Mitochondrial DNA variability to explore the relationship complexity of Schizothoracine (Teleostei: Cyprinidae) Syed Mudasir Ahmad • Farooz Ahmad Bhat • Masood-ul Hassan Balkhi • Bilal Ahmad Bhat Received: 18 March 2014 / Accepted: 27 October 2014 / Published online: 4 November 2014 Ó Springer International Publishing Switzerland 2014 Abstract Despite numerous studies on the taxonomy of a highly complex group of schizothoracine (snow trouts), with over five recognized species from Kashmir, India (Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus) based on traditional morphological data, the relationships between these species is poorly understood and the taxonomic validity is still under debate. To resolve the evolutionary relationships among these species, we sequenced mitochondrial fragments, including 16Sr RNA, Cytb and the D-loop. Separate analyses of 16S and Cytb showed intermixing of the species and 16S was found more conserved than Cytb. The D-loop was found highly vari- able and showed length variation between and within species. Length variation was observed in di-nucleotide (TA) n microsatellite repeats with a variable number of repeat units (n = 7–14) that did not show heteroplasmy. Central conserved sequence blocks (CSBs) in D-loop sequences were found comparable to other vertebrate species. All phylogenetic reconstructions recovered the focal taxa as a monophyletic clade within the schizothoracines. Analyses with combined mitochondrial data sets showed close genetic relationships of all the five species. In addition to a close relationship between S. niger and S. curvifrons, two distinct groupings of S. ecoscinus and S. plagiostomus were supported by all the analyses. This study gives an insight into molecular phylogeny of the species and improves our understanding of historical and taxonomic relationships derived from morphological and ecological studies. Keywords Schizothoracines Á Complex group Á Mitochondrial DNA Á Microsatellite variation Introduction Schizothoracine fish, commonly called snow trouts, inhabit the entire network of snow and spring fed cool waters of rivers and streams of Jammu and Kashmir (India). The fish are believed to have migrated into waters of the region from Central Asiatic south slopes of the Himalayas and Sulaiman range (Das and Subla 1964). Subfamily Schizo- thoracinae (family Cyprinidae and order Cypriniformes) comprise 90 species in 12 genera. According to Cao et al. (1981) the subfamily Schizothoracinae originated from primitive barbine fishes distributed in Tibet during the late Tertiary, and subsequently evolved into more specialized groups following the uplift of Tibet. These fishes dominate the torrential mountain streams and plateau lakes of Central Asia, the Himalayas and Tibetan plateau. Based on present biogeography, Das and Subla (1963) suggested that the subfamily Schizothoracinae migrated during the early Tertiary from Southeast or South Asia to the great plain, which is now occupied by mountains of Central Asia, and was subsequently isolated by the uplift of the Himalayas Electronic supplementary material The online version of this article (doi:10.1007/s10709-014-9797-y) contains supplementary material, which is available to authorized users. S. M. Ahmad (&) Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology – Kashmir, Shuhama, Srinagar 190006, India e-mail: mudasirbio@gmail.com F. A. Bhat Á M. H. Balkhi Á B. A. Bhat Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences and Technology – Kashmir, Shuhama, Srinagar 190006, India 123 Genetica (2014) 142:507–516 DOI 10.1007/s10709-014-9797-y