ALBERT

Description: The Mozambique Ridge, a prominent basement high in the southwestern Indian Ocean, consists of four major geomorphological segments associated with numerous phases of volcanic activity in the Lower Cretaceous. The nature and origin of the Mozambique Ridge have been intensely debated with one hypothesis suggesting a Large Igneous Province origin. High-resolution seismic reflection data reveal a large number of extrusion centres with a random distribution throughout the southern Mozambique Ridge and the nearby Transkei Rise. Intra-basement reflections emerge from the extrusion centres and are interpreted to represent massive lava flow sequences. Such lava flow sequences are characteristic of eruptions leading to the formation of continental and oceanic flood basalt provinces, hence supporting a Large Igneous Province origin of the Mozambique Ridge. We observe evidence for widespread post-sedimentary magmatic activity that we correlate with a southward propagation of the East African Rift System. Based on our volumetric analysis of the southern Mozambique Ridge we infer a rapid sequential emplacement between ~131 Ma and ~125 Ma, which is similar to the short formation periods of other Large Igneous Provinces like the Agulhas Plateau.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.

Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.

Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.

Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.

Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.

Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.

Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.

Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.

Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.

Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.

Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.

Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.

Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.

Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.

Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.

Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.

Description: Author Posting. © The Authors, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 208 (2017): 1026-1042, doi:10.1093/gji/ggw435.

Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the subseafloor conductivity that is assumed to be isotropic. The deep water (ocean layer electrically much thicker than the overburden) seafloor EM response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a half-space, or a stronger and faster response. For an ocean whose electrical thickness is comparable to or much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. These transitions can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire subseafloor resistivity structure with the sea surface. A stronger and faster response occurs when guided energy flow is dominant, while a weaker and slower response occurs when the air interaction is dominant. However, at intermediate offsets for some models, the air interaction can partially or fully reverse the direction of energy flux in the reservoir layer toward rather than away from the source, resulting in a stronger and slower response. The Fréchet derivatives are dominated by preferential sensitivity to the reservoir layer conductivity for all water depths except at high frequencies, but also display a shift with offset from the galvanic to the inductive mode in the underburden and overburden due to the interplay of guided energy flow and the air interaction. This means that the sensitivity to the horizontal conductivity is almost as strong as to the vertical component in the shallow parts of the subsurface, and in fact is stronger than the vertical sensitivity deeper down. However, the sensitivity to horizontal conductivity is still weak compared to the vertical component within thin resistive regions. The horizontal sensitivity is gradually decreased when the water becomes deep. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioscience 67 (2017): 760–768, doi:10.1093/biosci/bix059.

Description: As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances.

Description: We would like to thank generous support from International Fund for Animal Welfare, the Bureau of Ocean Energy, and the Oak Foundation for funding support for the telemetry devices.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.

Description: Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.

Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 702, doi:10.3389/fmicb.2017.00702.

Description: The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.

Description: SS was supported by NSF grant OCE-1124272. This work was financed through the DFG Emmy Noether Grant BU 2606/1-1 to SB.

Description: Author Posting. © The Authors, 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 211 (2017): 1046–1061, doi:10.1093/gji/ggx360.

Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically-polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the sub-seafloor conductivity that is assumed to be transversely anisotropic, with a vertical-to-horizontal resistivity ratio of 3:1. For an ocean whose electrical thickness is comparable to that of the overburden, the seafloor electromagnetic response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a halfspace, or a stronger and faster response, and displays little to no evidence for the air interaction. For an ocean whose electrical thickness is much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets, and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. By comparison to the isotropic case with the same horizontal conductivity, transverse anisotropy stretches the Poynting vector and the electric field response from a thin resistive layer to much longer offsets. These phenomena can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire sub-seafloor resistivity structure with the sea surface. The Fréchet derivatives are dominated by preferential sensitivity to the vertical conductivity in the reservoir layer and overburden at short offsets. The horizontal conductivity Fréchet derivatives are weaker than to comparable to the vertical derivatives at long offsets in the substrate. This means that the sensitivity to the horizontal conductivity is present in the shallow parts of the subsurface. In the presence of transverse anisotropy, it is necessary to go to higher frequencies to sense the horizontal conductivity in the overburden as compared to an isotropic model with the same horizontal conductivity. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.

Description: This work was supported at WHOI by an Independent Research and Development award, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.

Description: A major uncertainty in determining the mass balance of the Antarctic ice sheet from measurements of satellite gravimetry, and to a lesser extent satellite altimetry, is the poorly known correction for the ongoing deformation of the solid Earth caused by glacial isostatic adjustment (GIA). Although much progress has been made in consistently modeling the ice-sheet evolution throughout the last glacial cycle, as well as the induced bedrock deformation caused by these load changes, forward models of GIA remain ambiguous due to the lack of observational constraints on the ice sheet's past extent and thickness and mantle rheology beneath the continent. As an alternative to forward-modeling GIA, we estimate GIA from multiple space-geodetic observations: Gravity Recovery and Climate Experiment (GRACE), Envisat/ICESat and Global Positioning System (GPS). Making use of the different sensitivities of the respective satellite observations to current and past surface-mass (ice mass) change and solid Earth processes, we estimate GIA based on viscoelastic response functions to disc load forcing. We calculate and distribute the viscoelastic response functions according to estimates of the variability of lithosphere thickness and mantle viscosity in Antarctica. We compare our GIA estimate with published GIA corrections and evaluate its impact in determining the ice-mass balance in Antarctica from GRACE and satellite altimetry. Particular focus is applied to the Amundsen Sea Sector in West Antarctica, where uplift rates of several centimetres per year have been measured by GPS. We show that most of this uplift is caused by the rapid viscoelastic response to recent ice-load changes, enabled by the presence of a low-viscosity upper mantle in West Antarctica. This paper presents the second and final contributions summarizing the work carried out within a European Space Agency funded study, REGINA (www.regina-science.eu).

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 2 (2016): 118, doi:10.3389/fmars.2015.00118.

Description: Characterization of dissolved organic matter (DOM) in terms of its composition and optical properties, with an eye toward ultimately understanding its deep ocean dynamics, is the currently active frontier in DOM research. We used UV-visible absorption spectroscopy and fluorescence excitation-emission matrix (EEM) spectroscopy to characterize DOM in the open ocean along sections of the U.S. CO2/CLIVAR Repeat Hydrography Project located in all the major ocean basins outside the Arctic. Despite large differences in fluorescence intensity between ocean basins, some variability patterns were similar throughout the global ocean, suggesting similar processes controlling the composition of the DOM. We find that commercially available single channel CDOM sensors are sensitive to the fluorescence of humic materials in the deep ocean and thermocline but not to the UVA-fluorescing and absorbing materials that characterize freshly produced CDOM in surface waters, revealing fundamental diversity in the DOM profile. In surface waters, UVA fluorescence and absorption signatures indicate the presence of freshly produced material and the process of bleaching removal, but in the upper mesopelagic and in the main thermocline these optical signatures are replaced by those of humic materials, with distribution patterns correlated to apparent oxygen utilization (AOU) and other signatures of remineralization. Empirical orthogonal function analysis (EOF) of the EEM data suggests the presence of two (unidentified) processes which convert “fresh” DOM to humic materials: one located in the surface ocean (shallower than 500 m) and one located in the main thermocline. These inferred humification processes represent less than 5% of the overall variability in oceanic humic DOM fluorescence, which appears to be dominated by terrestrial input and solar bleaching of humic materials.

Description: This research was supported by grants from NASA (grants NAG5-13277 and NNX14AG24G) and NSF (OCE-0241614 and OCE-0648541) to NN and D. A. Siegel.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 27, doi:10.3389/fmars.2016.00027.

Description: The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS) along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) using multiple analytical windows (MAWs) revealed three classes of iron-binding ligands present throughout the water column (L1−L3), whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2), and relatively constant concentrations of weaker ligands (L3) down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.

Description: RB, KB, and MC were supported by NSF OCE #10-2667 for the CCE-LTER program. MJ was funded by NSF ANT grant 0948378 and Harbor Branch Oceanographic Institute Foundation.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 4 (2016): 77, doi:10.3389/feart.2016.00077.

Description: Arctic deltas are dynamic and vulnerable regions that play a key role in land-ocean interactions and the global carbon cycle. Delta lakes may provide valuable historical records of the quality and quantity of fluvial fluxes, parameters that are challenging to investigate in these remote regions. Here we study lakes from across the Mackenzie Delta, Arctic Canada, that receive fluvial sediments from the Mackenzie River when spring flood water levels rise above natural levees. We compare downcore lake sediments with suspended sediments collected during the spring flood, using bulk (% organic carbon, % total nitrogen, δ13C, Δ14C) and molecular organic geochemistry (lignin, leaf waxes). High-resolution age models (137Cs, 210Pb) of downcore lake sediment records (n = 11) along with lamina counting on high-resolution radiographs show sediment deposition frequencies ranging between annually to every 15 years. Down-core geochemical variability in a representative delta lake sediment core is consistent with historical variability in spring flood hydrology (variability in peak discharge, ice jamming, peak water levels). Comparison with earlier published Mackenzie River depth profiles shows that (i) lake sediments reflect the riverine surface suspended load, and (ii) hydrodynamic sorting patterns related to spring flood characteristics are reflected in the lake sediments. Bulk and molecular geochemistry of suspended particulate matter from the spring flood peak and lake sediments are relatively similar showing a mixture of modern higher-plant derived material, older terrestrial permafrost material, and old rock-derived material. This suggests that deltaic lake sedimentary records hold great promise as recorders of past (century-scale) riverine fluxes and may prove instrumental in shedding light on past behavior of arctic rivers, as well as how they respond to a changing climate.

Description: Funding was provided by the US National Science Foundation as part of the Arctic Great Rivers Observatory (NSF-0732522 and NSF-1107774), as well as the Netherlands Organization for Scientific Research (Rubicon #825.10.022, and Veni #863.12.004). Additional funding for the lake coring was provided from WHOI through its Ocean and Climate Change Institute.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 22, doi:10.3389/fmars.2016.00022.

Description: Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean's interior on time scales of months to millennia. Here we present a measurement/synthesis/modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical, and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing, and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step toward our understanding of the Earth as an integrated system.

Description: The development of the EXPORTS Science Plan was supported by NASA Ocean Biology and Biogeochemistry program (award NNX13AC35G).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.

Description: Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.

Description: This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.

Description: Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.

Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 332, doi:10.3389/fmars.2017.00332.

Description: While sound scattering layers (SSLs) have been described previously from ice-covered waters in the Arctic, the existence of a viable mesopelagic community that also includes mesopelagic fishes in the Arctic has been questioned. In addition, it has been hypothesized that vertical migration would hardly exist in these areas. We wanted to check if deep scattering layers (DSLs) was found to the west and north of Svalbard (79°30′N−82°10′N) during autumn 2015, and if present; whether organisms in such DSLs undertook vertical migrations. Our null hypothesis was that there would be no evidence of diel vertical migration. Multi-frequency acoustic observations by hull mounted echo sounder (18, 38, and 120 kHz) revealed a DSL at depths ~210–510 m in areas with bottom depths exceeding ~600 m. Investigating eight geographical locations that differed with respect to time periods, light cycle and sea ice conditions, we show that the deeper layer of DSL displayed a clear ascending movement during night time and a descending movement during daytime. The high-light weighted mean depth (WMD) (343–514 m) with respect to backscattered energy was statistically deeper than the low-light WMD (179–437 m) for the locations studied. This behavior of the DSL was found to be consistent both when the sun was continuously above the horizon and after it started to set on 1 September, and both in open water and sea ice covered waters. The WMD showed an increasing trend, while the nautical area backscattering strength from the DSL showed a decreasing trend from south to north among the studied locations. Hydrographic observations revealed that the diel migration was found in the lower part of the north-flowing Atlantic Water, and was disconnected from the surface water masses above the Atlantic Water during day and night. The organisms conducting vertical migrations were studied by vertical and oblique hauls with zooplankton nets and pelagic trawls. These data suggest that these organisms were mainly various mesopelagic fishes, some few larger fishes, large zooplankton like krill and amphipods, and various gelatinous forms.

Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem” — (SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 5 (2017): cox061, doi:10.1093/conphys/cox061.

Description: Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.

Description: This work was supported by (1) the Center for Bioengineering Innovation at Northern Arizona University and (2) the New England Aquarium.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 1, doi:10.3389/fmars.2016.00001.

Description: The coccolithophore Emiliania huxleyi forms massive blooms and plays a critical role in global elemental cycles, sequestering significant amounts of atmospheric carbon dioxide on geological time scales via production of calcium carbonate coccoliths and emitting dimethyl sulfoniopropionate (DMSP), which has the potential for increasing atmosph-eric albedo. Because grazing in pelagic systems is a major top-down force structuring microbial communities, the influence of grazers on E. huxleyi populations has been of interest to researchers. Roles of DMSP (and related metabolites) in interactions between E. huxleyi and protist grazers have been investigated, however, little is known about the release of other metabolites that may influence, or be influenced by, such grazing interactions. We used high-resolution mass spectrometry in an untargeted approach to survey the suite of low molecular weight compounds released by four different E. huxleyi strains in response to grazing by the dinoflagellate Oxyrrhis marina. Overall, a strikingly small number of metabolites were detected from E. huxleyi and O. marina cells, but these were distinctly informative to construct metabolic footprints. At most, E. huxleyi strains shared 25% of released metabolites. Furthermore, there appeared to be no unified metabolic response in E. huxleyi strains to grazing; rather, these responses were strain specific. Concentrations of several metabolites also positively correlated with grazer activities, including grazing, ingestion, and growth rates; however, no single metabolite responded uniformly across all strains of E. huxleyi tested. Regardless, grazing clearly transformed the constituents of dissolved organic matter produced by these marine microbes. This study addresses several technical challenges, and presents a platform to further study the influence of chemical cues in aquatic systems and demonstrates the impact of strain diversity and grazing on the complexity of dissolved organic matter in marine systems.

Description: Funding for this work was provided by the Gordon and Betty Moore Foundation, Grant #3301 awarded to A Vardi, BAS. Van Mooy, K Bidle, MJ, and TM. Additional funding for this work was provided by an award from the Flatley Discovery Lab to TM.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 2 (2016): 202, doi:10.3389/fmars.2016.00202.

Description: Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning.

Description: This work was supported by FEDER funds, through the Competitiveness Factors Operational Programme - COMPETE, by national funds, through FCT - Foundation for Science and Technology, under project TRACE (PTDC/ MAR/74071/2006), and by regional funds, through DRCT/SRCTE, under projects MAPCET (M2.1.2/F/012/2011) and 2020 (M2.1.2/I/026/2011). We acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013. RP is supported by an FCT postdoctoral grant (SFRH/BPD/108007/2015); MAS is supported by Program Investigator FCT (IF/00943/2013) and MT was supported by a research fellowship under the Exploratory project (IF/00943/2013/CP1199/CT0001) that also paid the fees for this open-access publication. IF/00943/2013 and IF/00943/2013/CP1199/CT0001 are funded by FSE and MCTES, through POPH and QREN.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 7 (2016): 620, doi:10.3389/fphys.2016.00620.

Description: Vertebrates with laterally placed eyes typically exhibit preferential eye use for ecological activities such as scanning for predators or prey. Processing visual information predominately through the left or right visual field has been associated with specialized function of the left and right brain. Lateralized vertebrates often share a general pattern of lateralized brain function at the population level, whereby the left hemisphere controls routine behaviors and the right hemisphere controls emergency responses. Recent studies have shown evidence of preferential eye use in some invertebrates, but whether the visual fields are predominately associated with specific ecological activities remains untested. We used the European common cuttlefish, Sepia officinalis, to investigate whether the visual field they use is the same, or different, during anti-predatory, and predatory behavior. To test for lateralization of anti-predatory behavior, individual cuttlefish were placed in a new environment with opaque walls, thereby obliging them to choose which eye to orient away from the opaque wall to scan for potential predators (i.e., vigilant scanning). To test for lateralization of predatory behavior, individual cuttlefish were placed in the apex of an isosceles triangular arena and presented with two shrimp in opposite vertexes, thus requiring the cuttlefish to choose between attacking a prey item to the left or to the right of them. Cuttlefish were significantly more likely to favor the left visual field to scan for potential predators and the right visual field for prey attack. Moreover, individual cuttlefish that were leftward directed for vigilant scanning were predominately rightward directed for prey attack. Lateralized individuals also showed faster decision-making when presented with prey simultaneously. Cuttlefish appear to have opposite directions of lateralization for anti-predatory and predatory behavior, suggesting that there is functional specialization of each optic lobe (i.e., brain structures implicated in visual processing). These results are discussed in relation to the role of lateralized brain function and the evolution of population level lateralization.

Description: This work was supported by a post-doctoral study grant from the Fyssen Foundation to AS, and by a research grant “Sélavie” from the Fyssen Foundation to CJ-A. The Sholley Foundation provided partial support for the research in Woods Hole.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 137, doi:10.3389/fmars.2016.00137.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 105, doi:10.3389/fmars.2017.00105.

Description: Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to 〈20 μM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ~1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling- Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ~4.8 μM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.

Description: This work was funded by the Agouron Institute, grant AI-M010.16.1 WHO to OU, M. Sullivan, and VE, and the Millenium Science Initiative, grant IC 120019. Ship time was provided the Chilean National Commission for Scientific and Technological Research (CONICYT) grant AUB 150006/12806.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 11 (2017): 388, doi:10.3389/fncel.2017.00388.

Description: α-Synuclein is a presynaptic protein that regulates synaptic vesicle (SV) trafficking. In Parkinson’s disease (PD) and several other neurodegenerative disorders, aberrant oligomerization and aggregation of α-synuclein lead to synaptic dysfunction and neurotoxicity. Despite evidence that α-synuclein oligomers are generated within neurons under physiological conditions, and that altering the balance of monomers and oligomers contributes to disease pathogenesis, how each molecular species of α-synuclein impacts SV trafficking is currently unknown. To address this, we have taken advantage of lamprey giant reticulospinal (RS) synapses, which are accessible to acute perturbations via axonal microinjection of recombinant proteins. We previously reported that acute introduction of monomeric α-synuclein inhibited SV recycling, including effects on the clathrin pathway. Here, we report the effects of α-synuclein dimers at synapses. Similar to monomeric α-synuclein, both recombinant α-synuclein dimers that were evaluated bound to small liposomes containing anionic lipids in vitro, but with reduced efficacy. When introduced to synapses, the α-synuclein dimers also induced SV recycling defects, which included a build up of clathrin-coated pits (CCPs) with constricted necks that were still attached to the plasma membrane, a phenotype indicative of a vesicle fission defect. Interestingly, both α-synuclein dimers induced longer necks on CCPs as well as complex, branching membrane tubules, which were distinct from the CCPs induced by a dynamin inhibitor, Dynasore. In contrast, monomeric α-synuclein induced a buildup of free clathrin-coated vesicles (CCVs), indicating an inhibition of clathrin-mediated endocytosis at a later stage during the clathrin uncoating process. Taken together, these data further support the conclusion that excess α-synuclein impairs SV recycling. The data additionally reveal that monomeric and dimeric α-synuclein produce distinct effects on clathrin-mediated endocytosis, predicting different molecular mechanisms. Understanding what these mechanisms are could help to further elucidate the normal functions of this protein, as well as the mechanisms underlying PD pathologies.

Description: This study was supported by a research grant from the National Institutes of Health (NINDS/NIA R01NS078165 to JRM), research funds from the Marine Biological Laboratory (to JRM) and a research grant from Horizon 2020 Grant no. InCure EU Joint Programme—JPND (to LB).

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 232, doi:10.3389/fmars.2016.00232.

Description: The reactive oxygen species (ROS) superoxide has been implicated in both beneficial and detrimental processes in coral biology, ranging from pathogenic disease resistance to coral bleaching. Despite the critical role of ROS in coral health, there is a distinct lack of ROS measurements and thus an incomplete understanding of underpinning ROS sources and production mechanisms within coral systems. Here, we quantified in situ extracellular superoxide concentrations at the surfaces of aquaria-hosted Porites astreoides during a diel cycle. High concentrations of superoxide (~10's of nM) were present at coral surfaces, and these levels did not change significantly as a function of time of day. These results indicate that the coral holobiont produces extracellular superoxide in the dark, independent of photosynthesis. As a short-lived anion at physiological pH, superoxide has a limited ability to cross intact biological membranes. Further, removing surface mucus layers from the P. astreoides colonies did not impact external superoxide concentrations. We therefore attribute external superoxide derived from the coral holobiont under these conditions to the activity of the coral host epithelium, rather than mucus-derived epibionts or internal sources such as endosymbionts (e.g., Symbiodinium). However, endosymbionts likely contribute to internal ROS levels via extracellular superoxide production. Indeed, common coral symbionts, including multiple strains of Symbiodinium (clades A to D) and the bacterium Endozoicomonas montiporae LMG 24815, produced extracellular superoxide in the dark and at low light levels. Further, representative P. astreoides symbionts, Symbiodinium CCMP2456 (clade A) and E. montiporae, produced similar concentrations of superoxide alone and in combination with each other, in the dark and low light, and regardless of time of day. Overall, these results indicate that healthy, non-stressed P. astreoides and representative symbionts produce superoxide externally, which is decoupled from photosynthetic activity and circadian control. Corals may therefore produce extracellular superoxide constitutively, highlighting an unclear yet potentially beneficial role for superoxide in coral physiology and health.

Description: This work was supported by a Postdoctoral Fellowship from the Ford Foundation (JD), the National Science Foundation under grants OCE 1225801 (JD) and OCE 1233612 (AA), the Ocean and Climate Change Institute of the Woods Hole Oceanographic Institution (CH), a BIOS Grant in aid award (SM), the Sidney Stern Memorial Trust (CH and AA), as well as an anonymous donor.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 243, doi:10.3389/fmars.2016.00243.

Description: Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu) and nickel (Ni) in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS), and high-resolution electrospray ionization mass spectrometry (ESIMS). Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of [C20H21N4O8S2+M]+ (M = metal isotope) and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex). Molecular formulae of [C32H54N3O6S2Ni]+ and [C33H56N3O6S2Ni]+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as well as variability in the extent to which different metals in the same environment compete for ligand binding.

Description: Support was provided by the National Science Foundation (NSF) program in Chemical Oceanography (OCE-1356747, OCE-1233261, OCE-1233733, OCE-1233502, and OCE-1237034), the NSF Science and Technology Center for Microbial Oceanography Research and Education (C-MORE; DBI-0424599), the Gordon and Betty Moore Foundation (#3298 and 3934), and the Simons Foundation (#329108, DR).

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 2017, doi:10.3389/fmicb.2016.02017.

Description: Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

Description: MJ thanks the funding support of the National Science Foundations Grants NSF-OCE 1031718 and NSF-IOS 1326228.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 338, doi:10.3389/fmars.2017.00338.

Description: The Santa Maria di Leuca (SML) cold-water coral province (northern Ionian Sea) has the largest occurrence of a living white coral community currently known in the Mediterranean Sea. Madrepora oculata and Lophelia pertusa, identified as marking sensitive habitats of relevance by the General Fisheries Commission for the Mediterranean, have been observed heterogeneously distributed on the summits of several mounds. This particularly patchy and uneven distribution in addition to their importance for regional biodiversity highlights the need to better understand their environmental preferences and predict their distribution. Bathymetric data (40 m resolution) was used to derive seafloor characteristics. A fine scale index quantifying the landscape elevation (Bathymetric Position Index at 120 m resolution) was used to select all the elevated features considered as candidate morphologies for potential coral mounds. Statistics on 22 known coral topped mounds were computed. Two statistical methods were then used to identify other potential coral mounds based on predictive variables. The first method, the Geomorphometric proxies method, consists in computing basic statistics of terrain variables, using them for a step-by-step classification in a quantitative approach to select a subset of candidate morphologies. The second method consists in using a predictive Habitat Suitability Model (Maxent model). The Geomorphometric proxies method identified 736 potential coral mounds while the Maxent method predicted 1,252 potential coral mounds. A subset of 517 potential coral mounds was common to both methods. The analysis of the contribution of each variable with the Maxent method showed that the variable “Vector Ruggedness Measure” at a resolution of 5 pixels (200 m) contributed to 53% of the final Maxent model, followed by the “Terrain Texture” index (31%) at a resolution of 11 pixels (440 m). The common potential coral mounds are mainly located in an area characterized by a mass transport deposit, also called the mounds area because of the roughness of the seafloor, in accordance with the high proportional contribution of the noticeable first roughness index to the Maxent model. The results highlight the importance of the global conservation of the entire Province, with white coral probably widespread over the entire 600 km2 SML area.

Description: The Habitat Suitability model study was part of a post-doctoral grant funded by the “Agence de l'Eau Rhône Méditerranée & Corse” under Convention Number 2015 0348, Ifremer and ISMAR Bologna. We are grateful to all the participants and the P.I. of the Aplabes 2004; Aplabes 2005, HERMES M70-1, MEDECO 2007 (http://dx.doi.org/10.17600/7030090) and magic CoralFISH 2010 cruises. The authors also benefited from EU FP7 project CoralFish (Grant agreement number: 213144—http://www.eu-fp7-coralfish.net), the Flag Project Ritmare (Ricerca Italiana per il Mare), funded by the Italian Ministry of Universities and Research (MIUR) and the ESF COCARDE Network. FM was funded through a Ph. D. fellowship in Earth Sciences at the University of Milano-Bicocca.

Description: 〈span〉〈div〉Summary〈/div〉Seismic free oscillations, or normal modes, provide a convenient tool to calculate low-frequency seismograms in heterogeneous Earth models. A procedure called ‘full mode coupling’ allows the seismic response of the Earth to be computed. However, in order to be theoretically exact, such calculations must involve an infinite set of modes. In practice, only a finite subset of modes can be used, introducing an error into the seismograms. By systematically increasing the number of modes beyond the highest frequency of interest in the seismograms, we investigate the convergence of full-coupling calculations. As a rule-of-thumb, it is necessary to couple modes 1–2 mHz above the highest frequency of interest, although results depend upon the details of the Earth model. This is significantly higher than has previously been assumed. Observations of free oscillations also provide important constraints on the heterogeneous structure of the Earth. Historically, this inference problem has been addressed by the measurement and interpretation of splitting functions. These can be seen as secondary data extracted from low frequency seismograms. The measurement step necessitates the calculation of synthetic seismograms, but current implementations rely on approximations referred to as self- or group-coupling and do not use fully accurate seismograms. We therefore also investigate whether a systematic error might be present in currently published splitting functions. We find no evidence for any systematic bias, but published uncertainties must be doubled to properly account for the errors due to theoretical omissions and regularization in the measurement process. Correspondingly, uncertainties in results derived from splitting functions must also be increased. As is well known, density has only a weak signal in low-frequency seismograms. Our results suggest this signal is of similar scale to the true uncertainties associated with currently published splitting functions. Thus, it seems that great care must be taken in any attempt to robustly infer details of Earth's density structure using current splitting functions.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉In this paper, we propose a new wavelet-based 3-D inversion method for frequency-domain airborne electromagnetic (FDAEM) data. Instead of inverting the model in the space domain using a smoothing constraint, this new method recovers the model in the wavelet domain based on a sparsity constraint. In the wavelet domain, the model is represented by two types of coefficients, which contain both large- and fine-scale informations of the model, meaning the wavelet-domain inversion has inherent multiresolution. In order to accomplish a sparsity constraint, we minimize an L〈sub〉1〈/sub〉-norm measure in the wavelet domain that mostly gives a sparse solution. The final inversion system is solved by an iteratively reweighted least-squares method. We investigate different orders of Daubechies wavelets to accomplish our inversion algorithm, and test them on synthetic frequency-domain AEM data set. The results show that higher order wavelets having larger vanishing moments and regularity can deliver a more stable inversion process and give better local resolution, while the lower order wavelets are simpler and less smooth, and thus capable of recovering sharp discontinuities if the model is simple. At last, we test this new inversion algorithm on a frequency-domain helicopter EM (HEM) field data set acquired in Byneset, Norway. Wavelet-based 3-D inversion of HEM data is compared to L〈sub〉2〈/sub〉-norm-based 3-D inversion's result to further investigate the features of the new method.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉A monitoring method to grasp the spatio-temporal change in the interplate coupling in a subduction zone based on the spatial gradients of surface displacement rate fields is proposed. I estimated the spatio-temporal change in the interplate coupling along the plate boundary in northeastern (NE) Japan by applying the proposed method to the surface displacement rates based on global positioning system observations. The gradient of the surface velocities is calculated in each swath configured along the direction normal to the Japan Trench for time windows such as 0.5, 1, 2, 3 and 5 yr being shifted by one week during the period of 1997–2016. The gradient of the horizontal velocities is negative and has a large magnitude when the interplate coupling at the shallow part (less than approximately 50 km in depth) beneath the profile is strong, and the sign of the gradient of the vertical velocity is sensitive to the existence of the coupling at the deep part (greater than approximately 50 km in depth). The trench-parallel variation of the spatial gradients of a displacement rate field clearly corresponds to the trench-parallel variation of the amplitude of the interplate coupling on the plate interface, as well as the rupture areas of previous interplate earthquakes. Temporal changes in the trench-parallel variation of the spatial gradient of the displacement rate correspond to the strengthening or weakening of the interplate coupling. We can monitor the temporal change in the interplate coupling state by calculating the spatial gradients of the surface displacement rate field to some extent without performing inversion analyses with applying certain constraint conditions that sometimes cause over- and/or underestimation at areas of limited spatial resolution far from the observation network. The results of the calculation confirm known interplate events in the NE Japan subduction zone, such as the post-seismic slip of the 2003 M8.0 Tokachi-oki and 2005 M7.2 Miyagi-oki earthquakes and the recovery of the interplate coupling around the rupture area of the 1994 M7.6 Sanriku-Haruka-oki earthquake. The results also indicate the semi-periodic occurrence of slow slip events and the expansion of the area of slow slip events before the 2011 Tohoku-oki earthquake (M9.0) approaching the hypocentre of the Tohoku-oki earthquake.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We image the internal structure of the San Jacinto fault zone (SJFZ) in the trifurcation area southeast of Anza, California, with seismic records from dense linear and rectangular arrays. The examined data include recordings from more than 20 000 local earthquakes and nine teleseismic events. Automatic detection algorithms and visual inspection are used to identify 〈span〉P〈/span〉 and 〈span〉S〈/span〉 body waves, along with 〈span〉P〈/span〉- and 〈span〉S〈/span〉-types fault zone trapped waves (FZTW). The location at depth of the main branch of the SJFZ, the Clark fault, is identified from systematic waveform changes across lines of sensors within the dense rectangular array. Delay times of 〈span〉P〈/span〉 arrivals from teleseismic and local events indicate damage asymmetry across the fault, with higher damage to the NE, producing a local reversal of the velocity contrast in the shallow crust with respect to the large-scale structure. A portion of the damage zone between the main fault and a second mapped surface trace to the NE generates 〈span〉P〈/span〉- and 〈span〉S〈/span〉-types FZTW. Inversions of high-quality 〈span〉S〈/span〉-type FZTW indicate that the most likely parameters of the trapping structure are width of ∼70 m, 〈span〉S〈/span〉-wave velocity reduction of 60 per cent, 〈span〉Q〈/span〉 value of 60 and depth of ∼2 km. The local reversal of the shallow velocity contrast across the fault with respect to large-scale structure is consistent with preferred propagation of earthquake ruptures in the area to the NW.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The computational cost of quasi-〈span〉P〈/span〉 wave extrapolation depends on the complexity of the medium, and specifically the anisotropy. Our effective-model method splits the anisotropic dispersion relation into an isotropic background and a correction factor to handle this dependency. The correction term depends on the slope (measured using the gradient) of current wavefields and the anisotropy. As a result, the computational cost is independent of the nature of anisotropy, which makes the extrapolation efficient. A dynamic implementation of this approach decomposes the original pseudo-differential operator into a Laplacian, handled using the low-rank approximation of the spectral operator, plus an angular dependent correction factor applied in the space domain to correct for anisotropy. We analyse the role played by the correction factor and propose a new spherical decomposition of the dispersion relation. The proposed method provides accurate wavefields in phase and more balanced amplitudes than a previous spherical decomposition. Also, it is free of 〈span〉SV〈/span〉-wave artefacts. Applications to a simple homogeneous transverse isotropic medium with a vertical symmetry axis (VTI) and a modified Hess VTI model demonstrate the effectiveness of the approach. The Reverse Time Migration applied to a modified BP VTI model reveals that the anisotropic migration using the proposed modelling engine performs better than an isotropic migration.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Over the past 15 yr, numerical models of convection in Earth’s mantle have made a leap forward: they can now produce self-consistent plate-like behaviour at the surface together with deep mantle circulation. These digital tools provide a new window into the intimate connections between plate tectonics and mantle dynamics, and can therefore be used for tectonic predictions, in principle. This contribution explores this assumption. First, initial conditions at 30, 20, 10 and 0 Ma are generated by driving a convective flow with imposed plate velocities at the surface. We then compute instantaneous mantle flows in response to the guessed temperature fields without imposing any boundary conditions. Plate boundaries self-consistently emerge at correct locations with respect to reconstructions, except for small plates close to subduction zones. As already observed for other types of instantaneous flow calculations, the structure of the top boundary layer and upper-mantle slab is the dominant character that leads to accurate predictions of surface velocities. Perturbations of the rheological parameters have little impact on the resulting surface velocities. We then compute fully dynamic model evolution from 30 and 10 to 0 Ma, without imposing plate boundaries or plate velocities. Contrary to instantaneous calculations, errors in kinematic predictions are substantial, although the plate layout and kinematics in several areas remain consistent with the expectations for the Earth. For these calculations, varying the rheological parameters makes a difference for plate boundary evolution. Also, identified errors in initial conditions contribute to first-order kinematic errors. This experiment shows that the tectonic predictions of dynamic models over 10 My are highly sensitive to uncertainties of rheological parameters and initial temperature field in comparison to instantaneous flow calculations. Indeed, the initial conditions and the rheological parameters can be good enough for an accurate prediction of instantaneous flow, but not for a prediction after 10 My of evolution. Therefore, inverse methods (sequential or data assimilation methods) using short-term fully dynamic evolution that predict surface kinematics are promising tools for a better understanding of the state of the Earth’s mantle.〈/span〉

Description: We investigate the impact of the new LUNA rate for the nuclear reaction 22 Ne( p , ) 23 Na on the chemical ejecta of intermediate-mass stars, with particular focus on the thermally pulsing asymptotic giant branch (TP-AGB) stars that experience hot-bottom burning. To this aim, we use the PARSEC and COLIBRI codes to compute the complete evolution, from the pre-main sequence up to the termination of the TP-AGB phase, of a set of stellar models with initial masses in the range 3.0–6.0 M and metallicities Z i = 0.0005, 0.006 and 0.014. We find that the new LUNA measures have much reduced the nuclear uncertainties of the 22 Ne and 23 Na AGB ejecta that drop from factors of ~=10 to only a factor of few for the lowest metallicity models. Relying on the most recent estimations for the destruction rate of 23 Na, the uncertainties that still affect the 22 Ne and 23 Na AGB ejecta are mainly dominated by the evolutionary aspects (efficiency of mass-loss, third dredge-up, convection). Finally, we discuss how the LUNA results impact on the hypothesis that invokes massive AGB stars as the main agents of the observed O–Na anticorrelation in Galactic globular clusters. We derive quantitative indications on the efficiencies of key physical processes (mass-loss, third dredge-up, sodium destruction) in order to simultaneously reproduce both the Na-rich, O-poor extreme of the anticorrelation and the observational constraints on the CNO abundance. Results for the corresponding chemical ejecta are made publicly available.

Description: We fitted the 3–180 keV spectrum of all the observations of the neutron star low-mass X-ray binary 4U 1636–53 taken with the Rossi X-ray Timing Explorer using a model that includes a thermal Comptonization component. We found that in the low hard state the power-law index of this component, , gradually increases as the source moves in the colour–colour diagram. When the source undergoes a transition from the hard to the soft state drops abruptly; once the source is in the soft state increases again and then decreases gradually as the source spectrum softens further. The changes in , together with changes of the electron temperature, reflect changes of the optical depth in the corona. The lower kilohertz quasi-periodic oscillation (kHz QPO) in this source appears only in observations during the transition from the hard to the soft state, when the optical depth of the corona is high and changes depends strongly upon the position of the source in the colour–colour diagram. Our results are consistent with a scenario in which the lower kHz QPO reflects a global mode in the system that results from the resonance between the disc and/or the neutron star surface, and the Comptonizing corona.

Description: Supermassive stars (SMSs; ~10 5 M ) formed from metal-free gas in the early Universe attract attention as progenitors of supermassive black holes observed at high redshifts. To form SMSs by accretion, central protostars must accrete at as high rates as ~0.1–1 M yr –1 . Such protostars have very extended structures with bloated envelopes, like supergiant stars, and are called supergiant protostars (SGPSs). Under the assumption of hydrostatic equilibrium, SGPSs have density-inverted layers, where the luminosity becomes locally super-Eddington, near the surface. If the envelope matter is allowed to flow out, however, a stellar wind could be launched and hinder the accretion growth of SGPSs before reaching the supermassive regime. We examine whether radiation-driven winds are launched from SGPSs by constructing steady and spherically symmetric wind solutions. We find that the wind velocity does not reach the escape velocity in any case considered. This is because once the temperature falls below ~10 4 K, the opacity plummet drastically owing to the recombination of hydrogen and the acceleration ceases suddenly. This indicates that, in realistic non-steady cases, even if outflows are launched from the surface of SGPSs, they would fall back again. Such a ‘wind’ does not result in net mass-loss and does not prevent the growth of SGPSs. In conclusion, SGPSs will grow to SMSs and eventually collapse to massive black holes of ~10 5 M , as long as the rapid accretion is maintained.

Description: The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

Description: Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp . japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.

Description: Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard ( Gallotia galloti ) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from 〉20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti . However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.

Description: Streptococcus anginosus is a member of the normal oral flora that can become a pathogen causing pyogenic infections in humans. The genome of daptomycin-resistant strain J4206, originally isolated from a patient suffering from breakthrough bacteremia and septic shock at the University of Texas Health Science Center at San Antonio, was determined. The circular genome is 2,001,352 bp long with a GC content of 38.62% and contains multiple mobile genetic elements, including the phage-like chromosomal island SanCI that mediates a mutator phenotype, transposons, and integrative conjugative elements. Daptomycin resistance involves multiple alterations in the cell membrane and cell wall, and unique features were identified in J4206 that may contribute to resistance. A cluster of capsular polysaccharide (CPS) genes for choline metabolism and transport are present that may help neutralize cell surface charges, destabilizing daptomycin binding. Further, unique J4206 genes encoding sortases and LPXTG-target proteins that are involved in cell wall modification were present. The J4206 genome is phylogenetically closely related to the recently reported vancomycin-resistant SA1 strain; however, these genomes differ with SNPs in cardiolipin synthetase, histidine kinase yycG , teichoic acid modification genes, and other genes involved in cell surface modification. Transmission electron microscopy showed that the cell walls of both strains J4206 and SA1 were significantly thicker and more electron dense than daptomycin- and vancomycin-sensitive strain J4211. This comparative genomic study has identified unique genes as well as allelic variants in the J4206 genome that are involved in cell surface modification and thus might contribute to the acquisition of daptomycin resistance.

Description: Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events; however, it did not find evidence for a paleopolyploidization at the base of this family, which has previously been hypothesized on the basis of sequence data from a limited number of species. The obtained results and potential causes of these discrepancies are discussed.

Description: Elastic reverse time migration (RTM) can yield accurate subsurface information (e.g. PP and PS reflectivity) by imaging the multicomponent seismic data. However, the existing RTM methods are still insufficient to provide satisfactory results because of the finite recording aperture, limited bandwidth and imperfect illumination. Besides, the P - and S -wave separation and the polarity reversal correction are indispensable in conventional elastic RTM. Here, we propose an iterative elastic least-squares RTM (LSRTM) method, in which the imaging accuracy is improved gradually with iteration. We first use the Born approximation to formulate the elastic de-migration operator, and employ the Lagrange multiplier method to derive the adjoint equations and gradients with respect to reflectivity. Then, an efficient inversion workflow (only four forward computations needed in each iteration) is introduced to update the reflectivity. Synthetic and field data examples reveal that the proposed LSRTM method can obtain higher-quality images than the conventional elastic RTM. We also analyse the influence of model parametrizations and misfit functions in elastic LSRTM. We observe that Lamé parameters, velocity and impedance parametrizations have similar and plausible migration results when the structures of different models are correlated. For an uncorrelated subsurface model, velocity and impedance parametrizations produce fewer artefacts caused by parameter crosstalk than the Lamé coefficient parametrization. Correlation- and convolution-type misfit functions are effective when amplitude errors are involved and the source wavelet is unknown, respectively. Finally, we discuss the dependence of elastic LSRTM on migration velocities and its antinoise ability. Imaging results determine that the new elastic LSRTM method performs well as long as the low-frequency components of migration velocities are correct. The quality of images of elastic LSRTM degrades with increasing noise.

Description: Ribosomal RNAs (rRNAs) account for 〉60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.

Description: In general, the complex electrical resistivity in the subsurface is anisotropic. Despite this, algorithms for the tomographic inversion of complex resistivity data commonly assume isotropy, mainly due to the lack of anisotropic modelling and inversion schemes, potentially leading to artefacts in the inversion results in the presence of anisotropy. The development of an effective anisotropic complex resistivity inversion algorithm which utilizes the gradient information of some cost function benefits from understanding the characteristics of the problem's sensitivities, that is, the partial derivative of the impedance forward response with respect to the complex conductivities in the different spatial directions, as well as with respect to the different ratios of complex conductivities, that is, the different anisotropy ratios. We here derive expressions for these sensitivities and, based on a 2.5-D finite-element modelling algorithm, we compute and discuss sensitivity distributions as well as measurement response curves of typical surface and cross-borehole measurement configurations for 2-D subsurface anisotropic complex resistivity distributions. Depending on the electrode layout and measurement configuration, the sensitivity with respect to the conductivity in a particular direction shows a unique pattern, while for other directions sensitivity patterns are qualitatively similar. These sensitivity characteristics translate into important equivalences between impedance responses of local anisotropic and isotropic anomalies, for both magnitude and phase. Accordingly, with collinear surface arrays only the complex conductivity in the direction of the electrode layout can be unambiguously resolved, and with cross-borehole arrays only the conductivity in the vertical direction, provided an in-hole current injection is used. Nevertheless, anisotropy ratios involving these resolvable conductivity components are likewise detectable. The distinct shape of the measurement response curves, reflecting the distinct spatial patterns of the corresponding sensitivity distributions, suggest that optimized measurement configurations can be inferred for specific exploration questions involving electrical anisotropy and given electrode layouts. The gained insight into the characteristics of the sensitivity distributions of complex resistivity measurements in case of subsurface anisotropy should guide the implementation of effective anisotropic complex resistivity inversion schemes and lead to a routine use of such schemes in any resistivity and induced polarization surveys whenever subsurface electrical anisotropy could be encountered.

Description: The streaming potential phenomenon is an electrokinetic effect that occurs in porous media. It is characterized by an electrokinetic (EK) coefficient. The aim of this paper is to simulate the EK coefficient in unsaturated conditions using the Lattice Boltzmann method in a 2-D capillary channel. The multiphase flow is simulated with the model of Shan & Chen. The Poisson–Boltzmann equation is solved by implementing the model of Chai & Shi. The streaming potential response shows a non-monotonous behaviour due to the combination of the increase of charge density and decrease of flow velocity with decreasing water saturation. Using a potential of –20 mV at the air–water interface, an enhancement of a factor 5–30 of the EK coefficient, compared to the saturated state, can be observed due to the positive charge excess at this interface which is magnified by the fluid velocity away from the rock surface. This enhancement is correlated to the fractioning of the bubbles, and to the dynamic state of these bubbles, moving or entrapped in the crevices of the channel.

Description: We present the results of two-dimensional hydrodynamic simulations of self-gravitating circumbinary discs around binaries whose parameters match those of the circumbinary planet-hosting systems Kepler-16, Kepler-34 and Kepler-35. Previous work has shown that non-self-gravitating discs in these systems form an eccentric precessing inner cavity due to tidal truncation by the binary, and planets which form at large radii migrate until stalling at this cavity. Whilst this scenario appears to provide a natural explanation for the observed orbital locations of the circumbinary planets, previous simulations have failed to match the observed planet orbital parameters. The aim of this work is to examine the role of self-gravity in modifying circumbinary disc structure as a function of disc mass, prior to considering the evolution of embedded circumbinary planets. In agreement with previous work, we find that for disc masses between one and five times the minimum mass solar nebula (MMSN), disc self-gravity affects modest changes in the structure and evolution of circumbinary discs. Increasing the disc mass to 10 or 20 MMSN leads to two dramatic changes in disc structure. First, the scale of the inner cavity shrinks substantially, bringing its outer edge closer to the binary. Secondly, in addition to the eccentric inner cavity, additional precessing eccentric ring-like features develop in the outer regions of the discs. If planet formation starts early in the disc lifetime, these changes will have a significant impact on the formation and evolution of planets and precursor material.

Description: In this paper, we present a multiwavelength investigation of the star-forming complex IRAS 20286+4105, located in the Cygnus X region. Near-infrared K -band data are used to revisit the cluster/stellar group identified in previous studies. Radio continuum observations at 610 and 1280 MHz show the presence of a H ii region possibly powered by a star of spectral type B0–B0.5. The cometary morphology of the ionized region is explained by invoking the bow-shock model, where the likely association with a nearby supernova remnant is also explored. A compact radio knot with a non-thermal spectral index is detected towards the centre of the cloud. Mid-infrared data from the Spitzer Legacy Survey of the Cygnus X region show the presence of six Class I young stellar objects inside the cloud. Thermal dust emission in this complex is modelled using Herschel far-infrared data to generate dust temperature and column density maps. Herschel images also show the presence of two clumps in this region, the masses of which are estimated to be ~175 and 30 M . The mass–radius relation and the surface density of the clumps mean that they do not qualify as massive star-forming sites. An overall picture of a runaway star ionizing the cloud and a triggered population of intermediate-mass, Class I sources located towards the cloud centre emerges from this multiwavelength study. Variation in the dust emissivity spectral index is shown to exist in this region and is seen to have an inverse relation with the dust temperature.

Description: We present a modification of the method for reconstructing the stellar velocity ellipsoid (SVE) in disc galaxies. Our version does not need any parametrization of the velocity dispersion profiles and uses only one assumption that the ratio z / R remains constant along the profile or along several pieces of the profile. The method was tested on two galaxies from the sample of other authors and for the first time applied to three lenticular galaxies NGC 1167, NGC 3245 and NGC 4150, as well as to one Sab galaxy NGC 338. We found that for galaxies with a high inclination ( $i 〉 55^\circ \text{--}60^\circ$ ) it is difficult or rather impossible to extract the information about SVE, while for galaxies at an intermediate inclination the procedure of extracting is successful. For NGC 1167 we managed to reconstruct SVE, provided that the value of z / R is piecewise constant. We found z / R = 0.7 for the inner parts of the disc and z / R = 0.3 for the outskirts. We also obtained a rigid constraint on the value of the radial velocity dispersion R for highly inclined galaxies, and tested the result using the asymmetric-drift equation, provided that the gas rotation curve is available.

Description: This paper presents new results from the ongoing study of the unusual Lynx–Cancer void galaxy DDO 68, which has star-forming regions of record low metallicity [12+log (O/H) ~7.14]. The results include the following. (i) A new spectrum and photometry have been obtained with the 6-m SAO RAS telescope (BTA) for the luminous blue variable (LBV = DDO68-V1). Photometric data sets were complemented with others based on the Sloan Digital Sky Survey (SDSS) and the Hubble Space Telescope ( HST ) archive images. (ii) We performed an analysis of the DDO 68 supergiant shell (SGS) and the prominent smaller Hα arcs/shells visible in the HST image coupled with kinematic maps in Hα obtained with the Fabry–Perot interferometer (FPI) at the BTA. (iii) We compiled a list of about 50 of the most luminous stars (–9.1 mag 〈 M V 〈 –6.0 mag) identified from the HST images associated with the star-forming regions with known extremely low O/H. This is intended to pave the path for the current science to be investigated with the next generation of giant telescopes. We have confirmed earlier hints of significant variation of the LBV optical light, deriving its amplitude as V 3.7 mag for the first time. New data suggest that in 2008–2010 the LBV reached M V = –10.5 mag and probably underwent a giant eruption. We argue that the structure of star-forming complexes along the SGS (‘Northern Ring’) perimeter provides evidence for sequential induced star-formation episodes caused by the shell gas instabilities and gravitational collapse. The variability of some luminous extremely metal-poor stars in DDO 68 can currently be monitored with medium-size telescopes at sites with superb seeing.

Description: The number, distribution and properties of dwarf satellites are crucial probes of the physics of galaxy formation at low masses and the response of satellite galaxies to the tidal and gas dynamical effects of their more massive parent. To make progress, it is necessary to augment and solidify the census of dwarf satellites of galaxies outside the Local Group. Müller et al. presented 16 dwarf galaxy candidates near M83, but lacking reliable distances, it is unclear which candidates are M83 satellites. Using red-giant-branch stars from the HST /GHOSTS survey in conjunction with ground-based images from VLT/VIMOS, we confirm that one of the candidates, dw1335-29 – with a projected distance of 26 kpc from M83 and a distance modulus of $(m-M)_0 = 28.5^{+0.3}_{-0.1}$ – is a satellite of M83. We estimate an absolute magnitude M V  = –10.1 ± 0.4, an ellipticity of $0.40^{+0.14}_{-0.22}$ , a half-light radius of $656^{+121}_{-170}$  pc and [Fe/H] = $-1.3^{+0.3}_{-0.4}$ . Owing to dw1335-29's somewhat irregular shape and possible young stars, we classify this galaxy as a dwarf irregular or transition dwarf. This is curious, as with a projected distance of 26 kpc from M83, dw1335-29 is expected to lack recent star formation. Further study of M83's dwarf population will reveal if star formation in its satellites is commonplace (suggesting a lack of a hot gas envelope for M83 that would quench star formation) or rare (suggesting that dw1335-29 has a larger M83-centric distance, and is fortuitously projected to small radii).

Description: Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs.

Description: Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes. As a result, ratios of X/A divergence increase with increasing distance from genes and corresponding estimates of male mutation bias are significantly higher in intergenic regions near genes versus far from genes. Future studies in other species will need to carefully consider the effect that genomic location will have on estimates of male mutation bias.

Description: Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene ( Mx ) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus , thus predating the loss of Major Histocompatibility Complex class II ( MHCII ) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time.

Description: Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.

Description: Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus . Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.

Description: Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India.

Description: Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception of the nucleocapsid. Also, secondary structure predictions are only conserved across 50–80% of sites for most protein families, with the implication that 20–50% of sites do not have conserved secondary structure prediction. Furthermore, nonconserved structure sites are significantly less constrained in sequence divergence than either sites conserved in the secondary structure or sites conserved in loop. Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the 〉10,000 starting sites across all coronaviruses in this study. The identified sequence motif is found within the nonstructural protein (NSP) 12 and constitutes an antiviral target potentially effective against the present day and future coronaviruses. On shorter evolutionary timescales, the SARS and MERS clades have more sequence motifs fulfilling the criteria applied. Interestingly, many motifs map to NSP12 making this a prime target for coronavirus antivirals.

Description: Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae , the cause of mango malformation, and two isolates of F. proliferatum , one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression ( in vitro and in planta ) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum , the pathogenic versus endophytic life style.

Description: Seismic noise measurements (ambient vibrations) have been increasingly used in rock slope stability assessment for both investigation and monitoring purposes. Recent studies made on gravitational hazard revealed significant spectral amplification at given frequencies and polarization of the wave-field in the direction of maximum rock slope displacement. Different properties (resonance frequencies, polarization and spectral ratio amplitudes) can be derived from the spectral analysis of the seismic noise to characterize unstable rock masses. The objective here is to identify the dynamic parameters that could be used to gain information on prone-to-fall rock columns’ geometry. To do so, the dynamic response of prone-to-fall columns to seismic noise has been studied on two different sites exhibiting cliff-like geometry. Dynamic parameters (main resonance frequency and spectral ratio amplitudes) that could characterize the column decoupling were extracted from seismic noise and their variations were studied taking into account the external environmental parameter fluctuations. Based on this analysis, a two-dimensional numerical model has been set up to assess the influence of the rear vertical fractures identified on both sites on the rock column motion response. Although a simple relation was found between spectral ratio amplitudes and the rock column slenderness, it turned out that the resonance frequency is more stable than the spectral ratio amplitudes to characterize this column decoupling, provided that the elastic properties of the column can be estimated. The study also revealed the effect of additional remote fractures on the dynamic parameters, which in turn could be used for detecting the presence of such discontinuities.

Description: In this study, we present a new synthesis of GPS velocities for tectonic deformation within the Tibetan Plateau and its surrounding areas, a combined data set of ~1854 GPS-derived horizontal velocity vectors. Assuming that crustal deformation is localized along major faults, a block modelling approach is employed to interpret the GPS velocity field. We construct a 30-element block model to describe present-day deformation in western China, with half of them located within the Tibetan Plateau, and the remainder located in its surrounding areas. We model the GPS velocities simultaneously for the effects of block rotations and elastic strain induced by the bounding faults. Our model yields a good fit to the GPS data with a mean residual of 1.08 mm a –1 compared to the mean uncertainty of 1.36 mm a –1 for each velocity component, indicating a good agreement between the predicted and observed velocities. The major strike-slip faults such as the Altyn Tagh, Xianshuihe, Kunlun and Haiyuan faults have relatively uniform slip rates in a range of 5–12 mm a –1 along most of their segments, and the estimated fault slip rates agree well with previous geologic and geodetic results. Blocks having significant residuals are located at the southern and southeastern Tibetan Plateau, suggesting complex tectonic settings and further refinement of accurate definition of block geometry in these regions.

Description: Surface-related multiples have been utilized in the reverse-time migration (RTM) procedures, and additional illumination for subsurface can be provided. Meanwhile, many cross-talks are generated from undesired interactions between forward- and backward-propagated seismic waves. In this paper, subsequent to analysing and categorizing these cross-talks, we propose RTM of first-order multiples to avoid most undesired interactions in RTM of all-order multiples, where only primaries are forward-propagated and crosscorrelated with the backward-propagated first-order multiples. With primaries and multiples separated during regular seismic data processing as the input data, first-order multiples can be obtained by a two-step scheme: (1) the dual-prediction of higher-order multiples; and (2) the adaptive subtraction of predicted higher-order multiples from all-order multiples within local offset-time windows. In numerical experiments, two synthetic and a marine field data sets are used, where different cross-talks generated by RTM of all-order multiples can be identified and the proposed RTM of first-order multiples can provide a very interpretable image with a few cross-talks.

Description: We present high-resolution radio continuum observations with the Karl G. Jansky very large array at 6, 8.5, 11.5 and 15 GHz of the double-peaked emission-line galaxy 2MASXJ12032061+1319316. The radio emission has a prominent S-shaped morphology with highly symmetric radio jets that extend over a distance of ~1.5 arcsec (1.74 kpc) on either side of the core of size ~0.1 arcsec (116 pc). The radio jets have a helical structure resembling the precessing jets in the galaxy NGC 326 which has confirmed dual active galactic nuclei (AGN). The nuclear bulge velocity dispersion gives an upper limit of (1.56 ± 0.26) x 10 8 M for the total mass of nuclear black hole(s). We present a simple model of precessing jets in 2MASXJ1203 and find that the precession time-scale is around 10 5 yr: this matches the source lifetime estimate via spectral ageing. We find that the expected supermassive black hole (SMBH) separation corresponding to this time-scale is 0.02 pc. We used the double-peaked emission lines in 2MASXJ1203 to determine an orbital speed for a dual AGN system and the associated jet precession time-scale, which turns out to be more than the Hubble time, making it unfeasible. We conclude that the S-shaped radio jets are due to jet precession caused either by a binary/dual SMBH system, a single SMBH with a tilted accretion disc or a dual AGN system where a close pass of the secondary SMBH in the past has given rise to jet precession.

Description: In any flux-density limited sample of blazars, the distribution of the time-scale modulation factor t '/ t , which quantifies the change in observed time-scales compared to the rest-frame ones due to redshift and relativistic compression follows an exponential distribution with a mean depending on the flux limit of the sample. In this work, we produce the mathematical formalism that allows us to use this information in order to uncover the underlining rest-frame probability density function of measurable time-scales of blazar jets. We extensively test our proposed methodology using a simulated Flat Spectrum Radio Quasar population with a 1.5 Jy flux-density limit in the simple case (where all blazars share the same intrinsic time-scale), in order to identify limits of applicability and potential biases due to observational systematics and sample selection. We find that for monitoring with time intervals between observations longer than ~30 per cent of the intrinsic time-scale under investigation the method loses its ability to produce robust results. For time intervals of ~3 per cent of the intrinsic time-scale, the error of the method is as low as 1 per cent in recovering the intrinsic rest-frame time-scale. We applied our method to rotations of the optical polarization angle of blazars observed by RoboPol. We found that the intrinsic time-scales of the longest duration rotation event in each blazar follows a narrow distribution, well described by a normal distribution with mean 87 d and standard deviation 5 d. We discuss possible interpretations of this result.

Description: About one-third of X-ray-luminous clusters show smooth, Mpc-scale radio emission, known as giant radio haloes. One promising model for radio haloes is Fermi-II acceleration of seed relativistic electrons by compressible turbulence. The origin of these seed electrons has never been fully explored. Here, we integrate the Fokker–Planck equation of the cosmic ray (CR) electron and proton distributions when post-processing cosmological simulations of cluster formation and confront them with radio surface brightness and spectral data of Coma. For standard assumptions, structure formation shocks lead to a seed electron population that produces too centrally concentrated radio emission. Matching observations requires modifying properties of the CR population (rapid streaming; enhanced CR electron acceleration at shocks) or turbulence (increasing turbulent-to-thermal energy density with radius), but at the expense of fine-tuning. In a parameter study, we find that radio properties are exponentially sensitive to the amplitude of turbulence, which is inconsistent with small scatter in scaling relations. This sensitivity is removed if we relate the acceleration time to the turbulent dissipation time. In this case, turbulence above a threshold value provides a fixed amount of amplification; observations could thus potentially constrain the unknown CR seed population. To obtain sufficient acceleration, the turbulent magneto-hydrodynamics cascade has to terminate by transit time damping on CRs, i.e. thermal particles must be scattered by plasma instabilities. Understanding the small scatter in radio halo scaling relations may provide a rich source of insight on plasma processes in clusters.

Description: We measure a combination of gravitational lensing, galaxy clustering and redshift-space distortions (RSDs) called E G . The quantity E G probes both parts of metric potential and is insensitive to galaxy bias and 8 . These properties make it an attractive statistic to test lambda cold dark matter, general relativity and its alternate theories. We have combined CMASS Data Release 11 with CFHTLenS and recent measurements of β from RSD analysis, and find E G ( z  = 0.57) = 0.42 ± 0.056, a 13 per cent measurement in agreement with the prediction of general relativity E G ( z  = 0.57) = 0.396 ± 0.011 using the Planck 2015 cosmological parameters. We have corrected our measurement for various observational and theoretical systematics. Our measurement is consistent with the first measurement of E G using cosmic microwave background lensing in place of galaxy lensing at small scales, but shows 2.8 tension when compared with their final results including large scales. This analysis with future surveys will provide improved statistical error and better control over systematics to test general relativity and its alternate theories.

Description: Using a Bayesian framework, we quantify what current observations imply about the history of the epoch of reionization (EoR). We use a popular, three-parameter EoR model, flexible enough to accommodate a wide range of physically plausible reionization histories. We study the impact of various EoR observations: (i) the optical depth to the CMB measured by Planck 2016; (ii) the dark fraction in the Lyman α and β forests; (iii) the redshift evolution of galactic Lyα emission (so-called ‘Lyα fraction’); (iv) the clustering of Lyα emitters; (v) the IGM damping wing imprint in the spectrum of QSO ULASJ1120+0641; (vi) and the patchy kinetic Sunyaev–Zel'dovich signal. Combined, (i) and (ii) already place interesting constraints on the reionization history, with the epochs corresponding to an average neutral fraction of (75, 50, 25) per cent, constrained at 1 to $z= (9.21^{+1.22 }_{ -1.15}, 8.14^{+1.08 }_{ -1.00}, 7.26^{+1.13 }_{ -0.96})$ . Folding-in more model-dependent EoR observations [(iii)–(vi)], strengthens these constraints by tens of per cent, at the cost of a decrease in the likelihood of the best-fitting model, driven mostly by (iii). The tightest constraints come from (v). Unfortunately, no current observational set is sufficient to break degeneracies and constrain the astrophysical EoR parameters. However, model-dependent priors on the EoR parameters themselves can be used to set tight limits by excluding regions of parameter space with strong degeneracies. Motivated by recent observations of z ~ 7 faint, lensed galaxies, we show how a conservative upper limit on the virial temperature of haloes which host reionizing galaxies can constrain the escape fraction of ionizing photons to $f_{\rm esc} = 0.14^{+0.26 }_{ -0.09}$ .

Description: We present new time-resolved photometry of 74 cataclysmic variables (CVs), 47 of which are eclipsing. Thirteen of these eclipsing systems are newly discovered. For all 47 eclipsing systems, we show high cadence (1–20 s) light curves obtained with the high-speed cameras ULTRACAM and ULTRASPEC. We provide new or refined ephemerides, and supply mid-eclipse times for all observed eclipses. We assess the potential for light-curve modelling of all 47 eclipsing systems to determine their system parameters, finding 20 systems that appear to be suitable for future study. Systems of particular interest include V713 Cep, in which we observed a temporary switching-off of accretion; and ASASSN-14mv and CSS111019:233313–155744, which both have orbital periods well below the CV period minimum. The short orbital periods and light-curve shapes suggest that they may be double degenerate (AM CVn) systems or CVs with evolved donor stars.

Description: We have used the 610-MHz receivers of the Giant Metrewave Radio Telescope (GMRT) to detect associated H i 21-cm absorption from the z  = 1.2230 blazar TXS 1954+513. The GMRT H i 21-cm absorption is likely to arise against either the milliarcsecond-scale core or the one-sided milliarcsecond-scale radio jet, and is blueshifted by 328 km s –1 from the blazar redshift. This is consistent with a scenario in which the H i cloud giving rise to the absorption is being driven outwards by the radio jet. The integrated H i 21-cm optical depth is (0.716 ± 0.037) km s –1 , implying a high H i column density, $N_{\rm H\small {I}} = (1.305 \pm 0.067) \times ({ T_{\rm s}/100\,{\rm K}}) \times 10^{20}$  cm –2 , for an assumed H i spin temperature of 100 K. We use Nickel Telescope photometry of TXS 1954+513 to infer a high rest-frame 1216 Å luminosity of (4.1 ± 1.2)  x  10 23 W Hz –1 . The z  = 1.2230 absorber towards TXS 1954+513 is only the fifth case of a detection of associated H i 21-cm absorption at z  〉 1, and is also the first case of such a detection towards an active galactic nucleus (AGN) with a rest-frame ultraviolet (UV) luminosity 〉〉10 23 W Hz –1 , demonstrating that neutral hydrogen can survive in AGN environments in the presence of high UV luminosities.

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉We present the theory of parsimonious refraction interferometry and tomography where a densely populated refraction data set can be obtained from two reciprocal and several infill shot gathers. The assumptions are that the refraction arrivals are head waves, and a pair of reciprocal shot gathers and several infill shot gathers are recorded over the line of interest. Refraction traveltimes from these shot gathers are picked and spawned into 〈span style="font-style:italic;"〉O〈/span〉(〈span style="font-style:italic;"〉N〈/span〉〈sup〉2〈/sup〉) virtual refraction traveltimes generated by 〈span style="font-style:italic;"〉N〈/span〉 virtual sources, where 〈span style="font-style:italic;"〉N〈/span〉 is the number of geophones in the 2-D survey. The virtual traveltimes can be inverted to give the velocity tomogram. This enormous increase in the number of traveltime picks and associated rays, compared to the many fewer traveltimes from the reciprocal and infill shot gathers, allows for increased model resolution and a better condition number with the system of normal equations. A significant benefit is that the parsimonious survey and the associated traveltime picking can be an order-of-magnitude less time consuming than that for a standard refraction survey with a dense distribution of sources.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉We describe three achievements for a ground motion simulation. First, we propose a kinematic modelling in which rupture delay time is governed by an eikonal equation on a Riemannian manifold and develop a coupling method between the ground motion simulation and the eikonal solver. In general the rupture velocity distribution is not spatially uniform and the rupture propagation depends on a fault shape. So we derive the eikonal equation by considering the Riemannian metric of the fault surface and give a detailed discretization of its difference scheme to deal with a curved surface fault. Next, in order to explain the effect of spatially discontinuous non-uniformity of rupture velocity, we introduce an isochrones jumping intensity and obtain a new decomposed isochrones formula in general settings. It is known that the representation theorem with the Green's function can be rewritten into an expression with a contour integral by the isochrones theory. The new formula says that the known isochrones formula for ground velocity can be decomposed into a trend component and a disturbance component. The disturbance component consists of the isochrones jumping intensity. Finally, by applying our ground motion simulation coupled with the eikonal solver and the decomposed isochrones formula, we investigate some relations between the non-uniformity of the rupture velocity and pulse-like disturbance of the ground motion velocity. Our simulations show that the disturbance of velocity waveform corresponds with that of rate of change of isochrones band area. It turns out that the pulse-like disturbance of velocity waveform occurs when isochrones move across the region where rupture velocity varies discontinuously. Thus we can explain that the pulse-like disturbance of the ground motion velocity occurs when the isochrones jumping intensity has nonzero value. Moreover, as another example of application of our simulation and formula, we show a distinctive dependence of peak ground velocity upon parameters such as the rupture velocity and the distance between a fault and an observer.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉Over the last decades, electromagnetic methods have become an accepted tool for a wide range of geophysical exploration purposes and nowadays even for monitoring. Application to hydrocarbon monitoring, for example for enhanced oil recovery, is hampered by steel-cased wells, which typically exist in large numbers in producing oil fields and which distort electromagnetic fields in the subsurface. Steel casings have complex geometries as they are very thin but vertically extended; moreover, the conductivity contrast of steel to natural materials is in the range of six orders of magnitude. It is therefore computationally prohibitively costly to include such structures directly into the modelling grid, even for finite element methods. To tackle the problem we developed a method to describe steel-cased wells as series of substitute dipole sources, which effectively interact with the primary field. The new approach cannot only handle a single steel-cased well, but also an arbitrary number, and their interaction with each other. We illustrate the metal casing effect with synthetic 3-D modelling of land-based controlled source electromagnetic data. Steel casings distort electromagnetic fields even for large borehole-transmitter distances above 2 km. The effect depends not only on the distance between casing and transmitter, but also on the orientation of the transmitter to the borehole. Finally, we demonstrate how the presence of steel-cased wells can be exploited to increase the sensitivity and enhance resolution in the target region. Our results show that it is at least advisable to consider the distribution of steel-cased wells already at the planning phase of a controlled source electromagnetic field campaign.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉The volatile content in magmas is fundamental for the triggering and style of volcanic eruptions. Carbon dioxide, the second most abundant volatile component in magmas after H〈sub〉2〈/sub〉O, is the first to reach saturation upon ascent and depressurization. We investigate experimentally CO〈sub〉2〈/sub〉-bubble nucleation in trachybasalt and trachyte melts at high temperature and high pressure (〈span style="font-style:italic;"〉HT〈/span〉 and 〈span style="font-style:italic;"〉HP〈/span〉) through wetting-angle measurements on different (sialic, mafic or oxide) phenocryst phases. The presence of crystals lowers the supersaturation required for CO〈sub〉2〈/sub〉-bubble nucleation up to 37 per cent (heterogeneous nucleation, 〈span style="font-style:italic;"〉HeN〈/span〉), with a minor role of mineral chemistry. Different from H〈sub〉2〈/sub〉O-rich systems, feldspar crystals are effective in reducing required supersaturation for bubble nucleation. Our data suggest that leucite, the dominant 〈span style="font-style:italic;"〉liquidus〈/span〉 phase in ultrapotassic systems at shallow depth (i.e. 〈100 MPa), facilitates late-stage, extensive magma vesiculation through CO〈sub〉2〈/sub〉〈span style="font-style:italic;"〉HeN〈/span〉, which may explain the shifting of CO〈sub〉2〈/sub〉-rich eruptive systems towards an apparently anomalous explosive behaviour.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉The contribution of the GOCE gravity gradients to regional gravity field solutions is investigated in this study. We employ radial basis functions to recover the gravity field on regional scales over Amazon and Himalayas as our test regions. In the first step, four individual solutions based on the more accurate gravity gradient components 〈span style="font-style:italic;"〉Txx〈/span〉, 〈span style="font-style:italic;"〉Tyy〈/span〉, 〈span style="font-style:italic;"〉Tzz〈/span〉 and 〈span style="font-style:italic;"〉Txz〈/span〉 are derived. The 〈span style="font-style:italic;"〉Tzz〈/span〉 component gives better solution than the other single-component solutions despite the less accuracy of 〈span style="font-style:italic;"〉Tzz〈/span〉 compared to 〈span style="font-style:italic;"〉Txx〈/span〉 and 〈span style="font-style:italic;"〉Tyy〈/span〉. Furthermore, we determine five more solutions based on several selected combinations of the gravity gradient components including a combined solution using the four gradient components. The 〈span style="font-style:italic;"〉Tzz〈/span〉 and 〈span style="font-style:italic;"〉Tyy〈/span〉 components are shown to be the main contributors in all combined solutions whereas the 〈span style="font-style:italic;"〉Txz〈/span〉 adds the least value to the regional gravity solutions. We also investigate the contribution of the regularization term. We show that the contribution of the regularization significantly decreases as more gravity gradients are included. For the solution using all gravity gradients, regularization term contributes to about 5 per cent of the total solution. Finally, we demonstrate that in our test areas, regional gravity modelling based on GOCE data provide more reliable gravity signal in medium wavelengths as compared to pre-GOCE global gravity field models such as the EGM2008.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Defining variations in the behaviour of the geomagnetic field through geological time is critical to understanding the dynamics of Earth's core and its response to mantle convection and planetary evolution. Furthermore, the question of whether the axial dipole dominance of the recent palaeomagnetic field persists through the whole of Earth's history is fundamental to determining the reliability of palaeogeographic reconstructions and the efficacy of the magnetosphere in shielding Earth from solar wind radiation. Previous palaeomagnetic directional studies have suggested that the palaeofield had a complex configuration in the Devonian period (419–359 Ma). Here we present new high-quality palaeointensity determinations from rocks aged between 408 and 375 Ma from the Minusa Basin (southern Siberia), and the Kola Peninsula that enable the first reliable investigation of the strength of the field during this enigmatic period. Palaeointensity experiments were performed using the thermal Thellier, microwave Thellier and Wilson methods on 165 specimens from 25 sites. Six out of eight successful sites from the Minusa Basin and all four successful sites from the Kola Peninsula produced extremely low palaeointensities (〈10 μT). These findings challenge the uniformitarian view of the palaeomagnetic field: field intensities of nearly an order of magnitude lower than Neogene values (except during relatively rare geomagnetic excursions and reversals) together with the widespread appearance of strange directions found in the Devonian suggest that the Earth's field during this time may have had a dominantly multipolar geometry. A persistent, low intensity multipolar magnetic field and associated diminished magnetosphere would increase the impact of solar particles on the Earth's magnetosphere, ionosphere and atmosphere with potential major implications for Earth's climate and biosphere.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Glacial Isostatic Adjustment (GIA) models commonly assume a mantle with a viscoelastic Maxwell rheology and a fixed ice history model. Here, we use a Bayesian Monte Carlo approach with a Markov chain formalism to invert the global GIA signal simultaneously for the mechanical properties of the mantle and the volumes of the ice sheets, using as starting ice models two previously published ice histories. Two stress relaxing rheologies are considered: Burgers and Maxwell linear viscoelasticities. A total of 5720 global palaeo sea level records are used, covering the last 35 kyr. Our goal is not only to seek the model best fitting this data set, but also to determine and display the range of possible solutions with their respective probability of explaining the data. In all cases, our 〈span style="font-style:italic;"〉a posteriori〈/span〉 probability maps exhibit the classic character of solutions for GIA-determined mantle viscosity with two distinct peaks. What is new in our treatment is the presence of the bi-viscous Burgers rheology and the fact that we invert rheology jointly with ice history, in combination with the greatly expanded palaeo sea level records. The solutions tend to be characterized by an upper-mantle viscosity of around 5 × 10〈sup〉20〈/sup〉 Pa s with one preferred lower-mantle viscosities at 3 × 10〈sup〉21〈/sup〉 Pa s and the other more than 2 × 10〈sup〉22〈/sup〉 Pa s, a rather classical pairing. Best-fitting models depend upon the starting ice history and the stress relaxing law. A first peak (P1) has the highest probability only in the case with a Maxwell rheology and ice history based on ICE-5G, while the second peak (P2) is favoured for ANU-based ice history or Burgers stress relaxation. The latter solution also may satisfy lower-mantle viscosity inferences from long-term geodynamics and gravity gradient anomalies over Laurentia. P2 is also consistent with large Laurentian and Fennoscandian ice-sheet volumes at the Last Glacial Maximum (LGM) and smaller LGM Antarctic ice volume than in either ICE-5G or ANU. Exploration of a bi-viscous linear relaxing rheology in GIA now seems logical due to a new set of requirements to satisfy observations of transient post-seismic flow seen so ubiquitously in space gravimetry and other global geodetic data.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Earthquakes mainly occur in crust or mantle that is below a critical temperature for the tectonic strain-rate, $\dot{e}_t$, such that stress builds up to the breaking point before it can relax due to creep. Then long-range stress correlation gives rise to power law seismicity including large events. The limiting temperature depends on pressure, which is taken into account by finding a critical homologous temperature 〈span style="font-style:italic;"〉T〈/span〉〈sub〉Hc〈/sub〉 = 〈span style="font-style:italic;"〉T〈/span〉/〈span style="font-style:italic;"〉T〈/span〉〈sub〉M〈/sub〉 above which earthquakes are rarely observed (where 〈span style="font-style:italic;"〉T〈/span〉, 〈span style="font-style:italic;"〉T〈/span〉〈sub〉M〈/sub〉 are temperature and average melting temperature of constituent minerals). We find that 〈span style="font-style:italic;"〉T〈/span〉〈sub〉Hc〈/sub〉 for ocean plates is ∼0.55. For California earthquakes, it is also close to 0.55. The uppermost mantle layer of oceanic plates of thickness ∼50 km is composed of harzburgite and depleted peridotite from which basalt has been removed to form ocean crust. Thus it has a higher melting temperature than the peridotite of the surrounding mantle, or the lower halves of plates. Thicknesses of seismicity in deep subduction zones, determined from 2-D polynomial fits to a relocated catalogue, are ∼50 km, which suggests that the earthquake channel is confined to this layer. We construct models to find homologous temperatures in slabs, and find that seismicity thicknesses are also, on average, confined to 〈span style="font-style:italic;"〉T〈/span〉〈sub〉H〈/sub〉 ≤ 0.55 ± 0.05. The associated rheology is compared with that obtained from flexure models of ocean lithosphere. The brittle-ductile transition occurs where viscosity drops from high values in the cold cores of slabs to values of 10〈sup〉22〈/sup〉–10〈sup〉23〈/sup〉 Pa s, that is, where creep strain-rates become comparable to tectonic rates. The cut-off for deep earthquakes is not sharp. However they appear unlikely to occur if homologous temperature is high 〈span style="font-style:italic;"〉T〈/span〉〈sub〉H〈/sub〉 〉 0.55. Exceptions to the rule are anomalously deep earthquakes such as those beneath the Iceland and the Hawaiian hotspots, and the Newport Inglewood Fault. These are smaller events with short-range stress correlation, and can be explained if strain-rates are two to three orders of magnitude higher than those associated with earthquakes located where 〈span style="font-style:italic;"〉T〈/span〉〈sub〉H〈/sub〉 ≤ 0.55. We conclude that the brittle-ductile transition corresponds to the transition from long-range (regional) to short-range (localized on asperities) stress correlation.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉We introduce a wavefield gradiometry technique to estimate both isotropic and anisotropic local medium characteristics from short recordings of seismic signals by inverting a wave equation. The method exploits the information in the spatial gradients of a seismic wavefield that are calculated using dense deployments of seismic arrays. The application of the method uses the surface wave energy in the ambient seismic field. To estimate isotropic and anisotropic medium properties we invert an elliptically anisotropic wave equation. The spatial derivatives of the recorded wavefield are evaluated by calculating finite differences over nearby recordings, which introduces a systematic anisotropic error. A two-step approach corrects this error: finite difference stencils are first calibrated, then the output of the wave-equation inversion is corrected using the linearized impulse response to the inverted velocity anomaly. We test the procedure on ambient seismic noise recorded in a large and dense ocean bottom cable array installed over Ekofisk field. The estimated azimuthal anisotropy forms a circular geometry around the production-induced subsidence bowl. This conforms with results from studies employing controlled sources, and with interferometry correlating long records of seismic noise. Yet in this example, the results were obtained using only a few minutes of ambient seismic noise.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Reverberations of teleseismic compressional (〈span style="font-style:italic;"〉P〈/span〉-) waves within a glacier or ice sheet may mask signals associated with crustal structure beneath the ice. We remove the signal associated with the ice from teleseismic 〈span style="font-style:italic;"〉P〈/span〉-waves using a wavefield downward continuation and decomposition technique that depends on known ice layer properties such as ice thickness, velocity, and attenuation. We test the method using data from nine stations in Antarctica and one station in Greenland. We deconvolve the downward-continued seismic wave vectors to create 〈span style="font-style:italic;"〉P〈/span〉-wave receiver functions that minimize the ice-layer reverberations in order to better measure signals from deeper structures. The subsurface 〈span style="font-style:italic;"〉P〈/span〉-wave receiver functions have similar sensitivities to crustal structure as those calculated from stations installed on bedrock. Synthetic experiments indicate subsurface 〈span style="font-style:italic;"〉P〈/span〉-wave receiver functions can constrain crustal structure more tightly than surface 〈span style="font-style:italic;"〉P〈/span〉-wave receiver functions when ice layer properties are known. We model the subsurface 〈span style="font-style:italic;"〉P〈/span〉-wave receiver functions using a Markov chain Monte Carlo inversion and constrain the product of crustal thickness and the column-average crustal-slowness beneath the stations. Our subglacial shear speed and thickness estimates are consistent with previous investigations at most stations. At station SUMG in south-central Greenland, our results suggest a thicker crust than from previous estimates.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Usually, when inverting geodetic data to estimate the slip distributions on a fault, the area is made large enough to more than cover the rupture zone, with regularization producing regions of large slip with very small slip over the rest of the surface. We have developed a new inverse method which assumes that nonzero slip is confined to a rectangular region, and which jointly estimates, using Bayesian methods, the boundaries of this region as well as the slip distribution within it, using a smoothing parameter also determined as part of the inversion. Synthetic tests show that our method can successfully image deeper slip regions not resolved by previous methods, and does not produce spurious regions of nonzero slip. We apply our method to coseismic displacements measured by GPS for the 2009 L’Aquila earthquake, first determining the orientation of the fault assuming a simplified model with uniform slip, and then determining probability density functions for the location, length, and width of the rupture area and for the slip distribution. The standard deviation of slip is about 10 cm and describes a normal-faulting earthquake with a maximum slip of 88 ± 11 cm and seismic moment of $3.32_{-0.29}^{+0.30}\times 10^{18}$ N m.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Summary〈/div〉High-resolution models of seismic velocity variations constructed using body-wave tomography inform the study of the origin, fate and thermochemical state of mantle domains. In order to reliably relate these variations to material properties including temperature, composition and volatile content, we must accurately retrieve both the patterns and amplitudes of variations and quantify the uncertainty associated with the estimates of each. For these reasons, we image the mantle beneath North America with 〈span style="font-style:italic;"〉P〈/span〉-wave traveltimes from USArray using a novel method for 3-D probabilistic body-wave tomography. The method uses a Transdimensional Hierarchical Bayesian framework with a reversible-jump Markov Chain Monte Carlo algorithm in order to generate an ensemble of possible velocity models. We analyse this ensemble solution to obtain the posterior probability distribution of velocities, thereby yielding error bars and enabling rigorous hypothesis testing. Overall, we determine that the average uncertainty (1σ) of compressional wave velocity estimates beneath North America is ∼0.25 per cent 〈span style="font-style:italic;"〉dVP〈/span〉/〈span style="font-style:italic;"〉VP〈/span〉, increasing with proximity to complex structure and decreasing with depth. The addition of USArray data reduces the uncertainty beneath the Eastern US by over 50 per cent in the upper mantle and 25–40 per cent below the transition zone and ∼30 per cent throughout the mantle beneath the Western US. In the absence of damping and smoothing, we recover amplitudes of variations 10–80 per cent higher than a standard inversion approach. Accounting for differences in data coverage, we infer that the length scale of heterogeneity is ∼50 per cent longer at shallow depths beneath the continental platform than beneath tectonically active regions. We illustrate the model trade-off analysis for the Cascadia slab and the New Madrid Seismic Zone, where we find that smearing due to the limitations of the illumination is relatively minor.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉We demonstrate with synthetic and field data that with sufficiently dense sampling wave-equation-based methods such as reverse time migration (RTM), implicitly forming array receiver functions (ARFs), perform better resolution wise than migration of common conversion point (CCP) stacks of traditional receiver functions. However, even with modern array deployments the sampling requirement is typically not met for teleseismic (earthquake) data. To enable RTM imaging with sparsely (and irregularly) sampled wavefields at the surface, we use an intermediate reconstruction based on sparsity promoting optimization using a curvelet (or wave packet) representation of the data, as an important and necessary pre-processing step. To suppress artefacts, the curvelet coefficients are constrained to represent the range of known directions present in the data. We show that our proposed pre-processing procedure (which may be viewed as generating ‘missing’ traces) can produce artefact-free data for RTM even if only 20 per cent of necessary data are available in the original data set. With synthetic data, we also demonstrate that if the sampling criteria is not met, CCP can produce results that are superior over wave-equation methods such as RTM. As a proof-of-concept with field data, we image the structure of the crust beneath the Himalayas with passive-source RTM of teleseismic data from Hi-CLIMB project. For Hi-CLIMB data, the CCP and RTM results are similar because sampling is still too sparse for RTM and the structure is simple enough for successful CCP. Both results are improved by wavefield regularization and reveal that the Moho is continuous beneath most of the array, and not fragmented as suggested by some earlier studies.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉Elastic full waveform inversion (EFWI) aims to reduce the misfit between recorded and modelled multicomponent seismic data for deducing a detailed model of elastic parameters in the subsurface. Because the explicit computation and inversion of the Hessian matrix is extremely resource intensive, a gradient-based (rather than Hessian-based) minimization is generally applied for large-scale applications. However, the multiparameter trade-off effects cause cross-talks in the computed gradients and thus severely affect the convergence and the quality of the inverted model. Recently, preconditioning the gradients based on elastic wave mode decomposition has been suggested for mitigating the parameter trade-offs in the EFWI process. In this paper, we propose a mode decomposition (MD)-based EFWI approach in which the preconditioned gradients are obtained through the cross-correlation of the forward and decomposed adjoint wavefields in the time domain. Based on the decomposed Frechét derivatives, we explain the mechanism of this approach through analyses of Hessian and resolution matrices and comparison with the Gauss–Newton gradients. Numerical examples of a simple fluid-saturated model and the Marmousi-II model demonstrate that the MD-based preconditioned conjugate-gradient approach can mitigate the trade-off between the 〈span style="font-style:italic;"〉P〈/span〉- and 〈span style="font-style:italic;"〉S〈/span〉-wave velocities and achieve fast convergence without any Hessian-involved calculations.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉We use frequency domain methods usually applied to volcanic tremor to analyse ground based seismic recordings of a helicopter. We preclude misinterpretations of tremor sources and show alternative applications of our seismological methods. On a volcano, the seismic source can consist of repeating, closely spaced, small earthquakes. Interestingly, similar signals are generated by helicopters due to repeating pressure pulses from the rotor blades. In both cases the seismic signals are continuous and referred to as tremor. As frequency gliding is in this case merely caused by the Doppler effect, not a change in the source, we can use its shape to deduce properties of the helicopter and its flight path. We show in this analysis that the number of rotor blades, rotor revolutions per minute, helicopter speed, flight direction, altitude and location can be deduced from seismometer recordings. Access to GPS determined flight path data from the helicopter offers us a robust way to test our location method.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉An analytical solution is derived concerning the linear run-up for any given initial wave generated over a sloping bathymetry. Due to the simplicity of the linear formulation, complex transformations are unnecessary, hence the shoreline motion is directly obtained in terms of the initial wave. This result supports not only maximum run-up invariance between linear and nonlinear theories but also the time evolution of shoreline motion and velocity, exhibiting good agreement with the nonlinear theory. The present formulation also allows quantifying the shoreline motion numerically from a customized initial waveform, including non-smooth functions. This is useful for numerical tests, laboratory experiments or realistic cases in which the initial disturbance might be retrieved from seismic data rather than using a theoretical model. It is also shown that the run-up calculation for the real case studied is consistent with the field observations.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉In studies of the magnetic properties of soils, the frequency-dependent magnetic susceptibility percentage (〈span style="font-style:italic;"〉χ〈/span〉〈sub〉FD〈/sub〉%) is often used for the identification of ultrafine magnetically superparamagnetic/stable single-domain (SP/SSD) particles. This parameter is commonly used as an indicator for increased pedogenesis. In strongly magnetic soils, the SP/SSD magnetic signal (mostly bio-pedogenic) may be masked by lithological signals; making pedogenesis hard to detect. In this study, we compare results for the detection of ultrafine SP/SSD magnetic particles in andic soils using two instruments: a Bartington MS2B dual-frequency meter and an AGICO Kappabridge MFK1-FA. In particular, the study focuses on the effect of pedogenesis by investigating the relationship between specific soil magnetic and chemical properties (soil organic carbon and pH〈sub〉H2O〈/sub〉). The values of 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉FD〈/sub〉% obtained with the MS2B varied from 2.4 to 5.9 per cent, and mass-specific magnetic susceptibility (〈span style="font-style:italic;"〉χ〈/span〉〈sub〉LF〈/sub〉) from 283 to 1688 × 10〈sup〉−8〈/sup〉 m〈sup〉3〈/sup〉 kg〈sup〉−1〈/sup〉, while values of 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉FD〈/sub〉% and 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉LF〈/sub〉 obtained with the MFK1-FA varied from 2.7 to 8.2 per cent and from 299 to 1859 × 10〈sup〉−8〈/sup〉 m〈sup〉3〈/sup〉 kg〈sup〉−1〈/sup〉, respectively. Our results suggest that the detection of the SP/SSD magnetic fraction can be accomplished by comparing relative trends of 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉FD〈/sub〉% along the soil profile. Moreover, the discrimination between bio-pedogenic and lithogenic magnetic contributions in the SP/SSD fraction is possible by comparing the 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉FD〈/sub〉% and 〈span style="font-style:italic;"〉χ〈/span〉〈sub〉LF〈/sub〉 data determined in the fine earth (〈2 mm) and the coarse fraction (4–10 mm) samples down the soil profile.〈/span〉

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉We present and use a phase coherence approach to identify seismic signals that have similar path effects but different source time functions: co-located earthquakes and tremor. The method used is a phase coherence-based implementation of empirical matched field processing, modified to suit tremor analysis. It works by comparing the frequency-domain phases of waveforms generated by two sources recorded at multiple stations. We first cross-correlate the records of the two sources at a single station. If the sources are co-located, this cross-correlation eliminates the phases of the Green’s function. It leaves the relative phases of the source time functions, which should be the same across all stations so long as the spatial extent of the sources are small compared with the seismic wavelength. We therefore search for cross-correlation phases that are consistent across stations as an indication of co-located sources. We also introduce a method to obtain relative locations between the two sources, based on back-projection of interstation phase coherence. We apply this technique to analyse two tremor-like signals that are thought to be composed of a number of earthquakes. First, we analyse a 20 s long seismic precursor to a 〈span style="font-style:italic;"〉M〈/span〉 3.9 earthquake in central Alaska. The analysis locates the precursor to within 2 km of the mainshock, and it identifies several bursts of energy—potentially foreshocks or groups of foreshocks—within the precursor. Second, we examine several minutes of volcanic tremor prior to an eruption at Redoubt Volcano. We confirm that the tremor source is located close to repeating earthquakes identified earlier in the tremor sequence. The amplitude of the tremor diminishes about 30 s before the eruption, but the phase coherence results suggest that the tremor may persist at some level through this final interval.〈/span〉

Description: Recent photometric analyses of the colour–magnitude diagrams of young massive clusters (YMCs) have found evidence for splitting in the main sequence and extended main-sequence turn-offs, both of which have been suggested to be caused by stellar rotation. Comparison of the observed main-sequence splitting with models has led various authors to suggest a rather extreme stellar rotation distribution, with a minority (10–30 per cent) of stars with low rotational velocities and the remainder (70–90 per cent) of stars rotating near the critical rotation (i.e. near break-up). We test this hypothesis by searching for Be stars within two YMCs in the Large Magellanic Cloud (NGC 1850 and NGC 1856), which are thought to be critically rotating stars with decretion discs that are (partially) ionized by their host stars. In both clusters, we detect large populations of Be stars at the main-sequence turn-off (~30–60 per cent of stars), which supports previous suggestions of large populations of rapidly rotating stars within massive clusters.

Description: The mass of the Local Group (LG) is a crucial parameter for galaxy formation theories. However, its observational determination is challenging – its mass budget is dominated by dark matter that cannot be directly observed. To meet this end, the posterior distributions of the LG and its massive constituents have been constructed by means of constrained and random cosmological simulations. Two priors are assumed – the cold dark matter model that is used to set up the simulations, and an LG model that encodes the observational knowledge of the LG and is used to select LG-like objects from the simulations. The constrained simulations are designed to reproduce the local cosmography as it is imprinted on to the Cosmicflows-2 data base of velocities. Several prescriptions are used to define the LG model, focusing in particular on different recent estimates of the tangential velocity of M31. It is found that (a) different v tan choices affect the peak mass values up to a factor of 2, and change mass ratios of M M31 to M MW by up to 20 per cent; (b) constrained simulations yield more sharply peaked posterior distributions compared with the random ones; (c) LG mass estimates are found to be smaller than those found using the timing argument; (d) preferred Milky Way masses lie in the range of (0.6–0.8) x 10 12  M ; whereas (e) M M31 is found to vary between (1.0–2.0) x 10 12  M , with a strong dependence on the v tan values used.