Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes Wazir S. Lakra Æ M. Goswami Æ A. Gopalakrishnan Received: 31 December 2007 / Accepted: 3 April 2008 / Published online: 16 April 2008 Ó Springer Science+Business Media B.V. 2008 Abstract The partial sequences of 16S rRNA and cyto- chrome c oxidase subunit I (COI) mitochondrial genes were analyzed for species identification and phylogenetic relationships among the commercially important Indian sciaenids (Otolithes cuvieri, Otolithes ruber, Johnius dussumieri, Johnius elongatus, Johnieops vogleri, Oto- lithoides biauritus and Protonibea diacanthus). Sequence analysis of both genes revealed that the seven species fell into three distinct groups, which were genetically distant from each other and exhibited identical phylogenetic res- olution. Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the seven sciaenids indicating the usefulness of mtDNA-based approach in species identification. Keywords Sciaenids Á 16S rRNA Á COI Á mtDNA genes Á Phylogenetics Introduction The Family Sciaenidae in the Order Perciformes is widely distributed throughout the world with approximately 70 genera and 300 species including about 30 species from Indian waters [1, 2]. The Sciaenidae is a species rich family of primarily marine fishes with particularly high diversity in estuaries of the Atlantic, Pacific and Indian Oceans [3]. The sciaenids, popularly known as croakers or drums, contribute significantly to the world marine fisheries par- ticularly of the warm shallow seas and estuaries of North and South America, West Africa, South and South-East Asia [4]. The Indian sciaenids, including the present commercially important species (Otolithes cuvieri, Otoli- thes ruber, Johnius dussumieri, Johnius elongatus, Johnieops vogleri, Otolithoides biauritus and Protonibea diacanthus), contribute approximately 4.6% to the total Indian marine fish production. Conventionally, sciaenid fishes are identified using morphological, meristic and anatomical characters [5, 6]. However, considerable ambiguity exists due to morpho- logical similarity and overlapping meristic counts [6, 7]. Synonym citations in FishBase indicate the possibility of ambiguous identification with respect to some sciaenid species of genus Johnieops and Johnius [8]. Accurate identification of morphologically similar species is essen- tial for population dynamic assessment and fisheries management. Application of molecular tools can provide valuable information for species identification to comple- ment the taxonomic data and validation of systematic positions, phylogeny and other applications like fish product identification in trade monitoring [9]. Among the earlier studies on Indian sciaenids, allozyme markers have been used to document genetic variation in Johnieops dussumieri, Kathala axillaries, Pennahia macropthalmus and Otoloithes ruber [7]. Recently, RAPD markers have been used for molecular identification of five Indian sciaenids [10]. Mitochondrial DNA has been extensively studied in fish phylogenetics since mitochondrial 16S rRNA gene and the protein coding cytochrome c oxidase subunit I (COI) gene are highly conserved. These mitochondrial genes have been sequenced in various invertebrate and vertebrate taxa [11–17]. The well characterized COI gene has proved to be a robust evolutionary marker for the analysis of intraspe- cific and interspecific relationships in many marine fish and W. S. Lakra (&) Á M. Goswami Á A. Gopalakrishnan National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow 226002, UP, India e-mail: lakraws@hotmail.com 123 Mol Biol Rep (2009) 36:831–839 DOI 10.1007/s11033-008-9252-1