43 Phylogenetic analysis of fishes of the subfamily Schizothoracinae (Teleostei: Cyprinidae) from Indian Himalayas using cytochrome b gene ASHOKTARU BARAT, SHAHNAWAZ ALI, JYOTI SATI AND G. K. SIVARAMAN Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research Bhimtal - 263 136, Nainital, Uttaranchal, India e-mail: abarat58@hotmail.com ABSTRACT Molecular phylogeny of two genera containing five species fish of the subfamily Schizothoracinae distributed in the north and north-east Himalayas was investigated based on the partial 307 bp cytochrome b gene sequences. The sequence analysis data showed that 48 sites out of 307 (16%) were variable without any insertion or deletion. Rate of transition (4.8%) was higher than transversion (0.65%). A total of 12 haplotypes (h) were identified. No haplotype was shared by the five species. The nucleotide diversity (π) ranged from 0.00561 to 0.06073 with least between Schizothorax richardsonii and Schizothorax progastus. The phylogenetic tree, constructed by neighbour-joining, minimum evolution and maximum parsimony methods revealed similar results suggesting that S. richardsonii and S. progastus were more closely related to each other than the other species in the subfamily, which was also confirmed by the genetic distance data. The results indicate that cytochrome b gene is useful in analysing genetic variation as well as in unravelling phylogenetic relationship in the subfamily Schizothoracinae. Keywords: Cytochrome b, Genetic distance, Genetic diversity, Mitochondrial DNA, Phylogenetic relationship, Schizothoracinae Introduction Snow trouts belong to the subfamily Schizothoracinae (Family: Cyprinidae) which consists of 15 genera and over hundred species distributed all over the world (Mirza, 1991). The Indian snow trouts fall under seven genera, majority of which constitute an important part of coldwater fishery in the Himalayan region (Tilak, 1987). These are economically important fishes which inhabit fast flowing snow fed streams and lakes. Due to overexploitation, many of the species were listed as ‘endangered’ by the National Environmental Protection Agency and Endangered Species Scientific Commission (Yue and Chen, 1998). Classification of snow trouts at species level is generally based on classical, morphological and osteological methods. However, accurate identification of Schizothoracine fishes using morphological characters (e.g., dorsal and caudal fin rays count, length and weight, structure of scales, structure of jaws and lips etc.) is difficult due to intraspecific morphological variability and therefore sometimes causes error in proper identification of closely related species. Although, all the species of snow trouts are classified under the subfamily Schizothoracinae, ambiguity remains under the genus level. The taxonomic positions of these species vary according to different sources leading to improper identification of the species. There are several studies on classification of fishes under Schizothoracinae (Wu, 1984; Chen, 1998; Wu and Indian J. Fish., 59(1) : 43-47, 2012 Tan, 1991). Phylogenetic relationships among genera and species under Schizothoracinae have been investigated based on morphological characters, RAPD analysis (Chen and Chen, 2000; 2001) and mitochondrial cytochrome b gene sequence analysis (Dekui et al., 2004; Qi et al., 2005). Mitochondrial DNA (mtDNA) has been one of the most widely used molecular markers for studying intraspecific and interspecies variation in animals because of its simple genomic structure, high nucleotide substitution rate, lack of recombination and maternal inheritance (Avise, 1986; Billington and Hebert, 1988). The availability of mtDNA data has provided new perspectives on taxonomically debatable taxa and confusing questions of phylogeny (Groves and Shields, 1996). Among many mitochondrial genes, the mitochondrial cytochrome b gene has been widely used to study genetic variation (McVeigh and Davidson, 1991), phylogenetic relationships (Groves and Shields, 1996; Gilles et al., 1998; Xiao et al., 2001; Perdices et al., 2004; Bajpai and Tewari, 2010; Kumar et al., 2011), biogeographical patterns (Gilles et al., 2001; Xiao et al., 2001; Durand et al., 2002) and taxonomy (Burridge, 1999; Xiao et al., 2001) in many fishes and higher nvertebrates. The rate of evolution of the cytochrome b gene is appropriate for investigating events that have occurred within the last 20 million years, such as the evolution of the Cyprinidae (Irwin et al., 1991). In the present study, we analysed the cytochrome b sequences of five species of