Phylogeography of the widely distributed John Dory (Zeus faber, Actinopterygii: Zeiformes) reaffirms the prevalence of at least two deeply divergent clades.

The John Dory Zeus faber is a commercially exploited demersal fish species with a known distribution ranging from the Northeast Atlantic to parts of the Indian and Pacific oceans. A previous genetic survey using cytochrome c oxidase subunit I (COI) DNA barcodes suggested the presence of two geographically segregated taxonomic units within Z. faber. We revisit this hypothesis by expanding the number and geographic coverage of DNA barcodes, addressing a major data gap along parts of the Atlantic coast of Africa and conducting a comprehensive phylogeographic analysis. Our findings consolidated the existence of two highly divergent mitochondrial clades, Clade A and Clade B (mean K2P distance: 7.4%), with the transition zone between them located along the Atlantic coast of Morocco. Clade A exhibited no phylogeographic structure, with haplotypes shared between Northeast Atlantic and Mediterranean populations. Conversely, four geographically structured subclades (mean K2P distance: 0.9%) were detected within Clade B, extending south and eastward from Morocco to Japan and New Zealand. Historical demographic events driving allopatric divergence, along with oceanographic and environmental factors, likely shaped the current geographic distribution of the two clades. These findings not only prompt the need to re-evaluate the taxonomic status of Z. faber but also highlight the probable existence of multiple evolutionarily significant units (ESUs) that must be considered in the scope of stock assessment, fisheries management and conservation purposes.