Molecular phylogeny of the family Rajidae in the Korean waters

Abstract

Rajidae are unique among chondrichthyes with regards to their relatively high species diversity, yet differentiated with morphological conservatism. It is known that 5 genera and 11 species inhabit Korean waters. Their classification has been confused including undescribed and dubious species still to wait for revision or reassignment. The morphology based phylogenetic relationship of the skates shows polytomies indicating ambiguity among the species. The aim of the present study is to investigate the molecular phylogenetic relationship of the Rajidae species inhabiting Korean waters with calibration of divergence time using mitochondrial genomes and nuclear genes.All genus-level sampling ( >60% species-level) was made from the genera Okamejei, Dipturus, Hongeo, Raja, Bathyraja for analysis of intergeneric relationships. All the mitogenome seuence (16,742 ~ 16,976 bp) and two nuclear genes (RAG1: 904bp SCFD2: 582 bp) from 12 species were used for constructing the molecular phylogeny and Maximum Likelihood and Bayesian methods were applied. The molecular phylogeny showed clear resolution of the relationships among Rajidae species. The resulted was selected as a best tree (((Hongeo, (Dipturus, Raja)), Okamjei), Bathyraja) showing monophyletic interrelationships in the family comparing with the previous morphological and genetic studies. Furthermore, we got the full time-calibrated tree of Rajidae evolution. The fen confused including undescribed and dubious species still to wait for revision or reassignment. The morphology based phylogenetic relationship of the skates shows polytomies indicating ambiguity among the species. The aim of the present study is to investigate the molecular phylogenetic relationship of the Rajidae species inhabiting Korean waters with calibration of divergence time using mitochondrial genomes and nuclear genes.All genus-level sampling ( >60% species-level) was made from the genera Okamejei, Dipturus, Hongeo, Raja, Bathyraja for analysis of intergeneric relationships. All the mitogenome seuence (16,742 ~ 16,976 bp) and two nuclear genes (RAG1: 904bp SCFD2: 582 bp) from 12 species were used for constructing the molecular phylogeny and Maximum Likelihood and Bayesian methods were applied. The molecular phylogeny showed clear resolution of the relationships among Rajidae species. The resulted was selected as a best tree (((Hongeo, (Dipturus, Raja)), Okamjei), Bathyraja) showing monophyletic interrelationships in the family comparing with the previous morphological and genetic studies. Furthermore, we got the full time-calibrated tree of Rajidae evolution. The f