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.

Morphometric redefinition of the component chronospecies of the Globorotalia conoidea - G. inflata lineage in DSDP Hole 29-284

Phylo-zonations (or lineage-zonations) are based upon morphological changes within individual evolutionary lineages. These zonations, although potentially of use for stratigraphic subdivision and correlation, often suffer from a lack of quantitative exactness in the definitions of chronospecies. Thus exact reproducibility is hindered for stratigraphic determinations. The potential of morphometrically defined phylo-zonations is demonstrated on a temperate South Pacific Late Cenozoic lineage of planktonic foraminifera (Globorotalia conoidea through intermediate forms to Globorotalia inflata in DSDP Site 284) exhibiting phyletic gradualism. Our sampling interval is about 0.1 m.y. during the last 8 m.y. Changes in the number of chambers in the final whorl, test conicalness, percentage of keeled forms, and test roundness or inflatedness, are used to quantitatively define the following five chronospecies: G. conoidea (Late Miocene; 6.1->8.3 m.y.), G. conomiozea (latest Miocene ; 5.3-6.1 m.y.), G. puncticulata sphericomiozea (earliest Pliocene; 4.5-5.3 m.y.), G. puncticulata puncticulata (Early-Middle Pliocene; 2.9-4.5 m.y.), and G. inflata (Late Pliocene-Quaternary; 0-2.9 m.y.). This phylo-zonation is directly applicable to temperate cool subtropical Southern Hemisphere areas where the evolution took place (Kennett, 1967, 1973; Scott, 1979). It is still not known if the lineage occurs elsewhere; thus the applicability of the phylo-zonation over broader areas is still uncertain. Trends in general size and aperture shape seem to be climatically controlled, and thus may be only of local stratigraphic utility. The practical applications of morphometric phylo-zonation for stratigraphy is to a large extent dependent upon the amount of time and effort required to statistically define the trends. Experiments with large numbers of subsamples from this lineage demonstrate that accurate stratigraphic determinations are possible from measurements on only 15 specimens per sample, except for those very close to chronospecies boundaries.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Compilation of 220 sediment core d13C data from the glacial Atlantic Ocean

We compare a compilation of 220 sediment core d13C data from the glacial Atlantic Ocean with three-dimensional ocean circulation simulations including a marine carbon cycle model. The carbon cycle model employs circulation fields which were derived from previous climate simulations. All sediment data have been thoroughly quality controlled, focusing on epibenthic foraminiferal species (such as Cibicidoides wuellerstorfi or Planulina ariminensis) to improve the comparability of model and sediment core carbon isotopes. The model captures the general d13C pattern indicated by present-day water column data and Late Holocene sediment cores but underestimates intermediate and deep water values in the South Atlantic. The best agreement with glacial reconstructions is obtained for a model scenario with an altered freshwater balance in the Southern Ocean that mimics enhanced northward sea ice export and melting away from the zone of sea ice production. This results in a shoaled and weakened North Atlantic Deep Water flow and intensified Antarctic Bottom Water export, hence confirming previous reconstructions from paleoproxy records. Moreover, the modeled abyssal ocean is very cold and very saline, which is in line with other proxy data evidence.