Molecular phylogeny of the subfamily Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) inferred from complete mitochondrial genomes

• Molecular phylogeny of the subfamily Schizothoracinae with 4/5 genera.
• Phylogenetic evidence for the monophyly of Schizothoracinae
• Monophyly of the morphologically specialized schizothoracine group was confirmed.
• Interrelationships within Schizothoracinae and paraphyly of some included genera.

The schizothoracine fishes, members of the Teleost order Cypriniformes, are one of the most diverse group of cyprinids in the Qinghai–Tibetan Plateau and surrounding regions. However, taxonomy and phylogeny of these species remain unclear. In this study, we determined the complete mitochondrial genome of Schizopygopsis malacanthus. We also used the newly obtained sequence, together with 31 published schizothoracine mitochondrial genomes that represent eight schizothoracine genera and six outgroup taxa to reconstruct the phylogenetic relationships of the subfamily Schizothoracinae by different partitioned maximum likelihood and partitioned Bayesian inference at nucleotide and amino acid levels. The schizothoracine fishes sampled form a strongly supported monophyletic group that is the sister taxon to Barbus barbus. A sister group relationship between the primitive schizothoracine group and the specialized schizothoracine group + the highly specialized schizothoracine group was supported. Moreover, members of the specialized schizothoracine group and the genera Schizothorax, Schizopygopsis, and Gymnocypris were found to be paraphyletic.