Leveraging Transcriptomic Data to Expand Mitogenome Knowledge and Phylogenetic Inference in Cartilaginous Fishes

Despite their ecological and evolutionary importance, genetic data for chondrichthyans remains scarce. To address this, we assembled mitogenomes from RNA-seq data of eight elasmobranchs, including Urobatis jamaicensis, representing the first preliminary mitogenome assembly for Urotrygonidae derived from transcriptomic data. We integrated these sequences with 230 publicly available mitogenomes to form a final dataset of 238 taxa (11 chimaeras, 109 batoids, and 118 selachians), generating the most comprehensive chondrichthyan mitogenomic phylogeny as of May 2024. Our analyses reinforced the fundamental elasmobranch–chimaera split and resolved key taxonomic conflicts: they supported the newly proposed family Dichichthyidae while revealing the polyphyly of Odontaspididae. Furthermore, gene concordance factor (gCF) analysis identified ND5 as exhibiting the highest relative topological concordance among mitochondrial genes. Finally, our time-calibrated phylogeny demonstrated a temporal correspondence between major divergence events and historical mass extinctions. Overall, our findings refine the evolutionary framework of chondrichthyans and clarify the utility of individual mitochondrial genes in phylogenetic inference.