Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex

Many marine species once considered to be cosmopolitan are now recognised as cryptic species complexes. Mitochondrial markers are ubiquitously used to address phylogeographic questions, and have been used to identify some cryptic species complexes; however, their efficacy in inference of evolutionary processes in the nuclear genome has not been thoroughly investigated. We used double digest restriction site-associated DNA sequencing (ddRADseq) markers to quantify species boundaries in the widely distributed and high value common octopus, Octopus vulgaris, comparing genome-wide phylogenetic signal to that obtained from mitochondrial markers. Phylogenetic analyses, genome-wide concordance and species tree estimation based on 604 genome-wide ddRADseq loci revealed six species within the O. vulgaris group. Divergence time estimates suggested modern-day species evolved over the last 2.5 ma, during a period of global cooling. Importantly, our study identified significant phylogenetic discordance between mitochondrial and nuclear markers; genome-wide nuclear loci supported O. vulgaris sensu stricto and Type III (South Africa) as distinct species, which mtDNA failed to recognise. Our finding of conflicting phylogenetic signal between mitochondrial and nuclear markers has broad implications for many taxa. Improved phylogenetic resolution of O. vulgaris has significant implications for appropriate management of the group and will allow greater accuracy in global fisheries catch statistics.