DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Composition and age of volcanic rocks from the Sinii Utes Depression, Southern Primoye

New data are reported on structure of sections, chemical composition, and age of volcano-sedimentary and volcanic rocks from the Sinii Utes Depression in the Southern Primorye region. The Sinii Utes Depression is filled with two sequences: the lower sequence composed of sedimentary-volcanogenic coaliferous rocks (the stratotype of the Sinii Utes Formation) and the upper sequence consisting of tephroid with overlying basalts. This work considers chemical composition and problems of K-Ar dating of basalts. The uppermost basaltic flow has K-Ar age 22.0±1.0 Ma. The dates obtained for the middle and upper parts of lava flows are underestimated. It is explained by their heating due to combustion of brown coals of the Sinii Utes Formation underlying the lava flow. Calculations show that argon could only partly have been removed from the basalts owing to conductive heat transfer and was lost largely due to infiltration of hot gases in heterogeneous fissured medium. Basaltic volcanism on continental margins of the southern Primorye region and the adjacent Korean and Chinese areas at the Oligocene-Miocene boundary preceded Early-Middle Miocene spreading and formation of the Sea of Japan basin. Undifferentiated moderately alkaline basalts of intraplate affinity developed in the Amba Depression and some other structures of the southern Primorye region and intraplate alkali basalts of the Phohang Graben in the Korean Peninsula serve as indicators of incipient spreading regime in the Sea of Japan. Potassic basalt-trachybasalt eruptions occurred locally in riftogenic depressions and shield volcanoes. In some structures this volcanism was terminated by eruptions of intermediate and acid lavas. Such evolution of volcanism is explained by selective contamination of basaltic melts during their interaction with crustal acid material and generation of acid anatectic melts.

Availability of sequences of aquatic and terrestrial taxa in genetic databases (GenBank and BOLD - the Barcode of Life Database) in 2010, 2012 and 2016

Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61% of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78% for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63% respectively, while those for terrestrial NIS increased to 74 and 88% respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data - mostly aquatic ones - encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.

Biostratigraphy and magnetostratigraphy of ODP Leg 124 sites

During ODP Leg 124, late middle Eocene to Quaternary sediment sequences were recovered from 13 holes drilled at five sites in the Celebes and Sulu basins. Paleomagnetic measurements and biostratigraphic studies using calcareous nannofossils, planktonic and benthic foraminifers, radiolarians, and diatoms were completed and summarized here. Two Neogene sediment sections recovered in the Sulu Basin yielded excellent core recoveries and magnetic reversal records, allowing direct magnetobiostratigraphic correlations for the Pliocene and Quaternary at Site 768 and for the middle Miocene to Quaternary at Site 769. The interpolated ages of biohorizons are not consistent between sites and only a few of them are in good agreement with previous calibrations. The differences may be the results of redeposition by turbidity currents and selective dissolution of key fossils.