Resolving Taxonomic Conflicts in Trichiurus: Chromosome Genomics Clarifies Species and Informs Conservation of Populations in the Northwest Pacific

The Trichiuridae family, comprising ecologically and commercially important hairtails, has faced persistent taxonomic uncertainties due to historical misclassifications and conflicting morphological criteria. While molecular approaches have advanced understanding, mitochondrial-based phylogenies and misapplied nomenclature have obscured species boundaries and population dynamics. Here, we integrate a chromosome-level genome assembly of Trichiurus japonicus with whole-genome resequencing of congeneric species to resolve three centuries of taxonomic ambiguity. Combining phylogenomic, demographic, and selective sweep analyses, we resolve taxonomic uncertainties by redefining species boundaries, reconstructing population dynamics, and identifying genomic adaptations underpinning environmental resilience. We confirm T. japonicus and T. nanhaiensis as distinct species. Crucially, we identify a cryptic Indian Ocean-derived lineage, misclassified as T. lepturus in previous studies, as the novel species Trichiurus sp., underscoring the impact of commercial trade on taxonomic confusion. Population genomics reveals panmixia in T. japonicus across the Northwest Pacific, supporting unified stock management. Selective sweeps in T. japonicus pinpoint cold-resilient genes (metabolic, anti-apoptotic, visual), consistent with its demographic stability during Pleistocene glaciations. This study provides a genomic roadmap for disentangling taxonomic conflicts in morphologically cryptic taxa and advances strategies for sustainable fisheries management under climate change.