Gene sequences of the lichen Cetraria aculeata

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large-scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

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.

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.

Description of lithofacies associations and their interpreted settings from sequences of sediment core CRP-1 (Table 2)

Cape Roberts Project drillcore 1 was obtained from Roberts Ridge, a sea-floor high located at 77°S, 16 km offshore from Cape Roberts in western McMurdo Sound, Antarctica. The recovered core is about 147 m long with the upper 43.15 metres below the sea floor (revised figure) being dated as Quarternary and the older part of the sequence being Miocene. The core includes nine facies: sandy diamict, muddy diamict, gravel/conglomerate, mud(stone), clay(stone) and carbonate. These facies occure in associations that are repeated in particulare sequences throughout the core, and are interpreted as representing different depositional environments through time. Seven lithofacies associations are interpreted as representing offshore shelf, ice protected/below wave-base; prodeltaic/offshore shelf; delta front/sandy shelf; ice system; subglacial till/rainout diamict/debris flow diamicts singly or in combination; and a carbonate-rich shelf bank. The facies associations are used to infer that the Quaternary section represents deposition on a polar shelf with perhaps two or three glacial fluctuations. The Quaternary carbonate unit indicates a period of ice sheet retreat, but local glacial activity may have increased with an increase in costal precipitation. The Miocene section represents polythermal glacial systems. The older Miocene section is glacially dominated whereas the younger section is much less so. The glacially dominated section may provide evidence for a major glacial advance thar resulted un a low stand of global eustatic sea level at that time. After the low stand, eustatic sea level was gradually rising during deposition of the younger section dominated more by non-glacial processes.

Geochemistry of Albian to Santonian black shale sequences on the Demerara Rise, South American margin

Ocean Drilling Program Leg 207 recovered thick sequences of Albian to Santonian organic-carbon-rich claystones at five drill-sites on the Demerara Rise in the western equatorial Atlantic Ocean. Dark-colored, finely laminated, Cenomanian-Santonian black shale sequences contain between 2% and 15% organic carbon and encompass Oceanic Anoxic Events 2 and 3. High Rock-Eval hydrogen indices signify that the bulk of the organic matter in these sequences is marine in origin. However, d13Corg values lie mostly between -30 per mil and -27 per mil, and TOC/TN ratios range from 15 to 42, which both mimic the source signatures of modern C3 land plants. The contradictions in organic matter source indicators provide important implications about the depositional conditions leading to the black shale accumulations. The low d13Corg values, which are actually common in mid-Cretaceous marine organic matter, are consequences of the greenhouse climate prevailing at that time and an associated accelerated hydrologic cycle. The elevated C/N ratios, which are also typical of black shales, indicate depressed organic matter degradation associated with low-oxygen conditions in the water column that favored preservation of carbon-rich forms of marine organic matter over nitrogen-rich components. Underlying the laminated Cenomanian-Santonian sequences are homogeneous, dark-colored, lower to middle Albian siltstones that contain between 0.2% and 9% organic carbon. The organic matter in these rocks is mostly marine in origin, but it occasionally includes large proportions of land-derived material.

Major and trace element concentrations of sediments from the IODP Exp302 sites

We analyzed a suite of sediment samples recovered in the central Arctic Ocean for major, trace, and rare earth elements in order to assess changes in terrigenous source material throughout the Cenozoic. The terrigenous component consists of two end-members. Input from a shale-like composition dominates bulk sediments, especially those deposited during the Paleocene and since the Miocene, and may represent sediment supply from the eastern Laptev Sea. Therefore, even though the environment and transport mechanisms may have varied from ice free to ice dominated, sequences of the early Paleogene and later Neogene appear to have been influenced by a single major terrigenous source. This suggests similar transport capabilities and trajectories for both ocean and drift currents through significant parts of the Cenozoic. Influence from a more mafic source appears to be more important through the early Eocene to the middle Miocene and most likely represents material from the western Laptev Sea or Kara Sea. Thus, Eocene major changes in surface water productivity appear broadly synchronous with those in terrigenous provenance. A combination of regional sea level variations, local shelf processes, and transport mechanisms are among the more probable causes for the observed source changes. Although the assignment of sources using chemistry presently is constrained by a lack of data from certain regions (e.g., eastern Siberian Sea) our results generally agree with inferences based on mineralogy or radiogenic isotopes and shed further light on long-term reconstructions of the central Arctic Ocean.

Chemistry of igneous rocks from, the Celebes Sea basement

Major and trace elements, mineral chemistry, and Sr-Nd isotope ratios are reported for representative igneous rocks of Ocean Drilling Program Sites 767 and 770. The basaltic basement underlying middle Eocene radiolarianbearing red clays was reached at 786.7 mbsf and about 421 mbsf at Sites 767 and 770, respectively. At Site 770 the basement was drilled for about 106 m. Eight basaltic units were identified on the basis of mineralogical, petrographical, and geochemical data. They mainly consist of pillow lavas and pillow breccias (Units A, B, D, and H), intercalated with massive amygdaloidal lavas (Units Cl and C2) or relatively thin massive flows (Unit E). Two dolerite sills were also recognized (Units F and G). All the rocks studied show the effect of low-temperature seafloor alteration, causing almost total replacement of olivine and glass. Calcite, clays, and Fe-hydroxides are the most abundant secondary phases. Chemical mobilization due to the alteration processes has been evaluated by comparing elements that are widely considered mobile during halmyrolysis (such as low-field strength elements) with those insensitive to seafloor alteration (such as Nb). In general, MgO is removed and P2O5 occasionally enriched during the alteration of pillow lavas. Ti, Cs, Li, Rb, and K, which are the most sensitive indicators of rock/seawater interaction, are generally enriched. The most crystalline samples appear the least affected by chemical changes. Plagioclase and olivine are continuously present as phenocrysts, and clinopyroxene is confined in the groundmass. Textural and mineralogical features as well as crystallization sequences of Site 770 rocks are, in all, analogous to typical mid-ocean-ridge basalts (MORBs). Relatively high content of compatible trace elements, such as Ni and Cr, indicate that these rocks represent nearly primitive or weakly fractionated MORBs. All the studied rocks are geochemically within the spectrum of normal MORB compositional variation. Their Sr/Nd isotopic ratios plot on the mantle array (87Sr/87Sr 0.70324-0.70348 with 143Nd/144Nd 0.51298-0.51291) outside the field of Atlantic and Pacific MORBs. However, Sr and Nd isotopes are typical of both Indian Ocean MORBs and of some back-arc basalts, such as those of Lau Basin. The mantle source of Celebes basement basalts does not show a detectable influence of a subduction-related component. The geochemical and isotopic data so far obtained on the Celebes basement rocks do not allow a clear discrimination between mid-ocean ridge and back-arc settings.

Age determination and paleotemperatures of sediment core MD95-2043 in the Alboran Sea

Past sea surface temperature (SST) evolution in the Alboran Sea (western Mediterranean) during the last 50,000 years has been inferred from the study of C37 alkenones in International Marine Global Change Studies MD952043 core. This record has a time resolution of ~200 years allowing the study of millennial-scale and even shorter climatic changes. The observed SST curve displays characteristic sequences of extremely rapid warming and cooling events along the glacial period. Comparison of this Alboran record with delta18O from Greenland ice (Greenland Ice Sheet Project 2 core) shows a strong parallelism between these SST oscillations and the Dansgaard-Oeschger events. Five prominent cooling episodes standing out in the SST profile are accompanied by an anomalous high abundance of Neogloboquadrina pachyderma sinistral which is confined to the duration of these cold intervals. These features and the isotopic record reflect drastic changes in the surface hydrography of the Alboran Sea in association with Heinrich events Hl-5.

Planktonic foraminifera abundance in sediments of ODP Leg 170 sites

From October to December in 1996, Sites 1039 through 1043 were drilled on the lower continental slope and the bottom of the Middle American Trench. Planktonic foraminifers were obtained from 377 samples of the total 487 examined. The Pliocene- to Pleistocene-age sediments of Sites 1039 and 1043 are continuous from Zones N19 through N23. At Sites 1039 and 1040, middle Miocene sediments are also continuous, encompassing Zones N8 through N12. The sequences of the upper part of Sites 1040, 1041, 1042, and 1043 are décollements, tentatively assignable to Zone N19 for Sites 1040, 1041, and 1042 and to Zone N22 for Site 1043. The oldest sediments of these sites are assigned to Zone N7 (latest early Miocene), ~17 Ma in age.