title: An assessment of the DNA barcodes of Indian freshwater fishes.
abstract: Freshwater fishes in India are poorly known and plagued by many unresolved cryptic species complexes that masks some latent and endemic species. Limitations in traditional taxonomy have resulted in this crypticism. Hence, molecular approaches like DNA barcoding, are needed to diagnose these latent species. We have analyzed 1383 barcode sequences of 175 Indian freshwater fish species available in the databases, of which 172 sequences of 70 species were generated. The congeneric and conspecific genetic divergences were calculated using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree using the MEGA 5.1. DNA barcoding principle at its first hand approach, led to the straightforward identification of 82% of the studied species with 2.9% (S.E=0.2) divergence between the nearest congeners. However, after validating some cases of synonymy and mislabeled sequences, 5% more species were found to be valid. Sequences submitted to the database under different names were found to represent single species. On the other hand, some sequences of the species like Barilius barna, Barilius bendelisis and Labeo bata were submitted to the database under a single name but were found to represent either some unexplored species or latent species. Overall, 87% of the available Indian freshwater fish barcodes were diagnosed as true species in parity with the existing checklist and can act as reference barcode for the particular taxa. For the remaining 13% (21 species) the correct species name was difficult to assign as they depicted some erroneous identification and cryptic species complex. Thus, these barcodes will need further assay and inclusion of barcodes of more specimens from same and sister species.
authors.affiliation: Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
authors.forename: Mohua
authors.initials: M
authors.lastname: Chakraborty
authors.affiliation: Department of Biotechnology, Assam University, Silchar 788011, Assam, India. Electronic address: drsankarghosh@gmail.com.
authors.forename: Sankar Kumar
authors.initials: SK
authors.lastname: Ghosh
mesh_terms: D000818:Animals; D058893:DNA Barcoding, Taxonomic; D003576:Electron Transport Complex IV / Q000235:genetics; D005399:Fishes / Q000145:classification* / Q000235:genetics*; D005618:Fresh Water; D007194:India; D008969:Molecular Sequence Data
chemical_list: D003576:Electron Transport Complex IV
keywords: BLAST; BOLD; BOLD and Genbank; COI; COI gene; Cryptic species complex; Cytochrome C oxidase 1; DNA barcode; EDTA; Indian freshwater fishes; K2P; Kimura 2 parameter; MEGA; ML; Maximum Likelihood; NJ; NUMTs; Neighbor Joining; Neighbor Joining tree; S.E; Standard Error; barcode of life datasystem; basic local alignment search tool; dNTPs; deoxynucleotide triphosphates; ethylenediaminetetraacetic acid; molecular evolutionary genetic analysis; nuclear DNA originating from mitochondrial DNA sequences