Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in theOctopus vulgarisspecies complex

Abstract

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 siteassociated 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.

First molecular approach to the octopus fauna from the southern Caribbean

“…However, even a well-resolved gene tree can hardly resemble a species tree due to incomplete lineage sorting and DNA barcodes are known to decrease their performance on poorly sampled groups (Meyer & Paulay, 2005). Moreover, recent genome-wide findings on the O. vulgaris species complex (Amor et al, 2019) highlight that phylogenetic analyses using only mitochondrial DNA underestimate octopus species diversity. Thus, despite the better performance of our COI analysis, more informative nuclear markers are needed to complement our results.…”

Chromosome‐level genome assembly of the East Asian common octopus (Octopus sinensis) using PacBio sequencing and Hi‐C technology

“…Recently, it was clearly distinguished from O. vulgaris on the basis of molecular and morphological features and renamed O. sinensis (Amor et al, 2019;Amor et al, 2017;Gleadall, 2016). Mature O. sinensis individuals have a relatively broader head and shorter arms with fewer suckers than the European O. vulgaris (Gleadall, 2016).…”

Allopatric divergence drives the genetic structuring of an endangered alpine endemic lizard with a sky‐island distribution

“…Alternatively, analyses of our SNP dataset show that individuals from swKNP are most similar to other NSW individuals, however, a small amount of admixture is present with VIC. Differing signals between mtNDA and nuDNA are relatively common and in cases where nuclear data show greater levels of biogeographic structure, as we see here, hybridisation after isolation and secondary contact is often responsible (Toews & Brelsford, ; Amor et al ., ). Furthermore, mtDNA is likely to reflect more recent patterns that nuDNA, especially considering our SNP data were found to be neutrally evolving.…”