Genome skimming elucidates the evolutionary history of Octopoda.

Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.

Trace element concentrations, including Cd and Hg, in long-finned pilot whales (Globicephala melas edwardii) mass stranded on the New Zealand coast.

The Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii) is a top predator in the New Zealand pelagic food web, feeding predominantly on arrow squids. This study quantified trace element concentrations (Al, As, Cd, Co, Cr, Cu, Fe, Hg, Ni, Mn, Pb, Se, V, Zn) in four tissues (blubber, kidney, liver, muscle) from 21 individuals from stranding sites in New Zealand. Maximum Cd and Hg concentrations were measured in liver and kidney, respectively. Selenium had a positive correlation with Cd and Hg, suggesting the involvement of Se in Cd and Hg detoxification. Arrow squids from the whales' stomach contents were DNA barcoded and identified as Nototodarus sloanii. Trace element concentrations were measured in squid samples from the whale stomach contents. The significant correlation for Hg between the squid tissue and the whale tissue suggests that arrow squids play a major role in trace element uptake by G. m. edwardii.

Regional assessment of trace element concentrations in arrow squids (Nototodarus gouldi, N. sloanii) from New Zealand waters: Bioaccessibility and impact on food web and human consumers.

The New Zealand arrow squids, Nototodarus gouldi and N. sloanii, play an important role in the marine food web, and are both economically important fishery species. This study compares trace element concentrations (As, Cd, Co, Cr, Cu, Fe, Hg, Ni, Mn, Pb, U, and Zn) in these animals from different fishing locations within New Zealand's Exclusive Economic Zone (Auckland Islands, Chatham Rise, Dunedin, Golden Bay, Taranaki, and West Coast of the South Island). Muscular mantle (the tissue usually consumed by humans) and digestive gland tissue (the primary organ for trace element accumulation) concentrations were compared among regions, revealing size, species, and sampling location effects. Overall, N. gouldi had higher concentrations of As and Zn. The Taranaki region had the highest concentrations for Cd, Co, Cu, and Zn in both tissues analysed. To assess the bioaccessibility of these trace elements to humans, an in-vitro digestion simulation experiment was conducted, revealing bioavailable concentrations overall below the maximum levels presently considered tolerable for human consumption. However, the in-vitro digestion had no observable effect upon Cd concentrations in arrow squid mantle tissue (implying that the measured concentrations are bioaccessible to humans), and revealed that Cd had the highest potential impact on marine food webs and human health. Digestive gland concentrations in particular indicate that arrow squids can be considered important vectors for trace element transfer to top predators (mean concentration for Cd: 123 ± 148 µg g-1 dw), with region-specific differences.

Real-time PCR identification of lake whitefish Coregonus clupeaformis in the Laurentian Great Lakes.

The purpose of this study was to develop a real-time PCR assay to specifically identify lake whitefish Coregonus clupeaformis in larval fish assemblages based on a 122 bp amplicon from the mitochondrial genome. The efficiency of the reaction, as calculated from the standard curve, was 90.77% with the standard curve having an r(2) value of 0.998. Specificity of the assay provided single melt peak in a melt-curve analysis and amplification of only the target species. The assay successfully identified target DNA in as low as 0.1% proportion of a DNA mixture. This assay was designed on the portable Smart Cycler II platform and can be used in both field and laboratory settings to successfully identify C. clupeaformis.