Phylogeny of the Sepia pharaonis species complex (Cephalopoda: Sepiida) based on analyses of mitochondrial and nuclear DNA sequence data

Abstract

The pharaoh cuttlefish, Sepia pharaonis Ehrenberg, 1831, is a commercially fished species found from Japan to East Africa. Previous morphological and genetic work (the latter based on the 16S rRNA mitochondrial gene) suggested that S. pharaonis is a species complex, but relationships within the complex remained unresolved. To clarify these relationships, we have sequenced an additional mitochondrial gene region (cytochrome oxidase subunit I) and a nuclear gene region (rhodopsin) from over 50 specimens from throughout the range of S. pharaonis. We have also added sequence data from two specimens of Sepia ramani Neethiselvan, 2001, collected in southeastern India. Sepia ramani is a species that is morphologically very similar to S. pharaonis, and there is some question regarding its status as a distinct species. Phylogenetic analyses of a dataset comprising all three-gene regions revealed a monophyletic S. pharaonis complex consisting of a western Indian Ocean clade, a northeastern Australia clade, a Persian Gulf/Arabian Sea (‘Iranian’) clade, a western Pacific clade and a central Indian Ocean clade. Relationships among these clades remain somewhat poorly supported except for a clade comprising the Iranian clade, the western Pacific clade and the central Indian Ocean clade. One S. pharaonis specimen was collected in the Arabian Sea, but was found to be a member of the western Indian Ocean clade, suggesting that gene flow between these regions has either occurred recently or is ongoing. Both specimens of S. ramani are members of the S. pharaonis complex, but their mtDNA haplotypes are not closely related – one is a member of the central Indian Ocean clade, while the other is rather distantly related to the northeastern Australia clade. We suggest that ‘S. pharaonis’ may consist of several species, but morphological work is needed to clarify species-level taxonomy within this complex.