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  • Oxford University Press  (162,245)
  • American Institute of Physics (AIP)  (87,665)
  • 2020-2023  (41)
  • 2015-2019  (109,926)
  • 2010-2014  (139,943)
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  • 1
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    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publication Date: 2022-03-07
    Description: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Description: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Description: Published
    Description: 536–547
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-24
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Description: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Description: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Description: Published
    Description: 29–49
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Description: Published
    Description: 1394–1418
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
    Details
    Publication Date: 2022-09-01
    Description: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Description: Published
    Description: 1404–1420
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publication Date: 2022-09-16
    Description: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 7
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Description: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Description: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Description: 2023-07-04
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Description: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Description: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
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  • 11
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    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-26
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Description: Published
    Description: 1283–1297
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Description: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
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  • 13
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    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Description: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
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  • 14
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
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  • 16
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    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-02
    Description: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Description: Published
    Description: 452–464
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
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  • 17
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    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Description: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Description: Published
    Description: 704–718
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
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  • 18
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    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-24
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Description: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Description: Published
    Description: 151–170
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
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  • 19
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    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-15
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Description: Published
    Description: 1465–1477
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
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  • 20
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    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-22
    Description: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Description: Published
    Description: egab062
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
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  • 21
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    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Description: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Keywords: Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
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  • 22
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    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
    Details
    Publication Date: 2022-06-07
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Description: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Description: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Description: 2022-06-07
    Keywords: domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository Name: Woods Hole Open Access Server
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  • 23
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    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
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  • 24
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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  • 25
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    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Description: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Description: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
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    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Description: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Description: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Keywords: population structure ; connectivity ; migration ; gene flow
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    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Description: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Description: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Keywords: Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
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    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Description: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Description: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
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    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Description: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio-Environmental Synthesis Center under the US National Science Foundation Grant DBI-1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1-1).
    Keywords: Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
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    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2020. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Description: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Description: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Description: 2021-10-16
    Keywords: dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
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    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Description: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Description: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Description: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Description: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Keywords: porpoise's physical model ; metamaterials ; biosonar ; directional emission
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Description: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Description: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
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    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Description: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Description: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
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  • 39
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    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Description: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Description: This work was supported by the National Science Foundation [OCE-1356192].
    Keywords: Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
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    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Description: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Description: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Keywords: Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
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  • 41
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    Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms (2020)
    Oxford University Press
    In:  Integrative and Comparative Biology, 60 (6). pp. 1401-1413.
    Details
    Publication Date: 2022-01-07
    Description: Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.
    Type: Article , PeerReviewed
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    Great Policy Successes (2019)
    Oxford University Press
    Details
    Publication Date: 2024-03-23
    Description: "With so much media and political criticism of their shortcomings and failures, it is easy to overlook the fact that many governments work pretty well much of the time. Great Policy Successes turns the spotlight on instances of public policy that are remarkably successful. It develops a framework for identifying and assessing policy successes, paying attention not just to their programmatic outcomes but also to the quality of the processes by which policies are designed and delivered, the level of support and legitimacy they attain, and the extent to which successful performance endures over time. The bulk of the book is then devoted to 15 detailed case studies of striking policy successes from around the world, including Singapore's public health system, Copenhagen and Melbourne's rise from stilted backwaters to the highly liveable and dynamic urban centres they are today, Brazil's Bolsa Familia poverty relief scheme, the US's GI Bill, and Germany's breakthrough labour market reforms of the 2000s. Each case is set in context, its main actors are introduced, key events and decisions are described, the assessment framework is applied to gauge the nature and level of its success, key contributing factors to success are identified, and potential lessons and future challenges are identified. Purposefully avoiding the kind of heavy theorizing that characterizes many accounts of public policy processes, each case is written in an accessible and narrative style ideally suited for classroom use in conjunction with mainstream textbooks on public policy design, implementation, and evaluation.
    Keywords: public policy ; policy evaluation ; government ; governance ; social policy ; health policy ; economic policy ; thema EDItEUR::J Society and Social Sciences::JP Politics and government
    Language: English
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  • 43
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    Rotational motions from the 2016, Central Italy seismic sequence, as observed by an underground ring laser gyroscope (2019)
    Oxford University Press
    Details
    Publication Date: 2021-06-21
    Description: We present the analysis of rotational and translational ground motions from earthquakes recorded during October–November 2016, in association with the Central Italy seismic sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope and the three components of ground velocity from a broad-band seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories of the Istituto Nazionale di Fisica Nucleare. We collected dozens of events spanning the 3.5–5.9 magnitude range and epicentral distances between 30 and 70 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. Under the plane-wave approximation we process the data set in order to get an experimental estimation of the events backazimuth. Peak values of rotation rate (PRR) and horizontal acceleration (PGA) are markedly correlated, according to a scaling constant which is consistent with previous measurements from different earthquake sequences. We used a prediction model in use for Italy to calculate the expected PGA at the recording site, obtaining consequently predictions for PRR. Within the modelling uncertainties, predicted rotations are consistent with the observed ones, suggesting the possibility of establishing specific attenuation models for ground rotations, like the scaling of peak velocity and peak acceleration in empirical ground-motion prediction relationships. In a second step, after identifying the direction of the incoming wavefield, we extract phase-velocity data using the spectral ratio of the translational and rotational components. This analysis is performed over time windows associated with the P-coda, S-coda and Lg phase. Results are consistent with independent estimates of shear wave velocities in the shallow crust of the Central Apennines
    Description: Published
    Description: 705-715
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Rotational seismology ; Surface waves and free oscillations ; Wave propagation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Subsurface fluid distribution and possible seismic precursory signal at the Salse di Nirano mud volcanic field, Italy (2019)
    Oxford University Press
    Details
    Publication Date: 2019-03-13
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2015. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Mud volcanoes are geological systems often characterized by elevated fluid pressures at depth deviating from hydrostatic conditions. This near-critical state makes mud volcanoes particularly sensitive to external forcing induced by natural or man-made perturbations. We used the Nirano mud volcanic field as a natural laboratory to test pre- and post-seismic effects generated by distant earthquakes.We first characterized the subsurface structure of the Nirano mud volcanic field with a geoelectrical study. Next, we deployed a broad-band seismic station in the area to understand the typical seismic signal generated by the mud volcano. Seismic records show a background noise below 2 s, sometimes interrupted by pulses of drumbeatlike high-frequency signals lasting from several minutes to hours. To date this is the first observation of drumbeat signal observed in mud volcanoes. In 2013 June we recorded a M4.7 earthquake, that occurred approximately 60 km far from our seismic station. According to empirical estimations the Nirano mud volcanic field should not have been affected by the M4.7 earthquake. Yet, before the seismic event we recorded an increasing amplitude of the signal in the 10–20 Hz frequency band. The signal emerged approximately two hours before the earthquake and lasted for about three hours. Our statistical analysis suggests the presence of a possible precursory signal about 10 min before the earthquake.
    Description: Published
    Description: 907–917
    Description: 7A. Geofisica per il monitoraggio ambientale
    Description: JCR Journal
    Keywords: Tomography ; Gas and hydrate systems ; Earthquake interaction, forecasting, and prediction ; Seismicity and tectonics ; Volcano seismology ; Mud volcanism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Evaluation of earthquake stress parameters and its scaling during the 2016-2017 Amatrice-Norcia-Visso sequence—Part I (2019)
    Oxford University Press
    Details
    Publication Date: 2021-11-09
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2019. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: The Amatrice–Norcia–Visso sequence is characterized by complex behaviour that is somewhat atypical of main-shock–aftershock sequences, as there were multiple large main shocks that continued for months. In this study we focus on the Amatrice sequence (main shock 2016 August 24, Mw = 5.97) to evaluate the apparent stress values and magnitude-dependent scaling in order to improve our knowledge of processes that control small and large earthquakes within this active region of Italy. Apparent stress is proportional to the ratio of radiated seismic energy and seismic moment, and as such, these stress parameters play an important role in hazard prediction as they have a strong effect on the observed and predicted ground shaking. We analyse 83 events of the sequence from 2016 August 24 to October 16, within a radius of 20 km from the main shock and with an Mw ranging between 5.97 and 2.72. Taking advantage of the averaging nature of coda waves, we analyse coda-envelope-based spectral ratios between neighbouring event pairs.We use equations proposed byWalter et al. to consider stable, low-frequency and high-frequency spectral ratio levelswhich provide measures of the corner frequency and apparent stress ratios of the events within the sequence. The results demonstrate non-self-similar behaviour within the sequence, suggesting a change in dynamics between the largest events and the smaller aftershocks. The apparent stress and corner frequency estimates are compared to those obtained by Malagnini and Munaf`o who utilized hundreds of direct S-wave spectral ratio measurements to obtain their results. Although our analysis is based only on 83 events, our results are in very good agreement, demonstrating once more that the use of coda waves is very stable and provides lower variance measures than those using direct waves. A comparison with recent Central Apennines source scaling models derived from various seismic sequences (1997–1998 Colfiorito, 2002 San Giuliano di Puglia, 2009 L’Aquila) shows that the Amatrice sequence source scaling in this study is well represented by the models proposed by Pacor et al. and Malagnini and Mayeda.
    Description: Published
    Description: 446-455
    Description: 3T. Sorgente sismica
    Description: JCR Journal
    Keywords: Coda waves; Earthquake dynamics; Earthquake source observations; Amatrice ; earthquake stress parameters
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  • 46
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    Bayesian joint inversion of controlled source electromagnetic and magnetotelluric data to image freshwater aquifer offshore New Jersey (2019)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 1822-1837, doi: 10.1093/gji/ggz253.
    Description: Joint inversion of multiple electromagnetic data sets, such as controlled source electromagnetic and magnetotelluric data, has the potential to significantly reduce uncertainty in the inverted electrical resistivity when the two data sets contain complementary information about the subsurface. However, evaluating quantitatively the model uncertainty reduction is made difficult by the fact that conventional inversion methods—using gradients and model regularization—typically produce just one model, with no associated estimate of model parameter uncertainty. Bayesian inverse methods can provide quantitative estimates of inverted model parameter uncertainty by generating an ensemble of models, sampled proportional to data fit. The resulting posterior distribution represents a combination of a priori assumptions about the model parameters and information contained in field data. Bayesian inversion is therefore able to quantify the impact of jointly inverting multiple data sets by using the statistical information contained in the posterior distribution. We illustrate, for synthetic data generated from a simple 1-D model, the shape of parameter space compatible with controlled source electromagnetic and magnetotelluric data, separately and jointly. We also demonstrate that when data sets contain complementary information about the model, the region of parameter space compatible with the joint data set is less than or equal to the intersection of the regions compatible with the individual data sets. We adapt a trans-dimensional Markov chain Monte Carlo algorithm for jointly inverting multiple electromagnetic data sets for 1-D earth models and apply it to surface-towed controlled source electromagnetic and magnetotelluric data collected offshore New Jersey, USA, to evaluate the extent of a low salinity aquifer within the continental shelf. Our inversion results identify a region of high resistivity of varying depth and thickness in the upper 500 m of the continental shelf, corroborating results from a previous study that used regularized, gradient-based inversion methods. We evaluate the joint model parameter uncertainty in comparison to the uncertainty obtained from the individual data sets and demonstrate quantitatively that joint inversion offers reduced uncertainty. In addition, we show how the Bayesian model ensemble can subsequently be used to derive uncertainty estimates of pore water salinity within the low salinity aquifer.
    Description: We gratefully acknowledge funding support from National Science Foundation grants 1458392 and 1459035. We thank the captain and crew of the R.V. Marcus G. Langseth for a successful cruise and the Marine EM Lab at Scripps Institution of Oceanography for providing the instrumentation. We also thank Chris Armerding, Marah Dahn, John Desanto, Jimmy Elsenbeck, Matt Folsom, Keiichi Ishizu, Jeff Pepin, Charlotte Wiman and Georgie Zelenak for participating in the cruise. We gratefully acknowledge Alberto Malinverno for the idea to use a Monte Carlo scheme to estimate the distribution of pore fluid salinity, and William Menke for many constructive conversations and suggestions.
    Keywords: Controlled source electromagnetics (CSEM) ; Joint inversion ; Magnetotellurics ; Statistical methods ; Marine electromagnetics ; Probability distributions
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  • 47
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    Along-strike variation in slab geometry at the southern Mariana subduction zone revealed by seismicity through ocean bottom seismic experiments (2019)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2122-2135, doi: 10.1093/gji/ggz272.
    Description: We have conducted the first passive Ocean Bottom Seismograph (OBS) experiment near the Challenger Deep at the southernmost Mariana subduction zone by deploying and recovering an array of 6 broad-band OBSs during December 2016–June 2017. The obtained passive-source seismic records provide the first-ever near-field seismic observations in the southernmost Mariana subduction zone. We first correct clock errors of the OBS recordings based on both teleseismic waveforms and ambient noise cross-correlation. We then perform matched filter earthquake detection using 53 template events in the catalogue of the US Geological Survey and find 〉7000 local earthquakes during the 6-month OBS deployment period. Results of the two independent approaches show that the maximum clock drifting was ∼2 s on one instrument (OBS PA01), while the rest of OBS waveforms had negligible time drifting. After timing correction, we locate the detected earthquakes using a newly refined local velocity model that was derived from a companion active source experiment in the same region. In total, 2004 earthquakes are located with relatively high resolution. Furthermore, we calibrate the magnitudes of the detected earthquakes by measuring the relative amplitudes to their nearest relocated templates on all OBSs and acquire a high-resolution local earthquake catalogue. The magnitudes of earthquakes in our new catalogue range from 1.1 to 5.6. The earthquakes span over the Southwest Mariana rift, the megathrust interface, forearc and outer-rise regions. While most earthquakes are shallow, depths of the slab earthquakes increase from ∼100 to ∼240 km from west to east towards Guam. We also delineate the subducting interface from seismicity distribution and find an increasing trend in dip angles from west to east. The observed along-strike variation in slab dip angles and its downdip extents provide new constraints on geodynamic processes of the southernmost Mariana subduction zone.
    Description: We express our appreciation to the science parties and crew members of the R/V Shiyan 3 for deployment and collection of the OBS instruments during the Mariana expeditions. This study is supported by the Hong Kong Research Grant Council Grants (No. 14313816), Faculty of Science at CUHK, Chinese Academy of Sciences (No. Y4SL021001, QYZDY-SSW-DQC005, 133244KYSB20180029), the National Natural Science Foundation of China (No. 41890813, 91628301, 41676042, U1701641, 41576041, 91858207 and U1606401), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100). Generic Mapping Tools (Wessel & Smith 1991) and PSSAC (developed by Prof Lupei Zhu) are used for data analysis and figure preparation in this study. Constructive comments from Dr Lidong Bie and two anonymous reviewers are helpful in improving the manuscript.
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Subduction zone processes
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  • 48
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    How we can all stop killing whales: A proposal to avoid whale entanglement in fishing gear (2019)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in ICES Journal of Marine Science 76(4), (2010): 781-786, doi:10.1093/icesjms/fsy194.
    Description: Whales are federally protected by the Marine Mammal Protection Act; endangered species, such as the North Atlantic right whale, receive additional protection under the Endangered Species Act. However, their regulations have failed to satisfy conservation and animal welfare concerns. From 1990 to 2011 the North Atlantic right whale (Eubalaena glacialis, NARW) population grew at a mean of 2.8% annually. However, population trends reversed since 2011; the species is in decline, with only ∼100 reproductively active females remaining. This failure is driven by vessel collisions and increasingly fatal and serious entanglement in fixed fishing gear, whose rope strength has increased substantially. Chronic entanglement, drag, and associated morbidity have been linked to poor fecundity. Genuine solutions involve designating areas to be avoided and speed restrictions for ships and removing fishing trap ropes from the water column. A trap fishing closure for NARW habitat in the Cape Cod Bay (U.S.) area has been in place seasonally since 2015. 2017 mortalities in Eastern Canada elicited substantive management changes whereby the 2018 presence of NARW in active trap fishing areas resulted in an effective closure. To avoid these costly closures, the traditional trap fishery model of rope end lines attached to surface marker buoys has to be modified so that traps are marked virtually, and retrieved with gear that does not remain in the water column except during trap retrieval. Consumer demand for genuinely whale-safe products will augment and encourage the necessary regulatory changes so that trap fisheries conserve target and nontarget species.
    Description: I thank Mark Baumgartner, Scott Kraus, Tim Werner, Amy Knowlton, Heather Pettis, Scott Landry, Stormy Mayo, Fred Penney, and Beth Casoni for discussions on this topic and Natalie Renier for drawing Figures 5 and 6. Funding was provided by the Woods Hole Oceanographic Institution Independent Research and Development Program.
    Description: 2020-01-10
    Keywords: end line ; entanglement ; large whale ; rope removal ; trap
    Repository Name: Woods Hole Open Access Server
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    Constraints on the resistivity of the oceanic lithosphere and asthenosphere from seafloor ocean tidal electromagnetic measurements (2019)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International, 219(1), (2019): 464-478, doi:10.1093/gji/ggz315.
    Description: The electromagnetic (EM) field generated by ocean tidal flow is readily detectable in both satellite magnetic field data, and in ocean-bottom measurements of electric and magnetic fields. The availability of accurate charts of tidal currents, constrained by assimilation of modern satellite altimetry data, opens the possibility of using tidal EM fields as a source to image mantle electrical resistivity beneath the ocean basins, as highlighted by the recent success in defining the globally averaged lithosphere–asthenosphere boundary (LAB) with satellite data. In fact, seafloor EM data would be expected to provide better constraints on the structure of resistive oceanic lithosphere, since the toroidal magnetic mode, which can constrain resistive features, is a significant component of the tidal EM field within the ocean, but is absent above the surface (in particular in satellite data). Here we consider this issue in more detail, using a combination of simplified theoretical analysis and 1-D and 3-D numerical modelling to provide a thorough discussion of the sensitivity of satellite and seafloor data to subsurface electrical structure. As part of this effort, and as a step toward 3-D inversion of seafloor tidal data, we have developed a new flexible 3-D spherical-coordinate finite difference scheme for both global and regional scale modelling, with higher resolution models nested in larger scale solutions. We use the new 3-D model, together with Monte Carlo simulations of errors in tidal current estimates, to provide a quantitative assessment of errors in the computed tidal EM signal caused by uncertainty in the tidal source. Over the open ocean this component of error is below 0.01 nT in Bz at satellite height and 0.05 nT in Bx on the seafloor, well below typical signal levels. However, as coastlines are approached error levels can increase substantially. Both analytical and 3-D modelling demonstrate that the seafloor magnetic field is most sensitive to the lithospheric resistance (the product of resistivity and thickness), and is more weakly influenced (primarily in the phase) by resistivity of the underlying asthenosphere. Satellite data, which contain only the poloidal magnetic mode, are more sensitive to the conductive asthenosphere, but have little sensitivity to lithospheric resistance. For both seafloor and satellite data’s changes due to plausible variations in Earth parameters are well above error levels associated with source uncertainty, at least in the ocean interior. Although the 3-D modelling results are qualitatively consistent with theoretical analysis, the presence of coastlines and bathymetric variations generates a complex response, confirming that quantitative interpretation of ocean tidal EM fields will require a 3-D treatment. As an illustration of the nested 3-D scheme, seafloor data at five magnetic and seven electric stations in the northeastern Pacific (41○N, 165○W) are fit with trial-and-error forward modelling of a local domain. The simulation results indicate that the lithospheric resistance is roughly 7 × 108 Ωm2. The phase of the seafloor data in this region are inconsistent with a sharp transition between the resistive lithosphere and conductive asthenosphere.
    Description: This work has been supported by National Natural Science Foundation of China grants 41804072 and 41574104, and NSF grant EAR-1447109. Special thanks to Dr Benjamin Murphy who provided the conductivity-depth profile for 1-D earth model, Dr Min Ding who provided valuable discussion about the oceanic lithosphere and Dr Jeffery Love who provided comments on the stylistics of the manuscript.
    Keywords: Composition and structure of the mantle ; Pacific Ocean ; Electromagnetic theory ; Geomagnetic induction ; Satellite magnetics
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    Employing plant functional groups to advance seed dispersal ecology and conservation (2019)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aslan, C., Beckman, N. G., Rogers, H. S., Bronstein, J., Zurell, D., Hartig, F., Shea, K., Pejchar, L., Neubert, M., Poulsen, J., HilleRisLambers, J., Miriti, M., Loiselle, B., Effiom, E., Zambrano, J., Schupp, G., Pufal, G., Johnson, J., Bullock, J. M., Brodie, J., Bruna, E., Cantrell, R. S., Decker, R., Fricke, E., Gurski, K., Hastings, A., Kogan, O., Razafindratsima, O., Sandor, M., Schreiber, S., Snell, R., Strickland, C., & Zhou, Y. Employing plant functional groups to advance seed dispersal ecology and conservation. AoB Plants, 11(2), (2019):plz006, doi:10.1093/aobpla/plz006.
    Description: Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio‐Environmental Synthesis Center under the US National Science Foundation Grant DBI‐1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1- 1). Contributions by the authors C.A. led the development of the concepts, writing, and revising of the manuscript with input from N.G.B. and H.S.R. All authors contributed to the development of concepts and are listed in order of contribution and alphabetical order within each level of contribution.
    Keywords: dependency ; directed dispersal ; dispersal vectors ; generalization ; mutualism ; seed dispersal effectiveness
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    Keeping it light: (re)analyzing community-wide datasets without major infrastructure (2019)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.
    Description: DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
    Description: Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.).
    Keywords: reproducibility ; data reuse ; open data
    Repository Name: Woods Hole Open Access Server
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    A multitaper spectral estimator for time-series with missing data (2019)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2165-2178, doi: 10.1093/gji/ggz280.
    Description: A multitaper estimator is proposed that accommodates time-series containing gaps without using any form of interpolation. In contrast with prior missing-data multitaper estimators that force standard Slepian sequences to be zero at gaps, the proposed missing-data Slepian sequences are defined only where data are present. The missing-data Slepian sequences are frequency independent, as are the eigenvalues that define the energy concentration within the resolution bandwidth, when the process bandwidth is [−1/2,1/2) for unit sampling and the sampling scheme comprises integer multiples of unity. As a consequence, one need only compute the ensuing missing-data Slepian sequences for a given sampling scheme once, and then the spectrum at an arbitrary set of frequencies can be computed using them. It is also shown that the resulting missing-data multitaper estimator can incorporate all of the optimality features (i.e. adaptive-weighting, F-test and reshaping) of the standard multitaper estimator, and can be applied to bivariate or multivariate situations in similar ways. Performance of the missing-data multitaper estimator is illustrated using length of day, seafloor pressure and Nile River low stand time-series.
    Description: The length of day utilized in Section 3 are available from http://hpiers.obspm.fr. The pressure data used in Section 4 are available from https://doi.org/10.1029/2018JC014586. A Matlab function MDmwps.m to compute missing-data power spectra is available from the Mathworks file exchange website. The author thanks Jeff Park and editor F.J. Simons for thorough reviews. This work was supported by an Internal Research and Development award at WHOI, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
    Keywords: Fourier analysis ; Numerical approximations and analysis ; Statistical methods ; Time-series analysis
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    Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes (2019)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.
    Description: Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
    Description: Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67].
    Keywords: marine microbial eukaryote ; transcriptome assembly ; automated pipeline ; re-analysis
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    On the forward modelling of three-dimensional magnetotelluric data using a radial basis function-based meshfree method (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The investigation of using a novel radial basis function-based meshfree method for forward modelling magnetotelluric data is presented. The meshfree method, which can be termed radial basis function-based finite difference (RBF-FD), uses only a cloud of unconnected points to obtain the numerical solution throughout the computational domain. Unlike mesh-based numerical methods (for example, grid-based finite difference, finite volume and finite element), the meshfree method has the unique feature that the discretization of the conductivity model can be decoupled from the discretization used for numerical computation, thus avoiding traditional expensive mesh generation and allowing complicated geometries of the model be easily represented. To accelerate the computation, unstructured point discretization with local refinements are employed. Maxwell’s equations in the frequency domain are re-formulated using $\mathbf {A}$-ψ potentials in conjuction with the Coulomb gauge condition, and are solved numerically with a direct solver to obtain magnetotelluric responses. A major obstacle in applying common meshfree methods in modelling geophysical electromagnetic data is that they are incapable of reproducing discontinuous fields such as the discontinuous electric field over conductivity jumps, causing spurious solutions. The occurrence of spurious, or non-physical, solutions when applying standard meshfree methods is removed here by proposing a novel mixed scheme of the RBF-FD and a Galerkin-type weak-form treatment in discretizing the equations. The RBF-FD is applied to the points in uniform conductivity regions, whereas the weak-form treatment is introduced to points located on the interfaces separating different homogeneous conductivity regions. The effectiveness of the proposed meshfree method is validated with two numerical examples of modelling the magnetotelluric responses over three-dimensional conductivity models.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Constraining Crustal Structure in the Presence of Sediment: A Multiple Converted Wave Approach (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Receiver functions are sensitive to sharp seismic velocity variations with depth and are commonly used to constrain crustal thickness. The H-κ stacking method of Zhu and Kanamori (〈span〉2000〈/span〉) is often employed to constrain both the crustal thickness (H) and ${V_P}$/${V_S}$ ratio ($\kappa $) beneath a seismic station using P-to-s converted waves (Ps). However, traditional H-κ stacks require an assumption of average crustal velocity (usually ${V_P}$). Additionally, large amplitude reverberations from low velocity shallow layers, such as sedimentary basins, can overprint sought-after crustal signals, rendering traditional H-$\ \kappa $ stacking uninterpretable. We overcome these difficulties in two ways. When S-wave reverberations from sediment are present, they are removed by applying a resonance removal filter allowing crustal signals to be clarified and interpreted. We also combine complementary Ps receiver functions, Sp receiver functions, and the post-critical P wave reflection from the Moho (SP〈sub〉m〈/sub〉p) to remove the dependence on an assumed average crustal ${V_P}$. By correcting for sediment and combining multiple data sets, the crustal thickness, average crustal P-wave velocity, and crustal ${V_P}$/${V_S}$ ratio is constrained in geologic regions where traditional H-$\ \kappa $ stacking fails, without making an initial P-wave velocity assumption or suffering from contamination by sedimentary reverberations.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Erratum to: Complex-conductivity monitoring to delineate aquifer pore clogging during nanoparticles injection (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉In the original version of this article the author, Adrian Flores Orozco, was incorrectly listed. This has now been corrected and the publisher apologises for the error.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Upper-mantle density structure in the Philippine Sea and adjacent region and its relation to tectonics (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The evolution of the Philippine Sea Plate (PSP) since Jurassic is one of the key issues in the dynamics of lithosphere and mantle. The related studies benefited mostly from seismic tomography which provides velocity structures in the upper mantle. However, the upper-mantle structure is not well resolved compared to the continental areas due to the lack of seismic data in the Philippine Sea. We employ a 3-D gravity inversion constrained by an initial model based on the 〈span〉S〈/span〉-wave tomography (SL2013sv; Schaeffer & Lebedev 2013) to image the density structure of the upper mantle of the PSP and adjacent region. The resulting model shows a three-layer pattern of vertical high-low-high density variation in the upper mantle under the PSP. The thin high-density layer evidences for strong oceanic lithosphere in the West Philippine Sea. The relatively low dense mantle located below the PSP possibly originates from the asthenosphere. The PSP differs from the Pacific and the Indian-Australian plates in the whole depth range, while its structure is similar to the eastern Eurasian and Sunda plates. In the depth range, 200–300 km, the relative high-density zone beneath PSP extends to the Sunda Plate and to the eastern Eurasian Plate. We further estimated the conversion factor of our density model and the velocity model (SL2013sv; Schaeffer & Lebedev 2013) in order to locate the changes of compositional effects in the upper mantle. The negative conversion factor indicates that the compositional changes primarily affect the density anomalies beneath the PSP. We, therefore, describe the layered density structures as ‘sandwich’ pattern, which is unique and different from adjacent regions.〈/span〉
    Print ISSN: 2051-1965
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    Spurious low velocity zones in joint inversions of surface waves and receiver functions (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Low-velocity layers within the crust can indicate the presence of melt and lithologic differences with implications for crustal composition and formation. Seismic wave conversions and reverberations across the base of the crust or intracrustal discontinuities, analysed using the receiver function method, can be used to constrain crustal layering. This is commonly accomplished by inverting receiver functions jointly with surface wave dispersion. Recently, the proliferation of model-space search approaches has made this technique a workhorse of crustal seismology. We show that reverberations from shallow layers such as sedimentary basins produce spurious low-velocity zones when inverted for crustal structure with surface wave data of insufficiently high frequency. Therefore, reports of such layers in the literature based on inversions using receiver function data should be re-evaluated. We demonstrate that a simple resonance-removal filter can suppress these effects and yield reliable estimates of crustal structure, and advocate for its use in receiver-function based inversions.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Dynamic rupture and earthquake sequence simulations using the wave equation in second-order form (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We present a numerical method for simulating both single-event dynamic ruptures and earthquake sequences with full inertial effects in antiplane shear with rate-and-state fault friction. We use the second-order form of the wave equation, expressed in terms of displacements, discretized with high-order-accurate finite difference operators in space. Advantages of this method over other methods include reduced computational memory usage and reduced spurious high frequency oscillations. Our method handles complex geometries, such as non-planar fault interfaces and free surface topography. Boundary conditions are imposed weakly using penalties. We prove time stability by constructing discrete energy estimates. We present numerical experiments demonstrating the stability and convergence of the method, and showcasing applications of the method, including the transition in rupture style from crack-like ruptures to slip pulses for strongly rate-weakening friction and the simulation of earthquake sequences in a viscoelastic solid with a fully dynamic coseismic phase.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    On seismic ambient noise cross-correlation and surface-wave attenuation (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉We derive a theoretical relationship between the cross correlation of ambient Rayleigh waves (seismic ambient noise) and the attenuation parameter α associated with Rayleigh-wave propagation. In particular, we derive a mathematical expression for the multiplicative factor relating normalized cross correlation to the Rayleigh-wave Green’s function. Based on this expression, we formulate an inverse problem to determine α from cross correlations of recorded ambient signal. We conduct a preliminary application of our algorithm to a relatively small instrument array, conveniently deployed on an island. In our setup, the mentioned multiplicative factor has values of about 2.5 to 3, which, if neglected, could result in a significant underestimate of α. We find that our inferred values of α are reasonable, in comparison with independently obtained estimates found in the literature. Allowing α to vary with respect to frequency results in a reduction of misfit between observed and predicted cross correlations.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Shallow crustal imaging using distant, high-magnitude earthquakes (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Global phases, viz. seismic phases that travel through the Earth’s core, can be used to locally image the crust by means of seismic interferometry. This method is known as Global Phase Seismic Interferometry (GloPSI). Traditionally, GloPSI retrieves low-frequency information (up to 1 Hz). Recent studies, however, suggest that there is high-frequency signal present in the coda of strong, distant earthquakes. This research quantifies the potential of these high-frequency signals, by analysing recordings of a multitude of high-magnitude earthquakes (≥6.4 〈span〉M〈/span〉〈sub〉w〈/sub〉) and their coda on a selection of permanent USArray stations. Nearly half of the 〈span〉P, PKP〈/span〉 and PKIKP phases are recorded with a signal-to-noise ratio of at least 5 dB at 3 Hz. To assess the viability of using the high-frequency signal, the second half of the paper highlights two case studies. First, a known sedimentary structure is imaged in Malargüe, Argentina. Secondly, the method is used to reveal the structure of the Midcontinent Rift below the SPREE array in Minnesota, USA. Both studies demonstrate that structural information of the shallow crust (≤5 km) below the arrays can be retrieved. In particular, the interpreted thickness of the sedimentary layer below the Malargüe array is in agreement with earlier studies in the same area. Being able to use global phases and direct 〈span〉P〈/span〉-phases with large epicentral distances (〉80°) to recover the Earth’s sedimentary structure suggests that GloPSI can be applied in an industrial context.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Source localization and joint velocity model building using wavefront attributes (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The localization of passive seismic sources in form of microseismic tremors as well as large-scale earthquakes is a key issue in seismology. While most previous studies are assuming fairly good knowledge of the underlying velocity model, we propose an automatic spatial localization and joint velocity model building scheme that is independent of detailed 〈span〉a priori〈/span〉 information. The first step is a coherence analysis, estimating so-called wavefront attributes to locally describe the wavefield in terms of slopes and curvatures. In a similar fashion, we also obtain an initial guess of the source excitation times of the recorded events. The wavefront attributes constitute the input for wavefront tomography which represents the next step of the workflow and allows for a refinement of the previously evaluated source excitation times while simultaneously approximating the velocity distribution. In a last step, we use the final estimate of the velocity distribution and compute the respective image function by reverse time modelling to gain the source locations. This paper introduces the theoretical concept of our proposed approach for the general 3-D case. We analyse the feasibility of our strategy and the influences of different acquisition settings by means of a synthetic 2-D data example. In a final 3-D field data example we use the workflow to localize a deep earthquake without relying on a given velocity model. The approach can deal with high levels of noise and low signal amplitudes, respectively, as well as sparse geophone sampling. The workflow generally delivers good approximations of the long-wavelength velocity variations along with accurate source locations.〈/span〉
    Print ISSN: 2051-1965
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    Topics: Geosciences
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    Slip distribution of the 2017 Mw6.6 Bodrum–Kos earthquake: resolving the ambiguity of fault geometry (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The 2017 July 20, 〈span〉M〈/span〉〈sub〉w〈/sub〉6.6 Bodrum–Kos earthquake occurred in the Gulf of Gökova in the SE Aegean, a region characterized by N–S extension in the backarc of the easternmost Hellenic Trench. The dip direction of the fault that ruptured during the earthquake has been a matter of controversy where both north- and south-dipping fault planes were used to model the coseismic slip in previous studies. Here, we use seismic (seismicity, main shock modelling, aftershock relocations and aftershock mechanisms using regional body and surface waves), geodetic (GPS, InSAR) and structural observations to estimate the location, and the dip direction of the fault that ruptured during the 2017 earthquake, and the relationship of this event to regional tectonics. We consider both dip directions and systematically search for the best-fitting locations for the north- and south-dipping fault planes. Comparing the best-fitting planes for both dip directions in terms of their misfit to the geodetic data, proximity to the hypocenter location and Coulomb stress changes at the aftershock locations, we conclude that the 2017 earthquake ruptured a north-dipping fault. We find that the earthquake occurred on a 20–25 km long, ∼E–W striking, 40° north-dipping, pure normal fault with slip primarily confined between 3 and 15 km depth, and the largest slip exceeding 2 m between depths of 4 and 10 km. The coseismic fault, not mapped previously, projects to the surface within the western Gulf, and partly serves both to widen the Gulf and separate Kos Island from the Bodrum Peninsula of SW Anatolia. The coseismic fault may be an extension of a mapped, north-dipping normal fault along the south side of the Gulf of Gökova. While all of the larger aftershocks are consistent with N–S extension, their spatially dispersed pattern attests to the high degree of crustal fracturing within the basin, due to rapid trenchward extension and anticlockwise rotation within the southeastern Aegean.〈/span〉
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    Processing harmonic EM noise with multiple or unstable frequency content in surface NMR surveys (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The harmonic electromagnetic noise produced by anthropic electrical structures is a critical component of the global noise affecting geophysical signals and increasing data uncertainty. It is composed of a series of harmonic signals whose frequencies are multiple integers of the fundamental frequency specific to the electrical noise source. To date, most model-based noise removal strategies assume that the fundamental frequency constraining the harmonic noise is single and constant over the duration of the geophysical record. In this paper, we demonstrate that classical harmonic processing methods lose efficacy when these assumptions are not valid. We present several surface nuclear magnetic resonance field data sets, which testify the increasing probability of recording the harmonic noise with such multiple or unstable frequency content. For each case (multiple frequencies or unstable frequency) we propose new processing strategies, namely, the 〈span〉2-D grid-search〈/span〉 and the 〈span〉segmentation〈/span〉 approach, respectively, which efficiently manage to remove the harmonic noise in these difficult conditions. In the process, we also apply a fast frequency estimator called the Nyman, Gaiser and Saucier estimation method, which shows equivalent performance as classical estimators while allowing a reduction of the computing time by a factor of 2.5.〈/span〉
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    A combinatorial approach to determine earthquake magnitude distributions on a variable slip-rate fault (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Combinatorial methods are used to determine the spatial distribution of earthquake magnitudes on a fault whose slip rate varies along strike. Input to the problem is a finite sample of earthquake magnitudes that span 5 kyr drawn from a truncated Pareto distribution. The primary constraints to the problem are maximum and minimum values around the target slip-rate function indicating where feasible solutions can occur. Two methods are used to determine the spatial distribution of earthquakes: integer programming and the greedy-sequential algorithm. For the integer-programming method, the binary decision vector includes all possible locations along the fault where each earthquake can occur. Once a set of solutions that satisfy the constraints is found, the cumulative slip misfit on the fault is globally minimized relative to the target slip-rate function. The greedy algorithm sequentially places earthquakes to locally optimize slip accumulation. As a case study, we calculate how earthquakes are distributed along the megathrust of the Nankai subduction zone, in which the slip rate varies significantly along strike. For both methods, the spatial distribution of magnitudes depends on slip rate, except for the largest magnitude earthquakes that span multiple sections of the fault. The greedy-sequential algorithm, previously applied to this fault (Parsons et al., 2012), tends to produce smoother spatial distributions and fewer lower magnitude earthquakes in the low slip-rate section of the fault compared to the integer-programming method. Differences in results from the two methods relate to how much emphasis is placed on minimizing the misfit to the target slip rate (integer programming) compared to finding a solution within the slip-rate constraints (greedy sequential). Specifics of the spatial distribution of magnitudes also depend on the shape of the target slip-rate function: that is, stepped at the section boundaries versus a smooth function. This study isolates the effects of slip-rate variation along a single fault in determining the spatial distribution of earthquake magnitudes, helping to better interpret results from more complex, interconnected fault systems.〈/span〉
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    The contemporary force balance in a wide accretionary wedge: numerical models of the southcentral Hikurangi margin of New Zealand (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The southcentral Hikurangi subduction margin (North Island, New Zealand) has a wide, low-taper accretionary wedge that is frontally accreting a 〉3-km-thick layer of sediments, with deformation currently focused near the toe of the wedge. We use a geological model based on a depth-converted seismic section, together with physically realistic parameters for fluid pressure, and sediment and décollement friction based on laboratory experiments, to investigate the present-day force balance in the wedge. Numerical models are used to establish the range of physical parameters compatible with the present-day wedge geometry and mechanics. Our analysis shows that the accretionary wedge stability and taper angle require either high to moderate fluid pressure on the plate interface, and/or weak frictional strength along the décollement. The décollement beneath the outer wedge requires a relatively weaker effective strength than beneath the inner (consolidated) wedge. Increasing density and cohesion with depth make it easier to attain a stable taper within the inner wedge, while anything that weakens the wedge—such as high fluid pressures and weak faults—make it harder. Our results allow a near-hydrostatic wedge fluid pressure, sublithostatic fluid overpressure at the subduction interface, and friction coefficients compatible with measurements from laboratory experiments on weak clay minerals.〈/span〉
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    Gravitational field calculation in spherical coordinates using variable densities in depth (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We present a new methodology to compute the gravitational fields generated by tesseroids (spherical prisms) whose density varies with depth according to an arbitrary continuous function. It approximates the gravitational fields through the Gauss–Legendre Quadrature along with two discretization algorithms that automatically control its accuracy by adaptively dividing the tesseroid into smaller ones. The first one is a preexisting 2-D adaptive discretization algorithm that reduces the errors due to the distance between the tesseroid and the computation point. The second is a new density-based discretization algorithm that decreases the errors introduced by the variation of the density function with depth. The amount of divisions made by each algorithm is indirectly controlled by two parameters: the distance-size ratio and the delta ratio. We have obtained analytical solutions for a spherical shell with radially variable density and compared them to the results of the numerical model for linear, exponential, and sinusoidal density functions. The heavily oscillating density functions are intended only to test the algorithm to its limits and not to emulate a real world case. These comparisons allowed us to obtain optimal values for the distance-size and delta ratios that yield an accuracy of 0.1 per cent of the analytical solutions. The resulting optimal values of distance-size ratio for the gravitational potential and its gradient are 1 and 2.5, respectively. The density-based discretization algorithm produces no discretizations in the linear density case, but a delta ratio of 0.1 is needed for the exponential and most sinusoidal density functions. These values can be extrapolated to cover most common use cases, which are simpler than oscillating density profiles. However, the distance-size and delta ratios can be configured by the user to increase the accuracy of the results at the expense of computational speed. Finally, we apply this new methodology to model the Neuquén Basin, a foreland basin in Argentina with a maximum depth of over 5000 m, using an exponential density function.〈/span〉
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    Mechanical energy balance and apparent fracture toughness for dykes in elastoplastic host rock with large-scale yielding. (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The dynamics of dyke emplacement are typically modeled by assuming an elastic rheology for the host rock. However, the resulting stress field predicts significant shear failure in the region surrounding the dyke tip. Here, we model the dyking process in an elastic-perfectly plastic host rock in order to simulate distributed shear fracturing and subsequent frictional slip on the fracture surfaces. The fluid mechanical aspects of the magma are neglected as we are interested only in the fracture mechanics of the process. Magma overpressure in dykes is typically of the same order of magnitude as the yield stress of the host rock in shear, especially when the pressure effect of volatiles exsolving from the magma is taken into account. Under these conditions, the plastic deformation zone has spatial dimensions that approach the length of the dyke itself, and concepts based on linear elastic fracture mechanics (LEFM) no longer apply. As incremental plasticity is path dependent, we describe two geologically meaningful endmember cases, namely dyke propagation at constant driving pressure, and gradual inflation of a pre-existing crack. For both models, we find that plastic deformation surrounding the fracture tip enhances dyke opening, and thus increases the energy input into the system due to pressure work integrated over the fracture wall. At the same time, energy is dissipated by plastic deformation. Dissipation in the propagation model is greater by about an order of magnitude than it is in the inflation model because the propagating dyke tip leaves behind it a broad halo of deformation due to plastic bending and unbending in the relict process zone. The net effect is that plastic deformation impedes dyke growth in the propagation model, while it enhances dyke growth in the inflation model. The results show that, when the plastic failure zone is large, a single parameter such as fracture toughness is unable to capture the physics that underpin the resistance of a fracture or dyke against propagation. In these cases, plastic failure has to be modeled explicitly for the given conditions. We provide analytical approximations for the propagation forces and the maximum dyke aperture for the two endmember cases, that is, the propagating dyke and the dyke formed by inflation of a crack. Furthermore, we show that the effect of plasticity on dyke energetics, together with an overestimate of magma pressure when interpreting dyke aspect ratios using elastic host rock models, offers a possible explanation for the long-standing paradox that laboratory measurements of fracture toughness of rocks consistently indicate values about two orders of magnitude lower than those derived from dyke observations.〈/span〉
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    3-D mechanical analysis of complex reservoirs: a novel mesh-free approach (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Building geomechanical models for induced seismicity in complex reservoirs poses a major challenge, in particular if many faults need to be included. We developed a novel way of calculating induced stress changes and associated seismic moment response for structurally complex reservoirs with tens to hundreds of faults. Our specific target was to improve the predictive capability of stress evolution along multiple faults, and to use the calculations to enhance physics-based understanding of the reservoir seismicity. Our methodology deploys a mesh-free numerical and analytical approach for both the stress calculation and the seismic moment calculation. We introduce a high-performance computational method for high-resolution induced Coulomb stress changes along faults, based on a Green's function for the stress response to a nucleus of strain. One key ingredient is the deployment of an octree representation and calculation scheme for the nuclei of strain, based on the topology and spatial variability of the mesh of the reservoir flow model. Once the induced stress changes are evaluated along multiple faults, we calculate potential seismic moment release in a fault system supposing an initial stress field. The capability of the approach, dubbed as MACRIS (〈strong〉M〈/strong〉echanical 〈strong〉A〈/strong〉nalysis of 〈strong〉C〈/strong〉omplex 〈strong〉R〈/strong〉eservoirs for 〈strong〉I〈/strong〉nduced 〈strong〉S〈/strong〉eismicity) is proven through comparisons with finite element models. Computational performance and suitability for probabilistic assessment of seismic hazards are demonstrated though the use of the complex, heavily faulted Gullfaks field.〈/span〉
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    Quick determination of earthquake source parameters from GPS measurements: a study of suitability for Taiwan (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We test the feasibility of GPS-based rapid centroid moment tensor (GPS CMT) methods for Taiwan, one of the most earthquake prone areas in the world. In recent years, Taiwan has become a leading developer of seismometer-based earthquake early warning systems, which have successfully been applied to several large events. The rapid determination of earthquake magnitude and focal mechanism, important for a number of rapid response applications, including tsunami warning, is still challenging because of the limitations of near-field inertial recordings. This instrumental issue can be solved by an entirely different observation system: a GPS network. Taiwan is well posed to take advantage of GPS because in the last decade it has developed a very dense network. Thus, in this research, we explore the suitability of the GPS CMT inversion for Taiwan. We retrospectively investigate six moderate to large (〈span〉M〈/span〉〈sub〉w〈/sub〉6.0 ∼ 7.0) earthquakes and propose a resolution test for our model, we find that the minimum resolvable earthquake magnitude of this system is ∼〈span〉M〈/span〉〈sub〉w〈/sub〉5.5 (at 5 km depth). Our tests also suggest that the finite fault complexity, often challenging for the near-field methodology, can be ignored under such good station coverage and thus, can provide a fast and robust solution for large earthquake directly from the near field. Our findings help to understand and quantify how the proposed methodology could be implemented in real time and what its contributions could be to the overall earthquake monitoring system.〈/span〉
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    Effects of lateral heterogeneity on time-domain processing parameters (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Time-domain processing of seismic reflection data has always been an important engine that is routinely utilized to produce seismic images and to expeditiously construct subsurface models. The conventional procedure involves analysing parameters related to the derivatives of reflection traveltime with respect to offset including normal moveout (NMO) velocities (second-order derivatives) and quartic coefficients (fourth-order derivatives). In this study, we propose to go beyond the typical assumption of 1-D laterally homogeneous medium when relating those ‘processing’ parameters to the subsurface medium parameters and take into account the additional influences from lateral heterogeneity including curved interfaces and smoothly variable velocities. We fill in the theoretical gap from previous studies and develop a general framework for such connection in layered anisotropic media. We show that in general, the influences of lateral heterogeneity get accumulated from all layers via a recursive relationship according to the Fermat’s principle and can be approximately quantified in terms of the lateral derivatives of the layer interface surfaces and velocities. Based on the same general principle, we show that our approach can also be used to study the lateral heterogeneity effects on diffraction traveltime and its second-order derivative related to time-migration velocity. In this paper, we explicitly specify expressions for NMO and time-migration velocities with the influences from both types of heterogeneity suitable for 2-D data sets and also discuss possible extensions of the proposed theory to 3-D data sets and to parameters related to higher-order traveltime derivatives. Using numerical examples, we demonstrate that the proposed theory can lead to more accurate reflection and diffraction traveltime predictions in comparison with those obtained based on the 1-D assumption. Both the proposed theoretical framework and its numerical testing for forward traveltime computation presented in this study aid in understanding the effects from lateral heterogeneity on time-processing parameters and also serve as an important basis for designing an efficient technique to separate those influences in important processes such as Dix inversion for a more accurate subsurface model in the future.〈/span〉
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    Methods to isolate retrograde and prograde Rayleigh-wave signals (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Estimating shear wave velocity with depth from Rayleigh-wave dispersion data is limited by the accuracy of fundamental and higher mode identification and characterization. In many cases, the fundamental mode signal propagates exclusively in retrograde motion, while higher modes propagate in prograde motion. It has previously been shown that differences in particle motion can be identified with multicomponent recordings and used to separate prograde from retrograde signals. Here we explore the domain of existence of prograde motion of the fundamental mode, arising from a combination of two conditions: (1) a shallow, high-impedance contrast and (2) a high Poisson ratio material. We present solutions to isolate fundamental and higher mode signals using multicomponent recordings. Previously, a time-domain polarity mute was used with limited success due to the overlap in the time domain of fundamental and higher mode signals at low frequencies. We present several new approaches to overcome this low-frequency obstacle, all of which utilize the different particle motions of retrograde and prograde signals. First, the Hilbert transform is used to phase shift one component by 90° prior to summation or subtraction of the other component. This enhances either retrograde or prograde motion and can increase the mode amplitude. Secondly, we present a new time–frequency domain polarity mute to separate retrograde and prograde signals. We demonstrate these methods with synthetic and field data to highlight the improvements to dispersion images and the resulting dispersion curve extraction.〈/span〉
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    Tomography of crust and lithosphere in the western Indian Ocean from noise cross-correlations of land and ocean bottom seismometers (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We use seismic noise cross-correlations to obtain a 3-D tomography model of 〈span〉SV〈/span〉-wave velocities beneath the western Indian Ocean, in the depth range of the oceanic crust and uppermost mantle. The study area covers 2000 × 2000 km〈sup〉2〈/sup〉 between Madagascar and the three spreading ridges of the Indian Ocean, centred on the volcanic hotspot of La Réunion. We use seismograms from 38 ocean bottom seismometers (OBSs) deployed by the RHUM-RUM project and 10 island stations on La Réunion, Madagascar, Mauritius, Rodrigues, and Tromelin. Phase cross-correlations are calculated for 1119 OBS-to-OBS, land-to-OBS, and land-to-land station pairs, and a phase-weighted stacking algorithm yields robust group velocity measurements in the period range of 3–50 s. We demonstrate that OBS correlations across large interstation distances of 〉2000 km are of sufficiently high quality for large-scale tomography of ocean basins. Many OBSs yielded similarly good group velocity measurements as land stations. Besides Rayleigh waves, the noise correlations contain a low-velocity wave type propagating at 0.8–1.5 km s〈sup〉−1〈/sup〉 over distances exceeding 1000 km, presumably Scholte waves travelling through seafloor sediments. The 100 highest-quality group velocity curves are selected for tomographic inversion at crustal and lithospheric depths. The inversion is executed jointly with a data set of longer-period, Rayleigh-wave phase and group velocity measurements from earthquakes, which had previously yielded a 3-D model of Indian Ocean lithosphere and asthenosphere. Robust resolution tests and plausible structural findings in the upper 30 km validate the use of noise-derived OBS correlations for adding crustal structure to earthquake-derived tomography of the oceanic mantle. Relative to crustal reference model CRUST1.0, our new shear-velocity model tends to enhance both slow and fast anomalies. It reveals slow anomalies at 20 km depth beneath La Réunion, Mauritius, Rodrigues Ridge, Madagascar Rise, and beneath the Central Indian spreading ridge. These structures can clearly be associated with increased crustal thickness and/or volcanic activity. Locally thickened crust beneath La Réunion and Mauritius is probably related to magmatic underplating by the hotspot. In addition, these islands are characterized by a thickened lithosphere that may reflect the depleted, dehydrated mantle regions from which the crustal melts where sourced. Our tomography model is available as electronic supplement.〈/span〉
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    A geothermal application for GOCE satellite gravity data: modelling the crustal heat production and lithospheric temperature field in Central Europe (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Since the completion of the Gravity field and steady-state Ocean Circulation Explorer mission (GOCE), global gravity models of uniform quality and coverage are available. We investigate their potential of being useful tools for estimating the thermal structure of the continental lithosphere, through simulation and real-data test in Central-Eastern Europe across the Trans-European Suture Zone. Heat flow, measured near the Earth surface, is the result of the superposition of a complex set of contributions, one of them being the heat production occurring in the crust. The crust is enriched in radioactive elements respect to the underlying mantle and crustal thickness is an essential parameter in isolating the thermal contribution of the crust. Obtaining reliable estimates of crustal thickness through inversion of GOCE-derived gravity models has already proven feasible, especially when weak constraints from other observables are introduced. We test a way to integrate this in a geothermal framework, building a 3-D, steady state, solid Earth conductive heat transport model, from the lithosphere–asthenosphere boundary to the surface. This thermal model is coupled with a crust-mantle boundary depth resulting from inverse modelling, after correcting the gravity model for the effects of topography, far-field isostatic roots and sediments. We employ a mixed space- and spectral-domain based forward modelling strategy to ensure full spectral coherency between the limited spectral content of the gravity model and the reductions. Deviations from a direct crustal thickness to crustal heat production relationship are accommodated using a subsequent substitution scheme, constrained by surface heat flow measurements, where available. The result is a 3-D model of the lithosphere characterised in temperature, radiogenic heat and thermal conductivity. It provides added information respect to the lithospheric structure and sparse heat flow measurements alone, revealing a satisfactory coherence with the geological features in the area and their controlling effect on the conductive heat transport.〈/span〉
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    Interferometric time-lapse velocity analysis: application to a salt-water disposal well in British Columbia, Canada (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We investigate the possibility of passive monitoring of a salt-water disposal well in British Columbia, Canada, using continuously recorded ambient seismic noise. We find seismic velocity variations induced by a reduction of injection pressure in an effort to mitigate an elevated level of seismicity, most likely associated with the disposal of salt water. The relative velocity variations are derived from time-shifts measured between consecutive cross-correlation functions for each station pair in a surface array composed of five broad-band seismometers. The probable driving mechanisms responsible for the velocity changes are reduced pore pressures and/or lowered poroelastic stresses beyond the injection wellbore, respectively. Hydrologic data (e.g. snow and rainfall), noise energy trends and fluctuations in the incident direction of dominant noise sources do not correlate with the estimated relative velocity variations. Velocity variations are detected ahead of the zone of induced seismicity, thus indicating that seismic interferometry may aid in mitigation efforts to reduce the risk of induced seismicity by (1) providing verifiable and repeatable measurements of physical changes within the surrounding area and (2) providing hard constraints for modelling efforts to constrain how and where pore-pressure fronts change.〈/span〉
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    A physically based model for the electrical conductivity of water-saturated porous media (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Electrical conductivity is one of the most commonly used geophysical method for reservoir and environmental studies. Its main interest lies in its sensitivity to key properties of storage and transport in porous media. Its quantitative use therefore depends on the efficiency of the petrophysical relationship to link them. In this work, we develop a new physically based model for estimating electrical conductivity of saturated porous media. The model is derived assuming that the porous media is represented by a bundle of tortuous capillary tubes with a fractal pore-size distribution. The model is expressed in terms of the porosity, electrical conductivity of the pore liquid and the microstructural parameters of porous media. It takes into account the interface properties between minerals and pore water by introducing a surface conductivity. Expressions for the formation factor and hydraulic tortuosity are also obtained from the model derivation. The model is then successfully compared with published data and performs better than previous models. The proposed approach also permits to relate the electrical conductivity to other transport properties such as the hydraulic conductivity.〈/span〉
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    Removing mantle lithosphere under orogens: delamination versus convective thinning (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Thinning of the lithosphere under continental collisional orogens is often attributed to delamination or convective thinning. Both processes remove part or all of the mantle lithosphere that has become denser and gravitationally unstable. Previous studies mostly focused on the different thermomagmatic consequences of these two processes; the dynamic links between them, and the critical conditions for one or the other process to dominate lithosphere thinning, remain uncertain. Here, we used high-resolution thermomechanical models with various rheology (linear viscous, power-law viscous and/or the extended Drucker–Prager plasticity) to systematically investigate the dynamics of delamination and convective thinning under collisional orogens. Our results show that convective thinning is favoured in models of linear (Newtonian) viscous rheology and low viscosity $({10^{19}}\!-\! {10^{20}}\,\,{\rm{Pa}} \, {\rm{s}})$. Power-law viscous rheology promotes strain localization, which reduces the effective viscosity and may lead to localized rising of the asthenosphere to the crustal base, thus triggering delamination. Further strain localization and stronger delamination are predicted with inclusion of plastic rheology in the model. These results indicate that convective thinning and delamination are dynamically linked and can occur in the same orogeny. Their relative dominance during orogenesis may be distinguished by the resulting spatiotemporal evolutions of thermal perturbation, magmatism and elevation changes. We applied the models to show that the evolution of the Central Anatolian Plateau is consistent with the dominance of convective thinning, whereas delamination played a major role in thinning the mantle lithosphere under central-northern Tibetan Plateau.〈/span〉
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    Anthropogenic seismicity as aftershocks for geo-resource production? Implications for Mmax estimates (reservoir impoundment cases) (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Developing a model for anthropogenic seismic hazard remains an open challenge whatever the geo-resource production. We analyse the (〈span〉M〈/span〉〈sub〉max〈/sub〉) largest reported magnitude on each site where (RTS) Reservoir Triggered Seismicity in documented (37 events, 1933–2008), for aftershocks of reservoir impoundment loading. We relate each reservoir impoundment to its magnitude-equivalent 〈span〉M〈/span〉*〈sub〉reservoir〈/sub〉 = 〈span〉M〈/span〉*(〈span〉L〈/span〉〈sub〉r〈/sub〉). We use (〈span〉L〈/span〉〈sub〉r〈/sub〉) the reservoir length as a proxy for a rupture length of the reservoir main shock-equivallent. This latter is derived from the empirical relationship that exists for tectonic earthquake among magnitude and rupture length. We resolve (i) 〈span〉M〈/span〉〈sub〉max〈/sub〉 for RTS are bounded by 〈span〉M〈/span〉*〈sub〉reservoir〈/sub〉 at a 95 per cent confidence level; (ii) in average 〈span〉M〈/span〉〈sub〉max〈/sub〉 are smaller than 〈span〉M〈/span〉*〈sub〉reservoir〈/sub〉 by 2.2 units (iii) 50 per cent of the 〈span〉M〈/span〉〈sub〉max〈/sub〉 occurrence is within 2 ± 1 yr from the reservoir impoundment. These triggering patterns support the signature of fluid driven seismicity during the slow reservoir impoundment emerges as a weaker efficiency (larger Δ〈span〉M〈/span〉 = 〈span〉M〈/span〉*〈sub〉reservoir〈/sub〉 – 〈span〉M〈/span〉〈sub〉max〈/sub〉) to trigger 〈span〉M〈/span〉〈sub〉max〈/sub〉 events than from earthquake interactions.〈/span〉
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    Holocene slip rate of the frontal thrust in the western Qilian Shan, NE Tibetan Plateau (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The activities of frontal thrusts in the northern Qilian Shan are critical for understanding the deformation of the Qilian Shan and the northeastern Tibetan Plateau. In this study, we estimate the slip rate of the active Fodongmiao–Hongyazi thrust along the northern margin of the Qilian Shan. High-resolution satellite imagery interpretations and detailed field investigations suggest that the fault displaced late Pleistocene terraces and formed fresh prominent north-facing fault scarps. To quantify the slip rate of the fault, we measured the displacements along the fault scarps using an unmanned aerial vehicle system and dated the displaced geomorphic surfaces using optically stimulated luminescence (OSL) and 〈sup〉14〈/sup〉C methods. The vertical slip rate of the fault is estimated at 1.0 ± 0.3 mm yr〈sup〉−1〈/sup〉 for the western segment. The slip rates for two branches in the eastern segment are 0.3 ± 0.1 and 0.6 ± 0.1 mm yr〈sup〉−1〈/sup〉. Using a fault dip of 40 ± 10°, we constrain the corresponding shortening rates to 1.4 ± 0.5 and 1.2 ± 0.4 mm yr〈sup〉−1〈/sup〉, respectively. The rates are consistent with values over different timescales, which suggests steady rock uplift and northeastward growth of the western Qilian Shan. Crustal shortening occurs mainly on the range-bounding frontal thrust.〈/span〉
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    A computational method for earthquake cycles within anisotropic media (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We present a numerical method for the simulation of earthquake cycles on a 1-D fault interface embedded in a 2-D homogeneous, anisotropic elastic solid. The fault is governed by an experimentally motivated friction law known as rate-and-state friction which furnishes a set of ordinary differential equations which couple the interface to the surrounding volume. Time enters the problem through the evolution of the ordinary differential equations along the fault and provides boundary conditions for the volume, which is governed by quasi-static elasticity. We develop a time-stepping method which accounts for the interface/volume coupling and requires solving an elliptic partial differential equation for the volume response at each time step. The 2-D volume is discretized with a second-order accurate finite difference method satisfying the summation-by-parts property, with boundary and fault interface conditions enforced weakly. This framework leads to a provably stable semi-discretization. To mimic slow tectonic loading, the remote side-boundaries are displaced at a slow rate, which eventually leads to earthquake nucleation at the fault. Time stepping is based on an adaptive, fourth-order Runge–Kutta method and captures the highly varying timescales present. The method is verified with convergence tests for both the orthotropic and fully anisotropic cases. An initial parameter study reveals regions of parameter space where the systems experience a bifurcation from period one to period two behaviour. Additionally, we find that anisotropy influences the recurrence interval between earthquakes, as well as the emergence of aseismic transients and the nucleation zone size and depth of earthquakes.〈/span〉
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    Palaeomagnetism of Late Triassic volcanic rocks from the western margin of Khorat Basin, Thailand and its implication for ambiguous inclination shallowing in Mesozoic sediments of Indochina (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Palaeomagnetic constraints are essential factors in the reconstruction of the Mesozoic convergence of Eastern Asia blocks. As one of the key blocks, Indochina was constrained only by sedimentary-rocks-derived palaeomagnetic data. To evaluate whether the palaeomagnetic data used to restore the Late Triassic position of Indochina suffered inclination shallowing effects, we conducted a palaeomagnetic and geochronologic study on a coeval volcanic clastic rocks sequence in the western margin of the Khorat Basin, Thailand. The U-Pb SIMS dating on zircons indicates the age of the sampling section is between 205.1 ± 1.5 and 204.7 ± 1.4 Ma. Site mean directions are D〈sub〉g〈/sub〉/I〈sub〉g〈/sub〉 = 217.2°/−39.4° (κ〈sub〉g〈/sub〉 = 45.1, α〈sub〉95g〈/sub〉 = 10.1°) before and D〈sub〉s〈/sub〉/I〈sub〉s〈/sub〉 = 209.2°/−44.5° (κ〈sub〉s〈/sub〉 = 43.8, α〈sub〉95s〈/sub〉 = 10.2°) after tilt correction. The new data set indicates a positive reversal test result at ‘Category C’ level. The characteristic remanent magnetization recorded by the coexistent magnetite and hematite is interpreted to be primary remanence acquired during the initial cooling of the volcanic clastic rocks. The consistence of the corresponding palaeolatitudes derived from the volcanic clastic rocks and the former reported sedimentary rocks suggests that there is probably no significant inclination shallowing bias in the sedimentary-rocks-derived palaeomagnetic data. Therefore, the estimates of the Late Triassic position of Indochina are confirmed to be reliable. The Indochina Block had collided to the southern margin of Eurasia by the Late Triassic and played an important role in the Mesozoic convergence of the Eastern Asia blocks.〈/span〉
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    A non-perturbative method for gravitational potential calculations within heterogeneous and aspherical planets (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉We present a numerically exact method for calculating the internal and external gravitational potential of aspherical and heterogeneous planets. Our approach is based on the transformation of Poisson’s equation into an equivalent equation posed on a spherical computational domain. This new problem is solved in an efficient iterative manner based on a hybrid pseudospectral/spectral element discretization. The main advantage of our method is that its computational cost reflects the planet’s geometric and structural complexity, being in many situations only marginally more expensive than boundary perturbation theory. Several numerical examples are presented to illustrate the method’s efficacy and potential range of applications.〈/span〉
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    A generalized Rytov approximation for accurate calculation of phase variation in strong perturbation media (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉In the case of long-range propagation of forward scattering, due to the accumulation of phase changes caused by the velocity perturbations, the validity of the Born approximation will be violated. In contrast, the phase-change accumulation can be handled by the Rytov approximation, which has been widely used for long-distance propagation with only forward scattering or small-angle scattering involved. However, the weak scattering assumption (i.e. small velocity perturbation) in the Rytov approximation limits its scope of application. To address this problem, we analyse the integral kernel of the Rytov transform using the Wentzel-Kramers-Brillouin-Jeffreys (WKBJ) approximation and we demonstrate that the integral kernel is a function of velocity perturbation and scattering angle. By applying a small scattering angle approximation, we show that the phase variation has a linear relationship with the slowness perturbation, no matter how strong the magnitude of perturbation is. Therefore, the new integral equation is then referred to as the generalized Rytov approximation (GRA) because it overcomes the weak scattering assumption of the Rytov approximation. To show the limitations of the Rytov approximation and the advantages of the proposed GRA method, first we design a two-layer model and we analytically calculate the errors introduced by the small scattering angle assumption using plane wave incidence. We show that the phase (traveltime) variations predicted by the GRA are always more accurate than the Rytov approximation. Particularly, the GRA produces accurate phase variations for the normal incident plane wave regardless of the magnitude of velocity perturbation. Numerical examples using Gaussian anomaly models demonstrate that the scattering angle has a crucial impact on the accuracy of the GRA. If the small scattering angle assumption holds, the GRA can produce an accurate phase approximation even if the velocity perturbation is very strong. On the contrary, both the first-order Rytov approximation and the GRA fail to get satisfying results when the scattering angle is large enough. The proposed GRA method has the potential to be used for traveltime modelling and inversion for large-scale strong perturbation media.〈/span〉
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    Mapping geologic features onto subducted slabs (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Estimating the location of geologic and tectonic features on a subducting plate is important for interpreting their spatial relationships with other observables including seismicity, seismic velocity and attenuation anomalies, and the location of ore deposits and arc volcanism in the over-riding plate. Here we present two methods for estimating the location of predictable features such as seamounts, ridges and fracture zones on the slab. One uses kinematic reconstructions of plate motions, and the other uses multidimensional scaling to flatten the slab onto the surface of the Earth. We demonstrate the methods using synthetic examples and also using the test case of fracture zones entering the Lesser Antilles subduction zone. The two methods produce results that are in good agreement with each other in both the synthetic and real examples. In the Lesser Antilles, the subducted fracture zones trend northwards of the surface projections. The two methods begin to diverge in regions where the multidimensional scaling method has its greatest likely error. Wider application of these methods may help to establish spatial correlations globally.〈/span〉
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    Detection of weak seismic sequences based on arrival time coherence and empiric network detectability: an application at a near fault observatory (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Microseismic monitoring is a primary tool for understanding and tracking the progress of mechanical processes occurring in active rock fracture systems. In geothermal or hydrocarbon fields or along seismogenic fault systems, the detection and location of microseismicity facilitates resolution of the fracture system geometry and the investigation of the interaction between fluids and rocks, in response of stress field perturbations. Seismic monitoring aims to detect locate and characterize seismic sources. The detection of weak signals is often achieved at the cost of increasing the number of false detections, related to transient signals generated by a range of noise sources, or related to instrumental problems, ambient conditions or human activity that often affect seismic records. A variety of fast and automated methods has been recently proposed to detect and locate microseismicity based on the coherent detection of signal anomalies, such as increase in amplitude or coherent polarization, at dense seismic networks. While these methods proved to be very powerful to detect weak events and to reduce the magnitude of completeness, a major problem remains to discriminate among weak seismic signals produced by microseismicity and false detections. In this work, the microseimic data recorded along the Irpinia fault zone (Southern Apennines, Italy) are analysed to detect weak, natural earthquakes using one of such automated, migration-based, method. We propose a new method for the automatic discrimination of real vs false detections, which is based on empirical data and information about the detectability (i.e. detection capability) of the seismic network. Our approach allows obtaining high performances in detecting earthquakes without requiring a visual inspection of the seismic signals and minimizing analyst intervention. The proposed methodology is automated, self-updating and can be tuned at different success rates.〈/span〉
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    A multitaper spectral estimator for time-series with missing data (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉A multitaper estimator is proposed that accommodates time-series containing gaps without using any form of interpolation. In contrast with prior missing-data multitaper estimators that force standard Slepian sequences to be zero at gaps, the proposed missing-data Slepian sequences are defined only where data are present. The missing-data Slepian sequences are frequency independent, as are the eigenvalues that define the energy concentration within the resolution bandwidth, when the process bandwidth is $[ { - 1/2,\,\,\,1/2} )$ for unit sampling and the sampling scheme comprises integer multiples of unity. As a consequence, one need only compute the ensuing missing-data Slepian sequences for a given sampling scheme once, and then the spectrum at an arbitrary set of frequencies can be computed using them. It is also shown that the resulting missing-data multitaper estimator can incorporate all of the optimality features (i.e. adaptive-weighting, 〈span〉F〈/span〉-test and reshaping) of the standard multitaper estimator, and can be applied to bivariate or multivariate situations in similar ways. Performance of the missing-data multitaper estimator is illustrated using length of day, seafloor pressure and Nile River low stand time-series.〈/span〉
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    Full-waveform matching of VP and VS models from surface waves (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉The analysis of surface wave dispersion curves (DCs) is widely used for near-surface 〈span〉S〈/span〉-wave velocity (VS) reconstruction. However, a comprehensive characterization of the near-surface requires also the estimation of 〈span〉P〈/span〉-wave velocity (VP). We focus on the estimation of both VS and VP models from surface waves using a direct data transform approach. We estimate a relationship between the wavelength of the fundamental mode of surface waves and the investigation depth and we use it to directly transform the DCs into VS and VP models in laterally varying sites. We apply the workflow to a real data set acquired on a known test site. The accuracy of such reconstruction is validated by a waveform comparison between field data and synthetic data obtained by performing elastic numerical simulations on the estimated VP and VS models. The uncertainties on the estimated velocity models are also computed.〈/span〉
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    Seismic signal recognition by unsupervised machine learning (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Seismic signal recognition can serve as a powerful auxiliary tool for analysing and processing ever-larger volumes of seismic data. It can facilitate many subsequent procedures such as first-break picking, statics correction, denoising, signal detection, events tracking, structural interpretation, inversion and imaging. In this study, I propose an automatic technique of seismic signal recognition taking advantage of unsupervised machine learning. In the proposed technique, seismic signal recognition is considered as a problem of clustering data points. All the seismic sampling points in time domain are clustered into two clusters, that is, signal or non-signal. The hierarchical clustering algorithm is used to group these sampling points. Four attributes, that is, two short-term-average-to-long-term-average ratios, variance and envelope are investigated in the clustering process. In addition, to quantitatively evaluate the performance of seismic signal recognition properly, I propose two new statistical indicators, namely, the rate between the total energies of original and recognized signals (RTE), and the rate between the average energies of original and recognized signals (RAE). A large number of numerical experiments show that when the signal is slightly corrupted by noise, the proposed technique performs very well, with recognizing accuracy, precision and RTE of nearly 1 (i.e. 100 per cent), recall greater than 0.8 and RAE about 1–1.3. When the signal is moderately corrupted by noise, the proposed technique can hold recognizing accuracy about 0.9, recognizing precision nearly to 1, RTE about 0.9, recall around 0.6 and RAE about 1.5. Applications of the proposed technique to real microseismic data induced from hydraulic fracturing and reflection seismic data demonstrate its feasibility and encouraging prospect.〈/span〉
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    The Mount Meron infrasound array: an infrasound array without a noise reduction system (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Measurements of seismo-acoustic events by collocated seismic and infrasound arrays allow for studying the two wavefields that were produced by the same event. However, some of the scientific and technical constraints on the building of the two technologies are different and may be contradicting. For the case of a new station, an optimal design that will satisfy the constraints of the two technologies can be found. However, in the case of upgrading an existing array by adding the complementing technology, the situation is different. The site location, the array configuration and physical constraints are fixed and may not be optimal for the complementing technology, which may lead to rejection of the upgrade. The International Monitoring System (IMS) for the verification of the Comprehensive Nuclear-Test-Ban Treaty (CTBT) includes 37 seismic arrays and 51 infrasound arrays. Although the CTBT verification regime is fixed in the treaty, an upgrade of the existing arrays by adding more technologies is possible.The Mount Meron seismic array (MMAI), which is part of the IMS, is composed of 16 sites. Microbarometers were installed at five MMAI sites to form the Mount Meron infrasound array. Due to regulation and physical constraints, it was not possible to relocate the sites nor to install analogue noise reduction filters (i.e. a pipe array). In this study, it is demonstrated that the installation of the MMAI infrasound array is beneficial despite the non-optimal conditions. It is shown that the noise levels of the individual array sites are between the high and median global noise levels. However, we claim that the more indicative measures are the noise levels of the beams of interest, as demonstrated by analysing the microbaroms originated from the Mediterranean Sea. Moreover, the ability to detect events relevant to the CTBT is demonstrated by analysing man-made events during 2011 from the Libya region.〈/span〉
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    The effect of stress changes on time-dependent earthquake probabilities for the central Wasatch fault zone, Utah, USA (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Static and quasi-static Coulomb stress changes produced by large earthquakes can modify the probability of occurrence of subsequent events on neighbouring faults. This approach is based on physical (Coulomb stress changes) and statistical (probability calculations) models, which are influenced by the quality and quantity of data available in the study region. Here, we focus on the Wasatch fault zone (WFZ), a well-studied active normal fault system having abundant geological and palaeoseismological data. Palaeoseismological trench investigations of the WFZ indicate that at least 24 large, surface-faulting earthquakes have ruptured the fault's five central, 35–59-km long segments since ∼7 ka. Our goal is to determine if the stress changes due to the youngest palaeoevents have significantly modified the present-day probability of occurrence of large earthquakes on each of the segments. For each segment, we modelled the cumulative (coseismic + post-seismic) Coulomb stress changes (∆CFS〈sub〉cum〈/sub〉) due to earthquakes younger than the most recent event on the segment in question and applied the resulting values to the time-dependent probability calculations. Results from the Coulomb stress modelling suggest that the Brigham City, Salt Lake City, and Provo segments have accumulated ∆CFS〈sub〉cum〈/sub〉 larger than 10 bar, whereas the Weber segment has experienced a stress decrease of 5 bar, in the scenario of recent rupture of the Great Salt Lake fault to the west. Probability calculations predict high probability of occurrence for the Brigham City and Salt Lake City segments, due to their long elapsed times (〉1–2 ka) when compared to the Weber, Provo and Nephi segments (〈1 ka). The range of calculated coefficients of variation has a large influence on the final probabilities, mostly in the case of the Brigham City segment. Finally, when the Coulomb stress and the probability models are combined, our results indicate that the ∆CFS〈sub〉cum〈/sub〉 resulting from earthquakes post-dating the youngest events on each of the five segments substantially affects the probability calculations for three of the segments: Brigham City, Salt Lake City and Provo. The probability of occurrence of a large earthquake in the next 50 yr on these three segments may, therefore, be underestimated if a time-independent approach, or a time-dependent approach that does not consider ∆CFS, is adopted.〈/span〉
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    Exploration of continuous seismic recordings with a machine learning approach to document 20 yr of landslide activity in Alaska (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Quantifying landslide activity in remote regions is difficult because of the numerous complications that prevent direct landslide observations. However, building exhaustive landslide catalogues is critical to document and assess the impacts of climate change on landslide activity such as increasing precipitation, glacial retreat and permafrost thawing, which are thought to be strong drivers of the destabilization of large parts of the high-latitude/altitude regions of the Earth. In this study, we take advantage of the capability offered by seismological observations to continuously and remotely record landslide occurrences at regional scales. We developed a new automated machine learning processing chain, based on the Random Forest classifier, able to automatically detect and identify landslide seismic signals in continuous seismic records. We processed two decades of continuous seismological observations acquired by the Alaskan seismic networks. This allowed detection of 5087 potential landslides over a period of 22 yr (1995–2017). We observe an increase in the number of landslides for the period and discuss the possible causes.〈/span〉
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    A scalar radiative transfer model including the coupling between surface and body waves (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉To describe the energy transport in the seismic coda, we introduce a system of radiative transfer equations for coupled surface and body waves in a scalar approximation. Our model is based on the Helmholtz equation in a half-space geometry with mixed boundary conditions. In this model, Green’s function can be represented as a sum of body waves and surface waves, which mimics the situation on Earth. In a first step, we study the single-scattering problem for point-like objects in the Born approximation. Using the assumption that the phase of body waves is randomized by surface reflection or by interaction with the scatterers, we show that it becomes possible to define, in the usual manner, the cross-sections for surface-to-body and body-to-surface scattering. Adopting the independent scattering approximation, we then define the scattering mean free paths of body and surface waves including the coupling between the two types of waves. Using a phenomenological approach, we then derive a set of coupled transport equations satisfied by the specific energy density of surface and body waves in a medium containing a homogeneous distribution of point scatterers. In our model, the scattering mean free path of body waves is depth dependent as a consequence of the body-to-surface coupling. We demonstrate that an equipartition between surface and body waves is established at long lapse-time, with a ratio which is predicted by usual mode counting arguments. We derive a diffusion approximation from the set of transport equations and show that the diffusivity is both anisotropic and depth dependent. The physical origin of the two properties is discussed. Finally, we present Monte Carlo solutions of the transport equations which illustrate the convergence towards equipartition at long lapse-time as well as the importance of the coupling between surface and body waves in the generation of coda waves.〈/span〉
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    Study on the layout of GNSS sites for strike-slip faults (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉In the profile analysis of faults, the distribution of GNSS sites directly affects the accuracy of the results of slip rate and locking depth. This paper discusses strategies for designing the layout of GNSS stations perpendicular to strike-slip faults in terms of site spacing and the Minimum Effective Distance, which is 20 times the locking depth of the fault. Three layout models are proposed considering the complexity of strike-slip faults: (1) Equal spacing layout, in which many stations are deployed in the far field, only a few are deployed in the near field. (2) Equal deformation layout, in which stations are densely arranged in the near field and sparsely arranged in the far field according to the frequency of deformation curve. (3) Equal slope spacing layout, in which stations are arranged according to the nonlinear degree of the deformation curve, with dense distribution in regions with high nonlinearity and sparse distribution in approximately linear regions. The three models were used to redistribute the sites in the Qiaojia to Dongchuan segment of the Xiaojiang fault profile, and their performances were compared with that of the current sites distribution of the segment. The results showed that model 1 is optimal for fitting the accuracy of slip rate and model 3 is optimal for the accuracy of locking depth. Overall, model 3 appears to be the best choice, considering that the accuracy of the locking depth is more difficult to control. One of the main purposes of deployment is to identify the seismogenic depth of the fault. With the locking depth of the fault gradually approaching the depth of the seismogenic layer during an interseismic period, the accuracy of observations of sites deployed at a preset value of historical seismogenic depth of the fault would improve.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    How HY-2A/GM altimeter performs in marine gravity derivation: assessment in the South China Sea (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉HY-2A is China's first satellite altimeter mission, launched in Aug. 2011. Its geodetic mission (GM) started from 2016 March 30 till present, collecting sea surface heights for about five 168-d cycles. To test how the HY-2A altimeter performs in marine gravity derivation, we use the least-squares collocation method to determine marine gravity anomalies on 1′ × 1′ grids around the South China Sea (covering 0°–30°N, 105°E–125°E) from the HY-2A/GM-measured geoid gradients. We assess the qualities of the HY-2A/GM-derived gravity over different depths and areas using the bias and tilt-adjusted ship-borne gravity anomalies from the U.S. National Centers for Environmental Information (NCEI) and the Second Institute of Oceanography, Ministry of Natural Resources (MNR) of P. R. China. The RMS difference between the HY-2A/GM-derived and the NCEI ship-borne gravity is 5.91 mGal, and is 5.33 mGal when replacing the HY-2A value from the Scripps Institution of Oceanography (SIO) V23.1 value. The RMS difference between the HY-2A/GM-derived and the MNR ship-borne gravity is 2.90 mGal, and is 2.76 mGal when replacing the HY-2A value from the SIO V23.1 value. The RMS difference between the HY-2A and SIO V23.1 value is 3.57 mGal in open sea areas at least 20 km far away from the coast. In general, the difference between the HY-2A/GM-derived gravity and ship-borne gravity decreases with decreasing gravity field roughness and increasing depth. HY-2A results in the lowest gravity accuracy in areas with islands or reefs. Our assessment result suggests that HY-2A can compete with other Ku-band altimeter missions in marine gravity derivation.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 95
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    Post-critical SsPmp and its applications to Virtual Deep Seismic Sounding (VDSS) 2. 1D imaging of the crust/mantle and joint constraints with receiver functions (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Virtual Deep Seismic Sounding (VDSS) has emerged as a novel method to image the crust-mantle-boundary (CMB) and potentially other lithospheric boundaries. In Part 1 (Liu et al., 2018), we showed that the arrival time and waveform of post-critical 〈span〉SsPmp〈/span〉, the post-critical reflection phase at the CMB used in VDSS, is sensitive to several different attributes of the crust and upper mantle. Here, we synthesize our methodology of deriving Moho depth, average crustal 〈span〉Vp〈/span〉 and uppermost-mantle 〈span〉Vp〈/span〉 from single-station observations of post-critical 〈span〉SsPmp〈/span〉 under a 1D assumption. We first verify our method with synthetics and then substantiate it with a case study using the Yellowknife and POLARIS arrays in the Slave Craton, Canada. We show good agreement of crustal and upper-mantle properties derived with VDSS with those given by previous active-source experiments and our own P receiver functions (PRF) in our study area. Finally, we propose a PRF-VDSS joint analysis method to constrain average crustal 〈span〉Vp〈/span〉/〈span〉Vs〈/span〉 ratio and composition. Our PRF-VDSS joint analysis shows that the southwest Slave Craton has an intermediate crustal composition, most consistent with a Mesoarchean age.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 96
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    Adjoint inversion of the thermal structure of Southeastern Australia (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The variation of temperature in the crust is difficult to quantify due to the sparsity of surface heat flow observations and lack of measurements on the thermal properties of rocks at depth. We examine the degree to which the thermal structure of the crust can be constrained from Curie depth and surface heat flow data in Southeastern Australia. We cast the inverse problem of heat conduction within a Bayesian framework and derive its adjoint so we can efficiently find the optimal model that best reproduces the data and prior information on the thermal properties of the crust. Efficiency gains obtained from the adjoint method facilitates a detailed exploration of thermal structure in SE Australia, where we predict high temperatures within Precambrian rocks of 650 〈sup〉○〈/sup〉C due to relatively high rates of heat production (0.9–1.4 μW m〈sup〉−3〈/sup〉). In contrast, temperatures within dominantly Phanerozoic crust reach only 520 〈sup〉○〈/sup〉C at the Moho due to the low rates of heat production in Cambrian mafic volcanics. A combination of Curie depth and heat flow data are required to constrain the uncertainty of lower crustal temperatures to ± 73 〈sup〉○〈/sup〉C. We also show that parts of the crust are unconstrained if either dataset is omitted from the inversion.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Receiver function mapping of mantle transition zone discontinuities beneath Alaska using scaled 3D velocity corrections (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The mantle transition zone is the region between the globally observed major seismic velocity discontinuities around depths of 410 and 660 km and is important for determining the style of convection and mixing between the upper and the lower mantle. In this study, P-to-S converted waves, or receiver functions, are used to study these discontinuities beneath the Alaskan subduction zone, where the Pacific plate subducts underneath the North American plate. Previous tomographic models do not agree on the depth extent of the subducting slab, therefore improved imaging of the Earth structure underneath Alaska is required. We use 27,800 high quality radial receiver functions to make common conversion point stacks. Upper mantle velocity anomalies are accounted for by two recently published regional tomographic S-wave velocity models. Using these two tomographic models, we show that the discontinuity depths within our CCP stacks are highly dependent on the choice of velocity model, between which velocity anomaly magnitudes vary greatly. We design a quantitative test to show whether the anomalies in the velocity models are too strong or too weak, leading to over- or under-corrected discontinuity depths. We also show how this test can be used to rescale the 3D velocity corrections in order to improve the discontinuity topography maps. After applying the appropriate corrections, we find a localised thicker mantle transition zone and an uplifted 410 discontinuity, which show that the slab has clearly penetrated into the mantle transition zone. Little topography is seen on the 660 discontinuity, indicating that the slab has probably not reached the lower mantle. In the southwest, P410s arrivals have very small amplitudes or no significant arrival at all. This could be caused by water or basalt in the subducting slab, reducing the strength at the 410, or by topography on the 410 discontinuity, preventing coherent stacking. In the southeast of Alaska, a thinner mantle transition zone is observed. This area corresponds to the location of a slab window, and thinning of the mantle transition zone may be caused by hot mantle upwellings.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Processing automatic seismic event detections: an iterative sorting algorithm improving earthquake hypocentres using inter-event cross-correlation (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉We present an iterative classification scheme using inter-event cross-correlation to update an existing earthquake catalogue with similar events from a list of automatic seismic event detections. The algorithm automatically produces catalogue quality events, with improved hypocentres and reliable P and S arrival time information. Detected events are classified into four event categories with the purpose of using the top category, with the highest assessed event quality and highest true-to-false ratio, directly for local earthquake tomography without additional manual analysis. The remaining categories have varying proportions of lower quality events, quality being defined primarily by the number of observed phase onsets, and can be viewed as different priority groups for manual inspection to reduce the time spent by a seismic analyst. A list of 3348 event detections from the geothermally active volcanic region around Hengill, southwest Iceland, produced by our migration and stack detector (Wagner et al. 2017), was processed using a reference catalogue of 1108 manually picked events from the same area. P and S phase onset times were automatically determined for the detected events using correlation time lags with respect to manually picked phase arrivals from different multiple reference events at the same station. A significant improvement of the initial hypocentre estimates was achieved after re-locating the detected events using the computed phase onset times. The differential time dataset resulting from the correlation was successfully used for a double-difference re-location of the final updated catalogue. The routine can potentially be implemented in real-time seismic monitoring environments in combination with a variety of seismic event/phase detectors.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    A scalar radiative transfer model including the coupling between surface and body waves (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉To describe the energy transport in the seismic coda, we introduce a system of radiative transfer equations for coupled surface and body waves in a scalar approximation. Our model is based on the Helmholtz equation in a half-space geometry with mixed boundary conditions. In this model, Green’s function can be represented as a sum of body waves and surface waves, which mimics the situation on Earth. In a first step, we study the single-scattering problem for point-like objects in the Born approximation. Using the assumption that the phase of body waves is randomized by surface reflection or by interaction with the scatterers, we show that it becomes possible to define, in the usual manner, the cross-sections for surface-to-body and body-to-surface scattering. Adopting the independent scattering approximation, we then define the scattering mean free paths of body and surface waves including the coupling between the two types of waves. Using a phenomenological approach, we then derive a set of coupled transport equations satisfied by the specific energy density of surface and body waves in a medium containing a homogeneous distribution of point scatterers. In our model, the scattering mean free path of body waves is depth dependent as a consequence of the body-to-surface coupling. We demonstrate that an equipartition between surface and body waves is established at long lapse-time, with a ratio which is predicted by usual mode counting arguments. We derive a diffusion approximation from the set of transport equations and show that the diffusivity is both anisotropic and depth dependent. The physical origin of the two properties is discussed. Finally, we present Monte-Carlo solutions of the transport equations which illustrate the convergence towards equipartition at long lapse-time as well as the importance of the coupling between surface and body waves in the generation of coda waves.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Rotating double-diffusive convection in stably stratified planetary cores (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉In planetary fluid cores, the density depends on temperature and chemical composition, which diffuse at very different rates. This leads to various instabilities, bearing the name of double-diffusive convection. We investigate rotating double-diffusive convection (RDDC) in fluid spheres. We use the Boussinesq approximation with homogeneous internal thermal and compositional source terms. We focus on the finger regime, in which the thermal gradient is stabilising whereas the compositional one is destabilising. First, we perform a global linear stability analysis in spheres. The critical Rayleigh numbers drastically drop for stably stratified fluids, yielding large-scale convective motions where local analyses predict stability. We evidence the inviscid nature of this large-scale double-diffusive instability, enabling the determination of the marginal stability curve at realistic planetary regimes. In particular, we show that in stably stratified spheres, the Rayleigh numbers 〈span〉Ra〈/span〉 at the onset evolve like 〈span〉Ra〈/span〉 ∼ 〈span〉Ek〈/span〉〈sup〉−1〈/sup〉, where 〈span〉Ek〈/span〉 is the Ekman number. This differs from rotating convection in unstably stratified spheres, for which 〈span〉Ra〈/span〉 ∼ 〈span〉Ek〈/span〉〈sup〉−4/3〈/sup〉. The domain of existence of inviscid convection thus increases as 〈span〉Ek〈/span〉〈sup〉−1/3〈/sup〉. Second, we perform nonlinear simulations. We find a transition between two regimes of RDDC, controlled by the strength of the stratification. Furthermore, far from the RDDC onset, we find a dominating equatorially anti-symmetric, large-scale zonal flow slightly above the associated linear onset. Unexpectedly, a purely linear mechanism can explain this phenomenon, even far from the instability onset, yielding a symmetry breaking of the nonlinear flow at saturation. For even stronger stable stratification, the flow becomes mainly equatorially-symmetric and intense zonal jets develop. Finally, we apply our results to the early Earth core. Double diffusion can reduce the critical Rayleigh number by four decades for realistic core conditions. We suggest that the early Earth core was prone to turbulent RDDC, with large-scale zonal flows.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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