc World Maricult Soc 10:873–9.
   Google Scholar
• Hickerson MJ, Meyer CP, Moritz C. (2006). DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55:729–39.
   PubMed Web of Science ®Google Scholar
• Hogg ID, Hebert PDN. (2004). Biological identification of springtails (Collembola: Hexapoda) from the Canadian Arctic, using mitochondrial DNA barcodes. Can J Zool 82:749–54.
   Web of Science ®Google Scholar
• Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, Bankvander M, Chase MW, et al. (2009). A DNA barcode for land plants. Proc Nat Acad Sci USA 106:12794–7.
   PubMed Web of Science ®Google Scholar
• Hurwood DA, Dammannagoda S, Krosch MN, Hyungtaek J, Salin KR, Youssef MABH, de Bruyn M, Mather PB. (2014). Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii). Freshwater Sci 33:217–31.
   Web of Science ®Google Scholar
• Jayachandran KV. (2001). Palaemonid prawns biodiversity, taxonomy, biology and management. New Hampshire: Science Publishers Inc. p 624.
   Google Scholar
• Johnson DS. (1973). Notes on some species of the genus Macrobrachium (Crustacea: Decapoda: Caridea: Palaemonidae). J Singapore Nat Acad Sci 3:273–91.
   Google Scholar
• Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. (2005). Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–74.
   PubMed Web of Science ®Google Scholar
• Lee MSY. (2004). The molecularisation of taxonomy. Invert Syst 18:1–6.
   Web of Science ®Google Scholar
• Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2.
   PubMed Web of Science ®Google Scholar
• Lindenfelser ME. (1984). Morphometric and allozyme congruence: Evolution in the prawn Macrobrachium rosenbergii (Decapoda: Palaemonidae). Syst Zool 33:195–204.
   Google Scholar
• Liu MY, Cai YX, Tzeng CS. (2007). Molecular systematics of the freshwater prawn genus Macrobrachium Bate, 1868 (Crustacea: Decapoda: Palaemonidae) inferred from mtDNA sequences, with emphasis on East Asian Species. Zool Stud 46:272–89.
   Web of Science ®Google Scholar
• Luiz HGP, Marlon FP, Robert H, Fausto F, Claudio O. (2011). DNA barcoding reveals hidden diversity in the Neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Parana Basin of Brazil. Mitochondrial DNA 22:87–96.
   PubMed Web of Science ®Google Scholar
• Malecha SR. (1977). Genetics and selective breeding of Macrobrachium rosenbergii. In: Hanson JA, Goodwin HL, editors. Shrimp and prawn farming in the western hemisphere. Stroudsberg, PA, USA: Dowden, Hutchinson and Ross. p 328–55.
   Google Scholar
• Malecha SR. (1987). Selective breeding and intraspecific hybridization of crustaceans. In: Proceedings of the world symposium on selection, hybridization, and genetic engineering in aquaculture, vol. 1. Berlin, Germany. p 323–36–.
   Google Scholar
• Mathews LM, Schubart CD, Neigel JE, Felder DL. (2002). Genetic, ecological, and behavioural divergence between two sibling snapping shrimp species (Crustacea: Decapoda: Alpheus). Mol Ecol 11:1427–37.
   PubMed Web of Science ®Google Scholar
• Miller AD, Murphy NP, Burridge CP, Austin CM. (2005). Complete mitochondrial DNA sequences of the Decapod Crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7:339–49.
   PubMed Web of Science ®Google Scholar
• Murphy NP, Austin CM. (2004). Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crusatcea: Decapoda: Palaemonidae): Biogeography, taxonomy and the convergent evolution of abbreviated larval development. Zool Scripta 34:187–97.
   Web of Science ®Google Scholar
• Nass NMK, Nass S. (1963). Intramitochondrial fibers with DNA characteristics. J Cell Biol 19:593–629.
   PubMed Web of Science ®Google Scholar
• Palumbi SR, Benzie J. (1991). Large mitochondrial DNA differences between morphologically similar Penaeid shrimp. Mol Mar Biol Biotechnol 1:27–34.
   PubMedGoogle Scholar
• Ratnasingham S, Hebert PDN. (2007). BOLD: The barcode of life data system. Mol Ecol Notes 7:355–64. (www.barcodinglife.org).
   PubMed Web of Science ®Google Scholar
• Rougerie R, Haxaire J, Kitching IJ, Hebert PDN. (2012). DNA barcode and morphology reveal a hybrid hawkmoth in Tahiti (Lepidoptera: Sphingidae). Invert Syst 26:445–50.
   Web of Science ®Google Scholar
• Schubart CD. (2009). Mitochondrial DNA and Decapod Phylogenies: The Importance of Pseudogenes and Primer Optimization. Decapod crustacean pylogenetics. Boca Raton, FL: CRC Press, Taylor & Francis Group. p 47–9.
   Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9.
   PubMed Web of Science ®Google Scholar
• Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. (2003). A plea for DNA taxonomy. Trends Ecol E 18:70–4.
   Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–82.
   PubMed Web of Science ®Google Scholar
• Vences M, Thomas M, Bonett RM, Vieites DR. (2005). Deciphering amphibian diversity through DNA barcoding: Chances and challenges. Philos Trans R Soc Lond B Biol Sci 360:1859–68.
   PubMed Web of Science ®Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. (2005). DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–57.
   PubMed Web of Science ®Google Scholar
• Will KW, Mishler BD, Wheeler QD. (2005). The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–51.
   PubMed Web of Science ®Google Scholar
• Wilson K, Cahill V, Bailment E, Benzie J. (2000). The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: Are malacostracan crustaceans more closely related to insects than to branchiopods? Mol Biol Evol 17:863–74.
   PubMed Web of Science ®Google Scholar
• Wowor D, Ng PKL. (2001). Identity of the Giant Prawn, Macrobrachium rosenbergii (De Man, 1879) (Crustacea: Decapoda: Caridea: Palaemonidae). In: Proceedings of the Fifth International Crustacean Congress, Melbourne, Australia.
   Google Scholar
• Wowor D, Ng PKL. (2007). The giant freshwater prawns of the Macrobrachium rosenbergii species group (Crustacea: Decapoda: Caridea: Palaemonidae). Raffles Bull Zool 55:321–36.
   Web of Science ®Google Scholar
• Wowor D, Ng PKL. (2008). Case 3428. Palaemon rosenbergii De Man, 1879 (currently Macrobrachium rosenbergii; Crustacea, Decapoda): Proposed conservation of usage by designation of a neotype. Bull Zool Nomenclature 6:288–92.
   Google Scholar
• Zhang J. (2011). Species identification of marine fishes in China with DNA barcoding. Evid-Based Complement Alternat Med 10 Article ID 978253.
   Web of Science ®Google Scholar