Genomic Divergence Between <scp> <i>Octopus vulgaris</i> </scp> and Its Undescribed Sister Species From the South Atlantic and Indian Ocean

ABSTRACT Molecular data are widely used to resolve complex phylogenetic relationships between cryptic species, particularly in cases where morphological features are insufficient to confirm taxonomic distinctness. For benthic shallow‐water octopuses, several successes and failures have been reported when attempting to delineate species using individual nuclear or mitochondrial markers. In this study, we investigated the potential of shallow random shotgun sequencing to assess the phylogenetic placement of an undescribed southern hemisphere lineage within the Octopus vulgaris species complex, which could not be conclusively delimited using single‐marker approaches. A total of 338 nuclear loci, along with complete mitochondrial genomes, were generated for two specimens presently classified as Octopus vulgaris (Type III) that originated from the southeastern Atlantic coast of South Africa and Amsterdam Island in the southern Indian Ocean. Our combined phylogenomic approach reveals that this lineage is genetically distinct from O. vulgaris sensu stricto (ss) from the Mediterranean and the northeast Atlantic, as well as from the closely related O. sinensis from East Asia. A further separation of O. vulgaris (Type III) into distinct South African and Amsterdam Island lineages cannot be proven. These findings add to the growing body of evidence that supports O. vulgaris Type III as a genetically distinct lineage within the O. vulgaris species complex, and emphasise that the taxonomic classification of this southern hemisphere lineage warrants re‐evaluation.