ALBERT

Description: The relationships between trachytes and peralkaline rhyolites (i.e. pantellerites and comendites), which occur in many continental rift systems, oceanic islands and continental intraplate settings, is unclear. To fill this gap, we have performed phase equilibrium experiments on two representative metaluminous trachytes from Pantelleria to determine both their pre-eruptive equilibration conditions (pressure, temperature, H2O content and redox state) and liquid lines of descent. Experiments were performed in the temperature range 750–950 C, pressure 0 5–1 5 kbar and fluid saturation conditions with XH2O [¼H2O/(H2OþCO2)] ranging between zero and unity. Redox conditions were fixed below the nickel–nickel oxide buffer (NNO). The results show that at 950 C and melt water contents (H2Omelt) close to saturation, trachytes are at liquidus conditions at all pressures. Clinopyroxene is the liquidus phase, being followed by iron-rich olivine and alkali feldspar. Comparison of experimental and natural phases (abundances and compositions) yields the following pre-eruptive conditions: P¼160 5 kbar, T¼925625 C, H2Omelt¼261wt %, and fO2 between NNO– 0 5 and NNO– 2. A decrease in temperature from 950 C to 750 C, as well as of H2Omelt, promotes a massive crystallization of alkali feldspar to over 80 wt %. Iron-bearing minerals show gradual iron enrichment when T and fO2 decrease, trending towards the compositions of the phenocrysts of natural pantellerites. Despite the metaluminous character of the bulk-rock compositions, residual glasses obtained after 80 wt % crystallization evolve toward comenditic compositions, owing to profuse alkali feldspar crystallization, which decreases the Al2O3 of the melt, leading to a consequent increase in the peralkalinity index [PI¼molar (Na2OþK2O)/Al2O3]. This is the first experimental demonstration that peralkaline felsic derivatives can be produced by low-pressure fractional crystallization of metaluminous mafic magmas. Our results show that the pantelleritic magmas of basalt–trachyte–rhyolite igneous suites require at least 95 wt % of parental basalt crystallization, consistent with trace element evidence. Redox conditions, through their effect on Fe–Ti oxide stabilities, control the final iron content of the evolving melt.

Description: Published

Description: 559- 588

Description: 2V. Struttura e sistema di alimentazione dei vulcani

Description: JCR Journal

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 6 (2018): coy049, doi:10.1093/conphys/coy049.

Description: Male baleen whales have long been suspected to have annual cycles in testosterone, but due to difficulty in collecting endocrine samples, little direct evidence exists to confirm this hypothesis. Potential influences of stress or adrenal stress hormones (cortisol, corticosterone) on male reproduction have also been difficult to study. Baleen has recently been shown to accumulate steroid hormones during growth, such that a single baleen plate contains a continuous, multi-year retrospective record of the whale’s endocrine history. As a preliminary investigation into potential testosterone cyclicity in male whales and influences of stress, we determined patterns in immunoreactive testosterone, two glucocorticoids (cortisol and corticosterone), and stable-isotope (SI) ratios, across the full length of baleen plates from a bowhead whale (Balaena mysticetus), a North Atlantic right whale (Eubalaena glacialis) and a blue whale (Balaenoptera musculus), all adult males. Baleen was subsampled at 2 cm (bowhead, right) or 1 cm (blue) intervals and hormones were extracted from baleen powder with methanol, followed by quantification of all three hormones using enzyme immunoassays validated for baleen extract of these species. Baleen of all three males contained regularly spaced peaks in testosterone content, with number and spacing of testosterone peaks corresponding well to SI data and to species-specific estimates of annual baleen growth rate. Cortisol and corticosterone exhibited some peaks that co-occurred with testosterone peaks, while other glucocorticoid peaks occurred independent of testosterone peaks. The right whale had unusually high glucocorticoids during a period with a known entanglement in fishing gear and a possible disease episode; in the subsequent year, testosterone was unusually low. Further study of baleen testosterone patterns in male whales could help clarify conservation- and management-related questions such as age of sexual maturity, location and season of breeding, and the potential effect of anthropogenic and natural stressors on male testosterone cycles.

Description: This work was supported by (1) the Arizona Board of Regents Technology Research Initiative Fund; (2) the Center for Bioengineering Innovation at Northern Arizona University; (3) the Greenland Institute of Natural Resources; (4) the Woods Hole Oceanographic Institution Ocean Life Institute and (5) Fisheries and Ocean Canada’s (DFO) Priorities and Partnership Strategic Initiatives Fund and Oceans Protection Plan.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Epigenetics 4 (2018): dvy005, doi:10.1093/eep/dvy005.

Description: There is growing evidence that environmental toxicants can affect various physiological processes by altering DNA methylation patterns. However, very little is known about the impact of toxicant-induced DNA methylation changes on gene expression patterns. The objective of this study was to determine the genome-wide changes in DNA methylation concomitant with altered gene expression patterns in response to 3, 3’, 4, 4’, 5-pentachlorobiphenyl (PCB126) exposure. We used PCB126 as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 10 nM PCB126 for 24 h (water-borne exposure) and brain and liver tissues were sampled at 7 days post-exposure in order to capture both primary and secondary changes in DNA methylation and gene expression. We used enhanced Reduced Representation Bisulfite Sequencing and RNAseq to quantify DNA methylation and gene expression, respectively. Enhanced reduced representation bisulfite sequencing analysis revealed 573 and 481 differentially methylated regions in the liver and brain, respectively. Most of the differentially methylated regions are located more than 10 kilobases upstream of transcriptional start sites of the nearest neighboring genes. Gene Ontology analysis of these genes showed that they belong to diverse physiological pathways including development, metabolic processes and regeneration. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and energy metabolism in response to polychlorinated biphenyl exposure. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting that the relationship between methylation and gene expression is dynamic and complex, involving multiple layers of regulation.

Description: This work was supported by the National Institute of Health Outstanding New Environmental Scientist Award to NA (NIH R01ES024915) and Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) grant P01ES021923 and National Science Foundation Grant OCE-1314642 to M. Hahn, J. Stegeman, NA and SK].

Description: Author Posting. © The Authors, 2018. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 215 (2018): 1072–1087, doi:10.1093/gji/ggy203.

Description: An earthquake rupture process can be kinematically described by rupture velocity, duration and spatial extent. These key kinematic source parameters provide important constraints on earthquake physics and rupture dynamics. In particular, core questions in earthquake science can be addressed once these properties of small earthquakes are well resolved. However, these parameters of small earthquakes are poorly understood, often limited by available data sets and methodologies. The Incorporated Research Institutions for Seismology Community Wavefield Experiment in Oklahoma deployed ∼350 three-component nodal stations within 40 km2 for a month, offering an unprecedented opportunity to test new methodologies for resolving small earthquake finite source properties in high resolution. In this study, we demonstrate the power of the nodal data set to resolve the variations in the seismic wavefield over the focal sphere due to the finite source attributes of an M2 earthquake within the array. The dense coverage allows us to tightly constrain rupture area using the second moment method even for such a small earthquake. The M2 earthquake was a strike-slip event and unilaterally propagated towards the surface at 90 per cent local S-wave speed (2.93 km s−1). The earthquake lasted ∼0.019 s and ruptured Lc ∼70 m and Wc ∼45 m. With the resolved rupture area, the stress-drop of the earthquake is estimated as 7.3 MPa for Mw 2.3. We demonstrate that the maximum and minimum bounds on rupture area are within a factor of two, much lower than typical stress-drop uncertainty, despite a suboptimal station distribution. The rupture properties suggest that there is little difference between the M2 Oklahoma earthquake and typical large earthquakes. The new three-component nodal systems have great potential for improving the resolution of studies of earthquake source properties.

Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. JM was partially supported by SCEC grant #17177 at Woods Hole Oceanographic Institution. This research was supported by the Southern California Earthquake Center (Contribution No. 8014). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038.

Description: Author Posting. © The Authors, 2018. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 215 (2018): 942–958, doi:10.1093/gji/ggy316.

Description: Surface waves recorded by global arrays have proven useful for locating tectonic earthquakes and in detecting slip events depleted in high frequency, such as glacial quakes. We develop a novel method using an aggregation of small- to continental-scale arrays to detect and locate seismic sources with Rayleigh waves at 20–50 s period. The proposed method is a hybrid approach including first dividing a large aperture aggregate array into Delaunay triangular subarrays for beamforming, and then using the resolved surface wave propagation directions and arrival times from the subarrays as data to formulate an inverse problem to locate the seismic sources and their origin times. The approach harnesses surface wave coherence and maximizes resolution of detections by combining measurements from stations spanning the whole U.S. continent. We tested the method with earthquakes, glacial quakes and landslides. The results show that the method can effectively resolve earthquakes as small as ∼M3 and exotic slip events in Greenland. We find that the resolution of the locations is non-uniform with respect to azimuth, and decays with increasing distance between the source and the array when no calibration events are available. The approach has a few advantages: the method is insensitive to seismic event type, it does not require a velocity model to locate seismic sources, and it is computationally efficient. The method can be adapted to real-time applications and can help in identifying new classes of seismic sources.

Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. This work was supported by National Science Foundation grant EAR-1358520 at Scripps Institution of Oceanography, UC San Diego.

Description: Author Posting. © The Author(s), 2018. 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 214 (2018): 2224–2235, doi:10.1093/gji/ggy201.

Description: The key kinematic earthquake source parameters: rupture velocity, duration and area, shed light on earthquake dynamics, provide direct constraints on stress drop, and have implications for seismic hazard. However, for moderate and small earthquakes, these parameters are usually poorly constrained due to limitations of the standard analysis methods. Numerical experiments by Kaneko and Shearer demonstrated that standard spectral fitting techniques can lead to roughly one order of magnitude variation in stress-drop estimates that do not reflect the actual rupture properties even for simple crack models. We utilize these models to explore an alternative approach where we estimate the rupture area directly. For the suite of models, the area averaged static stress drop is nearly constant for models with the same underlying friction law, yet corner-frequency-based stress-drop estimates vary by a factor of 5–10 even for noise-free data. Alternatively, we simulated inversions for the rupture area as parametrized by the second moments of the slip distribution. A natural estimate for the rupture area derived from the second moments is A = πLcWc, where Lc and Wc are the characteristic rupture length and width. This definition yields estimates of stress drop that vary by only 10 per cent between the models but are slightly larger than the true area averaged values. We simulate inversions for the second moments for the various models and find that the area can be estimated well when there are at least 15 available measurements of apparent duration at a variety of take-off angles. The improvement compared to azimuthally averaged corner-frequency-based approaches results from the second moments accounting for directivity and removing the assumption of a circular rupture area, both of which bias the standard approach. We also develop a new method that determines the minimum and maximum values of rupture area that are consistent with a particular data set at the 95 per cent confidence level. For the Kaneko and Shearer models with 20+ randomly distributed observations and ∼10 per cent noise levels, we find that the maximum and minimum bounds on rupture area typically vary by a factor of two and that the minimum stress drop is often more tightly constrained than the maximum.

Description: This work was supported by USGS NEHRP Award G17AP00029. The research was supported by the Southern California Earthquake Center (SCEC; Contribution No. 8013). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038. YK was supported by both public funding from the Government of New Zealand and the Royal Society of New Zealand’s Rutherford Discovery Fellowship.

Description: Author Posting. © The Authors, 2018. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 215 (2018): 713–735, doi:10.1093/gji/ggy313.

Description: Gas flux in volcanic conduits is often associated with long-period oscillations known as seismic tremor (Lesage et al.; Nadeau et al.). In this study, we revisit and extend the ‘magma wagging’and ‘whirling’models for seismic tremor, in order to explore the effects of gas flux on the motion of a magma column surrounded by a permeable vesicular annulus (Jellinek & Bercovici; Bercovici et al.; Liao et al.). We find that gas flux flowing through the annulus leads to a Bernoulli effect, which causes waves on the magma column to become unstable and grow. Specifically, the Bernoulli effects are associated with torques and forces acting on the magma column, increasing its angular momentum and energy. As the displacement of the magma column becomes large due to the Bernoulli effect, frictional drag on the conduit wall decelerates the motions of the column, restoring them to small amplitude. Together, the Bernoulli effect and the damping effect contribute to a self-sustained wagging-and-whirling mechanism that help explain the longevity of long-period seismic tremor.

Description: This work was supported by National Science Foundation grants EAR-1344538 and EAR-1645057

Description: Author Posting. © The Authors, 2018. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 215 (2018): 460–473, doi:10.1093/gji/ggy152.

Description: In this work, we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine-learning techniques. Non-negative matrix factorization is used to determine grain-size end-members from sediment surface samples. Four end-members were found, which well represent the variety of sediments in the study area. A radial basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.

Description: This work was funded through DFG Research Center/Cluster of Excellence ‘The Ocean in the Earth System’ and was part of MARUM Research Area SD

Description: Author Posting. © Author(s), 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 212 (2018): 1429–1449, doi:10.1093/gji/ggx488.

Description: We conducted detailed analyses of a global array of trenches, revealing systematic intra- and intertrench variations in plate bending characteristics. The intratrench variations of the Manila and Mariana Trenches were analysed in detail as end-member cases of the relatively young (16–36 Ma) and old (140–160 Ma) subducting plates, respectively. Meanwhile, the intertrench variability was investigated for a global array of additional trenches including the Philippine, Kuril, Japan, Izu-Bonin, Aleutian, Tonga-Kermadec, Middle America, Peru, Chile, Sumatra and Java Trenches. Results of the analysis show that the trench relief (W0) and width (X0) of all systems are controlled primarily by the faulting-reduced elastic thickness near the trench axis (Tme) and affected only slightly by the initial unfaulted thickness (TMe) of the incoming plate. The reduction in Te has caused significant deepening and narrowing of trench valleys. For the cases of relatively young or old plates, the plate age could be a dominant factor in controlling the trench bending shape, regardless the variations in axial loadings. Our calculations also show that the axial loading and stresses of old subducting plates can vary significantly along the trench axis. In contrast, the young subducting plates show much smaller values and variations in axial loading and stresses.

Description: This work was supported by Chinese Academy of Sciences Grants (Y4SL021001, QYZDY-SSW-DQC005, YZ201325 and YZ201534), National Natural Science Foundation of China Grants (91628301, U1606401, 41376063 and 41706056) and HKSAR Research Grant Council Grants (24601515, 14313816).

Description: 〈span〉〈div〉Summary〈/div〉The strength of the lithosphere plays a key role in the formation and evolution of tectonic plate boundaries. Localized lithospheric deformation associated with plate tectonics requires a mechanism for weakening across the entire width of the lithosphere, including the strongest cold ductile region. We explore the microphysics of weakening of lithospheric materials, and in particular the coupled evolution of mineral grain size and intragranular defects and their control on lithospheric strength. We propose a model for the interaction between grain-boundaries and dislocation density to reduce the net free energy of grains during dynamic recrystallization (DRX). The driving forces for DRX arise from heterogeneity in dislocation density and grain boundary curvature. Our model shows that grain growth driven by variation in grain boundary curvature can be impeded by variation in dislocation density; this occurs because as the grains grow, to minimize their surface energy, their dislocation density and associated internal energy may increase and offset the driving forces for grain growth. The correlation between grain size and dislocation density can for example arise because the dislocation accumulation in smaller grains is suppressed due to the large stress that is needed to bend and elongate a short dislocation (as dictated by the small grain size), while the larger grains can have long dislocations and reach a steady state dislocation density dictated by the applied stress. In a lithospheric setting, slower grain growth means that it would require less mechanical work to establish weak localized shear zones through grain damage, and retard the healing of previously damaged zones. Furthermore, the competition of two different time-scales - that of grain growth and the dislocation kinetics - can lead to oscillating behavior over 1 to 10 years as the grain size and dislocation density advance towards their steady states. These oscillations are likely to have an effect on the rheology of lithospheric rocks, e.g. their strengthening and weakening through time, and have a potential application to geological processes such as postseismic creep in ductile shear zones.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Locating and monitoring passive seismic sources provides us important information for studying subsurface rock deformation, injected fluid migration, regional stress conditions as well as fault rupture mechanism. In this paper, we present a novel passive-source monitoring approach using vector-based elastic time-reversal imaging. By solving the elastic wave equation using observed multicomponent records as boundary conditions, we first compute back-propagated elastic wavefields in the subsurface. Then, we separate the extrapolated wavefields into compressional (P-wave) and shear (S-wave) modes using the vector Helmholtz decomposition. A zero-lag cross-correlation imaging condition is applied to the separated pure-mode vector wavefields to produce passive-source images. We compare imaging results using three implementations, i.e., dot-product, energy and power. Numerical experiments demonstrate that the power imaging condition gives us the highest resolution and is less sensitive to the presence of random noises. To capture the propagation of microseismic fracture and earthquake rupture, we modify the traditional zero-lag cross-correlation imaging condition by summing the multiplication of the separated P- and S-wavefields within local time windows, which enables us to capture the temporal and spatial evolution of earthquake rupture. 2D and 3D numerical examples demonstrate that the proposed method is capable of accurately locating point sources, as well as delineating dynamic propagation of hydraulic fracture and earthquake rupture.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Magnitudes of differential stress in the lithosphere, especially in the crust, are still disputed. Earthquake-based stress drop estimates indicate median values 〈 10 MPa whereas the lateral variation of gravitational potential energy per unit area (〈span〉GPE〈/span〉) across significant relief indicates stress magnitudes of ca. 100 MPa in average across a 100 km thick lithosphere between the Indian lowland and the Tibetan plateau. These standard 〈span〉GPE〈/span〉-based stress estimates correspond to membrane stresses, because they are associated with a deformation that is uniform with depth. We show here with new analytical results that lateral variations in 〈span〉GPE〈/span〉 can also cause bending moments and related bending stresses of several hundreds of MPa. Furthermore, we perform two-dimensional thermo-mechanical numerical simulations (1) to evaluate estimates for membrane and bending stresses based on 〈span〉GPE〈/span〉 variations, (2) to quantify minimum crustal stress magnitudes that are required to maintain the topographic relief between Indian lowland and Tibetan plateau for ca. 10 Ma and (3) to quantify the corresponding relative contribution of crustal strength to the total lithospheric strength. The numerical model includes viscoelastoplastic deformation, gravity and heat transfer. The model configuration is based on density fields from the CRUST1.0 data set and from a geophysically and petrologically constrained density model based on 〈span〉in situ〈/span〉 field campaigns. The numerical results indicate that values of differential stress in the upper crust must be 〉 ca. 180 MPa, corresponding to a friction angle of ca. 10°, to maintain the topographic relief between lowland and plateau for 〉 10 Ma. The relative contribution of crustal strength to total lithospheric strength varies considerably laterally. In the region between lowland and plateau and inside the plateau the depth-integrated crustal strength is approximately equal to the depth-integrated strength of the mantle lithosphere. Simple analytical formulae predicting the lateral variation of depth-integrated stresses agree with numerically calculated stress fields, which show both the accuracy of the numerical results and the applicability of simple, rheology-independent, analytical predictions to highly variable, rheology-dependent, stress fields. Our results indicate that (1) crustal strength can be locally equal to mantle lithosphere strength and that (2) crustal stresses must be at least one order of magnitude larger than median stress drops in order to support the plateau relief over a duration of ca. 10 Ma.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Scanning magnetometers are increasingly used to characterize the magnetization of mineral grains in rock samples. Up-scaling this measurement technique to large numbers of individual particles is hampered by the intrinsic non-uniqueness of potential-field inversion. Here it is shown that this problem can be circumvented by adding tomographic information that determines the location of the possible field sources. Standard potential theory is used to prove a uniqueness theorem which completely characterizes the mathematical background of the corresponding source-localized inversion. It exactly resolves under which conditions a potential field measurement on a surface can be uniquely decomposed into signals from the different source regions. The intrinsic non-uniqueness of potential field inversion prevents that the source distribution inside the tomographically outlined regions can be recovered, but the potential field of each region is uniquely defined. For scanning magnetometers in rock magnetism, this result implies that magnetic dipole vectors of large numbers of individual magnetic particles can be reliably reconstructed from surface scans of the magnetic field, if the particle positions are independently determined. This provides an incentive to improve scanning methods for future paleomagnetic applications.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The most common earthquake forecasting models assume that the magnitude of the next earthquake is independent from the past. This feature severely limits the capability to forecast large earthquakes with high probabilities. Here we investigate empirically on the magnitude-independence assumption, exploring if: i) background and triggered earthquakes have the same frequency-magnitude distribution, ii) variations of seismicity in the space-time-magnitude domain encode some information on the future earthquakes size. For this purpose, and to verify the stability of the findings, we consider seismic catalogues covering different space-time-magnitude windows, such as the Alto Tiberina Near Fault Observatory (TABOO), the California and Japanese seismic catalogues. Our approach is inspired by the nearest-neighbour method proposed by Baiesi & Paczuski (2004) and elaborated by Zaliapin et al. (2008) to distinguish between triggered and background earthquakes. Here we implement the same metric-based correlation to identify the precursory seismicity of any triggered earthquake; this allows us to analyse, for each triggered earthquake, the space-time-magnitude distribution of the seismicity that likely contributed to its occurrence. Our results show that the magnitude-independence assumption holds reasonably well in all catalogues, with a remarkable exception that is consistent with a previous independent study; this departure from the magnitude-independence assumption shows that larger events tend to nucleate at a higher distance from the ongoing sequence. We also notice that the reliability of this assumption may depend on the spatial scale considered; it holds for seismic catalogues of large areas, but we identify possible departures in small areas, reflecting different ways to release locally seismic energy. Finally, we come across an important issue that may lead to misleading results in similar studies, i.e., if a seismic catalogue appears overall complete above a fixed magnitude threshold, it may still yield spurious signals into the analysis. Specifically, we show that some significant departures from the magnitude-independence assumption do not survive when considering spatiotemporal variations of the magnitude of completeness.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Vp/Vs models provide important complementary information to Vp and Vs models, relevant to lithology, rock damage, partial melting, water saturation, etc. However, seismic tomography using body-wave traveltime data from local or regional earthquakes does not constrain Vp/Vs well due to the different resolution of Vp and Vs models, with the Vp models usually better constrained than Vs. Since surface-wave data are most sensitive to Vs, which leads to complementary strengths with respect to body-wave data, we jointly invert body- and surface-wave data to better resolve the Vp/Vs models. In order to show the robustness of our joint inversion method, we compare the results to other approaches, including dividing Vp by Vs models and Vp/Vs parameterization with body-wave or both body- and surface-wave data, using synthetic data and real data from the southern California plate boundary region. We confirm that Vp/Vs models from body-wave inversion obtained by division tend to include artifacts, even when both Vp and Vs models seem reasonable. The joint inversion with Vp/Vs parameterization is found to improve the Vp/Vs ratio model significantly and the resultant Vp/Vs model shows more geologically consistent features, such as high Vp/Vs along fault traces at shallow depths likely indicating fault-related damage. The Vp/Vs model also exhibits contrasts at intermediate depths along the Peninsular Range compositional boundary, and high Vp/Vs in the lower crust near the Salton Sea region correlated with high heat flow and may indicate partial melting. The improved Vp/Vs as well as individual Vp and Vs models are useful for earthquake relocation, high-resolution Moho depth imaging, and interpretation of other data and tectonic evolution in the region.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Interpretation of surface fault scarps and palaeoseismic trenches is a key component of estimating fault slip rates, earthquake recurrence rates and maximum magnitudes for hazard assessments. Often these analyses rely on the assumption that successive earthquakes all breached the surface and that the ruptures are recorded topographically, or by the deposits exposed in a trench. The M〈sub〉〈span〉w〈/span〉〈/sub〉7.2 1992 Suusamyr earthquake, Kyrgyzstan, is an apparently problematic case for such analyses because its ruptures show significant displacement but are only mapped as having broken the surface along small, disparate portions of the fault. Here we present the results of surveys conducted along the Suusamyr Fault to establish whether that is the case. Two sets of ruptures were identified following the earthquake. They are unusually short for their displacement and are separated by a 25 km gap. Using satellite imagery, high-resolution digital elevation models and palaeoseismic trenching we first reassess the distribution of the 1992 ruptures and then reconstruct the Holocene earthquake record to establish the extent to which the 1992 earthquake is representative of the rupture behaviour of this fault. We find evidence for at least two prehistoric surface rupturing earthquakes in the Holocene: one ∼3 ka and one 〉8 ka that, along with the modern event, gives recurrence intervals of ∼3 kyr and ∼5 kyr. Within spatial gaps between segments of the 1992 ruptures there are clear prehistoric surface ruptures and the ruptures in each prehistoric earthquake were discontinuous. We conclude that there is significant variability in the surface rupture pattern of successive earthquakes on the Suusamyr Fault, with implications for the completeness of palaeoseismic records obtained from thrust scarps.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We provide a six-component (6-C) polarization model for 〈span〉P〈/span〉-, 〈span〉SV〈/span〉-, 〈span〉SH〈/span〉-, Rayleigh-, and Love-waves both inside an elastic medium as well as at the free surface. It is shown that single-station 6-C data comprised of three components of rotational motion and three components of translational motion provide the opportunity to unambiguously identify the wave type, propagation direction, and local 〈span〉P〈/span〉- and 〈span〉S〈/span〉-wave velocities at the receiver location by use of polarization analysis. To extract such information by conventional processing of three-component (3-C) translational data would require large and dense receiver arrays. The additional rotational components allow the extension of the rank of the coherency matrix used for polarization analysis. This enables us to accurately determine the wave type and wave parameters (propagation direction and velocity) of seismic phases, even if more than one wave is present in the analysis time window. This is not possible with standard, pure-translational 3-C recordings. In order to identify modes of vibration and to extract the accompanying wave parameters, we adapt the multiple signal classification algorithm (MUSIC). Due to the strong nonlinearity of the MUSIC estimator function, it can be used to detect the presence of specific wave types within the analysis time window at very high resolution. We show how the extracted wavefield properties can be used, in a fully automated way, to separate the wavefield into its different wave modes using only a single 6-C recording station. As an example, we apply the method to remove surface wave energy while preserving the underlying reflection signal and to suppress energy originating from undesired directions, such as side-scattered waves.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The Sentinel-1 mission comprises two synthetic aperture radar satellites, each with a 12 day orbital repeat, orbiting 6 days apart within a narrow tube. The mission design promises the ability to respond quickly to earthquakes with InSAR, and to facilitate production of interferograms with good interferometric correlation globally. We report on our efforts to study global seismicity using Sentinel-1 Interferometric Wide-Swath data between April 2015 and December 2016. We select 35 potentially detectable terrestrial earthquakes in the range 5.5 ≤ 〈span〉Mw〈/span〉 ≤ 7.8 on the basis of their locations, depths and magnitudes, and process the first post-event interferogram with the shortest possible time-span for each using the ISCE software. We evaluate each interferogram for earthquake deformation signals by visual inspection. We can identify deformation signals attributable to earthquakes in 18 of these interferograms (51%); a further six interferograms (17%) have ambiguous interferometric phase affected by tropospheric noise. 11 events (31%) could not be identified from their interferograms. The majority of these failed detections were due to interferogram decorrelation, particularly apparent for earthquakes that occurred between 15°N and 15°S, where climate conditions promote dense vegetation. The majority of the ambiguous interferograms are affected by tropospheric noise, suggesting that techniques to mitigate such noise could improve detection performance. The largest event we do not detect with Sentinel-1 data is a 〈span〉Mw〈/span〉7.0 earthquake that occurred in Vanuatu in April 2016; we also fail to detect the 2016 〈span〉Mw〈/span〉6.2 Kurayoshi earthquake in one out of two possible 24-day interferograms. We propose these as upper and lower estimates on the magnitude of completeness for earthquakes studied with Sentinel-1 data; to raise the magnitude of completeness we suggest that more frequent (e.g. six day) recurrence may be necessary in low latitude areas.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The correct estimation of site-specific attenuation is crucial for the assessment of seismic hazard. Downhole instruments provide in this context valuable information to constrain attenuation directly from data. In this study, we apply an interferometric approach to this problem by deconvolving seismic motions recorded at depth with those recorded at the surface. In doing so, incident and surface-reflected waves can be separated. We apply this technique not only to earthquake data but also to recordings of ambient vibrations. We compute the transfer function between incident and surface-reflected waves in order to infer frequency dependent quality factors for S-waves. The method is applied to a 87 m deep borehole sensor and a co-located surface instrument situated at a hard-rock site in West Bohemia/Vogtland, Germany. We show that the described method provides comparable attenuation estimates using either earthquake data or ambient noise for frequencies between 5-15 Hz. Moreover, a single hour of noise recordings seems to be sufficient to yield stable deconvolution traces and quality factors, thus, offering a fast and easy way to derive attenuation estimates from borehole recordings even in low to mid seismicity regions.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Injection of CO〈sub〉2〈/sub〉 into tight reservoirs produces both gravity change and ground deformation, which provide great opportunities for more accurate coupled inverse modelling. In this study, we incorporate signals generated from several synthetic models to estimate the CO〈sub〉2〈/sub〉 distribution in the reservoir. A relationship is found that connects density variations to volumetric changes associated with injected CO〈sub〉2〈/sub〉, taking advantage of a common set of model parameters for both gravitational and geo-mechanical inverse modelling. This is achieved by assuming that the injected CO〈sub〉2〈/sub〉 increases pressure in the reservoir, which in turn generates extra porosity that is then filled in by the CO〈sub〉2〈/sub〉 mass in the generated space. Tikhonov regularization, supported by the Generalized Cross Validation (GCV) technique for finding the optimized model, is used to solve the ill-posed inverse problems. The results indicate that with a combination of gravity and ground deformation monitoring, the uncertainty and ambiguity in gravimetric modelling due to high levels of noise is mitigated by implementing highly accurate ground deformation measurements, which normally have a higher signal to noise ratio.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉As the number of seismic sensors grows, it is becoming increasingly difficult for analysts to pick seismic phases manually and comprehensively, yet such efforts are fundamental to earthquake monitoring. Despite years of improvements in automatic phase picking, it is difficult to match the performance of experienced analysts. A more subtle issue is that different seismic analysts may pick phases differently, which can introduce bias into earthquake locations. We present a deep-neural-network-based arrival-time picking method called ”PhaseNet” that picks the arrival times of both P and S waves. Deep neural networks have recently made rapid progress in feature learning, and with sufficient training, have achieved super-human performance in many applications. PhaseNet uses three-component seismic waveforms as input and generates probability distributions of P arrivals, S arrivals, and noise as output. We engineer PhaseNet such that peaks in the probability distributions provide accurate arrival times for both P and S waves. PhaseNet is trained on the prodigious available data set provided by analyst-labeled P and S arrival times from the Northern California Earthquake Data Center. The dataset we use contains more than seven hundred thousand waveform samples extracted from over thirty years of earthquake recordings. We demonstrate that PhaseNet achieves much higher picking accuracy and recall rate than existing methods when applied to the waveforms of known earthquakes, which has the potential to increase the number of S-wave observations dramatically over what is currently available. This will enable both improved locations and improved shear wave velocity models.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The low frequency earthquakes (LFEs) that constitute tectonic tremor are often inferred to be slow: to have durations of 0.2 to 0.5 s, a factor of 10 to 100 longer than those of typical 〈span〉MW〈/span〉 1-2 earthquakes. Here we examine LFEs near Parkfield, CA in order to assess several proposed explanations for LFEs’ long durations. We determine LFE rupture areas and location distributions using a new approach, similar to directivity analysis, where we examine how signals coming from various locations within LFEs’ finite rupture extents create differences in the apparent source time functions recorded at various stations. We use synthetic ruptures to determine how much the LFE signals recorded at each station would be modified by spatial variations of the source-station travel time within the rupture area given various possible rupture diameters, and then compare those synthetics with the data. Our synthetics show that the methodology can identify inter-station variations created by heterogeneous slip distributions or complex rupture edges, and thus lets us estimate LFE rupture extents for unilateral or bilateral ruptures. To obtain robust estimates of the sources’ similarity across stations, we stack signals from thousands of LFEs, using an empirical Green’s function approach to isolate the LFEs’ apparent source time functions from the path effects. Our analysis of LFEs in Parkfield implies that LFEs’ apparent source time functions are similar across stations at frequencies up to 8 to 16 Hz, depending on the family. The inter-station coherence observed at these relatively high frequencies, or short wavelengths (down to 0.2 to 0.5 km), suggest that LFEs in each of the 7 families examined occur on asperities. They are clustered in patches with sub-1-km diameters. The individual LFEs’ rupture diameters are estimated to be smaller than 1.1 km for all families, and smaller than 0.5 km and 1 km for the two shallowest families, which were previously found to have 0.2-s durations. Coupling the diameters with the durations suggests that it is possible to model these 〈span〉MW〈/span〉 1-2 LFEs with earthquake-like rupture speeds: around 70% of the shear wave speed. However, that rupture speed matches the data only at the edge of our uncertainty estimates for the family with highest coherence. The data for that family are better matched if LFEs have rupture velocities smaller than 40% of the shear wave speed, or if LFEs have different rupture dynamics. They could have long rise times, contain composite sub-ruptures, or have slip distributions that persist from event to event.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉On June 24, 2015, a 230,000 cubic metre landslide slid into the triangle bayou at the intersection of the Yangtze and Daning Rivers and generated a river tsunami that ran up 6.2 metres on the opposite shoreline at Wushan town. The slope failure and resulting waves killed two people and damaged many shipping facilities. Based on field surveys and eyewitness observations, we apply the ‘Tsunami Squares’ method to model the Hongyanzi landslide and its generated waves. Landslide simulations indicate a maximum impact velocity of ∼16 m/s that matches well with an eyewitness video. The computed post-slide mass stopped on the near riverbed with a shape fitting the observed geological profile. Tsunami simulations reveal a large region of wave impacts that coincide with the observed runup heights. The successful reproduction of the dynamics of this landslide-generated river tsunami emphasizes the capacity and efficiency of Tsunami Squares modeling in emergency reaction and risk assessment.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Improvement of global 3D Earth density and velocity models is based in part on measurements of Earth’s normal mode eigenfrequencies and splitting function coefficients. Despite many methods developed inconsistency in measurements still exists and it is difficult to understand which results are more precise, that is which methods introduce less systematic biases in the measurements. Therefore, the main goal of this study is to test the performances of typically used techniques in low-frequency normal mode studies: the optimal sequence estimation stacking method and the autoregressive method in the frequency domain, where validation of the estimates is performed with the phasor walkout method. Motivations for their utilization are their easy and fast implementation and their accurate performances when it comes to eigenfrequency estimates. For this purpose, we first perform the analysis with synthetic seismograms in order to evaluate how the station distributions and noise levels impact the estimates of eigenfrequencies and structure coefficients. Synthetic seismograms are calculated for a 3D realistic Earth model, which includes Earth’s rotation as well as ellipticity and other lateral heterogeneities. They were computed by means of normal mode summation and a perturbation theory for modes up to 1 mHz. The three methods above are also applied to long-period seismometer and superconducting gravimeter data recorded after six earthquakes of magnitude greater than 8.3. Finally, our study shows that the optimal sequence estimation is sensitive to the station distribution under the noise influence, while the autoregressive method for frequency estimation gives us reasonable estimates within the estimated error bars. Moreover, we present new estimates of eigenfrequencies and Q-factors for 〈sub〉0〈/sub〉S〈sub〉2, 0〈/sub〉S〈sub〉3, 2〈/sub〉S〈sub〉1〈/sub〉 and 〈sub〉3〈/sub〉S〈sub〉1〈/sub〉 multiplets. A new value for the 〈span〉c〈/span〉〈sub〉20〈/sub〉 structure coefficient of 〈sub〉0〈/sub〉S〈sub〉2〈/sub〉 multiplet −0.7233 ± 0.0623 μHz is obtained.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We propose a novel approach to compute the gravity field due to density anomaly in both outside and inside of the solid Earth with high accuracy and efficiency. The high accuracy comes from the direct employment of the analytic gravitation solution between any point on a two-dimensional (2D) plane in the horizontal direction and individual mass cubes. The high computational efficiency comes from two aspects: 1, the application of the highly efficient 2D discrete convolution algorithm; and 2, a newly developed algorithm for the optimized computation of the weight coefficient matrix. Numerical examples for applying to compare with analytical solutions demonstrated its excellent accuracy. Comparison with other state-of-the-art gravity modeling algorithm has proved that this algorithm has superior performance in both accuracy and efficiency. Application to analyze real topography demonstrated the practicality. This algorithm will be an attractive candidate for carrying out the forward modeling step in geophysical inversion problems with the claimed and proved advantages.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We assess the stress field that drives lithospheric deformation, focusing on the active New Zealand plate boundary zone between the Australian and Pacific plates. Here there is a rich database for the horizontal velocity field and crustal structure, used to derive gravitational potential energy (GPE). We solve the stress balance equations, in the context of a thin sheet model of a viscously deforming lithosphere, for characteristic deviatoric stresses and viscosities, defined as the integral of these with depth (divided by the layer thickness), using the stress method of Flesch 〈span〉et al.〈/span〉 (2001), where the input parameters are the fields of strain rate and GPE that apply to the sheet. Synthetic tests show that the stress method is able to resolve the stress field to high (20 per cent) levels of noise in the input strain rates, and the mean stress is a very robust feature of the inversions, regardless of noise levels. We invert for the stress and viscosity fields in New Zealand, calculating the field of GPE from topography/bathymetry and crustal data, and the field of strain rates from either a long term (multi millennial) velocity field inferred from the rate and pattern of Quaternary faulting, or a short term (decadal) velocity field directly observed with decadal Global Positioning System (GPS) measurements. In addition, we consider the effect of shear stresses on the subducted plate interface along the Hikurangi Margin (5–15 MPa), or regionally. We explore the effect of GPE on the inversion results by calculating these for a range of deforming layers (ie thin sheet with 35–150 km thickness), in effect sampling the lithospheric strength in the crust and mantle. The results show that the derived stress magnitudes (square root second invariant of the stress deviator) are in the range 0–35 MPa, with mean values of 13 ± 1 MPa for all models, comparable to typical earthquake stress drops. Gravitationally induced stresses account for approximately half of the full deviatoric stress. Effective characteristic viscosities are 0.5 - 5 × 10〈sup〉21〈/sup〉 Pas in the deforming zone, with an approximate inverse relation between strain rate and viscosity, most likely controlled by thermal structure and/or lithology.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉I present a source-independent fracture imaging method to use passive seismic data for mapping subwavelength natural fractures. Unlike conventional source-dependent imaging that often adopts reflection-type seismic imaging with known source that is not available in passive seismic surveys, the proposed fracture imaging approach relies on the transmission and diffraction data without the need for source information. I assume that passive seismic data can be decomposed into two types of data: primary transmission wave data and diffraction (coda) wave data. The imaging formula states that primary waves should coincide with coda waves at scatterer points at the time of scattering. Instead of generating source wavefields in the conventional imaging method, the proposed method only need to propagate transmission wave data and diffraction wave data from the receiver arrays and apply an imaging condition to produce an image of fractures. This imaging procedure can be used for processing P-wave or S-wave. In synthetic examples, I evaluate the proposed method in several aspects: inaccurate source location, inaccurate velocity model, sparse receivers and irregular receiver spacing, elastic data, and joint surface and borehole acquisitions. I found that the proposed approach performed well (or even better) comparable to source-dependent fracture imaging when assuming exact source information is known. With perturbed source locations with random shifts (e.g., estimated source location with errors), however, fractures were missing in the source-dependent fracture imaging results but the proposed approach was not influenced. In the presence of velocity errors and sparse and irregular receiver spacing, the proposed method produces better fracture images than the source-dependent imaging results.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We introduce a formalism for estimating local spatial averages of the core-mantle boundary (CMB) radial magnetic field and its time derivatives, based on magnetic field observations collected by low-Earth-orbit satellites. This provides a useful alternative to conventional core field modelling based on global spherical harmonic basis functions, where noise in the polar regions maps into all harmonics, and model regularization and spectral truncation are required. A powerful perspective offered by the proposed technique is formal appraisal of the spatial resolution and variance of the resulting field averages. We use the Green’s functions for the Neumann boundary value problem to link the satellite observations to the radial magnetic field on the CMB and estimate field averages using a modified Backus-Gilbert inversion approach. Our approach builds on the Subtractive Optimally Localized Averages (SOLA) method developed in helioseismology, that seeks averaging kernels as close as possible to a chosen target kernel. We are able to account for both internal and external field sources and can easily incorporate data error covariance information, for example describing along-track serial error correlation. As a proof of concept we present a global map collecting local estimates of the radial main field (MF) constructed on a grid at the CMB with one degree spacing in latitude and longitude, derived from one month of three component vector magnetic field data collected by the 〈span〉Swarm〈/span〉 satellite trio, using data from dark and geomagnetically quiet times. Using sums and differences of the field components taken along track and in the east-west direction we obtain estimates with spatial resolution kernel widths varying between 18 and 54 degrees depending on the latitude, and a standard deviation of approximately 10μT (i.e. 5% of the mean CMB field amplitude). The morphology of our CMB radial field map agrees well with results from conventional spherical harmonic field models. In a second application, we determine local estimates of the average rate of change, or secular variation (SV), of the radial field at the CMB, initially considering two year time windows, and performing the analysis on data collected by either the 〈span〉Swarm〈/span〉 or CHAMP satellites. We obtain stable local estimates of the SV at the CMB, and present maps of estimates with averaging kernel widths of approximately 42, 33 and 30 degrees on the equator, with corresponding standard derivations of 0.25, 2.5 and 5 μT/yr. By subtracting SV estimates constructed at different epochs we are able to calculate the local aggregated secular acceleration (SA) and to study its time changes. Differencing SV estimates 2 years apart, and considering an averaging kernel width of 42 degrees on the equator, we obtain SA maps very similar to those found in the CHAOS-6-x7 field model truncated at SH degree 10. Using our approach we are able to directly control the width of the spatial averaging kernel and the length of the time window, enabling us to directly study the robustness of the inferred SA. Pushing to higher resolution in time, considering one year differences of SV estimates constructed using one year windows, we are able to track the evolution of coherent SA structures in time-longitude plots at the equator. At 25° W in mid 2007 we find a distinctive SA ’cross-over’ event, with strong, oppositely signed and adjacent, SA features rapidly changing sign within a year. Our method is well suited for studying such spatio-temporally localized SA events at high resolution; there will be further opportunities for such investigations as the time series of data provided by the 〈span〉Swarm〈/span〉 mission lengthens.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The evolution of the ratio between P- and S-wave velocity (〈span〉V〈/span〉〈sub〉P〈/sub〉/〈span〉V〈/span〉〈sub〉S〈/sub〉) with increasing fluid-saturated porosity is computed for isotropic rocks containing spheroidal pores. The ratio 〈span〉V〈/span〉〈sub〉P〈/sub〉/〈span〉V〈/span〉〈sub〉S〈/sub〉 is shown to either decrease or increase with increasing porosity, depending on the aspect ratio α of the pores, fluid to solid bulk modulus ratio ζ, and Poisson’s ratio ν〈sub〉0〈/sub〉 of the solid constituents of the rock. A critical initial Poisson’s ratio ν〈sub〉0, crit〈/sub〉 is computed, separating cases where 〈span〉V〈/span〉〈sub〉P〈/sub〉/〈span〉V〈/span〉〈sub〉S〈/sub〉 increases (if ν〈sub〉0〈/sub〉 〈 ν〈sub〉0, crit〈/sub〉) or 〈span〉decreases〈/span〉 (if ν〈sub〉0〈/sub〉 〉 ν〈sub〉0, crit〈/sub〉) with increasing porosity. For thin cracks and highly compressible fluids, ν〈sub〉0, crit〈/sub〉 is approximated by 0.157 ζ/α, whereas for spherical pores ν〈sub〉0, crit〈/sub〉 is given by 0.2 + 0.8ζ. When ν〈sub〉0〈/sub〉 is close to ν〈sub〉0, crit〈/sub〉, the evolution of 〈span〉V〈/span〉〈sub〉P〈/sub〉/〈span〉V〈/span〉〈sub〉S〈/sub〉 with increasing fluid-saturated porosity is near neutral and depends on subtle changes in pore shape and fluid properties. This regime is found to be relevant to partially dehydrated serpentinites in subduction zones (porosity of aspect ratio near 0.1 and ζ in the range 0.01–0.1), and makes detection of these rocks and possibly elevated fluid pressures difficult from 〈span〉V〈/span〉〈sub〉P〈/sub〉/〈span〉V〈/span〉〈sub〉S〈/sub〉 only.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Secondary microseismic sources emit seismic waves over long time spans. Reoccurring signals with similar slowness and frequency therefore arrive at seismic arrays. Blind source separation techniques can be used to identify and isolate such reoccurring signals from other signals and from diffuse seismic noise. Along these lines, we use non-negative matrix factorization as blind source separation technique to decompose continuous seismic array records. We model the recorded energy as a mixture of a few components with static slowness-frequency and time dependent amplitudes. Components and amplitudes are fitted to optimally explain the recorded seismic energy over time. These components represent secondary microseismic signals with quasi-static slowness-frequency vector and fluctuating amplitude. Each fitted component reveals the geographical origin (through the slowness-frequency vector) and time evolution of an active secondary microseism with high precision because it is separated from other signals and diffuse seismic noise. Furthermore, relative travel times can be automatically extracted for the signals that correspond to a specific component that can potentially be used in tomographic studies. We show two examples of seismic signals that were extracted with this technique, one focusing on P-waves from the typhoons Goni and Atsani, and another showing secondary microseism PKP signals from typhoon Glenda.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Locating microseismic events is essential for many areas of seismology including volcano and earthquake monitoring and reservoir engineering. Due to the large number of microseismic events in these settings, an automated seismic location method is required to perform real time seismic monitoring. The measurement environment requires a precise and noise-resistant event location method for seismic monitoring. In this paper, we apply Multichannel Coherency Migration (MCM) to automatically locate microseismic events of induced and volcano-tectonic seismicity using sparse and irregular monitoring arrays. Compared to other migration-based methods, in spite of the often sparse and irregular distribution of the monitoring arrays, the MCM can show better location performance and obtain more consistent location results with the catalogue obtained by manual picking. Our MCM method successfully locates many triggered volcano-tectonic events with local magnitude smaller that 0, which demonstrates its applicability on locating very small earthquakes. Our synthetic event location example at a carbon capture and storage site shows that continuous and coherent drilling noise in industrial settings will pose great challenges for source imaging. However, automatic quality control techniques including filtering in the frequency domain and weighting are used to automatically select high quality data, and can thus effectively reduce the effects of continuous drilling noise and improve source imaging quality. The location performance of the MCM method for synthetic and real microseismic datasets demonstrates that the MCM method can perform as a reliable and automatic seismic waveform analysis tool to locate microseismic events.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The unification of local height systems has been a classical geodetic problem for a long time, the main challenges of which are the estimation of offsets between different height systems and the correction of tilts along the levelling lines. It has been proposed to address these challenges with clock networks. The latest generation of optical clocks as well as the dedicated frequency links, e.g., optical fibres, are now approaching to deliver the comparison of frequencies at the level of 1.0 × 10〈sup〉−18〈/sup〉. It corresponds to an accuracy of about 1.0 cm in height difference. Clock networks can thus serve as a powerful tool to connect local height systems. To verify the idea, we carried out simulations using the EUVN/2000 (European Unified Vertical Network) as a priori input. Four local height systems were simulated from the EUVN/2000 by introducing individual offsets and tilts, and were re-unified by using measurements in clock networks. The results demonstrate the great potential of clock networks for height system unification. In case that the offsets between different height systems and tilts along national levelling lines in both longitudinal and latitudinal directions are considered, three or four clocks measurements for each local region are sufficient for the unification. These clocks are to be interconnected and should be properly arranged so that they can sense the levelling tilts where necessary. Our results also indicate that even clocks with one magnitude poorer accuracy than the desired ones can still unify the height systems to some extent, but it may cause a shift for the re-unified system.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We investigate slip-distribution models of the 2011 Tohoku earthquake, with a particular focus on diffracted tsunamis and uplift-induced waves along the back-arc region of the Japanese Island Arc.The 2011 Tohoku earthquake produced a large amplitude tsunami that diffracted around Kyushu Island before reaching Korea. At the same time, this earthquake co-seismically induced short-period small-amplitude sea waves in the East Sea. We performed tsunami simulations using seven fault models of the Tohoku earthquake to examine whether the models can accurately reproduce the observed waveforms in the open sea of the western Pacific Ocean, the South Sea of Korea, and the coast of the East Sea. For each fault model, we investigate tsunami features due to geomorphological characteristics of the Korean Peninsula in the Korea offshore. To determine which slip distribution model shows a good performance in the tsunami simulations, we set three criteria; the delay time between observations and synthetic waveforms, the normalized mean residual, and the normalized RMS misfit. Depending on the study region, all models show varying degrees of accuracy. The fault dimensions and the amount of slip have a larger effect on the RMS misfit then the slip distribution patterns of the fault models for observations along the Korean coast and the western coast of Japan.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉The study of radiation patterns in poroelastic media allows us to visually explore the possibility of reconstructing crucial model properties describing reservoir rocks, and to examine the coupling effects between different parameters during full-waveform inversion (FWI). In this paper, we derive analytical formulae for the radiation patterns of single parameter perturbations in fluid-saturated porous media by deriving scattered wavefields based on plane-wave theory and the far-field approximation. We illustrate these scattered wavefields via their radiation patterns expressed as a function of the angle between the incident and scattered waves. To simplify the algebra, we consider poroelastic waves at seismic (low) frequencies, where the fast compressional wave and shear wave are propagating modes but the slow compressional wave is severely dispersive. To verify our derivation of the analytical radiation patterns, we also compute them numerically by perturbing one parameter at a single point, keeping the other parameters fixed at their background values. We find that all the analytical radiation patterns match the wavefronts of the numerically computed scattered wavefields, well indicating that our derivations are correct. Parameters such as the solid density, fluid density, viscosity of the fluid, and intrinsic permeability, have similar radiation patterns and thus show strong coupling effects. Therefore, we anticipate difficulties in recovering these parameters in a multi-parameter FWI procedure. In an attempt to mitigate these trade-offs, we analyze different parameterizations which result in different radiation patterns. As the patterns that we observe are similar to those of the elastic case, we anticipate that parameter separation might be easier when inverting for velocities than for moduli.〈/span〉

Description: 〈span〉〈div〉Abstract〈/div〉In the Sea of Marmara, areas of gas seepage or cold seeps are tightly related to the faults system and understanding the spatial and temporal dynamics in gas-related processes is crucial for geohazard mitigation. Although acoustic surveys proved to be efficient in detecting and locating cold seeps, temporal variability or trends in the gas-related processes are still poorly understood. Two arrays of 10 ocean bottom seismometers were deployed in the western part of the Sea of Marmara in 2011 and 2014, respectively. In addition to the local seismic events, the instruments recorded a large number of short duration events and long-lasting tremors. Short duration events are impulsive signals with duration 〈 1 s, amplitude well above the noise level and a frequency spectrum with one or two narrow peaks. They are not correlated from one site to another, suggesting a very local source. Tremors consist of sequences of clustered impulsive signals lasting for minutes to more than an hour with a multi-peak frequency spectrum. Based on evidence of known seepage and by analogy with volcanic and hydrothermal models, we suggest that short duration events and tremors are associated with gas migration and seepage. There is a relationship between tremors associated with gas emission and the local seismicity, although not systematic. Rather than triggering gas migration out of the seabed, locally strong earthquakes act as catalysts when gas is already present or gas emission is already initiated.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Long-period Rayleigh wave Horizontal to Vertical amplitude (H/V) ratios at a station provide information about local earth structure that is complementary to phase velocity. However, a number of studies (Ferreira and Woodhouse, 2007; Lin 〈span〉et al.〈/span〉, 2012) have observed that significant scatter appears in these measurements making it difficult to use H/V ratio measurements to resolve earth structure. Some of the scatter in these measurements has been attributed to local geological structure while some has remained unaccounted for. Most Global Seismographic Network (GSN) stations contain two nearby high-quality broadband seismometers (e.g. in the same vault, but on different piers or in different boreholes). For each broadband sensor in the IRIS/USGS component of the GSN, we estimate H/V ratios of fundamental mode Rayleigh waves using M 〉 6.5 earthquakes from 2001 to 2018 (around 19,000 measurements). We compute these ratios at a number of discrete periods (25, 50, 75, 100, and 150 s) and find that for well-isolated Rayleigh waves (windows where the correlation coefficients between radial and the phase-shifted vertical components are greater than 0.9) significant scatter in H/V ratios occurs between co-located sensors (greater than 25 per cent at 100 s period). This suggests the scatter in H/V ratio measurements can be at least partially attributed to extremely local phenomena such as sensor emplacement in the vault. We also find that H/V ratios can vary as a function of event back-azimuth, indicating that care must be taken when computing average ratios for a station, as a large number of events from a given region could bias H/V ratio measurements at a station.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We analyse noise characteristics of spatial and temporal correlation of 260 continuous GPS sites from Crustal Movement Observation Network of China (CMONOC). These data sets were mainly collected between 2010 and 2016, with an average of 6 yr of position time-series. In the functional analysis, a clear regional dependence of seasonal movements has been observed and other significant periodic signals are detected nearby the GPS draconitic period and its harmonics. The distribution of these periodic signals shows a spatial correlation, along with non-negligible local inconsistencies. In the stochastic analysis, impacts of the periodicities on the noise assessment have been investigated and Maximum likelihood estimation is used to study noise properties for deseasonalized residual time-series having the seasonal signals removed and filtered residual time-series having other periodic signals removed further. We demonstrate that for both solutions, the flicker noise is thought to be the dominant time-correlated noise and velocity uncertainties may be underestimated 8–10 times if assuming a pure white noise. Ignoring the periodicities could bias the estimation of noise amplitude, spectral index and velocity uncertainty. After removing the periodic signals, the median flicker noise magnitude shows an average of ∼10 per cent reductions and the noise process shifts closer towards white noise. A correlation between the index variations and RMS variations has been observed, indicating that the index varies more significantly for sites with more periodic signals removed. Besides, the spectral index in the vertical component has a better spatial correlation than that in the horizontal and the spatial distribution of the index of deseasonalized solutions seems to correlate well with the amplitudes of seasonal signals, probably implying common sources of spatial variations of these characteristics. Furthermore, analyses of intersite correlations indicate that the correlation induced from the periodic signals displays a similar pattern to the deseasonalized solutions, confirming that the period pattern is spatially correlated and can induce time-series correlations. Finally, the stochastic processes of the common mode noise are predominantly featured by spatially correlated flicker and white noise over a wide range, consistent with previous results.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉As temperature increases with depth and the creep resistance of rock decreases exponentially, a high-viscosity sub-lithospheric layer, just beneath the ‘elastic’ lithosphere is expected to exist. Depending on the temperature profile, a low-viscosity asthenosphere may also exist if the temperature deeper down gets high enough. Since the temperature profile is expected to change laterally – especially from below the oceans to cratonic areas underneath continents, rock properties of the lithosphere, high-viscosity sub-lithosphere and low-viscosity asthenosphere are expected to change laterally. Our aim is to constrain sub-lithospheric properties (depth, thickness and viscosity), lateral lithospheric thickness variations and asthenospheric properties using observed GIA data. A Coupled Laplace-Finite Element Method is used to compute gravitationally self-consistent sea level with time-dependent coastline and rotational feedback in addition to changes in deformation, gravity and the state of stress. We start with the VM5a-ICE-6G_C model combination and then modify the lithospheric, sub-lithospheric and asthenospheric properties (including lateral thickness variation) while keeping the mantle viscosities the same as VM5a. Through this study, we confirm that the sub-lithospheric and asthenospheric properties can significantly affect the predicted global relative sea level (RSL), present-day gravity rate-of-change (g-dot) and uplift rate (u-dot) in Laurentia and Fennoscandia. In addition, incorporating the elastic lithosphere with lateral thickness variation, sub-lithosphere and asthenosphere can improve the fit to global RSL, but the predicted peak values of g-dot and u-dot in Laurentia may decrease slightly but not significant enough to affect the fit to the observed data. Our results prefer an elastic lithosphere that has maximum thickness of 140 km under continental cratons but reduces to 60 km underneath the oceans. The results preferred depth of the asthenospheric bottom is around 190–200 km with asthenospheric viscosity around 10〈sup〉20〈/sup〉Pa s. Finally, we show that the best laterally heterogeneous mantle model we found in previous publication when combined with the lithosphere with lateral thickness variaion gives the best fit to global RSL and peak g-dot and u-dot in Laurentia simultaneously.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We implement an analytical model based on flexural deflection of a thin elastic disc to investigate the magnitude of lithospheric decompression caused by deglaciation at upper crustal magmatic reservoirs. Considering a published numerical climate model describing the space–time evolution of deglaciation after the Last Glacial Maximum (LGM) along the Southern Volcanic Zone (SVZ) of the Andes, we demonstrate that changes in pressure at upper crustal levels (〈10 km depth) at the scale of several hundred years are of the order of 10–100 MPa. Total decompression and decompression rate (300–150 kPa yr〈sup〉−1〈/sup〉) are 1–2 orders of magnitude larger than values previously estimated by other authors who assume that glacial loads are supported by an elastic half-space, that is, of infinite elastic thickness. The large decompression caused by flexural unbending of an elastic plate of finite thickness as assumed here can easily surpass the tensile strength of rocks (5–20 MPa), creating adequate conditions for failure of the reservoir walls, dike propagation inside and outside the reservoir and the eventual collapse of the reservoir accompanying an explosive eruption. We apply our results to the analysis of post-glacial eruptions of SVZ volcanoes, which erupted large volumes (〉10 km〈sup〉3〈/sup〉) of mafic ignimbrites hundreds to thousands of years after deglaciation onset. We show that this time lag is necessary to achieve a decompression of several tens of megapascals at depths of several kilometres that are consistent with the location of magmatic reservoirs as estimated by independent petrologic, seismic and/or geodetic studies. Moreover the northward increase of this time lag is in agreement with a smaller size of the Andean ice cap in the north than in the south during the LGM. For wet, volatile-rich magmas typical of subduction zones, the effect of large decompression at upper crustal reservoirs caused by flexural unbending of the lithosphere after deglaciation could play a major role in promoting large explosive eruptions through devolatization of the magma, during past deglaciation events as demonstrated here for the LGM along the SVZ and current accelerated ice retreat caused by climate change over large segments of subduction-related arcs at higher latitudes.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉The unification of local height systems has been a classical geodetic problem for a long time, the main challenges of which are the estimation of offsets between different height systems and the correction of tilts along the levelling lines. It has been proposed to address these challenges with clock networks. The latest generation of optical clocks as well as the dedicated frequency links, for example optical fibres, are now approaching to deliver the comparison of frequencies at the level of 1.0 × 10〈sup〉−18〈/sup〉. It corresponds to an accuracy of about 1.0 cm in height difference. Clock networks can thus serve as a powerful tool to connect local height systems. To verify the idea, we carried out simulations using the EUVN/2000 (European Unified Vertical Network) as 〈span〉apriori〈/span〉 input. Four local height systems were simulated from the EUVN/2000 by introducing individual offsets and tilts, and were reunified by using measurements in clock networks. The results demonstrate the great potential of clock networks for height system unification. In case that the offsets between different height systems and tilts along national levelling lines in both longitudinal and latitudinal directions are considered, three or four clocks measurements for each local region are sufficient for the unification. These clocks are to be interconnected and should be properly arranged so that they can sense the levelling tilts where necessary. Our results also indicate that even clocks with one magnitude poorer accuracy than the desired ones can still unify the height systems to some extent, but it may cause a shift for the reunified system.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Waveform backprojection (BP) is a key technique of earthquake-source imaging, which has been widely used for extracting information of earthquake source evolution that cannot be obtained by kinematic source inversion. The technique enjoys considerable popularity, owing to the simplicity of its implementation and the robustness of its processing, but the physical meaning of BP images has remained elusive. In this study, we reviewed the mathematical representation of BP and hybrid BP (HBP) methods, following the pioneering work of Fukahata 〈span〉et al〈/span〉. (〈a href="http://academic.oup.com/gji#bib15"〉2014〈/a〉), to clarify the physical implications of BP images. We found that signal intensity in BP and HBP images is scaled with the amplitude of the Green’s function that corresponds to a unit-step slip, which results in the signal intensity being depth dependent. We propose variants of BP and HBP, which we call kinematic BP and HBP, respectively, to relate the BP signal intensity to slip motion of an earthquake by modifying the normalizing factors used in the original BP and HBP methods. The original BP and HBP images remain useful for assessing the spatiotemporal strength of the wave radiation, which scales with the amplitude of the Green’s function, whereas the kinematic BP and HBP methods are suitable for imaging the slip motion that is responsible for the high-frequency radiation produced during the source-rupture process.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉 〈strong〉Moment Tensors of hydraulically induced AEs:〈/strong〉 Hydraulic fracturing is an important technique in the development of enhanced geothermal systems and unconventional resources. Although the fracture modes induced by hydraulic fracturing influence the recovery efficiency of the resources, the current understanding of this relationship is insufficient. In this study, we considered the acoustic emissions (AEs) induced during hydraulic fracturing under uniaxial loading conditions in the laboratory, and applied a moment tensor analysis by carefully correcting the coupling condition and directivity of AE transducers. Experiments were conducted for two types of Kurokami–jima granite samples: those with a rift plane perpendicular (Type H) or parallel (Type V) to the expected direction of fracture propagation (i.e. along the loading axis). In the experiments, both sample types experienced a significant number of shear, tensile and compressive events. The dominant fracture mode for Type H samples is found to be tensile events in which the fracture plane is parallel to the loading axis, whereas for Type V samples, shear events are dominant. This difference suggests that the dominant fracture modes induced by hydraulic fracturing are highly dependent on the relationship between the direction of fracture propagation and orientation of pre-existing weak planes.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We present a sensitivity analysis aimed at testing whether observables related to glacial isostatic adjustment can support or refute the occurrence of a low viscosity melt-rich layer (MRL) above the mantle transition zone, as required by the ‘transition-zone water-filter’ model (Bercovici & Karato 2003). In total, 1600 model runs were performed sampling a range of MRL thicknesses (1, 10 and 20 km) and viscosities (10〈sup〉15〈/sup〉–10〈sup〉19〈/sup〉 Pa·s), plausible viscosity values in the upper and lower mantle regions and four distinct ice histories. To determine decay time constraints, we consider relative sea level (RSL) data from two sites [Ångerman River (ÅR), Sweden and Richmond Gulf (RG), Canada] and use a new method of observational sea level data correction. Comparing model output of postglacial decay times and ${\skew{6}\dot{J}_2}$ to observational constraints, we find numerous possible solutions, largely as a result of parameter trade-off. The investigated observables are sensitive to the existence of an MRL and reasonable variations in its thickness and viscosity. The magnitude and nature of this sensitivity varies between the two data types as well as the adopted background viscosity structure. Decay time results from either considered location do not strictly support or exclude MRL existence. However, both locations offer MRL viscosity requirements for given thicknesses, with ÅR being more restrictive. RG constraints allow MRL viscosities as low as 10〈sup〉16〈/sup〉 Pa·s (10 km) and 10〈sup〉17〈/sup〉 Pa·s (20 km). ÅR results narrow these permitted viscosity ranges to 10〈sup〉18〈/sup〉 Pa·s or greater for both 10 and 20 km MRL thicknesses. In the case of a 1 km thick MRL, ÅR constraints permit the viscosity to be as low as 10〈sup〉17〈/sup〉 Pa·s, whereas those of RG permit any MRL viscosity. The decay time observations are satisfied by only a small subset of ‘background’ mantle viscosities (regardless of the MRL properties), none of which support a spherically symmetric solution of Earth viscosity. Finally, comparing model output to the observed ${\skew{6}\dot{J}_2}$ value did not provide any constraints on MRL properties. However, our results show that this observable has a strong preference for viscosity values in the lower mantle that are equal to or greater than 10〈sup〉22〈/sup〉 Pa·s.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We investigated an 〈span〉M〈/span〉〈sub〉w〈/sub〉 ∼ 6.2 earthquake doublet on the border of the USA and Canada using ALOS2 Light-of-Sight displacements and GPS measurements. We selected three L-band ALOS-2 interfergorams with temporal baselines of one yr to extract coseismic deformation maps, in which master and slave images were both acquired in July. A subpixel-based alignment and another range spectral splitting techniques under the GAMMA InSAR software framework were applied to improve the interferometric coherence and reduce the effects of phase anomalies in two of the three interferometric pairs due to either ionospheric delay or a potential focusing issues in the generation of the ALOS2 SLC data. The updated interferograms convincingly reveal deformation fringe patterns produced by the two earthquakes. We conducted a nonlinear geophysical inversion to estimate the geometric parameters of the earthquakes with the InSAR and GPS measurements. The best-fitting model shows that a thrust faulting on a reverse fault and left-lateral strike-slip faulting on a nearly vertical fault with the centroid depths of 9.3±0.6 and 8.4±0.7 km, respectively, are most likely responsible for the earthquake doublet. The eastern Denali fault (EDF) and Duke River fault are major active faults in the region and the earthquake doublet could be due to reactivation of the part of the two faults system.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉In this paper, we present a series of mathematical abstractions for seismologically relevant wave equations discretized using finite-element methods, and demonstrate how these abstractions can be implemented efficiently in computer code. Our motivation is to mitigate the combinatorial complexity present when considering geophysical waveform modelling and inversion, where a variety of spatial discretizations, material models, and boundary conditions must be considered simultaneously. We accomplish this goal by first considering three distinct classes of abstract mathematical models: (1) those representing the physics of an underlying wave equation, (2) those describing the discretization of the chosen equation onto a finite-dimensional basis and (3) those describing any spatial transforms. A full representation of the discrete wave equation can then be constructed using a hierarchical nesting of models from each class. Additionally, each class is functionally orthogonal to the others, and with certain restrictions models within one class can be interchanged independently from changes in another. We then show how this recasting of the relevant equations can be implemented concisely in computer software using an abstract object-oriented design, and discuss how recent developments in the numerical and computational sciences can be naturally incorporated. This builds to a set of results where we demonstrate how the developments presented can lead to an implementation capable of multiphysics waveform simulations in completely unstructured domains, on both hypercubical and simplical spectral-element meshes, in both two and three dimensions, while remaining concise, efficient and maintainable.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Traveltime approximation plays an important role in seismic data processing, for example, anisotropic parameter estimation and seismic imaging. By exploiting seismic traveltimes, it is possible to improve the accuracy of anisotropic parameter estimation and the resolution of seismic imaging. Conventionally, the traveltime approximations in anisotropic media are obtained by expanding the anisotropic eikonal equation in terms of the anisotropic parameters and the elliptically anisotropic eikonal equation based on perturbation theory. Such an expansion assumes a small perturbation and weak anisotropy. In a realistic medium, however, the assumption of small perturbation likely breaks down. We present a retrieved zero-order deformation equation that creates a map from the anisotropic eikonal equation to a linearized partial differential equation system based on the homotopy analysis method. By choosing the linear and nonlinear operators in the retrieved zero-order deformation equation, we develop new traveltime approximations that allow us to compute the traveltimes for a medium of arbitrarily strength anisotropy. A comparison of the traveltimes and their errors from the homotopy analysis method and from the perturbation method suggests that the traveltime approximations provide a more reliable result in strongly anisotropic media.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Guided waves in a water layer overlaying an elastic half-space are known as normal modes. They are often present in seismic recordings at long offsets in shallow-water environment and generally considered coherent noise. The normal modes, however, carry important information about the near-surface and, as demonstrated by a number of authors, can be used to obtain the shallow velocity model. There is a growing evidence that the latter needs not to be isotropic due to various geological reasons. Motivated by that, we consider the normal-mode propagation in case the elastic half-space exhibits orthorhombic anisotropy. We derive the period equation that describes the normal-mode phase velocity dispersion. To simplify the complicated expression, we present acoustic and ellipsoidal orthorhombic approximations. We also outline the approach towards the group velocity and group azimuth calculation and apply it to the ellipsoidal case to obtain concise and intuitive expressions. Using numerical test, we study the relation between phase and group domains in elastic orthorhombic case. The deviation between velocities and azimuths in these domains is the strongest for low frequencies and it rapidly decreases with increasing frequency. For higher frequencies, the anisotropy effects of the underlaying half-space are barely detectable since the observed signal is composed mainly of the direct acoustic wave, resulting in the two domains being nearly indistinguishable.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Understanding why Earth’s lithosphere is divided into several plates while other terrestrial bodies have unbroken lids is a long-standing challenge, often addressed with the help of numerical modelling. A key mechanism defining the transition between these two convective regimes is the formation of shear zones that cut through the entire lithosphere in regions with high stresses. Here we present a modelling study in which lithospheric stresses resulting from small-scale convection in the upper mantle are analysed. We perform model simulations that include elasticity and a free surface and evaluate how these physical complexities affect stress distribution inside the lithosphere, which in turn controls the depths of yielding and the possible initiation of subduction. We show that the spatial distribution of stress is significantly altered by the presence of elastic deformation only when the model lithosphere acts as a thick plate capable of bending. Whether or not this is the case depends on the viscosity model. For an Arrhenius viscosity limited by a cut-off value that produces an essentially rigid lid, flexure dominates the observed lithospheric stress pattern in simulations with a free surface. The amplitudes of the stress are, when a free surface is assumed but elasticity is neglected, largely overestimated. Including both a free surface and elasticity results in stresses with maximum amplitudes close to those observed in the traditional models with a viscous rheology and a free-slip upper boundary, suggesting that having no additional complexity is, in a way, better than employing just a free surface. We also demonstrate how the use of impermeable free-slip side boundaries can result in the formation of unnatural, laterally locked convection cells, and bias the results of a parametric study. For each point in the parameter space, we perform several simulations with slightly different initial temperature fields in order to statistically eliminate the occurrence of locked states.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉The design of an array configuration is an important task in array seismology during experiment planning. Often the array response function (ARF), which depends on the relative position of array stations and frequency content of the incoming signals, is used as the array design criterion. In practice, additional constraints and parameters have to be taken into account, for example, land ownership, site-specific noise levels or characteristics of the seismic sources under investigation. In this study, a flexible array design framework is introduced that implements a customizable scenario modelling and optimization scheme by making use of synthetic seismograms. Using synthetic seismograms to evaluate array performance makes it possible to consider additional constraints. We suggest to use synthetic array beamforming as an array design criterion instead of the ARF. The objective function of the optimization scheme is defined according to the monitoring goals, and may consist of a number of subfunctions. The array design framework is exemplified by designing a seven-station small-scale array to monitor earthquake swarm activity in Northwest Bohemia/Vogtland in central Europe. Two subfunctions are introduced to verify the accuracy of horizontal slowness estimation; one to suppress aliasing effects due to possible secondary lobes of synthetic array beamforming calculated in horizontal slowness space and the other to reduce the event’s mislocation caused by miscalculation of the horizontal slowness vector. Subsequently, a weighting technique is applied to combine the subfunctions into one single scalar objective function to use in the optimization process.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We develop a new method for measuring ellipticity of Rayleigh waves from ambient noise records by degree-of-polarization (DOP) analysis. The new method, named DOP-E, shows a good capability to retrieve accurate ellipticity curves separated from incoherent noise. In order to validate the method we perform synthetic tests simulating noise in a 1-D earth model. We also perform measurements on real data from Antarctica and Northern Italy. Observed curves show a good fit with measurements from earthquake records and with theoretical ellipticity curves. The inversion of real data measurements for 〈span〉vS〈/span〉 structure shows a good agreement with previous models. In particular, the shear-wave structure beneath Concordia station shows no evidence of a significant layer of liquid water at the base of the ice. The new method can be used to measure ellipticity at high frequency and therefore it will allow the imaging of near-surface structure, and possibly of temporal changes in subsurface properties. It promises to be useful to study near-surface processes in a wide range of geological settings, such as volcanoes, fault zones and glaciers.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉The interaction of subducted oceanic lithosphere with the discontinuities of the mantle transition zone (MTZ) provides insight into the composition and temperature of the subducted slab as well as potential melting of the slab or the surrounding mantle and loss of volatiles from the slab. Detailed mapping of the structure of the MTZ will help to better understand how slabs transport material and volatiles into the mantle and how phase transitions affect the slab dynamics. Here we use a dense network of seismic stations in northern Anatolia to image the structure of the MTZ discontinuities in detail using 〈span〉P〈/span〉-wave receiver functions. With a station spacing of about 7 km and a surface footprint of ∼35 km × ∼70 km, analysing receiver functions calculated from teleseismic earthquakes that occurred during an ∼18-month deployment produced clear images of where the MTZ interacts with the Tethys/Cyprus slabs that either lie flat on the 660-km discontinuity or pass into the lower mantle. We observe an undulating 660-km discontinuity depressed by up to 30 km and a slightly depressed (1–2 km) 410-km discontinuity, apparently undisturbed by the slab. The MTZ is thickened to ∼270 km as result of the cool slab in the MTZ influencing the 660-km discontinuity and includes an arrival at ∼520-km depth likely from the top of a flat lying slab or a discontinuity related to a solid–solid phase transition in the olivine component of the mantle. We find evidence for low-velocity zones both above and below the 410-km discontinuity and above the 660-km discontinuity. The low-velocity zones around the 410-km discontinuity might be the result of hydration of the MTZ from the slab and upward convection of MTZ material into the upper mantle. The origin of the low-velocity zone around the 660-km discontinuity is less clear and could be related to sedimentation of subducted mid-ocean ridge basalts. The small footprint of the seismic array provides accurate information on the structure of the MTZ in an area influenced by subduction and shows small-scale changes in MTZ structure that might be lost in studies covering larger areas with sparser sampling.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We perform non-linear time-series analysis on a harmonic tremor seismogram recorded at 830 m away from the centre of the crater during the 2011 eruption at Shinmoedake, Japan. We found features suggesting the existence of period doubling bifurcation in the harmonic tremor signal, implying that the harmonic tremor might be generated by a non-linear process. In order to quantify the non-linearity in the harmonic tremor signal, we measure the correlation dimension 〈span〉D〈/span〉 and the maximal Lyapunov exponent λ. For one short but stable segment of the harmonic tremor seismogram, we obtained 〈span〉D〈/span〉 = 1.12 and λ = 0.03 s〈sup〉−1〈/sup〉. This result implies that the stable oscillation of the harmonic tremor is predominantly a limit cycle with small amounts of chaos present. We then use surrogate data analysis to check that our measurements of 〈span〉D〈/span〉 and λ do not include any false positive detection of non-linearity. Limit cycles imply that the harmonic tremor is generated by self-sustained oscillations. We show that the autonomous Julian tremor model is able to exhibit period doubling bifurcation. We also show that the non-autonomous Julian tremor model with a step like increase and decrease in input pressure is able to exhibit oscillations of varying amplitude while keeping a constant frequency spectrum. Both phenomena were observed at Shinmoedake. We also demonstrate that the non-autonomous Julian tremor model with a transient input pressure is able to exhibit long period-like events in addition to harmonic tremor-like events, implying that the same non-linear mechanism could be responsible for the generation of both type of events.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Reservoir models are numerical representations of the subsurface petrophysical properties such as porosity, volume of minerals and fluid saturations. These are often derived from elastic models inferred from seismic inversion in a two-step approach: first, seismic reflection data are inverted for the elastic properties of interest (such as density, 〈span〉P〈/span〉-wave and 〈span〉S〈/span〉-wave velocities); these are then used as constraining properties to model the subsurface petrophysical variables. The sequential approach does not ensure a proper propagation of uncertainty throughout the entire geo-modelling workflow as it does not describe a direct link between the observed seismic data and the resulting petrophysical models. Rock physics models link the two domains. We propose to integrate seismic and rock physics modelling into an iterative geostatistical seismic inversion methodology. The proposed method allows the direct inference of the porosity, volume of shale and fluid saturations by simultaneously integrating well-logs, seismic reflection data and rock physics model predictions. Stochastic sequential simulation is used as the perturbation technique of the model parameter space, a calibrated facies-dependent rock physics model links the elastic and the petrophysical domains and a global optimizer based on cross-over genetic algorithms ensures the convergence of the methodology from iteration to iteration. The method is applied to a 3-D volume extracted from a real reservoir data set of a North Sea reservoir and compared to a geostatistical seismic AVA.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉We investigate slip-distribution models of the 2011 Tohoku earthquake, with a particular focus on diffracted tsunamis and uplift-induced waves along the backarc region of the Japanese Island Arc. The 2011 Tohoku earthquake produced a large amplitude tsunami that diffracted around Kyushu Island before reaching Korea. At the same time, this earthquake coseismically induced short-period small-amplitude sea waves in the East Sea. We performed tsunami simulations using seven fault models of the Tohoku earthquake to examine whether the models can accurately reproduce the observed waveforms in the open sea of the western Pacific Ocean, the South Sea of Korea, and the coast of the East Sea. For each fault model, we investigate tsunami features due to geomorphological characteristics of the Korean Peninsula in the Korea offshore. To determine which slip distribution model shows a good performance in the tsunami simulations, we set three criteria; the delay time between observations and synthetic waveforms, the normalized mean residual, and the normalized RMS misfit. Depending on the study region, all models show varying degrees of accuracy. The fault dimensions and the amount of slip have a larger effect on the RMS misfit then the slip distribution patterns of the fault models for observations along the Korean coast and the western coast of Japan.〈/span〉

Description: 〈span〉〈div〉Abstract〈/div〉Economically important deposits of nickel-copper and platinum group elements tend to be associated with small mafic-ultramafic intrusions characterized by compositional layering. Our rock magnetic study of an exploration drill core recovered from a typical small intrusion from the recently discovered Kun-Man'e ore field have found that concentration-independent hysteresis parameters of the studied rocks generally co-vary with petrological characteristics, such as major element abundances and compositions of olivine and clinopyroxene. Although monoclinic pyrrhotite and defect-poor magnetite both contribute to magnetic properties of the samples, we argue that hysteresis parameters are not affected significantly by pyrrhotite content. Rather, the variations in the hysteresis parameters reflect variations in median grain-size of magnetite crystals. The correlation between the rock-magnetic grain-size indicators and geochemical crystallization temperature indicators suggests that the size of magnetite crystals is controlled by cooling regime. Compared to conventional laborious crystal size distribution (CSD) studies, rock magnetic measurements can provide a quick and sensitive way to evaluate CSD of magmatic magnetite in mafic and ultramafic rocks.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉The Reykjanes geothermal system is a high-temperature seawater system situated in SW-Iceland. Interferometric analysis of the Sentinel-1 satellite synthetic aperture radar (InSAR) data has been used to determine a time series of ground deformation induced by geothermal utilization between April 2015 and October 2017. Surface displacements have been estimated at coherent pixels, indicating a steady and linear subsidence within a sub-circular bowl centered on the well field at a maximum near-vertical rate of about 25 mm/yr, together with horizontal contraction. The average line-of-sight (LOS) displacement rates from ascending and descending tracks are inverted to determine the characteristics of the deformation source at depth, modeling the geothermal reservoir as a body of simple geometry within an elastic half space. The results indicate a deformation source at about 1 km depth contracting at a rate of (0.7–0.9) × 10〈sup〉5〈/sup〉 m〈sup〉3〈/sup〉/yr during the 2015–2017 period. Using pressure and temperature monitoring data at 900 m depth as well as an analysis of the reservoir structure and rock properties, we infer that the recent estimated volume change can be attributed to processes in the steam cap situated in the topmost part of the geothermal reservoir, in the 800–1200 m depth range. Processes involve a combination of compaction under pressure decrease and/or thermal contraction due to cooling of the rocks within or near the steam cap. The steam cap expanded in response to a sudden pressure drop resulting from the increase in extraction of geothermal fluids for a new power plant in 2006.〈/span〉

Description: 〈span〉〈div〉Abstract〈/div〉The seismic speed and anisotropy are two methods frequently used to image the assembly inside the Earth. We study the crust assembly beneath the Biga Peninsula and the surrounding area in Northwest Turkey using the accelerometer and broadband recordings where short-to-medium period (5-20 s) Love-Rayleigh surface waves are utilized to extract the group-phase speed data (fundamental mode). Single-station and two-station techniques are engaged to understand the detected surface waves for the speed and anisotropy assemblies. The single-station group speeds are inverted in a tomographic approach to attain the two-dimensional group speed diagrams. The least-squares inversion procedure is utilized to find the speed-depth profiles (one-dimensional) under each grid location. The one-dimensional results are cooperatively inferred to attain the three-dimensional appearance of the S-wave speeds below the measured region. This process is reiterated for Love and Rayleigh waves. Isotropic configuration is not sufficient to concurrently describe the present detected Love-Rayleigh surface waves. Vertical transverse isotropic crust assembly is found to better elucidate the detected data showing the Rayleigh-Love discrepancy. Complex arrangement of sills and dykes due to the widespread plutonic and volcanic activity in the region linked to the interaction between the Turkish plate and the African plate (northward subducting) is thought to depict the crust assembly deformations causing the detected long-wavelength vertical transverse isotropy. The mineral orientation within horizontal sills and vertical dykes following the magma flow, which is independent of seismic wavelength, adds to the detected anisotropy. The upper crust vertical transverse isotropy is mostly negative; i.e. SV-wave is faster than SH-wave, which is assumed to be due to the existence of dykes. The middle-to-lower crust vertical transverse isotropy is commonly positive; i.e. SH-wave is faster than SV-wave, which is assumed to be due to the existence of sills. The two-station analyses operating on cross-correlograms give analogous vertical transverse isotropic results to those of the single-station estimates.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The representative elementary volume (REV) is a critically important concept in fractured rock investigations as it tells us at what scale the fractured domain can be represented by an anisotropic tensor as opposed to requiring the details of each individual fracture for modeling purposes. Whereas the REV size and corresponding tensor characteristics for the hydraulic conductivity (〈span〉K〈/span〉) in fractured rock have been the subject of numerous previous investigations, no studies to date have focused on the electrical conductivity (σ). This is despite the fact that geoelectrical measurements are arguably the most popular means of geophysically investigating fractured rock, typically via azimuthal resistivity surveying where the observed electrical anisotropy is commonly used to infer hydraulic characteristics. In this paper, we attempt to fill this void and present a systematic numerical study of the impacts of changes in fracture-network properties on the REV size and equivalent tensor characteristics for both the electrical and hydraulic conductivities. We employ a combined statistical and numerical approach where the size of the REV is estimated from the conductivity variability observed across multiple stochastic fracture-network realizations for various domain sizes. Two important differences between fluid and electric current flow in fractured media are found to lead to significant differences in the REV size and tensor characteristics for σ and 〈span〉K〈/span〉; these are the greater importance of the matrix in the electrical case and the single-power instead of cubic dependence of electric current flow upon aperture. Specifically, the REV for the electrical conductivity will always be smaller than that for the hydraulic conductivity, and the corresponding equivalent tensor will exhibit less anisotropy, often with notably different principal orientations. These findings are of key importance for the eventual interpretation of geoelectrical measurements in fractured rock, where we conclude that extreme caution must be taken when attempting to make the link to hydraulic properties.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉Stress is a crucial factor that affects the permeability, and the influence of stress on permeability has been studied extensively by many investigators. In this article the relationship between confining pressure and permeability is investigated. For this purpose, a void ratio- pressure model based on the theory of incompressible elastic porous media is first proposed, then, based on the model and Kozeny-Carman equation, a new pressure–permeability relationship is proposed. Finally the relationship is utilized to predict the permeability of coal and mudstone under different confining pressure, and these predictions are compared with other models and found to be in better agreement with experimental data reported recently.〈/span〉

Description: 〈span〉〈div〉Abstract〈/div〉We perform nonlinear time series analysis on a harmonic tremor seismogram recorded at 830 m away from the centre of the crater during the 2011 eruption at Shinmoedake, Japan. We found features suggesting the existence of period doubling bifurcation in the harmonic tremor signal, implying that the harmonic tremor might be generated by a nonlinear process. In order to quantify the nonlinearity in the harmonic tremor signal, we measure the correlation dimension 〈span〉D〈/span〉 and the maximal Lyapunov exponent λ. For one short but stable segment of the harmonic tremor seismogram, we obtained 〈span〉D〈/span〉 = 1.12 and λ = 0.03 s〈sup〉−1〈/sup〉. This result implies that the stable oscillation of the harmonic tremor is predominantly a limit cycle with small amounts of chaos present. We then use surrogate data analysis to check that our measurements of 〈span〉D〈/span〉 and λ do not include any false positive detection of nonlinearity. Limit cycles imply that the harmonic tremor is generated by self-sustained oscillations. We show that the autonomous Julian tremor model [〈span〉Julian〈/span〉, 1994] is able to exhibit period doubling bifurcation. We also show that the non-autonomous Julian tremor model with a step like increase and decrease in input pressure is able to exhibit oscillations of varying amplitude while keeping a constant frequency spectrum. Both phenomena were observed at Shinmoedake. We also demonstrate that the non-autonomous Julian tremor model with a transient input pressure is able to exhibit long period-like events in addition to harmonic tremor-like events, implying that the same nonlinear mechanism could be responsible for the generation of both type of events.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We present a joint analysis of newly acquired gravity and teleseismic data in the North Tanzanian Divergence, where the lithospheric break-up is at its earliest stage. The impact of a mantle upwelling in more mature branches of the East African Rift has been extensively studied at a lithospheric scale. However, few studies have been completed that relate the deep-seated mantle anomaly detected in broad regional seismic tomography with the surface deformation observed in the thick Archaean Pan-African suture zone located in North Tanzania. Our joint inversion closes the gap between local and regional geophysical studies, providing velocity and density structures from the surface down to ca. 250 km depth with new details. Our results support the idea of a broad mantle upwelling rising up to the lithosphere and creating a thermal modification along its path. However, our study clearly presents an increasing amplitude of the associated anomaly both in velocity and density above 200 km depth, which cannot be solely explained by a temperature rise. We infer from our images the combined impact of melt (2-3%), composition and hydration that accompany the modification of a thick heterogenous cratonic lithosphere are a response to the hot mantle rising. The detailed images we obtained in density and velocity assert that Archaean and Proterozoic units interact with the mantle upwelling to restrict the lithosphere modifications within the Magadi-Natron-Manyara rift arm. The composition and hydration variations associated with those units equilibrate the thermal erosion of the craton root and allow for its stability between 100 and 200 km depth. Above 80 km depth, the crustal part is strongly affected by intruding bodies (melt and gas) which produces large negative anomalies in both velocity and density beneath the main magmatic centers. In addition to the global impact of a superplume, the velocity and density anomaly pattern suggests a 3D distribution of the crust and mantle lithospheric stretching, which is likely to be controlled by inherited fabrics and enhanced by lateral compositional and hydration variations at the Tanzanian craton-orogenic belt boundary.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉We report palaeomagnetic and K–Ar geochronologic results of two volcanic sequences from Ethiopia. The Belessa section, dated around 29–30 Ma and spanning ∼1 km in thickness, is related to the Oligocene Afro-Arabian traps, whereas the ∼700-m-thick Debre Sina section was emplaced during the Miocene in two periods around 10–11 and 14–15 Ma. We sampled 67 flows of predominantly basaltic rocks near Belessa and 59 rhyolitic to trachybasaltic flows near Debre Sina. From a geodynamic viewpoint, the magnetostratigraphy of the Belessa sequence confirms that the Ethiopian traps were emplaced at a minimum rate of ∼1 m/kyr, with a possible acceleration of the volume of volcanism over time. To provide insight into the evolution of the geomagnetic field in the Afro-Arabian region over the past 30 Myr, we combined our results with previous studies in the same area. Recentred directional distributions were elongated in the meridian plane, in coherence with field models for a dipole-dominated field. The dispersion 〈span〉S〈/span〉 of the virtual geomagnetic poles, representative of the vigour of palaeosecular variation, was approximately 50% higher during the 10–30 Ma interval than during the past 5 Myr. As the reversal frequency 〈span〉f〈/span〉 was more than two times lower during the Early Oligocene than during the Plio-Pleistocene, it appears that 〈span〉S〈/span〉 and 〈span〉f〈/span〉 are uncorrelated in this near-equatorial region. It remains an open question whether this apparent decoupling is ascribable to a local anomaly, is only sporadic in time, or represents a general feature of the geodynamo.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The non-linear interaction of ocean surface waves produces coherent infrasound noise—microbaroms—between 0.1 and 0.5 Hz. Microbaroms propagate through the atmosphere over thousands of kilometres due to low absorption and efficient ducting between the ground and the stratopause. These signals are globally and permanently detected by the International Monitoring System (IMS) infrasound network, which has been established to monitor compliance with the Comprehensive Nuclear-Test-Ban Treaty. At the International Data Centre (IDC) in Vienna, where IMS data are routinely processed, microbarom detections appear in overlapping frequency bands, and are treated as false alarms. Therefore, understanding the variability in microbarom detections is essential to support the IDC in the reduction of the false alarm rate. In this study, microbarom amplitudes and the direction of arrivals at the German infrasound station IS26 were modelled. For the simulations, the source was described by an operational ocean wave interaction model, and the signal amplitude was modelled using a semi-empirical attenuation relation. This relation strongly depends on middle atmosphere (MA; i.e. 15–90 km altitude) dynamics; however, vertical temperature and wind profiles, provided by numerical weather prediction (NWP) models, exhibit significant biases and differences when compared with high-resolution lidar soundings in altitudes where infrasound signals propagate. To estimate uncertainties in the modelled amplitude, a fully autonomous lidar for MA temperature measurements was installed at IS26. Temperature and wind perturbations, considering observed biases and deviations, were added to the operational high-resolution atmospheric model analysis produced by the European Centre for Medium-Range Weather Forecasts. Such uncertainties in horizontal winds and temperature strongly impact propagation conditions, explaining almost 97 per cent of the actual detections, compared to 77 per cent when using the direct output of the NWP model only. Incorporating realistic wind and temperature uncertainties in NWP models can thus significantly improve the understanding of microbarom detections as well as the detection capability of a single station throughout the year.〈/span〉

Description: 〈span〉〈div〉Summary〈/div〉The interaction of subducted oceanic lithosphere with the discontinuities of the mantle transition zone (MTZ) provides insight into the composition and temperature of the subducted slab as well as potential melting of the slab or the surrounding mantle and loss of volatiles from the slab. Detailed mapping of the structure of the MTZ will help to better understand how slabs transport material and volatiles into the mantle and how phase transitions affect the slab dynamics. Here we use a dense network of seismic stations in northern Anatolia to image the structure of the MTZ discontinuities in detail using P-wave receiver functions. With a station spacing of about 7 km and a surface footprint of ∼35 km by ∼70 km, analysing receiver functions calculated from teleseismic earthquakes that occurred during an ∼18 month deployment produced clear images of where the mantle transition zone interacts with the Tethys/Cyprus slabs that either lie flat on the 660-km discontinuity or pass into the lower mantle. We observe an undulating 660-km discontinuity depressed by up to 30 km and a slightly depressed (1–2 km) 410-km discontinuity, apparently undisturbed by the slab. The MTZ is thickened to ∼270 km as result of the cool slab in the MTZ influencing the 660-km discontinuity and includes an arrival at ∼520-km depth likely from the top of a flat lying slab or a discontinuity related to a solid-solid phase transition in the olivine component of the mantle. We find evidence for low-velocity zones both above and below the 410-km discontinuity and above the 660-km discontinuity. The low velocity zones around the 410-km discontinuity might be the result of hydration of the MTZ from the slab and upward convection of MTZ material into the upper mantle. The origin of the low velocity zone around the 660-km discontinuity is less clear and could be related to sedimentation of subducted mid-ocean ridge basalts. The small footprint of the seismic array provides accurate information on the structure of the MTZ in an area influenced by subduction and shows small-scale changes in MTZ structure that might be lost in studies covering larger areas with sparser sampling.〈/span〉

Description: 〈span〉〈div〉SUMMARY〈/div〉Long-period Rayleigh wave horizontal to vertical amplitude (H/V) ratios at a station provide information about local earth structure that is complementary to phase velocity. However, a number of studies have observed that significant scatter appears in these measurements making it difficult to use H/V ratio measurements to resolve earth structure. Some of the scatter in these measurements has been attributed to local geological structure while some has remained unaccounted for. Most Global Seismographic Network (GSN) stations contain two nearby high-quality broad-band seismometers (e.g. in the same vault, but on different piers or in different boreholes). For each broad-band sensor in the IRIS/USGS component of the GSN, we estimate H/V ratios of fundamental mode Rayleigh waves using 〈span〉M〈/span〉 〉 6.5 earthquakes from 2001 to 2018 (around 19 000 measurements). We compute these ratios at a number of discrete periods (25, 50, 75, 100 and 150 s) and find that for well-isolated Rayleigh waves (windows where the correlation coefficients between radial and the phase-shifted vertical components are greater than 0.9) significant scatter in H/V ratios occurs between colocated sensors (greater than 25 per cent at 100 s period). This suggests the scatter in H/V ratio measurements can be at least partially attributed to extremely local phenomena such as sensor emplacement in the vault. We also find that H/V ratios can vary as a function of event backazimuth, indicating that care must be taken when computing average ratios for a station, as a large number of events from a given region could bias H/V ratio measurements at a station.〈/span〉

Description: In their recent review, Bailey et al. (2017) make the compelling case that indirect genetic effects (IGEs) should be more widely incorporated into behavioral ecology research. IGEs occur whenever the trait of one individual is affected by the genotype of another “interacting” individual, usually via one or more “social cues.” IGEs create an additional source of heritable variation that can influence an individual’s trait expression above and beyond any direct contributions of its genotype (direct genetic effect [DGE]) and the environment ( Lynch and Walsh 1998 ). When conspecifics interact, as is the case for behavioral interactions, they make up part of an individual’s “social environment” and because these interacting partners are themselves genetically variable, additional heritable variation can be generated. So why does this matter? A key outcome of IGEs is that traits affected by them can evolve not only due to direct genetic variation but also due to evolution of the social environment itself ( Wolf et al. 1998 ).

Description: Behavior is rapidly flexible and highly context-dependent, which poses obvious challenges to researchers attempting to dissect its causes. However, over a century of unresolved debate has also focused on whether the very flexibility and context-dependence of behavior lends it a unique role in the evolutionary origins and patterns of diversity in the Animal Kingdom. Here, we propose that both challenges can benefit from studying how indirect genetic effects (IGEs: the effects of genes expressed in one individual on traits in another individual) shape behavioral phenotypes. We provide a sketch of the theoretical framework that grounds IGEs in behavioral ecology research and focus on recent advances made from studies of IGEs in areas of behavioral ecology such as sexual selection, sexual conflict, social dominance, and parent–offspring interactions. There is mounting evidence that IGEs have important influences on behavioral phenotypes associated with these processes, such as sexual signals and preferences and behaviors which function to manipulate interacting partners. IGEs can also influence both responses to selection and selection itself, and considering IGEs refines evolutionary predictions and provides new perspectives on the origins of seemingly perplexing behavioral traits. A key unresolved question, but one that has dominated the behavioral sciences for over a century, is whether behavior is more likely than other types of traits to contribute to evolutionary change and diversification. We advocate taking advantage of an IGE approach to outline falsifiable hypotheses and a general methodology to rigorously test this frequently proposed, yet still contentious, special role of behavior in evolution.

Description: The notion that behavioral traits “must often take the lead in evolution” because they are “especially plastic” ( West-Eberhard 2003 ) sits somewhat uncomfortably with standard quantitative genetic theory. Under simple models, plasticity actually slows evolution: more plastic traits have greater variance, reduced heritability and so lowered expected selection response. Here, Bailey et al. (2017) highlight the tantalizing possibility that indirect genetic effects (IGEs) could reconcile these contrasting positions. They provide a neat structured list of questions to guide empirical efforts, effectively asking:

Description: The key proposal in Bailey et al. (2018) is that evolutionary processes may be misinterpreted if indirect genetic effects (IGEs) are not taken into consideration. Further, that such processes are a fundamental part of behavior and thus the genetic analysis of behavior and its evolution must take into account IGEs. The authors present a very convincing case for this proposal both from theoretical argument and empirical evidence.

Description: There is growing evidence for consistent among-individual variation in individual sociability (e.g., tendency to be sociable) in a number of species. However, sexes often differ in their social behaviors, as well as the selection pressures which they experience. This may translate into differences in repeatability of sociability, although this has not yet been tested. Here, we investigated whether eastern water dragons ( Intellegama leseurii ) exhibited evidence of consistent among-individual variation (i.e., repeatability) in 4 different measurements of sociability. Specifically, we measured sociability in 4 ways (degree, centrality, proportion of time spent being social, and number of preferences), and tested whether there was evidence for sex differences in the repeatability of these sociability measurements, or whether observed levels of repeatability could be explained by a stable social environment. Our findings provide new evidence for sex differences in social personality: we found that males were significantly repeatable in 3 of 4 sociability measurements (degree, centrality, and proportion of time spent being social), whereas females were not. Further, we found that these differences were not a result of differences in the dynamics of the social environment. We discuss our findings in the context of sexual selection, as well as sex differences in the evolutionary drivers of social behavior.

Description: When foraging in their natural environment, many animals readily complement their personal knowledge with additional social information. To balance the costs and benefits of copying others, animals have to discern situations in which it is more advantageous to use social rather than personal information. Here, we used foraging bumblebees ( Bombus terrestris ) in a controlled laboratory setting and showed that the difficulty of a foraging task affects how the bees weight the 2 types of information. We used artificial flowers to devise easy and difficult discriminatory tasks, and tested the influence of floral and social cues on decision making. When facing an easy discrimination task, foraging bees were likely to rely on personal information and were only marginally affected by social information. By contrast, they prioritized social over personal information when flower discrimination was difficult and therefore the probability of making errors was higher. In summary, bees are able to use social and personal information to optimize foraging decisions in a flexible way.

Description: We propose that indirect genetic effects (IGEs) represent an appealing way to dissect the genetics and evolutionary dynamics of complex phenotypes studied in behavioral ecology. IGEs are complementary to inclusive fitness approaches, but as Kruuk and Wilson (2018) observe, are distinct because they do not require assumptions about relatedness (see also McGlothlin et al. 2014 and McDonald et al. 2017 ). Thus, IGEs open up the opportunity to study any social interaction and any trait expressed in a social interaction (See Roff 2018 ). These features of IGEs have enabled behavioral ecologists to study behavior from a slightly different perspective, as an evolutionary feedback process that links individuals and their environments through genes.

Description: By definition, teaching is both cooperative and costly and so we appreciate Cordony’s (2017) commentary in this spirit. We also agree that the cost of teaching in the superb fairy-wren ( Malurus cyaneus ) system can and should be more fully explored. Kleindorfer, Hoi, et al. (2014) quantified a cost of incubation calling ( Colombelli-Négrel et al. 2012 ) to fairy-wren mothers through the detection of higher egg predation at nests with more incubation calls. The commentary raises 2 main concerns: that 1) Kleindorfer, Hoi, et al. (2014) misinterpreted the operational definition of cost in animal teaching by Caro and Hauser (1992) and its operational interpretation by Thornton and Raihani (2010) , because 2) nest predation is neither an immediate nor a personal cost to the mother.

Description: Although numerous aquatic and terrestrial species adorn their surface with items secured from their surroundings, termed decorating, the physical and environmental factors that drive this behavior are often unclear. One of the best-known examples of this phenomenon are the decorator crabs (Majoidea), with almost 75% of species known to decorate. Here, we examined patterns of decorating in a coral reef-associated majoid, Camposcia retusa , to identify what factors determine patterns of, and investment in, decorating. Observations of natural decoration patterns indicate this species primarily decorate with sponges, fleshy and filamentous algae, and detritus. Decorations were primarily distributed on the carapace and hind walking legs which may reflect exoskeleton morphology. However, decoration cover did not decline with size, as is observed in some other majoid species, suggesting the factors driving decoration investment remain consistent throughout growth stages. From behavioral experiments, we determined that nonuniform decorating is a result of active selection, with crabs preferentially decorating their hind legs and carapace, with only small items placed on the carapace. Decorating in C. retusa appears to function primarily as an antipredator response, with crabs decorating at higher rates when access to shelter is limited. This study is the first to quantify the decorating habits of C. retusa and suggests that behaviorally-mediated decorating has a primary antipredator function. This study also highlights the value of manipulative behavioral experiments as a tool for assessing the behavioral mechanisms that drive decorating in animals.

Description: Pathogens are ubiquitous in nature and typically entail major fitness costs in their hosts. These costs can be particularly important when individuals exhibit poor immune defenses, as it is often the case during early developmental stages. Hence, selection should favor parental strategies limiting the risks of pathogen exposure and infection in their offspring. In this study, we investigated 1) whether females of the European earwig Forficula auricularia avoid areas contaminated with spores of the entomopathogenic fungus Metarhizium brunneum prior to and at egg laying, as well as 2) whether spore presence entails an increase in females’ investment into both pre-hatching forms of care and clutch quantity and quality. Our results first show that females did not avoid contaminated areas prior to and at egg laying. However, females returned to their eggs faster in presence of living spores compared to UV-killed or no spores. They were also more likely to construct a nest when in presence of both living and UV-killed spores (but only in one studied population). Finally, we found that spore presence did not influence maternal investment into egg grooming, egg gathering and egg defense, as well as into clutch quantity and quality. Overall, our results demonstrate that earwig females do not avoid contaminated environments, but could mitigate the associated costs of pathogen exposure by adjusting their level of egg care. These findings emphasize the importance of pathogens in the evolution of pre-hatching parental care and, more generally, in the emergence and maintenance of family life in nature.

Description: In this paper, we examined both stated norms of sex preference and actual sex-biases in parental investment in a Tibetan pastoralist society. We collected detailed demographic data on infant mortality, infant feeding, the length of interbirth intervals, and a decision when giving gifts, to examine sex-biased parental investment. Our results indicate a mismatch between self-reported son preference and measures of actual parental investment that favor daughters. We interpret this female-biased parental investment as a possible response to daughters generating more economic resources. However, the stated sex preferences of both sexes reflect cultural norms that appear to have remained unchanged over a long period, which may reflect the importance of male roles in the past. Our behavioral measures of parental investment are those most likely to be in the control of women (such as breastfeeding and interbirth interval), so this mismatch between stated and actual investment may be especially true of women.

Description: Behavioral syndromes are widely recognized as important for ecology and evolution, but most predictions about ecological impacts are based on conceptual models and are therefore imprecise. Borrowing insights from the theory of demographic heterogeneity, we derived insights about the population-dynamic effects of behavioral syndromes. If some individuals are consistently more aggressive than others, not just in interspecific contests, but also in foraging, mating, and antipredator behavior, then population dynamics could be affected by the resulting heterogeneity in demographic rates. We modeled a population with a boldness–aggressiveness syndrome (with the individual’s trait constant through life), showing that the mortality cost of boldness causes aggressive individuals to die earlier, on average, than their nonaggressive siblings. The equilibrium frequency of the aggressive type is strongly affected by the mortality cost of boldness, but not directly by the reproductive benefit of aggressiveness. Introducing aggressive types into a homogeneous nonaggressive population increases the average per-capita mortality rate at equilibrium; under many conditions, this reduces the equilibrium density. One such condition is that the reproductive benefit of aggression is frequency dependent and the population has evolved to equalize the expected fitness of the two types. Finally, if the intensity of aggressiveness can evolve, then the population is likely to evolve to an evolutionarily stable trait value under biologically reasonable assumptions. This analysis shows how a formal model can predict both how a syndrome affects population dynamics and how the population processes constrain evolution of the trait.

Description: “Motion dazzle” patterns are a form of defensive coloration suggested to prevent successful capture during motion by causing predators to misjudge the direction or speed of prey movement. Several studies have found results supporting this idea but little is known about the factors that favor the evolution of these antipredator colorations. A recent experimental study has suggested that the longitudinal striped patterns on the body of lizards can redirect attacks to the tail via the motion dazzle effect. Using a virtual predation experiment with humans and a phylogenetic comparative analysis, we show that evolution of longitudinal striped coloration is associated with prey size. Experiments showed that longitudinal stripes located at the anterior reduced lethal attacks (i.e., attacks directed to the anterior and centre ) but this benefit was greater for shorter prey. Our comparative analysis revealed a negative association between stripe occurrence and body length but no association between stripes and body width. Overall, our results suggest that the dazzle effect produced by stripes is more advantageous in shorter lizards than in longer ones and that the error induced by stripes might be distributed along the axis parallel to the prey trajectory. We discuss reasons why dazzle coloration could be associated with evolution of smaller body size in animals.

Description: The avian nest is an essential structure for offspring development. For adults, nest building entails costs in terms of time, energy, and exposure to predators and parasites. Amount and diversity of materials used for nest building depend on their availability and functionality in scenarios of sexual selection and parasitism. Green plants and feathers of different colors have been hypothesized to play key roles in offspring protection against pathogens, and we here experimentally assessed spotless starling ( Sturnus unicolor ) preferences for pigmented versus unpigmented feathers and for different green plants (aromatic vs. non-aromatic plants) as nest materials. We predicted a preferential selection of unpigmented feathers and aromatic plants according to the antimicrobial properties of these materials described in the literature. We evaluated these predictions during nest building and during egg-laying stages. As expected, starlings preferentially selected unpigmented feathers both before and during egg laying, while aromatic plants were preferentially selected only during the egg-laying stage. These results suggest that starlings prefer nest materials that enhance antimicrobial protection of their offspring. We also discuss some other, non-exclusive functions that might explain the observed preference for nest materials, especially with regard to their potential role in sexual signaling.

Description: There is ongoing debate about how and why the menstrual cycle affects women’s attraction to men. According to the dual sexuality hypothesis, women form pair-bond relationships with men who provide care but also obtain genetic benefits by biasing mating effort towards men with high-fitness genes during the fertile phase. By contrast, the commitment hypothesis proposes that attachment bonds with primary partners function to strengthen pair-bond relationships by enhancing in-pair attraction at the fertile phase, rather than extrapair attraction. We tested these hypotheses by measuring women’s daily sexual and emotional attraction towards men over the whole menstrual cycle. We employed 1) a urinary luteinizing hormone test to determine the day of ovulation, 2) a 5-part classification of menstrual cycle that identifies a distinct peri-ovulatory phase, and 3) individualized phase identification for each participant. There was a mid-cycle rise in extrapair sexual desire. Women gave and received more care from partners during the menstrual than the mid-cycle phases. Partner’s sexual attractiveness and mutual commitment did not moderate these findings. The results do not support either the dual sexuality or commitment hypotheses, and imply that female self-reported sexual desire is not strictly dependent on cyclic hormonal changes. Our results are more consistent with a recently proposed `spandrel’ hypothesis, positing cycle phase effects as a nonfunctional by-product of raised estradiol. Additionally, we found that, with the date of ovulation estimated by luteinizing hormone tests, 45% of ovulations were misclassified by the backward counting method, which urges caution in interpreting results based on counting methods.

Description: Corrigendum for “ Social conflict and costs of cooperation in meerkats are reflected in measures of stress hormones ”

Description: Kleptoparasitism (food stealing) is a significant behavior for animals that forage in social groups as it permits some individuals to obtain resources while avoiding the costs of searching for their own food. Evolutionary game theory has been used to model kleptoparasitism, with a series of differential equation-based compartmental models providing significant theoretical insights into behavior in kleptoparasitic populations. In this paper, we apply this compartmental modeling approach to kleptoparasitic behavior in a real foraging population of urban gulls ( Laridae ). Field data was collected on kleptoparasitism and a model developed that incorporated the same kleptoparasitic and defensive strategies available to the study population. Two analyses were conducted: 1) An assessment of whether the density of each behavior in the population was at an equilibrium. 2) An investigation of whether individual foragers were using Evolutionarily Stable Strategies in the correct environmental conditions. The results showed the density of different behaviors in the population could be at an equilibrium at plausible values for handling time and fight duration. Individual foragers used aggressive kleptoparasitic strategies effectively in the correct environmental conditions but some individuals in those same conditions failed to defend food items. This was attributed to the population being composed of 3 species that differed in competitive ability. These competitive differences influenced the strategies that individuals were able to use. Rather than gulls making poor behavioral decisions these results suggest a more complex 3-species model is required to describe the behavior of this population.

Description: In animal species in which parents provide food to their dependent young, offspring often display conspicuous begging signals. These solicitation behaviors are important components of parent–offspring communication, but it is currently unclear how they and the parental response covary with offspring dependency on parental food provisioning across species. Burying beetles ( Nicrophorus ) are well known for providing elaborate biparental care, including provisioning of begging larvae. By using a multispecies approach, we show that larval begging intensity, as well as the time parents spend provisioning, differ greatly between individuals of the 3 species: N. orbicollis , N. pustulatus , and N. vespilloides . Our results demonstrate that the most dependent offspring of N. orbicollis invest the most time in begging, whereas the most independent offspring of N. pustulatus invest the least amount of time in begging. Thus, we suggest that begging intensity differs due to intrinsic differences in nutritional need between the species rather than because of an arbitrary divergence in begging behavior. We further show that in all 3 species, females spend significantly more time provisioning than males, although there is considerable divergence between species in the extent to which females and males contribute to the provisioning of larvae. We discuss the potential selective factors leading to this diversification of offspring begging and parental provisioning in relation to the distinct variation in offspring dependence between the 3 species.

Description: Red, orange, and yellow carotenoid-based ornaments, which are widely used as sexual signals in many birds, fish, and reptiles, are known to exhibit multidimensional chromatic variation as a result of both the concentration and relative proportions of different constituent carotenoids with differing spectral properties. This is thought to reflect intrinsic variation in signaler quality, making it a useful basis for female choice. However, whether females are able to discriminate relevant variation in carotenoid concentration and/or composition independently of each other, and of other phenotypic or behavior traits, and if so, how this mediates their choice, is poorly understood. Here, female 3-spined sticklebacks ( Gasterosteus aculeatus ) were presented with computer-animated courting males that varied exclusively in the appearance of their carotenoid-based coloration; specifically, each male’s signal provided a perceptual match for carotenoid coloration expressed by live males with known underlying carotenoid content, thereby providing a biologically-relevant signal while precluding confounding traits influencing female choice. Females were able to discriminate between prospective mates solely on the basis of perceived variation in the allocation of carotenoids to males’ sexual signals, and exhibited a strong preference for males with coloration indicative of higher concentrations of carotenoids in their signal, rather than in response to perceived variation in the relative proportion of constituent carotenoids. This has important implications for our understanding of male signaling strategies and the information content of carotenoid-based sexual signals.

Description: Motivation The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis , where a large number of mutations instead occur simultaneously . A number of potential signatures of chromothripsis have been proposed. In this work, we provide a rigorous formulation and analysis of the ‘ability to walk the derivative chromosome’ signature originally proposed by Korbel and Campbell. In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction , which allows us to overcome some of the limitations of the original signature. Results We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion. Availability and implementation An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac . Contact loesper@carleton.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation The identification of microRNA (miRNA) target sites is important. In the past decade, dozens of computational methods have been developed to predict miRNA target sites. Despite their existence, rarely does a method consider the well-known competition and cooperation among miRNAs when attempts to discover target sites. To fill this gap, we developed a new approach called CCmiR, which takes the cooperation and competition of multiple miRNAs into account in a statistical model to predict their target sites. Results Tested on four different datasets, CCmiR predicted miRNA target sites with a high recall and a reasonable precision, and identified known and new cooperative and competitive miRNAs supported by literature. Compared with three state-of-the-art computational methods, CCmiR had a higher recall and a higher precision. Availability and implementation CCmiR is freely available at http://hulab.ucf.edu/research/projects/miRNA/CCmiR . Contact xiaoman@mail.ucf.edu or haihu@cs.ucf.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities [e.g. copy number variations (CNVs) and translocations] altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g. Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. Results In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions ( HiCnv ), (ii) to call inter-chromosomal translocations and their boundaries ( HiCtrans ) from Hi-C experiments and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities ( AveSim ) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing data among chromosomes with CNV events for a breast cancer cell line ( r  = 0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes and homogeneously staining regions. Considering the inherent limitations of existing techniques for karyotyping (i.e. missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100–300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. Availability and implementation CNV calling: https://github.com/ay-lab/HiCnv , Translocation calling: https://github.com/ay-lab/HiCtrans and Hi-C simulation: https://github.com/ay-lab/AveSim . Contact ferhatay@lji.org Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Cancer hallmarks, a concept that seeks to explain the complexity of cancer initiation and development, provide a new perspective of studying cancer signaling which could lead to a greater understanding of this complex disease. However, to the best of our knowledge, there is currently a lack of tools that support such hallmark-based study of the cancer signaling network, thereby impeding the gain of knowledge in this area. We present TROVE, an user-friendly software that facilitates hallmark annotation, visualization and analysis in cancer signaling networks. In particular, TROVE facilitates hallmark analysis specific to particular cancer types. Availability and implementation Available under the Eclipse Public License from: https://sites.google.com/site/cosbyntu/softwares/trove and https://github.com/trove2017/Trove . Contact hechua@ntu.edu.sg or assourav@ntu.edu.sg

Description: Summary High-throughput screening of the host transcriptional response to various viral infections provides a wealth of data, but utilization of microarray and next generation sequencing (NGS) data for analysis can be difficult. The Ho st T ranscriptional R esponse D ata B ase (HoTResDB), allows visitors to access already processed microarray and NGS data from non-human primate models of viral hemorrhagic fever to better understand the host transcriptional response. Availability HoTResDB is freely available at http://hotresdb.bu.edu Contact jhconnor@bu.edu

Description: Motivation Structural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (∼5 to 10) DNA molecules ∼50 Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. Results We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in an individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification—including two recent methods that also analyze linked-reads—on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Availability and implementation Software is available at compbio.cs.brown.edu/software . Contact braphael@princeton.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as carcinogenic exposures or cancer related aberrations of DNA maintenance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. The decomposition of a cancer genome’s mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. However, the results from different decomposition methods are not always consistent. Hence, one needs to be able to not only decompose a patient’s mutational profile into signatures but also establish the accuracy of such decomposition. Results We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes. We identified both very stable and highly unstable signatures, as well as signatures that previously have not been associated with breast cancer. We also provided additional support for the novel signatures. Our results emphasize the importance of assessing the confidence and stability of inferred signature contributions. Availability and implementation All tools developed in this paper have been implemented in an R package, called SignatureEstimation, which is available from https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi\#signatureestimation . Contact wojtowda@ncbi.nlm.nih.gov or przytyck@ncbi.nlm.nih.gov Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Brain imaging genetics, which studies the linkage between genetic variations and structural or functional measures of the human brain, has become increasingly important in recent years. Discovering the bi-multivariate relationship between genetic markers such as single-nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is one major task in imaging genetics. Sparse Canonical Correlation Analysis (SCCA) has been a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ 1 -norm or its variants to induce sparsity. The ℓ 0 -norm penalty is a perfect sparsity-inducing tool which, however, is an NP-hard problem. Results In this paper, we propose the truncated ℓ 1 -norm penalized SCCA to improve the performance and effectiveness of the ℓ 1 -norm based SCCA methods. Besides, we propose an efficient optimization algorithms to solve this novel SCCA problem. The proposed method is an adaptive shrinkage method via tuning τ . It can avoid the time intensive parameter tuning if given a reasonable small τ . Furthermore, we extend it to the truncated group-lasso (TGL), and propose TGL-SCCA model to improve the group-lasso-based SCCA methods. The experimental results, compared with four benchmark methods, show that our SCCA methods identify better or similar correlation coefficients, and better canonical loading profiles than the competing methods. This demonstrates the effectiveness and efficiency of our methods in discovering interesting imaging genetic associations. Availability and implementation The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/tlpscca/ . Contact dulei@nwpu.edu.cn or shenli@iu.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Modelling with multiple servers that use different algorithms for docking results in more reliable predictions of interaction sites. However, the scoring and comparison of all models by an expert is time-consuming and is not feasible for large volumes of data generated by such modelling. Results Quality ASsessment of DOcking Models (QASDOM) Server is a simple and efficient tool for real-time simultaneous analysis, scoring and ranking of data sets of receptor–ligand complexes built by a range of docking techniques. This meta-server is designed to analyse large data sets of docking models and rank them by scoring criteria developed in this study. It produces two types of output showing the likelihood of specific residues and clusters of residues to be involved in receptor–ligand interactions and the ranking of models. The server also allows visualizing residues that form interaction sites in the receptor and ligand sequence and displays 3D model structures of the receptor–ligand complexes. Availability http://qasdom.eimb.ru . Contact alexei.adzhubei@eimb.ru. Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Protein–protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein–protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein–protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods. Results On an independent test set of obligate and transient complexes, our IntPred predictor performs well (MCC = 0.370, ACC = 0.811, SPEC = 0.916, SENS = 0.411) and compares favourably with other methods. Overall, IntPred ranks second of six methods tested with SPPIDER having slightly better overall performance (MCC = 0.410, ACC = 0.759, SPEC = 0.783, SENS = 0.676), but considerably worse specificity than IntPred. As with SPPIDER, using an independent test set of obligate complexes enhanced performance (MCC = 0.381) while performance is somewhat reduced on a dataset of transient complexes (MCC = 0.303). The trade-off between sensitivity and specificity compared with SPPIDER suggests that the choice of the appropriate tool is application-dependent. Availability and implementation IntPred is implemented in Perl and may be downloaded for local use or run via a web server at www.bioinf.org.uk/intpred/ . Contact andrew@bioinf.org.uk or andrew.martin@ucl.ac.uk Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Motivation Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments. Results We combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated. Availability and implementation The app is publicly available in the Cytoscape app store. Contact guillaume.brysbaert@univ-lille1.fr Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Description: Summary Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner. Availability and implementation Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango . Contact jh22@sanger.ac.uk or sh16@sanger.ac.uk

Description: Summary MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc/ Contact contact-metexplore@inra.fr

Description: Motivation Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired. Results We developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development. Availability and implementation MATLAB and R version of SINCERITIES are freely available from the following websites: http://www.cabsel.ethz.ch/tools/sincerities.html and https://github.com/CABSEL/SINCERITIES . The single cell THP-1 and T2EC transcriptional profiles are available from the original publications ( Kouno et al. , 2013 ; Richard et al. , 2016 ). The in silico single cell data are available on SINCERITIES websites. Contact rudi.gunawan@chem.ethz.ch Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.