The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specimens and 31 egg cases from 26 skate species were barcoded. NJ and ML analyses showed that nearly all species exhibited unique barcodes or clusters of closely related haplotypes, except for Psammobatis normani/P. rudis and Dipturus trachyderma/D. argentinensis. The first pair was discriminated by NCD. BIN analysis recovered 17 groups, whereas ABGD recovered 23, better reflecting taxonomic diversity. In summary, 24 species were resolved by COI. Phylogeographic signals were observed for Amblyraja doellojuradoi and Zearaja brevicaudata. Compiling our results with data from BOLD, almost all the species occurring in the area possess barcodes, contributing to completing and curating the BOLD reference library, which constitutes an important tool for resolving taxonomic issues, tracing fishery products, and performing eDNA biomonitoring.

The Beagle Channel, located south of Tierra del Fuego (~54° S), is South America’s southernmost intracoastal ecosystem. Here, we applied environmental DNA metabarcoding using a partial sequence of the 12sRNA mitochondrial gene to evaluate the seasonal and spatial dynamics of marine vertebrate communities along the longitudinal gradient of the Beagle Channel. Water samples were collected across seasons and sites spanning the central and eastern sectors of the channel. Vertebrate DNA was amplified and analyzed against a custom reference database enriched with locally generated sequences. A total of 43 vertebrate taxa were detected, including 25 fish, 13 mammals, and 5 seabirds. Vertebrate assemblages were spatially structured along the longitudinal gradient of the Beagle Channel, with the central sector characterized by higher relative abundances of Fuegian sprat (Sprattus fuegensis), Southern elephant seal (Mirounga leonina), South American fur seal (Arctocephalus australis), and domestic species, whereas the eastern sector showed higher relative abundances of fish species including silversides (Odontesthes spp.), Magellanic rockcod (Paranotothenia magellanica), and striped rockcod (Trematomus hansoni), as well as mammals including southern sea lion (Otaria flavescens), North American beaver (Castor canadensis), and native grass mice (Abrothrix spp.). This spatial differentiation was associated with contrasting environmental conditions. No significant seasonal effect was detected. This study provides the first environmental DNA-based baseline of marine vertebrates on the Beagle Channel and validates this approach for ecosystem-scale biodiversity monitoring in subantarctic coastal environments.