Complete Mitochondrial Genome Analysis Reveals Genetic Diversity in the Narrow–Ridged Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) Across East Asian Waters

The narrow-ridged finless porpoise (<i>Neophocaena asiaeorientalis</i> Pilleri & Gihr 1972) is one of the most endangered cetacean species inhabiting East Asian waters. Complete mitogenome analysis offers accurate phylogenetic insights; however, complete mitogenome sequences for the narrow-ridged finless porpoise have so far been restricted to specific regions, mainly in China, and no sequences are available from Korean or Japanese populations. To address this gap, in this study, we developed a multiplex PCR primer panel to sequence the complete mitochondrial genome of the porpoise and sequenced 23 individuals of <i>N. a. sunameri</i>, a subspecies of <i>N. asiaeorientalis</i>, from Korean waters using next-generation sequencing. Phylogenetic analyses based on maximum likelihood and Bayesian inference revealed three major, well-supported monophyletic clades within the species. Two sequences of the Yangtze finless porpoise (<i>N. a. asiaeorientalis</i>), another subspecies, displayed significantly higher genetic divergence compared to <i>N. a. sunameri</i> sequences. The 23 mitochondrial genome sequences exhibited a nucleotide diversity of 0.142% and a haplotype diversity of 99.6%, with 22 unique haplotypes identified. These findings contribute to our understanding of the evolutionary history and genetic diversity of the species, providing valuable insights for future conservation efforts and further genetic research.