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  • Articles  (8,536)
  • Oxford University Press  (8,536)
  • 2020-2024  (477)
  • 2020-2023  (40)
  • 1960-1964  (5,070)
  • 1950-1954  (2,949)
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  • 1
    Publication Date: 2024-01-19
    Description: We performed seismic ambient noise tomography to investigate the shallow crustal structure around the Ivrea geophysical body (IGB) in the Ivrea-Verbano Zone (IVZ). We achieved higher resolution with respect to previous tomographic works covering the Western Alps, by processing seismic data collected by both permanent and temporary seismic networks (61 broad-band seismic stations in total). This included IvreaArray, a temporary, passive seismic experiment designed to investigate the IVZ crustal structure. Starting from continuous seismic ambient noise recordings, we measured and inverted the dispersion of the group velocity of surface Rayleigh waves (fundamental mode) in the period range 4–25 s. We obtained a new, 3-D vS model of the IVZ crust via the stochastic neighbourhood algorithm (NA), with the highest resolution between 3 to 40 km depth. The fast and shallow shear wave velocity anomaly associated with the IGB presents velocities of 3.6 km s−1 directly at the surface, in remarkable agreement with the location of the exposed lower-to-middle crustal and mantle outcrops. This suggests a continuity between the surface geological observations and the subsurface geophysical anomalies. The fast IGB structure reaches vS of 4 km s−1 at 20–25 km depth, at the boundary between the European and Adriatic tectonic plates, and in correspondence with the earlier identified Moho jump in the same area. The interpretation of a very shallow reaching IGB is further supported by the comparison of our new results with recent geophysical investigations, based on receiver functions and gravity anomaly data. By combining the new geophysical constraints and the geological observations at the surface, we provide a new structural interpretation of the IGB, which features lower crustal and mantle rocks at upper crustal depths. The comparison of the obtained vS values with the physical properties from laboratory analysis of local rock samples suggests that the bulk of the IGB consists of a combination of mantle peridotite, ultramafic and lower crustal rocks, bound in a heterogeneous structure. These new findings, based on vS tomography, corroborate the recent interpretation for which the Balmuccia peridotite outcrops are continuously linked to the IGB structure beneath. The new outcomes contribute to a multidisciplinary framework for the interpretation of the forthcoming results of the scientific drilling project DIVE. DIVE aims at probing the lower continental crust and its transition to the mantle, with two ongoing and one future boreholes (down to 4 km depth) in the IVZ area, providing new, complementary information on rock structure and composition across scales. In this framework, we constrain the upper crustal IGB geometries and lithology based on new evidence for vS, connecting prior crustal knowledge to recent active seismic investigations.
    Description: Published
    Description: 1089–1105
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2024-01-23
    Description: On the 9th of January 2020, an Mw 6.4 strike-slip earthquake took place north of the Asian margin of the Bering Sea. The earthquake occurred within the known reverse-right-lateral active fault zone, called Khatyrka–Vyvenka, which transverses the Koryak Highland from SE to NW and is thought to be a surface manifestation of the Asian portion of either the Bering plate boundary or the northern edge of the Alaskan stream. No other strong earthquake has ever been recorded in this remote uninhabited area and the few existing seismic stations provide poor quality earthquake locations.We adopt SAR interferometry (InSAR) technique to define an improved location of the Koryak 2020 earthquake and constrain the seismic source. The analysis of the 2020 event revealed a previously unknown active fault of left-lateral kinematics that is possibly hidden and strikes NWtransversely to the Khatyrka–Vyvenka fault zone. Although several mechanisms could account for left-lateral kinematics of this fault, we propose that the structure is part of a more extended NW fault structure, that formed in pre-neotectonic times and has played a role of a pre-existing rheological discontinuity. This revived NW structure together with a similar structure located easterly, so far aseismic, make the plate/stream boundary segmented, step-like in plan view. The step-like boundary geometry may be the result of internal transform deformation of a rigid plate, but it is better explained by deflections of the Alaskan stream edge at local crustal asperities, which are pre-Cenozoic terrains.
    Description: Published
    Description: 1412–1421
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Plate motion ; Radar interferometry ; Seismic cycle ; Asia
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2024-04-03
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: Estimation of local seismic response plays a key role in assessing local seismic hazard and particularly in the design of shaking scenarios. Modelling local seismic response involves knowing of the shear wave velocity (Vs) and quality factor (Qs) profiles for the site in question. The many techniques that have been developed to assess Vs in surface deposits produce reliable measurements of Vs , but these rarely correspond to direct measurements of Qs . The latter is often considered through damping measures from laboratory tests on small-scale soil samples, which can provide information primarily on intrinsic attenuation, neglecting the contribution of scattering effects. In this paper, using seismic recordings obtained at the surface and in boreholes at 100 m depth, we estimate an average value of Qs of some characteristic alluvial deposits of the Po Plain (northern Italy). Data come from a microseismic network which sampled an almost uniform lithology in the central Po Plain and consisted of three surface and four borehole stations with an interstation distance of about 2 km. The average value of Qs of the shallowest 100 m of the sedimentary strata, Qs100, is estimated by considering: (1) the high-frequency attenuation of seismic waves due to propagation through the corresponding stratigraphy and (2) the interference between incident and surface-reflected waves observed at borehole stations. We parametrize the first through k0_100, the difference between the values of the spectral decay parameter kappa (k) estimated at the surface and at the boreholes depth, respectively. We use the second in order to compute Vs100, the time-averaged Vs referred to the uppermost 100 m stratigraphy. We obtain: k0_100 = (11 ± 3) ms, Vs100 = (309 ± 11) m s −1 and Qs100 = 31 ± 10. At the surface, the estimated values of the site-specific kappa, k0, are found to range from 75 to 79 ms. As expected, these results are in good agreement with studies performed in other sites characterized by sandy or clayey lithologies, and can be usefully used in site response analysis at sites where the rigidity is mainly controlled by lithostatic pressure.
    Description: Comune di Minerbio (grant: “Sperimentazione ILG Minerbio”; grant number: 0913.010).
    Description: Published
    Description: 2075–2094
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquake ground motions ; Seismic attenuation ; Site effects ; Wave propagation ; Wave scattering and diffraction ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2024-03-19
    Description: Accurate quantification of seismic activity in volcanic regions is an important asset for im- proving hazard and risk assessment. This is especially true for densely populated areas, as in the case of Etna volcano (Southern Italy). There, the volcanic hazard is amplified by the seismic risk of acti ve faults, especiall y on the eastern flank of the volcano. In such a context, it is common to rely on moment magnitude ( M W ) to characterize seismicity and monitor the energy released during an eruption. In this study, we calculate the moment-based magnitude ( M W ) for selected seismic data sets, using different approaches in distinct magnitude ranges to cover the widest possible range of magnitude that characterizes Etna’s seismicity . Specifically , we computed the M W from a data set of moment tensor solutions of earthquakes that occurred in the magnitude range 3.4 ≤M L ≤4.8 during 2005–2020; we created a data set of seismic moment and associated M W for earthquakes 1.0 ≤M L 〈 3.4 obtained by analysing source spectra; we fine-tuned two relationships, for shallow and deep earthquakes, to obtain M W from response spectra. Finally, we calibrated a specific relationship between M W and M L for the Etna area earthquakes in the range 1.0 ≤M L ≤4.8. All the empirical relationships obtained in this study can be applied in real-time analysis of the seismicity to provide fast and robust information on the released seismic energy.
    Description: INGV-DPC 2012- 2021 agreement; B2 DPC-INGV 2019-2021 project; IMPACT Department strategic project ; ‘Project PE0000005–RETURN (NRRP)
    Description: Published
    Description: 2520-2534
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquak e source observations ; Earthquake hazards ; Time series analysis ; Full moment tensor
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2024-03-12
    Description: This study presents a new robust statistical framework, in which to measure relative differences, or deviations from a hypothetical reference value, of Gutenberg-Richter b-value. Moreover, it applies this method to recent seismicity in Italy, to find possible changes of earthquake magnitude distribution in time and space. The method uses bootstrap techniques, which have no prior assumptions about the distribution of data, keeping their basic features. Excluding Central Italy, no significative b-value variation is found, revealing that the frequency-magnitude distribution exponent is substantially stable or that data are not able to reveal hidden variations. Considering the small size of examined magnitude samples, we cannot definitively decide if the higher b-values in Central Italy, consistently founded by all applied tests, have a physical origin or result from a statistical bias. In any case, they indicate short-lived excursions which have a temporary nature and, therefore, cannot be associated solely to spatial variations in tectonic framework. Both the methodological issues and the results of the application to seismicity in Italy show that a correct assessing of b-value changes requests appropriate statistics, that accurately quantify the low accuracy and precision of b-value estimation for small magnitude samples.
    Description: Published
    Description: 729–740
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2024-03-12
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: We present the results from a fully unconstrained moment tensor inversion of induced seismic events in a complex and high seismic hazard region (Val d’Agri basin, Southern Italy). The study area hosts two well-documented cases of induced microseismicity linked to (i) a wastewater injection well of a giant oilfield (the largest in onshore Europe), and (ii) severe seasonal level changes of an artificial lake. In order to gather information on the non-doublecouple components of the source and to better understand the rupture mechanisms, we analyse seismic events recorded during daily injection tests in the disposal well. The computed moment tensors have significant non-double-couple components that correlate with the well-head injection pressure. The injection parameters strongly influence the rupture mechanism that can be interpreted as due to the opening/closing of a fracture network inside a fault zone of a pre-existing thrust fault. For the case of the reservoir-induced seismicity, no direct correlations are observed with the loading/unloading of the reservoir.
    Description: Published
    Description: 1617–1627
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2024-04-09
    Description: Serpentinites are polymineralic rocks distributed almost ubiquitously across the globe in active tectonic regions. Magnetite-rich serpentinites are found in the low-strain domains of serpen- tinite shear zones, which act as potential sites of nucleation of unstable slip. To assess the potential of earthquake nucleation in these materials, we investigate the link between me- chanical properties and fabric of these rocks through a suite of laboratory shear experiments. Our experiments were done at room temperature and cover a range of normal stress and slip velocity from 25 to 100 MPa and 0.3 to 300 μm s −1 , respecti vel y. We show that magnetite-rich serpentinites are ideal materials since they display strong sensitivity to the loading rate and are susceptible to nucleation of unstable slip, especially at low forcing slip velocities. We also aim at the integration of mechanical and microstructural results to describe the underlying mechanisms that produce the macroscopic behaviour. We show that mineralogical composi- tion and mineral structure dictates the coexistence of two deformation mechanisms leading to stable and unstable slip. The weakness of phyllosilicates allows for creep during the interseis- mic phase of the laboratory seismic cycle while favouring the restoration of a load-bearing granular framework, responsible of the nucleation of unstable events. During dynamic slip, fault zone shear fabric determines the mode of slip, producing either asymmetric or Gaussian slip time functions for either fast or slow events. We report rate/state friction parameters and integrate our mechanical data with microstructural observations to shed light on the mech- anisms dictating the complexity of laborator y ear thquakes. We show that mineralogical and fabric heterogeneities control fault slip behaviour.
    Description: Published
    Description: 1778–1797
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2024-05-27
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: We report on about 20 yr of relative gravity measurements, acquired on Mt. Somma–Vesuvius volcano in order to investigate the hydrological and volcano-tectonic processes controlling the present-day activity of the volcano. The retrieved long-term field of time gravity change (2003–2022) shows a pattern essentially related to the subsidence, which have affected the central part of the volcano, as detected by the permanent GNSS network and InSAR data. After reducing the observations for the effect of vertical deformation, no significant residuals are found, indicating no significant mass accumulation or loss within the volcanic system. In the north-western sector of the study area, at the border of the volcano edifice, however, significant residual positive gravity changes are detected which are associated to ground-water rebound after years of intense exploitation of the aquifers. On the seasonal timescale, we find that stations within the caldera rim are affected by the seasonal hydrological effects, while the gravity stations at the base of the Vesuvius show a less clear correlation. Furthermore, within the caldera rim a multiyear gravity transient is detected with an increase phase lasting about 4 yr followed by a slower decrease phase. Analysis of rain data seem to exclude a hydrological origin, hence, we hypothesize a deeper source related to the geothermal activity, which can be present even if the volcano is in a quiescent state. We infer the depth and volume of the source by inverting the spatial pattern of the gravity field at the peak of the transient. A volume of fluids of 9.5 × 107 m3 with density of 1000 kg m−3 at 2.3 km depth is capable to fit reasonably well the observations. To explain the gravity transient, simple synthetic models are produced, that simulate the ascent of fluids from a deep reservoir up to the depth of 2.3 km and a successive diffusion within the carbonate aquifer hosting the geothermal system. The whole process appears to not significantly affect the seismicity rate and the deformation of the volcano. This study demonstrates the importance of a 4-D gravity monitoring of a volcano to understand its complex gravity signals that cover different spatial and temporal scales. Discriminating the different contributions that mix up in the observed gravity changes, in particular those due to hydrologic/anthropogenic activities form those due to the geothermal dynamics, is fundamental for a complete and reliable evaluation of the volcano state.
    Description: Published
    Description: 1565–1580
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: In a recent work, we applied the every earthquake a precursor according to scale (EEPAS) probabilistic model to the pseudo-prospective forecasting of shallow earthquakes with magni- tude M 5.0 in the Italian region. We compared the forecasting performance of EEPAS with that of the epidemic type aftershock sequences (ETAS) forecasting model, using the most recent consistency tests developed within the collaboratory for the study of earthquake predictabil- ity (CSEP). The application of such models for the forecasting of Italian target earthquakes seems to show peculiar characteristics for each of them. In particular, the ETAS model showed higher performance for short-term forecasting, in contrast, the EEPAS model showed higher forecasting performance for the medium/long-term. In this work, we compare the performance of EEPAS and ETAS models with that obtained by a deterministic model based on the occur- rence of strong foreshocks (FORE model) using an alarm-based approach. We apply the two rate-based models (ETAS and EEPAS) estimating the best probability threshold above which we issue an alarm. The model parameters and probability thresholds for issuing the alarms are calibrated on a learning data set from 1990 to 2011 during which 27 target earthquakes have occurred within the analysis region. The pseudo-prospective forecasting performance is as- sessed on a validation data set from 2012 to 2021, which also comprises 27 target earthquakes. Tests to assess the forecasting capability demonstrate that, even if all models outperform a purely random method, which trivially forecast earthquake proportionally to the space–time occupied by alarms, the EEPAS model exhibits lower forecasting performance than ETAS and FORE models. In addition, the relative performance comparison of the three models demonstrates that the forecasting capability of the FORE model appears slightly better than ETAS, but the difference is not statistically significant as it remains within the uncertainty level. However, truly prospective tests are necessary to validate such results, ideally using new testing procedures allowing the analysis of alarm-based models, not yet available within the CSEP.
    Description: Published
    Description: 1541–1551
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction, forecasting and prediction ; Statistical seismology ; Comparison betwee earthquake forecasting methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2024-05-09
    Description: To understand the seismic hazard of a subduction zone, it is necessary to know the geometry, location and mechanical characteristics of the interplate boundary below which an oceanic plate is thrust downward. By considering the azimuthal dependence of converted P-to-S (Ps) amplitudes in receiver functions, we have detected the interplate boundary in the Makran subduction zone, revealing significant seismic anisotropy at the base of the accretionary wedge above the slab before it bends down beneath the Jaz Murian basin. This anisotropic feature aligns with a zone of reduced seismic velocity and a high primary/secondary wave velocity ratio (Vp/Vs), as documented in previous studies. The presence of this low-velocity highly anisotropic layer at the base of the accretionary wedge, likely representing a low-strength shear zone, could possibly explain the unusually wide accretionary wedge in Makran. Additionally, it may impact the location and width of the locked zone along the interplate boundary.
    Description: Iranian National Science Foundation (INSF)
    Description: Published
    Description: 64-74
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Keywords: Earthquake hazards, Seismic anisotropy, Crustal structure, Subduction zone processes ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: The Every Earthquake a Precursor According to Scale (EEPAS) forecasting model is a space– time point-process model based on the precursory scale increase (ψ ) phenomenon and associated predictive scaling relations. It has been previously applied to New Zealand, Cal- ifornia and Japan earthquakes with target magnitude thresholds varying from about 5–7. In all previous application, computations were done using the computer code implemented in Fortran language by the model authors. In this work, we applied it to Italy using a suite of computing codes completely rewritten in Matlab. We first compared the two software codes to ensure the convergence and adequate coincidence between the estimated model parameters for a simple region capable of being analysed by both software codes. Then, using the rewritten codes, we optimized the parameters for a different and more complex polygon of analysis using the Homogenized Instrumental Seismic Catalogue data from 1990 to 2011. We then perform a pseudo-prospective forecasting experiment of Italian earthquakes from 2012 to 2021 with Mw ≥ 5.0 and compare the forecasting skill of EEPAS with those obtained by other time in- dependent (Spatially Uniform Poisson, Spatially Variable Poisson and PPE: Proximity to Past Earthquakes) and time dependent [Epidemic Type Aftershock Sequence (ETAS)] forecasting models using the information gain per active cell. The preference goes to the ETAS model for short time intervals (3 months) and to the EEPAS model for longer time intervals (6 months to 10 yr).
    Description: Published
    Description: 1681–1700
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction ; forecasting and prediction ; Statistical seismology ; Earthquake forecasting
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2024-06-17
    Description: Thermobarometry provides a critical means of assessing locations of magma storage and dynamics in the lead-up to volcanic eruptions and crustal growth. A common approach is to utilise minerals that have compositions sensitive to changes in pressure and/or temperature, such as clinopyroxene, which is ubiquitous in mafic to intermediate magmas. However, clinopyroxene thermobarometry may carry significant uncertainty and require an appropriate equilibrium melt composition. In addition, the degree of magma undercooling (ΔT) affects clinopyroxene composition and zoning, with common sector zoning potentially obfuscating thermobarometry results. Here, we use a set of crystallisation experiments on a primitive trachybasalt from Mt. Etna (Italy) at ΔT = 25–233 °C, P = 400–800 MPa, H2O = 0–4 wt % and fO2 = NNO + 2, with clinopyroxene crystals defined by Al-rich zones (prisms and skeletons) and Al-poor zones (hourglass and overgrowths) to assess common equilibrium models and thermobarometric approaches. Under the studied conditions, our data suggest that the commonly applied Fe–Mg exchange (cpx-meltKdFe–Mg) is insensitive to increasing ΔT and may not be a reliable indicator of equilibrium. The combined use of DiHd (CaMgSi2O6 + CaFeSi2O6) and EnFs (Mg2Si2O6 + Fe2Si2O6) models indicate the attainment of equilibrium in both Al-rich and Al-poor zones for almost all investigated ΔT. In contrast, CaTs (CaAl2SiO6) and CaTi (CaTiAl2O6) models reveal substantial deviations from equilibrium with increasing ΔT, particularly in Al-rich zones. We postulate that this reflects slower diffusion of Al and Ti in the melt compared with Ca and Mg and recommend the concurrent application of these four models to evaluate equilibrium between clinopyroxene and melt, particularly for sector-zoned crystals. Thermobarometers calibrated with only isothermal–isobaric experiments closely reproduce experimental P–T at low ΔT, equivalent to natural phenocrysts cores and sector-zoned mantles. Models that also consider decompression experiments are most accurate at high ΔT and are therefore suitable for outermost phenocryst rims and groundmass microlites. Recent machine learning approaches reproduce P–T conditions across all ΔT conditions. Applying our experimental constraints to sector-zoned microphenocrysts and groundmass microlites erupted during the 1974 eccentric eruption at Mt. Etna, we highlight that both hourglass and prism sectors are suitable for thermobarometry, given that equilibrium is sufficiently tested for. The combination of DiHd, EnFs, CaTs and CaTi models identifies compositions closest to equilibrium with the bulk melt composition, and results in smaller differences in P–T calculated for hourglass and prism sectors compared with applying only DiHd and EnFs equilibrium models. This provides a framework to assess crystallisation conditions recorded by sector-zoned clinopyroxene crystals in mafic alkaline settings.
    Description: Published
    Description: egad074
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
    Keywords: Experimental Petrology ; Petrology ; Clinopyroxene ; Thermobarometry ; Experimental Petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2024-07-02
    Description: The joint ESA/NASA Mass-change And Geosciences International Constellation (MAGIC) has the objective to extend time-series from previous gravity missions, including an improvement of accuracy and spatio-temporal resolution. The long-term monitoring of Earth’s gravity field carries information on mass change induced by water cycle, climate change and mass transport processes between atmosphere, cryosphere, oceans and solid Earth. MAGIC will be composed of two satellite pairs flying in different orbit planes. The NASA/DLR-led first pair (P1) is expected to be in a near-polar orbit around 500 km of altitude; while the second ESA-led pair (P2) is expected to be in an inclined orbit of 65°–70° at approximately 400 km altitude. The ESA-led pair P2 Next Generation Gravity Mission shall be launched after P1 in a staggered manner to form the MAGIC constellation. The addition of an inclined pair shall lead to reduction of temporal aliasing effects and consequently of reliance on de-aliasing models and post-processing. The main novelty of the MAGIC constellation is the delivery of mass-change products at higher spatial resolution, temporal (i.e. subweekly) resolution, shorter latency and higher accuracy than the Gravity Recovery and Climate Experiment (GRACE) and Gravity Recovery and Climate Experiment Follow-On (GRACE-FO). This will pave the way to new science applications and operational services. In this paper, an overview of various fields of science and service applications for hydrology, cryosphere, oceanography, solid Earth, climate change and geodesy is provided. These thematic fields and newly enabled applications and services were analysed in the frame of the initial ESA Science Support activities for MAGIC. The analyses of MAGIC scenarios for different application areas in the field of geosciences confirmed that the double-pair configuration will significantly enlarge the number of observable mass-change phenomena by resolving smaller spatial scales with an uncertainty that satisfies evolved user requirements expressed by international bodies such as IUGG. The required uncertainty levels of dedicated thematic fields met by MAGIC unfiltered Level-2 products will benefit hydrological applications by recovering more than 90 per cent of the major river basins worldwide at 260 km spatial resolution, cryosphere applications by enabling mass change signal separation in the interior of Greenland from those in the coastal zones and by resolving small-scale mass variability in challenging regions such as the Antarctic Peninsula, oceanography applications by monitoring meridional overturning circulation changes on timescales of years and decades, climate applications by detecting amplitude and phase changes of Terrestrial Water Storage after 30 yr in 64 and 56 per cent of the global land areas and solid Earth applications by lowering the Earthquake detection threshold from magnitude 8.8 to magnitude 7.4 with spatial resolution increased to 333 km.
    Description: Published
    Description: 1288–1308
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2023-12-27
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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. All rights reserved.
    Description: The south-eastern sector of the Mount Etna, Italy, is characterized by numerous active faults, in particular the Belpasso–Ognina lineament, the Tremestieri–San Gregorio–Acitrezza fault, the Trecastagni fault and the Fiandaca–Nizzeti fault including the Timpe Fault System. Their activity is the result of both volcanism and tectonics. Here, we analyse the ground deformation occurred from 2016 to 2019 across those active faults by using the GNSS data acquired at 22 permanent stations and 35 campaign points observed by the Etna Observatory (INGV) and by the University of Catania. We also use the time-series of line of sight displacement of permanent scatterers SENTINEL-1 A-DInSAR obtained by using the P-SBAS tool of the ESA GEP-TEP (Geohazards Thematic Exploitation Platform) service. We discriminate the contributions of the regional tectonic strain, the inflations, the deflations of the volcano and the gravitational sliding in order to analyse the deformation along the faults of the south-eastern flank of Etna. The shallow and destructive Mw = 4.9 earthquake of 2018 December 26 occurred within the studied area two days after a dyke intrusion, that propagated beneath the centre of the volcano accompanied by a short eruption. Both GNSS and InSAR time-series document well those events and allow to investigate the post-seismic sliding across the faults of south-eastern flank. We analyse the slow slip events (SSE) that are observed in the GNSS and InSAR time-series in the vicinity of the Acitrezza fault. We quantify and discuss the tectonic origin of the Belpasso–Ognina lineament that we interpreted as a tear fault.
    Description: Published
    Description: 664–682
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: Satellite geodesy ; Transient deformation ; Interferometry ; Fractures ; fault ; Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    Publication Date: 2023-03-15
    Description: Ground shaking, whether it is due to natural or induced earthquakes, has always been a matter of concern since it correlates with structural/non-structural damage and can culminate in human anxiety. Industrial activities such as water injection, gas sequestration and waste fluid disposals, promote induced seismicity and consequent ground shaking that can hinder ongoing activities. Therefore, keeping in mind the importance of timely evaluation of a seismic hazard and its mitigation for societal benefits, the present study proposes specifically designed ground-motion prediction equations (GMPEs) from induced earthquakes in the St. Gallen geothermal area, Switzerland. The data analysed in this study consist of 343 earthquakes with magnitude −1.17 ≤ ML, corr ≤ 3.5 and hypocentral distance between 4 and 15 km. The proposed study is one of the first to incorporate ground motions from negative magnitude earthquakes for the development of GMPEs. The GMPEs are inferred with a two-phase approach. In the first phase, a reference model is obtained by considering the effect of source and medium properties on the ground motion. In the second phase the final model is obtained by including a site/station effect. The comparison between the GMPEs obtained in the present study with GMPEs developed for the other induced seismicity environments highlights a mismatch that is ascribed to differences in regional seismic environment and local site conditions of the respective regions. This suggests that, when dealing with induced earthquakes, GMPEs specific for the study should be inferred and used for both monitoring purposes and seismic hazard analyses.
    Description: Published
    Description: 820–832
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hudson, A. R., Peters, D. P. C., Blair, J. M., Childers, D. L., Doran, P. T., Geil, K., Gooseff, M., Gross, K. L., Haddad, N. M., Pastore, M. A., Rudgers, J. A., Sala, O., Seabloom, E. W., & Shaver, G. Cross-site comparisons of dryland ecosystem response to climate change in the US long-term ecological research network. Bioscience, 72(9), (2022): 889–907, https://doi.org/10.1093/biosci/biab134.
    Description: Long-term observations and experiments in diverse drylands reveal how ecosystems and services are responding to climate change. To develop generalities about climate change impacts at dryland sites, we compared broadscale patterns in climate and synthesized primary production responses among the eight terrestrial, nonforested sites of the United States Long-Term Ecological Research (US LTER) Network located in temperate (Southwest and Midwest) and polar (Arctic and Antarctic) regions. All sites experienced warming in recent decades, whereas drought varied regionally with multidecadal phases. Multiple years of wet or dry conditions had larger effects than single years on primary production. Droughts, floods, and wildfires altered resource availability and restructured plant communities, with greater impacts on primary production than warming alone. During severe regional droughts, air pollution from wildfire and dust events peaked. Studies at US LTER drylands over more than 40 years demonstrate reciprocal links and feedbacks among dryland ecosystems, climate-driven disturbance events, and climate change.
    Description: Funding was provided by the USDA-ARS SCINet Big Data Project (grant no. 0500–00093–001–00-D), and the National Science Foundation US LTER Program to New Mexico State University for the Jornada Basin (grant no. DEB 20–25166), Kansas State University for the Konza Prairie (grant no. DEB 2025849), the Kellogg Biological Station (grant no. DEB 1832042), Cedar Creek Ecosystem Science Reserve (grants no. DEB-1234162 and no. DEB-1831944), ARC (grant no. DEB-1637459), MCM (grant no. OPP-1637708), CAP (grant no. DEB-1832016), and SEV (grant no. DEB-1655499). Support was also provided by the Minnesota Supercomputer Institute and the University of Minnesota, Michigan State University AgBioResearch.
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  • 17
    Publication Date: 2023-02-17
    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 Geophysical Journal International 231(2),(2022): 1434–1445, https://doi.org/10.1093/gji/ggac257.
    Description: Makran subduction zone is very active with ∼38 mm yr−1 convergence rate and has experienced great earthquakes in the past. The latest great earthquake of 1945 Mw 8.1 event also triggered a large tsunami and led to ∼4000 casualties. However, due to incomplete historical seismicity records and poor modern instrumentation, earthquake mechanism, co-seismic slip and tsunami characteristics in Makran remain unclear. On 2017 February 17, an Mw 6.3 earthquake rattled offshore Pasni of Pakistan in the eastern Makran, marking the largest event after the 1945 Mw 8.1 earthquake with good geodetic and geophysical data coverage. We use a combination of seismicity, multibeam bathymetry, seismic profile, InSAR measurements and tide-gauge observation to investigate the seismogenic structure, co-seismic deformation, tsunami characteristics of this event and its implication for future major earthquakes. Our results indicate that (1) the earthquake occurred on the shallow-dipping (3°–4°) megathrust; (2) the megathrust co-seismically slipped 15 cm and caused ∼2–4 cm ground subsidence and uplift at Pasni; (3) our tsunami modelling reproduces the observed 5-cm-high small tsunami waveforms. The Pasni earthquake rupture largely overlaps the 1945 slip patch and disturbs the west and east megathrust segments that have not ruptured yet at least since 1765. With such stress perturbation and possible stress evolution effect from the 1945 earthquake, the unruptured patches may fail in the future. This study calls for more preparedness in mitigating earthquake and associated hazards in the eastern Makran.
    Description: his study is financially supported by the National Natural Science Foundation of China (Nos. 42076059, 41890813, 41976066 and 41976064), the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (No. GML2019ZD0205), Chinese Academy of Sciences (Nos. Y4SL021001, QYZDY-SSW-DQC005, 131551KYSB20200021, ISEE2021PY03, 133244KYSB20180029 and E1SL3C02), Guangdong Basic and Applied Basic Research Foundation (No. 2021B1515020098) and China–Pakistan Joint Research Centre on Earth Sciences.
    Keywords: Tsunamis ; Earthquake dynamics ; Earthquake hazards ; Seismicity and tectonics ; Subduction zone processes
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  • 18
    Publication Date: 2023-01-25
    Description: The Doldrums Megatransform System (~7–8°N, Mid-Atlantic Ridge) shows a complex architecture including four intra-transform ridge segments bounded by five active transform faults. Lower crustal rocks are exposed along the Doldrums and Vernadsky transform walls that bound the northernmost intra-transform ridge segment. The recovered gabbros are characterized by variably evolved chemical compositions, ranging from olivine gabbros to gabbronorites and oxide gabbros, and lack the most primitive gabbroic endmembers (troctolites, dunites). Notably, the numerous recovered gabbronorites show up to 20 vol. % of coarse-grained orthopyroxene. Although covariations in mineral and bulk-rock chemical compositions of the olivine and oxide gabbros define trends of crystallization from a common parental melt, the gabbronorites show elevated light over heavy rare earth elements (LREE/HREE) ratios in both bulk-rock and mineral compositions. These features are not consistent with a petrological evolution driven solely by fractional crystallization, which cannot produce the preferential enrichments in highly incompatible elements documented in the orthopyroxene-bearing lithologies. We suggest that gabbronorites crystallized from evolved melts percolating and partly assimilating a pre-existing olivine gabbro matrix. Saturation in orthopyroxene and selective enrichments in LREE relative to M-HREE are both triggered by an increase in assimilated crystal mass, which ranges from negligible in the oxide-gabbros to abundant in the gabbronorites. This melt–rock reaction process has been related to lateral melt migration beneath ridge-transform intersections, where variably evolved melts injected from the peripheral parts of the melting region towards the transform zone may interact with a gabbroic crystal mush to form abundant oxide-bearing gabbronoritic associations.
    Description: Published
    Description: egac086
    Description: 3A. Geofisica marina e osservazioni multiparametriche a fondo mare
    Description: JCR Journal
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  • 19
    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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  • 20
    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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  • 21
    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.].
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  • 22
    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.
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  • 23
    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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  • 24
    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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  • 25
    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
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  • 26
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    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
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  • 27
    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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  • 28
    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
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  • 29
    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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  • 30
    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.
    Repository Name: Woods Hole Open Access Server
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  • 31
    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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  • 32
    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.
    Repository Name: Woods Hole Open Access Server
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  • 33
    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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  • 34
    Publication Date: 2024-01-30
    Description: In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs 〉 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 35
    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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 36
    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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 37
    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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 38
    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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  • 39
    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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 40
    Publication Date: 2023-10-26
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 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. All rights reserved.
    Description: Relative location of microearthquakes that occurred at Mt Pollino (Italy) from 2011 to 2013 have been analyzed with the aim of a detailed imaging of the geometry of active faults. We identified 27 clusters composed of a number of earthquakes from 9 to 33, with local magnitude in the range 0.6–2.7. The relative location shows that the distribution of hypocentres in each cluster is characterized by extension from few tens of meters to at most 350 m. For each cluster the hypocentre distribution was fitted by a plane to infer the fault orientation, and results were compared with the fault plane solutions corresponding to the focal mechanism of earthquakes of the same cluster. The comparison shows a good agreement in most of the cases. The relative location analysis, generally applied to earthquakes with similar waveform, has been improved to permit also the relative location of earthquakes characterized by not similar signals. To achieve this purpose a modified procedure that overcome the condition of very similar waveforms has been applied to estimate the time delay between first pulses of the master events. The relative location of master events of all clusters shows a precise imaging of the relative position of all analysed sources and allows also to follow with high accuracy the evolution in time of the seismic swarm within the selected periods. The hypocentre position of master events and the nearly parallel fitting planes of any clusters suggest that most of the analyzed earthquakes were produced by different patches of the same fault. The final results depict a main fault plane characterized by NW–SE strike, dip of about 35–45° and depth between 4.5 and 6.5 km b.s.l. Focal mechanisms, used also to evaluate the local stress field, are mostly of normal type with few strike slip solutions for the shallowest events. This result is in good agreement with the local tectonic stress regime that is characterized by predominant NE–SW transtension, as inferred from structural, seismological and geophysical data.
    Description: Published
    Description: 637–648
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Persistence, memory, correlations, clustering, Spatial analysis, Crustal imaging, Earthquake source observations, Seismicity and tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 41
    Publication Date: 2023-10-31
    Description: Since the Mesozoic, central and eastern European tectonics have been dominated by the closure of the Tethyan Ocean as the African and European plates collided. In the Miocene, the edge of the East European Craton and Moesian Platform were reworked in collision during the Carpathian orogeny and lithospheric extension formed the Pannonian Basin. To investigate the mantle deformation signatures associated with this complex collisional-extensional system, we carry out SKS splitting analysis at 123 broad-band seismic stations in the region. We compare our measurements with estimates of lithospheric thickness and recent seismic tomography models to test for correlation with mantle heterogeneities. Reviewing splitting delay times in light of xenolith measurements of anisotropy yields estimates of anisotropic layer thickness. Fast polarization directions are mostly NW–SE oriented across the seismically slow West Carpathians and Pannonian Basin and are independent of geological boundaries, absolute plate motion direction or an expected palaeo-slab roll-back path. Instead, they are systematically orthogonal to maximum stress directions, implying that the indenting Adria Plate, the leading deformational force in Central Europe, reset the upper-mantle mineral fabric in the past 5 Ma beneath the Pannonian Basin, overprinting the anisotropic signature of earlier tectonic events. Towards the east, fast polarization directions are perpendicular to steep gradients of lithospheric thickness and align along the edges of fast seismic anomalies beneath the Precambrian-aged Moesian Platform in the South Carpathians and the East European Craton, supporting the idea that craton roots exert a strong influence on the surrounding mantle flow. Within the Moesian Platform, SKS measurements become more variable with Fresnel zone arguments indicating a shallow fossil lithospheric source of anisotropy likely caused by older tectonic deformation frozen in the Precambrian. In the Southeast Carpathian corner, in the Vrancea Seismic Zone, a lithospheric fragment that sinks into the mantle is sandwiched between two slow anomalies, but smaller SKS delay times reveal weaker anisotropy occurs mainly to the NW side, consistent with asymmetric upwelling adjacent to a slab, slower mantle velocities and recent volcanism.
    Description: Published
    Description: 2105–2118
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; geodynamics ; Seismic anisotropy and geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 42
    Publication Date: 2023-11-21
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 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. All rights reserved.
    Description: On 24 August 2016 at 01:36 UTC a ML6.0 earthquake struck several villages in central Italy, among which Accumoli, Amatrice and Arquata del Tronto. The earthquake was recorded by about 350 seismic stations, causing 299 fatalities and damage with macroseismic intensities up to 11. The maximum acceleration was observed at Amatrice station (AMT) reaching 916 cm s–2 on E–W component, with epicentral distance of 15 km and Joyner and Boore distance to the fault surface (RJB) of less than a kilometre. Motivated by the high levels of observed ground motion and damage, we generate broad-band seismograms for engineering purposes by adopting a hybrid method. To infer the low frequency seismograms, we considered the kinematic slip model by Tinti et al . The high frequency seismograms were produced using a stochastic finite-fault model approach based on dynamic corner-frequency. Broadband synthetic time-series were therefore obtained by merging the low and high frequency seismograms. Simulated hybrid ground motions were compared both with the observed ground motions and the ground-motion prediction equations (GMPEs), to explore their performance and to retrieve the region-specific parameters endorsed for the simulations. In the near-fault area we observed that hybrid simulations have a higher capability to detect near source effects and to reproduce the source complexity than the use of GMPEs. Indeed, the general good consistency found between synthetic and observed ground motion (both in the time and frequency domain), suggests that the use of regional-specific source scaling and attenuation parameters together with the source complexity in hybrid simulations improves ground motion estimations. To include the site effect in stochastic simulations at selected stations, we tested the use of amplification curves derived from HVRSs (horizontal-to-vertical response spectra) and from HVSRs (horizontal-to-vertical spectral ratios) rather than the use of generic curves according to NTC18 Italian seismic design code. We generally found a further reduction of residuals between observed and simulated both in terms of time histories and spectra.
    Description: Published
    Description: 1753–1779
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 43
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. 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. All rights reserved
    Description: This study describes a deep convolutional neural network (CNN) based technique for the prediction of intensity measurements (IMs) of ground shaking. The input data to the CNN model consists of multistation 3C broadband and accelerometric waveforms recorded during the 2016 Central Italy earthquake sequence for M $\ge$ 3.0. We find that the CNN is capable of predicting accurately the IMs at stations far from the epicenter and that have not yet recorded the maximum ground shaking when using a 10 s window starting at the earthquake origin time. The CNN IM predictions do not require previous knowledge of the earthquake source (location and magnitude). Comparison between the CNN model predictions and the predictions obtained with Bindi et al. (2011) GMPE (which require location and magnitude) has shown that the CNN model features similar error variance but smaller bias. Although the technique is not strictly designed for earthquake early warning, we found that it can provide useful estimates of ground motions within 15-20 sec after earthquake origin time depending on various setup elements (e.g., times for data transmission, computation, latencies). The technique has been tested on raw data without any initial data pre-selection in order to closely replicate real-time data streaming. When noise examples were included with the earthquake data, the CNN was found to be stable predicting accurately the ground shaking intensity corresponding to the noise amplitude.
    Description: Published
    Description: 1379–1389
    Description: 8T. Sismologia in tempo reale
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 44
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. 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. All rights reserved.
    Description: In volcanoes, topography, shallow heterogeneity and even shallow morphology can substan- tially modify seismic coda signals. Coda waves are an essential tool to monitor eruption dynamics and model volcanic structures jointly and independently from velocity anomalies: it is thus fundamental to test their spatial sensitivity to seismic path effects. Here, we apply the Multiple Lapse Time Window Analysis (MLTWA) to measure the relative importance of scattering attenuation vs absorption at Mount St Helens volcano before its 2004 erup- tion. The results show the characteristic dominance of scattering attenuation in volcanoes at lower frequencies (3–6 Hz), while absorption is the primary attenuation mechanism at 12 and 18 Hz. Scattering attenuation is similar but seismic absorption is one order of magnitude lower than at open-conduit volcanoes, like Etna and Kilauea, a typical behaviour of a (rela- tively) cool magmatic plumbing system. Still, the seismic albedo (measuring the ratio between seismic energy emitted and received from the area) is anomalously high (0.95) at 3 Hz. A radiative-transfer forward model of far- and near-field envelopes confirms this is due to strong near-receiver scattering enhancing anomalous phases in the intermediate and late coda across the 1980 debris avalanche and central crater. Only above this frequency and in the far-field diffusion onsets at late lapse times. The scattering and absorption parameters derived from MLTWA are used as inputs to construct 2-D frequency-dependent bulk sensitivity kernels for the S-wave coda in the multiple-scattering (using the Energy Transport Equations—ETE) and diffusive (AD, independent of MLTWA results) regimes. At 12 Hz, high coda-attenuation anomalies characterize the eastern side of the volcano using both kernels, in spatial correla- tion with low-velocity anomalies from literature. At 3 Hz, the anomalous albedo, the forward modelling, and the results of the tomographic imaging confirm that shallow heterogeneity beneath the extended 1980 debris-avalanche and crater enhance anomalous intermediate and late coda phases, mapping shallow geological contrasts. We remark the effect this may have on coda-dependent source inversion and tomography, currently used across the world to image and monitor volcanoes. At Mount St Helens, higher frequencies and deep borehole data are necessary to reconstruct deep volcanic structures with coda waves.
    Description: Scottish Alliance for Geosciences Environment and Society and the Kleinman Grant for Volcano Research
    Description: Published
    Description: 169-188
    Description: 1T. Struttura della Terra
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3IT. Calcolo scientifico
    Description: JCR Journal
    Keywords: NorthAmerica ; Wave scattering and diffraction. ; Codawaves ; Seismicattenuation ; Seismic tomography ; Volcano seismology ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 45
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. 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. All rights reserved.
    Description: To evaluate the site response using both empirical approaches (e.g. standard spectral ratio, ground motion models (GMMs), generalized inversion techniques, etc.) and numerical 1-D/2-D analyses, the definition of the reference motion, that is the ground motion recorded at stations unaffected by site-effects due to topographic, stratigraphic or basin effects, is needed. The main objective of this work is to define a robust strategy to identify the seismic stations that can be considered as reference rock sites, using six proxies for the site response: three proxies are related to the analysis of geophysical and seismological data (the repeatable site term from the residual analysis, the resonance frequencies from horizontal-to-vertical spectral ratios on noise or earthquake signals, the average shear wave velocity in the first 30 m); the remaining ones concern geomorphological and installation features (outcropping rocks or stiff soils, flat topography and absence of interaction with structures). We introduce a weighting scheme to take into account the availability and the quality of the site information, as well as the fulfillment of the criterion associated to each proxy. We also introduce a hierarchical index, to take into account the relevance of the proposed proxies in the description of the site effects, and an acceptance threshold for reference rock sites identification. The procedure is applied on a very large data set, composed by accelerometric and velocimetric waveforms, recorded in Central Italy in the period 2008–2018. This data set is composed by more than 30 000 waveforms relative to 450 earthquakes in the magnitude range 3.2–6.5 and recorded by more than 450 stations. A total of 36 out of 133 candidate stations are identified as reference sites: the majority of them are installed on rock with flat topography, but this condition is not sufficient to guarantee the absence of amplifications, especially at high frequencies. Seismological analyses are necessary to exclude stations affected by resonances. We test the impact of using these sites by calibrating a GMMs. The results show that for reference rock sites the median predictions are reduced down to about 45 per cent at short periods in comparison to the generic rock motions.
    Description: Published
    Description: 2053–2067
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 46
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. 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. All rights reserved.
    Description: We compile a data set of Rayleigh-wave phase velocities between pairs of stations, based on teleseismic events located on the same great circle as the two stations. We validate our observations against dispersion estimates based on ambient-noise cross correlations at the same station pairs. Discrepancies between the results of the two methods can in principle be explained by deviations in the wave propagation path between earthquake and receivers, due to lateral heterogeneity in the Earth’s structure, but the latter effect has, so far, not been precisely quantified nor corrected for. We implement an algorithm to measure the arrival angle of earthquake-generated surface waves and correct the dispersion measurements accordingly. Application to a data set from the Central-Western Mediterranean shows that the arrival-angle correction almost entirely accounts for the discrepancy in question, decreasing significantly the velocity bias for a wide range of periods.
    Description: Published
    Description: 1838–1844
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 47
    Publication Date: 2023-11-16
    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: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 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. All rights reserved.
    Description: Three dimensional attenuation images of Mt Etna volcano obtained by the analysis of Q-coda from local volcano-tectonic earthquakes are presented in this work. Seismic sources are confined inside the Etna structure with a maximum focal depth of 35 km below the sea level. The space distribution of the attenuation values was calculated by using 3-D weighting functions derived by the sensitivity kernels of Pacheco & Snieders and approximated by a polynomial interpolation, represented in the maps by using a backprojection method. Data were analyzed in four bands with central frequency placed at 1.5, 3, 6 and 12 Hz, respectively. We observed a frequency dependence of Q-coda with values that range from 55 at 1.5 Hz to 218 at 12 Hz. Q-coda space distribution in the Etna area shows almost uniformity in the average attenuation in the first 35 km below the surface. The images were derived with a resolution of 5 km. We observe as one of our main conclusions that Q-coda attenuation space anomalies are correlated with the areas of highest structural heterogeneities and are distributed along the well-known tectonic structures which characterize the crust in Mt Etna region. Previous and numerous velocity and attenuation images describing the structure of Mt Etna support our main conclusion: high Q-coda volumes almost coincide with the zones marked by high velocity and relative low total attenuation for direct waves.
    Description: Published
    Description: 544–558
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 48
    Publication Date: 2023-11-29
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. 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. All rights reserved.
    Description: On 24 January 2020 an Mw 6.8 earthquake occurred at 20:55 local time (17:55 UTC) in eastern Turkey, close to the town of Sivrice in the Elazığ province, causing widespread considerable seismic damage in buildings. In this study, we analyse the main features of the rupture process and the seismic ground shaking during the Elazığ earthquake. We first use Interferometric Synthetic Aperture Radar (InSAR) interferograms (Sentinel-1 satellites) to constrain the fault geometry and the coseismic slip distribution of the causative fault segment. Then, we utilize this information to analyse the ground motion characteristics of the main shock in terms of peak ground acceleration (PGA), peak ground velocity (PGV) and spectral accelerations. The absence of seismic registrations in near-field for this earthquake imposes major constraints on the computation of seismic ground motion estimations in the study area. To do this, we have used a stochastic finite-fault simulation method to generate high-frequency ground motions synthetics for the Mw 6.8 Elazığ 2020 earthquake. Finally, we evaluate the potential state of stress of the unruptured portions of the causative fault segment as well as of adjacent segments, using the Coulomb stress failure function variations. Modelling of geodetic data shows that the 2020 Elazığ earthquake ruptured two major slip patches (for a total length of about 40 km) located along the Pütürge segment of the well-known left-lateral strike-slip East Anatolian Fault Zone (EAFZ), with up to 2.3 m of slip and an estimated geodetic moment of 1.70 × 1019 Nm (equivalent to a Mw 6.8). The position of the hypocentre supports the evidence of marked WSW rupture directivity during the main shock. In terms of ground motion characteristics, we observe that the high-frequency stochastic ground motion simulations have a good capability to reproduce the source complexity and capture the ground motion attenuation decay as a function of distance, up to the 200 km. We also demonstrate that the design spectra corresponding to 475 yr return period, provided by the new Turkish building code is not exceeded by the simulated seismograms in the epicentral area where there are no strong motion stations and no recordings available. Finally, based on the Coulomb stress distribution computation, we find that the Elazığ main shock increased the stress level of the westernmost part of the Pütürge fault and of the adjacent Palu segment and as a result of an off-fault lobe.
    Description: Published
    Description: 1054–1068
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 49
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    Oxford University Press
    In:  EPIC3Conservation Physiology, Oxford University Press, 9(1), ISSN: 2051-1434
    Publication Date: 2024-01-01
    Description: We studied the ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded area in the North Sea. H. sanguineus is native to Japan and China but has successfully invaded the Atlantic coast of North America and Europe. In the invaded areas, H. sanguineus is becoming a keystone species as driver of community structure and the adults compete with the shore crab Carcinus maenas. Strong osmoregulatory abilities may confer the potential to use and invade coastal areas already earlier in the life cycle. We reared larvae and first juveniles at 24°C in seawater from hatching to intermoult of each developmental stage (zoea I-V, megalopa, crab I). We exposed each stage to a range of salinities (0–39 ppt) for 24 h, and then we quantified haemolymph osmolality, using nano-osmometry. In addition, we quantified osmolality in field-collected adults after acclimation to the test salinities for 6 days. Larvae of H. sanguineus were able to hyper-osmoregulate at low salinities (15 and 20 ppt) over the complete larval development, although the capacity was reduced at the zoeal stage V; at higher salinities (25–39 ppt), all larval stages were osmoconformers. The capacity to slightly hypo-regulate at high salinity appeared in the first juvenile. Adults were able to hyper-osmoregulate at low salinities and hypo-regulate at concentrated seawater (39 ppt). H. sanguineus showed a strong capacity to osmoregulate as compared to its native competitor C. maenas, which only hyper-regulates at the first and last larval stages and does not hypo-regulate at the juvenile-adult stages. The capacity of H. sanguineus to osmoregulate over most of the life cycle should underpin the potential to invade empty niches in the coastal zone (characterized by low salinity and high temperatures). Osmoregulation abilities over the whole life cycle also constitute a strong competitive advantage over C. maenas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 50
    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
    Repository Name: Woods Hole Open Access Server
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  • 51
    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
    Repository Name: Woods Hole Open Access Server
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  • 52
    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
    Type: Preprint
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  • 53
    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.
    Repository Name: Woods Hole Open Access Server
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  • 54
    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.
    Repository Name: Woods Hole Open Access Server
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  • 55
    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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  • 56
    Publication Date: 2021-07-22
    Description: Insects detect odors using an array of odorant receptors (ORs), which may expand through gene duplication. How and which new functions may evolve among related ORs within a species remain poorly investigated. We addressed this question by functionally characterizing ORs from the Eurasian spruce bark beetle Ips typographus, in which physiological and behavioral responses to pheromones, volatiles from host and nonhost trees, and fungal symbionts are well described. In contrast, knowledge of OR function is restricted to two receptors detecting the pheromone compounds (S)-(–)-ipsenol (ItypOR46) and (R)-(–)-ipsdienol (ItypOR49). These receptors belong to an Ips-specific OR-lineage comprising seven ItypORs. To gain insight into the functional evolution of related ORs, we characterized the five remaining ORs in this clade using Xenopus oocytes. Two receptors responded primarily to the host tree monoterpenes (+)-3-carene (ItypOR25) and p-cymene (ItypOR27). Two receptors responded to oxygenated monoterpenoids produced in larger relative amounts by the beetle-associated fungi, with ItypOR23 specific for (+)-trans-(1R, 4S)-4-thujanol, and ItypOR29 responding to (+)-isopinocamphone and similar ketones. ItypOR28 responded to the pheromone E-myrcenol from the competitor Ips duplicatus. Overall, the OR responses match well with those of previously characterized olfactory sensory neuron classes except that neurons detecting E-myrcenol have not been identified. The characterized ORs are under strong purifying selection and demonstrate a shared functional property in that they all primarily respond to monoterpenoids. The variation in functional groups among OR ligands and their diverse ecological origins suggest that neofunctionalization has occurred early in the evolution of this OR-lineage following gene duplication.
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  • 57
    Publication Date: 2021-08-19
    Description: Vulnerable marine ecosystems (VMEs) are typically fragile and slow to recover, making them likely to be substantially altered by disturbance. In the High Seas, regional fishery management organizations (RFMOs) are required to implement measures to prevent significant adverse impacts on VMEs. The objectives of the present study were to: update distribution models of VME indicator taxa in the South Pacific RFMO Convention Area; evaluate these against newly-collated independent field data to test the reliability of the presence-only habitat suitability models; and assess how well the updated models were able to predict into unsampled space. Ensemble habitat suitability models of 10 VME indicator taxa performed well using the newly collated data (AUC 〉 0.95, TSS 〉 0.76, and RMSE  0.93, TSS 〉 0.71, and RMSE
    Print ISSN: 1054-3139
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  • 58
    Publication Date: 2021-08-25
    Description: During the last few decades, many wild Atlantic salmon populations have declined dramatically. One possible contributing factor for the decline is reduced prey availability at sea. Here, we examine post-smolt diet and investigate if post-smolts show signs of selective feeding based on 2546 post-smolts sampled from west of Ireland to the northern Norwegian Sea over a 25-year period. We also test for changes over time in stomach fullness, diet, condition factor and body length. There was a clear reduction in condition factor for post-smolts sampled in the Norwegian Sea in the period 2003–2012. The post-smolt stomach fullness was also reduced in the same period. The reduction in condition factor is partly explained by reduced stomach fullness, including a reduction of highly energetic fish larvae and Amphipoda in the diet. Feeding on other prey, such as meso-zooplankton and insects, cannot substitute the high-quality fish larvae and Amphipoda in the post-smolt diet. This is the first study to document how salmon post-smolts feeding in the Norwegian Sea are affected by reduced feeding conditions. Possible causes for the observed changes in post-smolt feeding are ocean warming, decreased primary productivity, and reduced recruitment of important fish larvae.
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  • 59
    Publication Date: 2021-08-03
    Description: We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci—such as genes, proteins, genomic segments, and positions—as parameters. Using the Least Absolute Shrinkage and Selection Operator, ESL selects only the most important genomic loci to explain a given phylogenetic hypothesis or presence/absence of a trait. ESL models do not directly involve conventional parameters such as rates of substitutions between nucleotides, rate variation among positions, and phylogeny branch lengths. Instead, ESL directly employs the concordance of variation across sequences in an alignment with the evolutionary hypothesis of interest. ESL provides a natural way to combine different molecular and nonmolecular data types and incorporate biological and functional annotations of genomic loci in model building. We propose positional, gene, function, and hypothesis sparsity scores, illustrate their use through an example, and suggest several applications of ESL. The ESL framework has the potential to drive the development of a new class of computational methods that will complement traditional approaches in evolutionary genomics, particularly for identifying influential loci and sequences given a phylogeny and building models to test hypotheses. ESL’s fast computational times and small memory footprint will also help democratize big data analytics and improve scientific rigor in phylogenomics.
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  • 60
    Publication Date: 2021-08-03
    Description: Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.
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  • 61
    Publication Date: 2021-07-30
    Description: Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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  • 62
    Publication Date: 2021-08-15
    Description: Genetic variation and phenotypic plasticity are both important to adaptive evolution. However, how they act together on particular traits remains poorly understood. Here, we integrated phenotypic, genomic, and transcriptomic data from two allopatric but closely related congeneric oyster species, Crassostrea angulata from southern/warm environments and Crassostrea gigas from northern/cold environments, to investigate the roles of genetic divergence and plasticity in thermal adaptation. Reciprocal transplantation experiments showed that both species had higher fitness in their native habitats than in nonnative environments, indicating strong adaptive divergence. The southern species evolved higher transcriptional plasticity, and the plasticity was adaptive, suggesting that increased plasticity is important for thermal adaptation to warm climates. Genome-wide comparisons between the two species revealed that genes under selection tended to respond to environmental changes and showed higher sequence divergence in noncoding regions. All genes under selection and related to energy metabolism exhibited habitat-specific expression with genes involved in ATP production and lipid catabolism highly expressed in warm/southern habitats, and genes involved in ATP consumption and lipid synthesis were highly expressed in cold/northern habitats. The gene for acyl-CoA desaturase, a key enzyme for lipid synthesis, showed strong selective sweep in the upstream noncoding region and lower transcription in the southern species. These results were further supported by the lower free fatty acid (FFA) but higher ATP content in southern species and habitat, pointing to significance of ATP/FFA trade-off. Our findings provide evidence that noncoding variation and transcriptional plasticity play important roles in shaping energy metabolism for thermal adaptation in oysters.
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  • 63
    Publication Date: 2021-08-28
    Description: The fishery for Northern Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Eastern Canada, presents the most spectacular case of an exploited stock crashed in a few decades by an industrial bottom trawl fishery under a seemingly sophisticated management regime after half a millennium of sustainable fishing. The fishery, which had generated annual catches of 100000 to 200000 tonnes from the beginning of the 16th century to the 1950s,  peaked in 1968 at 810000 tonnes, followed by a devastating collapse and closure 24 years later. Since then, stock recovery may have been hindered by premature openings, with vessels targeting the remains of the cod population. Previous research paid little attention towards using multicentury time series to inform sustainable catches and recovery plans. Here, we show that a simple stock assessment model can be used to model the cod population trajectory for the entire period from 1508 to 2019 for which catch estimates are available. The model suggests that if fishing effort and mortality had been stabilized in the 1980s,  precautionary annual yields of about 200000 tonnes could have been sustained. Our analysis demonstrates the value of incorporating prior knowledge to counteract shifting baseline effects on reference points and contemporary perceptions of historical stock status.
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  • 64
    Publication Date: 2021-07-26
    Description: We present a simple model in which the bullets that produce the ‘Orion fingers’ (ejected by the BN/KL object) are interpreted as protoplanets or low-mass protostars in orbit around a high-mass star that has a supernova explosion. As the remnant of the SN explosion has only a small fraction of the mass of the pre-supernova star, the orbiting objects then move away in free trajectories, preserving their orbital velocity at the time of release. We show that a system of objects arranged in approximately coplanar orbits results in trajectories with morphological and kinematical characteristics resembling the Orion fingers. We show that, under the assumption of constant velocity motions, the positions of the observed heads of the fingers can be used to reconstruct the properties of the orbital structure from which they originated, resulting in a compact disc with an outer radius of ∼2.4 au.
    Print ISSN: 1745-3925
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  • 65
    Publication Date: 2021-08-13
    Description: Ecological interactions among marine zooplankton are poorly described because conventional sampling gears, such as plankton nets and traps, obscure the physical and biological environment that individuals experience. With in situ imagery, however, it is possible to resolve these interactions and potentially convert snapshot distributions into process-oriented oceanographic and ecological understanding. We describe a variety of imagery-detected ecological interactions with high spatial resolution in the northern Gulf of Mexico shelf waters (20–35 m bottom depth), providing new evidence of parasitism, predation, and life stage spatial structuring for different zooplankton groups. Chaetognaths were infected with an anteriorly attached, parasitic polychaete (1.1% of 33 824 individuals), and these infected chaetognaths were more common further offshore, south of a nearshore patch where unparasitized individuals reached concentrations of ∼90 m–3. Predation by Liriope spp. hydromedusae tended to occur in the shallowest 10–15 m, and doliolids formed distinct patches of different life stages, indicating that the environment is replete with sharp transitions among various ecological processes. Similar patterns in other marine ecosystems likely exist, and we encourage hybrid (machine/human expertise) approaches that broaden the scope for analysis of plankton images, which are rich sources of new ecological information and hypotheses yet to be examined quantitatively.
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  • 66
    Publication Date: 2021-07-01
    Description: Aspect sentiment classification is an important research topic in natural language processing and computational linguistics, assisting in automatically review analysis and emotional tendency judgement. Different from extant methods that focus on text sequence representations, this paper presents a network framework to learn representation from concurrence-words relation graph (LRCWG), so as to improve the Macro-F1 and accuracy. The LRCWG first employs the multi-head attention mechanism to capture the sentiment representation from the sentences which can learn the importance of text sequence representation. And then, it leverages the priori sentiment dictionary information to construct the concurrence relations of sentiment words with Graph Convolution Network (GCN). This assists in that the learnt context representation can keep both the semantics integrity and the features of sentiment concurrence-words relations. The designed algorithm is experimentally evaluated with all the five benchmark datasets and demonstrated that the proposed aspect sentiment classification can significantly improve the prediction performance of learning task.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
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  • 67
    Publication Date: 2021-07-01
    Description: Non-negative matrix factorization (NMF) is a powerful tool for data science researchers, and it has been successfully applied to data mining and machine learning community, due to its advantages such as simple form, good interpretability and less storage space. In this paper, we give a detailed survey on existing NMF methods, including a comprehensive analysis of their design principles, characteristics and drawbacks. In addition, we also discuss various variants of NMF methods and analyse properties and applications of these variants. Finally, we evaluate the performance of nine NMF methods through numerical experiments, and the results show that NMF methods perform well in clustering tasks.
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  • 68
    Publication Date: 2021-07-13
    Description: Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.
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  • 69
    Publication Date: 2021-07-01
    Description: The task of question generation (QG) aims to create valid questions and correlated answers from the given text. Despite the neural QG approaches have achieved promising results, they are typically developed for languages with rich annotated training data. Because of the high annotation cost, it is difficult to deploy to other low-resource languages. Besides, different samples have their own characteristics on the aspects of text contextual structure, question type and correlations. Without capturing these diversified characteristics, the traditional one-size-fits-all model is hard to generate the best results. To address this problem, we study the task of cross-lingual QG from an adaptive learning perspective. Concretely, we first build a basic QG model on a multilingual space using the labelled data. In this way, we can transfer the supervision from the high-resource language to the language lacking labelled data. We then design a task-specific meta-learner to optimize the basic QG model. Each sample and its similar instances are viewed as a pseudo-QG task. The asking patterns and logical forms contained in the similar samples can be used as a guide to fine-tune the model fitly and produce the optimal results accordingly. Considering that each sample contains the text, question and answer, with unknown semantic correlations among them, we propose a context-dependent retriever to measure the similarity of such structured inputs. Experimental results on three languages of three typical data sets show the effectiveness of our approach.
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  • 70
    Publication Date: 2021-10-25
    Description: Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origins of ecotypes are often inferred based on a phylogeny that clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which was surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
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  • 71
    Publication Date: 2021-06-02
    Description: We report the discovery of large amounts of previously undetected cold neutral atomic hydrogen (H i) around the core triplet galaxies in the nearby NGC 7232 galaxy group with MeerKAT. With a physical resolution of ∼1 kpc, we detect a complex web of low-surface-brightness H i emission down to a 4σ column density level of ∼1 × 1019 cm−2 (over 44  km s−1). The newly discovered H i streams extend over ∼20 arcmin corresponding to 140 kpc in projection. This is approximately three times the H i extent of the galaxy triplet (52 kpc). The H i debris has an H i mass of ∼6.6 × 109 M⊙, more than 50 per cent of the total H i mass of the triplet. Within the galaxy triplet, NGC 7233 and NGC 7232 have lost a significant amount of H i while NGC 7232B appears to have an excess of H i. The H i deficiency in NGC 7232 and NGC 7233 indicates that galaxy–galaxy interaction in the group concentrates on this galaxy pair while the other disc galaxies have visited them over time. In comparison to the AMIGA sample of isolated galaxies, we find that with regards to its total H i mass the NGC 7232/3 galaxy triplet is not H i-deficient. Despite the many interactions associated to the triplet galaxies, no H i seems to have been lost from the group (yet).
    Print ISSN: 0035-8711
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  • 72
    Publication Date: 2021-07-01
    Description: In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically interacting proteins, hyponastic leaves 1 (HYL1) and Dicer-like 1 (DCL1). However, the evolutionary history and structural basis of the HYL1–DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 in vitro and in Arabidopsis thaliana to better understand the origin and evolution of the HYL1–DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (∼500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two dsRNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1–DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in A. thaliana was sufficient to rescue many key aspects of plant development disrupted by HYL1− knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1–DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant “developmental toolkit.”
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  • 73
    Publication Date: 2021-07-02
    Description: Historically it has been difficult to study the evolution of bacterial small RNAs (sRNAs) across distantly related species. For example, identifying homologs of sRNAs is often difficult in genomes that have undergone multiple structural rearrangements. Also, some types of regulatory sRNAs evolve at rapid rates. The high degree of genomic synteny among divergent host-restricted bacterial lineages, including intracellular symbionts, is conducive to sRNA maintenance and homolog identification. In turn, symbiont genomes can provide us with novel insights into sRNA evolution. Here, we examine the sRNA expression profile of the obligate symbiont of psyllids, Carsonella ruddii, which has one of the smallest cellular genomes described. Using RNA-seq, we identified 36 and 32 antisense sRNAs (asRNAs) expressed by Carsonella from the psyllids Bactericera cockerelli (Carsonella-BC) and Diaphorina citri (Carsonella-DC), respectively. The majority of these asRNAs were associated with genes that are involved in essential amino acid biosynthetic pathways. Eleven of the asRNAs were conserved in both Carsonella lineages and the majority were maintained by selection. Notably, five of the corresponding coding sequences are also the targets of conserved asRNAs in a distantly related insect symbiont, Buchnera. We detected differential expression of two asRNAs for genes involved in arginine and leucine biosynthesis occurring between two distinct Carsonella-BC life stages. Using asRNAs identified in Carsonella, Buchnera, and Profftella which are all endosymbionts, and Escherichia coli, we determined that regions upstream of these asRNAs encode unique conserved patterns of AT/GC richness, GC skew, and sequence motifs which may be involved in asRNA regulation.
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  • 74
    Publication Date: 2021-06-27
    Description: Prior and extensive plastic rewiring of a transcriptional network, followed by a functional switch of the conserved transcriptional regulator, can shape the evolution of a new network with diverged functions. The presence of three distinct iron regulatory systems in fungi that use orthologous transcriptional regulators suggests that these systems evolved in that manner. Orthologs of the transcriptional activator Sef1 are believed to be central to how iron regulatory systems developed in fungi, involving gene gain, plastic network rewiring, and switches in regulatory function. We show that, in the protoploid yeast Lachancea kluyveri, plastic rewiring of the L. kluyveri Sef1 (Lk-Sef1) network, together with a functional switch, enabled Lk-Sef1 to regulate TCA cycle genes, unlike Candida albicans Sef1 that mainly regulates iron-uptake genes. Moreover, we observed pervasive nonfunctional binding of Sef1 to its target genes. Enhancing Lk-Sef1 activity resuscitated the corresponding transcriptional network, providing immediate adaptive benefits in changing environments. Our study not only sheds light on the evolution of Sef1-centered transcriptional networks but also shows the adaptive potential of nonfunctional transcription factor binding for evolving phenotypic novelty and diversity.
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  • 75
    Publication Date: 2021-06-15
    Description: Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. Taricha newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance by sequencing the entire Nav gene family in newts and related salamanders. We show that moderate TTX resistance evolved early in the salamander lineage in three of the six Nav paralogs, preceding the proposed appearance of tetrodotoxic newts by ∼100 My. TTX-bearing newts possess additional unique substitutions across the entire Nav gene family that provide physiological TTX resistance. These substitutions coincide with signatures of positive selection and relaxed purifying selection, as well as gene conversion events, that together likely facilitated their evolution. We also identify a novel exon duplication within Nav1.4 encoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons of Nav1.4. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to a common selection pressure.
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  • 76
    Publication Date: 2021-06-27
    Description: Emergence of resistant bacteria during antimicrobial treatment is one of the most critical and universal health threats. It is known that several stress-induced mutagenesis and heteroresistance mechanisms can enhance microbial adaptation to antibiotics. Here, we demonstrate that the pathogen Bartonella can undergo stress-induced mutagenesis despite the fact it lacks error-prone polymerases, the rpoS gene and functional UV-induced mutagenesis. We demonstrate that Bartonella acquire de novo single mutations during rifampicin exposure at suprainhibitory concentrations at a much higher rate than expected from spontaneous fluctuations. This is while exhibiting a minimal heteroresistance capacity. The emerged resistant mutants acquired a single rpoB mutation, whereas no other mutations were found in their whole genome. Interestingly, the emergence of resistance in Bartonella occurred only during gradual exposure to the antibiotic, indicating that Bartonella sense and react to the changing environment. Using a mathematical model, we demonstrated that, to reproduce the experimental results, mutation rates should be transiently increased over 1,000-folds, and a larger population size or greater heteroresistance capacity is required. RNA expression analysis suggests that the increased mutation rate is due to downregulation of key DNA repair genes (mutS, mutY, and recA), associated with DNA breaks caused by massive prophage inductions. These results provide new evidence of the hazard of antibiotic overuse in medicine and agriculture.
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  • 77
    Publication Date: 2021-06-16
    Description: DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the “domestication syndrome”. We therefore explored the possibility that DLX5/6 played a role in human evolution and “self-domestication” comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams–Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (〉105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.
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  • 78
    Publication Date: 2021-06-27
    Description: Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.
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  • 79
    Publication Date: 2021-08-14
    Description: While the importance of early life survival and growth variations for population dynamics is well documented, there is still a relatively limited understanding of how survival and growth is affected by the species’ spatial distribution. Using Barents Sea spatial bottom survey data (1994–2018), we study the spatiotemporal variability of the juvenile Atlantic cod (Gadus morhua) growth and survival. We used indices of the spatial distribution of juvenile cod at age-1 to study the role of distribution for the change in abundance and mean body size through their second winter of life (from age-1 to age-2). Over the 24 years analysed, we found that the location where the age-1 cod are in the Barents Sea matters for their growth and survival. We found that year-classes growing up in the western Barents Sea have higher mortality but faster growth than year-classes distributed farther east. Our results indicate that the biotic and abiotic conditions encountered at the settlement location may influence the spatial survival and growth of age-1 cod and subsequently the population dynamics. Our results underscore the importance of distribution for survival and growth early in life and by providing this essential information has implications for stock assessment and spatial fisheries management.
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  • 80
    Publication Date: 2021-07-01
    Description: Motivation Personalized medicine aims at providing patient-tailored therapeutics based on multi-type data toward improved treatment outcomes. Chronotherapy that consists in adapting drug administration to the patient’s circadian rhythms may be improved by such approach. Recent clinical studies demonstrated large variability in patients’ circadian coordination and optimal drug timing. Consequently, new eHealth platforms allow the monitoring of circadian biomarkers in individual patients through wearable technologies (rest-activity, body temperature), blood or salivary samples (melatonin, cortisol) and daily questionnaires (food intake, symptoms). A current clinical challenge involves designing a methodology predicting from circadian biomarkers the patient peripheral circadian clocks and associated optimal drug timing. The mammalian circadian timing system being largely conserved between mouse and humans yet with phase opposition, the study was developed using available mouse datasets. Results We investigated at the molecular scale the influence of systemic regulators (e.g. temperature, hormones) on peripheral clocks, through a model learning approach involving systems biology models based on ordinary differential equations. Using as prior knowledge our existing circadian clock model, we derived an approximation for the action of systemic regulators on the expression of three core-clock genes: Bmal1, Per2 and Rev-Erbα. These time profiles were then fitted with a population of models, based on linear regression. Best models involved a modulation of either Bmal1 or Per2 transcription most likely by temperature or nutrient exposure cycles. This agreed with biological knowledge on temperature-dependent control of Per2 transcription. The strengths of systemic regulations were found to be significantly different according to mouse sex and genetic background. Availability and implementation https://gitlab.inria.fr/julmarti/model-learning-mb21eccb. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
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  • 81
    Publication Date: 2021-06-15
    Description: Since graph learning could preserve the structure information of the samples to improve the learning ability, it has been widely applied in both shallow learning and deep learning. However, the current graph learning methods still suffer from the issues such as outlier influence and model robustness. In this paper, we propose a new dynamic graph neural network (DGCN) method to conduct semi-supervised classification on multi-view data by jointly conducting the graph learning and the classification task in a unified framework. Specifically, our method investigates three strategies to improve the quality of the graph before feeding it into the GCN model: (i) employing robust statistics to consider the sample importance for reducing the outlier influence, i.e. assigning every sample with soft weights so that the important samples are with large weights and outliers are with small or even zero weights; (ii) learning the common representation across all views to improve the quality of the graph for every view; and (iii) learning the complementary information from all initial graphs on multi-view data to further improve the learning of the graph for every view. As a result, each of the strategies could improve the robustness of the DGCN model. Moreover, they are complementary for reducing outlier influence from different aspects, i.e. the sample importance reduces the weights of the outliers, both the common representation and the complementary information improve the quality of the graph for every view. Experimental result on real data sets demonstrates the effectiveness of our method, compared to the comparison methods, in terms of multi-class classification performance.
    Print ISSN: 0010-4620
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  • 82
    Publication Date: 2021-10-28
    Description: This article investigates the local economic cost of hosting refugees. Using administrative data in France, we show that the opening of small housing centers for refugees decreases the economic activity in hosting municipalities. We demonstrate that this downturn is related to a decline in the population by around 2% due to fewer people moving to hosting municipalities. We show that this avoidance behavior of natives results from prejudices, and is unlikely to be driven by a labor market supply shock from the arrival of refugees. We also estimate the aggregate cost of hosting refugees.
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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  • 83
    Publication Date: 2021-03-11
    Description: Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 84
    Publication Date: 2021-05-14
    Description: Spectral clustering is widely applied in real applications, as it utilizes a graph matrix to consider the similarity relationship of subjects. The quality of graph structure is usually important to the robustness of the clustering task. However, existing spectral clustering methods consider either the local structure or the global structure, which can not provide comprehensive information for clustering tasks. Moreover, previous clustering methods only consider the simple similarity relationship, which may not output the optimal clustering performance. To solve these problems, we propose a novel clustering method considering both the local structure and the global structure for conducting nonlinear clustering. Specifically, our proposed method simultaneously considers (i) preserving the local structure and the global structure of subjects to provide comprehensive information for clustering tasks, (ii) exploring the nonlinear similarity relationship to capture the complex and inherent correlation of subjects and (iii) embedding dimensionality reduction techniques and a low-rank constraint in the framework of adaptive graph learning to reduce clustering biases. These constraints are considered in a unified optimization framework to result in one-step clustering. Experimental results on real data sets demonstrate that our method achieved competitive clustering performance in comparison with state-of-the-art clustering methods.
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  • 85
    Publication Date: 2021-04-30
    Description: Laplacian support vector machine (LapSVM) is an extremely popular classification method and relies on a small number of labels and a Laplacian regularization to complete the training of the support vector machine (SVM). However, the training of SVM model and Laplacian matrix construction are usually two independent process. Therefore, In this paper, we propose a new adaptive LapSVM method to realize semi-supervised learning with a primal solution. Specifically, the hinge loss of unlabelled data is considered to maximize the distance between unlabelled samples from different classes and the process of dealing with labelled data are similar to other LapSVM methods. Besides, the proposed method embeds the Laplacian matrix acquisition into the SVM training process to improve the effectiveness of Laplacian matrix and the accuracy of new SVM model. Moreover, a novel optimization algorithm considering primal solver is proposed to our adaptive LapSVM model. Experimental results showed that our method outperformed all comparison methods in terms of different evaluation metrics on both real datasets and synthetic datasets.
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  • 86
    Publication Date: 2021-09-03
    Description: Catch data from bottom trawl surveys are used in various ways (e.g. stock assessments, fisheries management, and ecosystem studies) to represent trends in fish populations across space, time, season, or size. Relative abundance indices assume constant capture efficiency, and area-swept abundance requires an estimate of capture efficiency. Therefore, it is important to develop a predictive understanding of the interaction between fish and survey gear. We conducted experiments to test two primary factors that influence the efficiency of survey trawls at capturing demersal groundfish: (1) footrope escapement—estimated by attaching a collection bag beneath the primary trawl, and (2) herding of the sweeps/doors—estimated by varying sweep length. Random forest models were used to disentangle the herding effect from patterns caused by environmental variables. Contrary to common assumptions, footrope efficiency was incomplete (〈 100%) and herding was non-trivial (〉 0%), which introduces a bias in population metrics that rely on such assumptions. This bias varied by species and depended upon the relative strength of the counteracting effects of footrope escapement and herding. Our findings suggest that trawl efficiency should be estimated (not assumed) to derive area-swept abundance, and relative abundance indices should account for size-based efficiency and changing size compositions.
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  • 87
    Publication Date: 2021-09-09
    Description: Incorporating ecological covariates into fishery stock assessments may improve estimates, but most covariates are estimated with error. Model selection criteria are often used to identify support for covariates, have some limitations and rely on assumptions that are often violated. For a more rigorous evaluation of ecological covariates, we used four popular selection criteria to identify covariates influencing natural mortality or recruitment in a Bayesian stock assessment of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska. Within this framework, covariates were incorporated either as fixed effects or as latent variables (i.e. covariates have associated error). We found most support for pink salmon increasing natural mortality, which was selected by three of four criteria. There was ambiguous support for other fixed effects on natural mortality (walleye pollock and the North Pacific Gyre Oscillation) and recruitment (hatchery-released juvenile pink salmon and a 1989 regime shift). Generally, similar criteria values among covariates suggest no clear evidence for a consistent effect of any covariate. Models with covariates as latent variables were sensitive to prior specification and may provide potentially very different results. We recommend using multiple criteria and exploring different statistical assumptions about covariates for their use in stock assessment.
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  • 88
    Publication Date: 2021-07-23
    Description: The enormous mammal’s lifespan variation is the result of each species’ adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.
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  • 89
    Publication Date: 2021-07-28
    Description: Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus, the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the “tigrina” morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species.
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  • 90
    Publication Date: 2021-07-26
    Description: How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.
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  • 91
    Publication Date: 2021-07-29
    Description: Microbes living in plant tissues—endophytes—are mainly studied in crop plants where they typically colonize the root apoplast. Trees—a large carbon source with a high capacity for photosynthesis—provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant–endophyte interaction in buds of adult Scots pine, where Methylorubrum species live inside the meristematic cells. The endosymbiont Methylorubrum extorquens DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here, we studied gene expression and metabolites of the pine host induced by M. extorquens DSM13060 infection. Malic acid was produced by pine to potentially boost M. extorquens colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of CUL1 and HYL1, and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of GLP1-7 and ALE2, and suppressed flowering, root hair and lateral root formation by downregulation of AGL8, plantacyanin, GASA7, COW1 and RALFL34. Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes CUL1, ETR2, ERF3, HYL, GLP1-7 and CYP71 were highly expressed in the shoot apical meristem, rarely in needles and not in stem or root tissues. Low expression of MERI5, CLH2, EULS3 and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, downregulation of senescence and cell death-associated genes and induction of ononitol biosynthesis.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 92
    Publication Date: 2021-07-28
    Description: Although Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of the Bactria–Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events that impacted the demography and population structure of this region, we generated 27 genome-wide single-nucleotide polymorphism capture data sets of Late Iron Age individuals around the Historical Kushan time period (∼2100–1500 BP) from three sites in South Uzbekistan. Overall, Bronze Age ancestry persists into the Iron Age in Uzbekistan, with no major replacements of populations with Steppe-related ancestry. However, these individuals suggest diverse ancestries related to Iranian farmers, Anatolian farmers, and Steppe herders, with a small amount of West European Hunter Gatherer, East Asian, and South Asian Hunter Gatherer ancestry as well. Genetic affinity toward the Late Bronze Age Steppe herders and a higher Steppe-related ancestry than that found in BMAC populations suggest an increased mobility and interaction of individuals from the Northern Steppe in a Southward direction. In addition, a decrease of Iranian and an increase of Anatolian farmer-like ancestry in Uzbekistan Iron Age individuals were observed compared with the BMAC populations from Uzbekistan. Thus, despite continuity from the Bronze Age, increased admixture played a major role in the shift from the Bronze to the Iron Age in southern Uzbekistan. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting more widespread admixture among local populations.
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  • 93
    Publication Date: 2021-07-24
    Description: Although rapid evolution of pericentromeric satellite DNA repeats is theorized to promote hybrid incompatibility (HI) (Yunis and Yasmineh 1971; Henikoff et al. 2001; Ferree and Barbash 2009; Sawamura 2012; Jagannathan and Yamashita 2017), how divergent repeats affect hybrid cells remains poorly understood. Recently, we demonstrated that sequence-specific DNA-binding proteins cluster satellite DNA from multiple chromosomes into “chromocenters,” thereby bundling chromosomes to maintain the entire genome in a single nucleus (Jagannathan et al. 2018, 2019). Here, we show that ineffective clustering of divergent satellite DNA in the cells of Drosophila hybrids results in chromocenter disruption, associated micronuclei formation, and tissue atrophy. We further demonstrate that previously identified HI factors trigger chromocenter disruption and micronuclei in hybrids, linking their function to a conserved cellular process. Together, we propose a unifying framework that explains how the widely observed satellite DNA divergence between closely related species can cause reproductive isolation.
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  • 94
    Publication Date: 2021-08-18
    Description: Exploitation is one of the major drivers of change in marine ecosystems. Following discovery in 1775, South Georgia saw sequential overexploitation of living resources, including seals, whales, and fish. Although exploitation is now tightly regulated, the ecosystem is still recovering. Marbled rockcod, Notothenia rossii (Richardson 1844), was the first fish species to be commercially exploited and high catches between 1967 and 1972 resulted in dramatic stock decline. Here, we use 30 years of trawl survey data to provide the first evidence of a sustained increase in the N. rossii population starting two decades after the prohibition of targeted fishing in 1985. The way species respond to change is mediated in part by trophic relationships with other organisms. We present the first multi-year, spatially-resolved comparison of adult N. rossii diet at South Georgia, highlighting a variable diet with less reliance on Antarctic krill than previously thought. Life history factors and possible heavy predation on early life stages might have delayed their recovery while diet plasticity potentially supported recent population growth. Due to the dynamic ecosystem at South Georgia and questions over catch reports from the period of heaviest exploitation, it is unlikely the current ecosystem could support a recovery to estimated pre-exploitation levels.
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  • 95
    Publication Date: 2021-07-21
    Description: Coexistence and cooperation between dogs and humans over thousands of years have supported convergent evolutionary processes in the two species. Previous studies found that Eurasian dogs evolved into a distinct geographic cluster. In this study, we used the genomes of 242 European dogs, 38 Southeast Asian indigenous (SEAI) dogs, and 41 gray wolves to identify adaptation of European dogs . We report 86 unique positively selected genes in European dogs, among which is LCT (lactase). LCT encodes lactase, which is fundamental for the digestion of lactose. We found that an A-to-G mutation (chr19:38,609,592) is almost fixed in Middle Eastern and European dogs. The results of two-dimensional site frequency spectrum (2D SFS) support that the mutation is under soft sweep . We inferred that the onset of positive selection of the mutation is shorter than 6,535 years and behind the well-developed dairy economy in central Europe. It increases the expression of LCT by reducing its binding with ZEB1, which would enhance dog’s ability to digest milk-based diets. Our study uncovers the genetic basis of convergent evolution between humans and dogs with respect to diet, emphasizing the import of the dog as a biomedical model for studying mechanisms of the digestive system.
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  • 96
    Publication Date: 2021-08-13
    Description: Since 1996, the European Union has required that fishery products of 35 fish species or groups of species, including crustaceans and cephalopods, be graded before being landed on the basis of commercial size-categories. A multi-stage sampling scheme to estimate catch-at-length and catch-at-age compositions of total annual landings has been conducted in Portuguese waters since 2009. All species and their size-categories are sampled concurrently from random trips within representatively selected site-days annually. In an effort to improve cost-efficiency of the biological catch sampling of commercial landings in Portugal, a size- category sampling scheme was tested during 2017, taking advantage of the stratification of horse mackerel landings, induced by the mandatory grading of landings by size-category. The total number of site-days (primary sampling units), fish boxes sampled, and specimens of horse mackerel sampled for length and age across strata during the pilot study were 30%, 57%, and 12% of the sampling carried out under the standard concurrent scheme, respectively. The assignment of horse mackerel length to the six commercial size-categories was highly consistent across site-days. Our study shows that the concurrent sampling, where trips are subsampled within site-days, could miss some size-categories by chance, resulting in poor estimates of catch-at-length especially for small fish present at the market during a site-day. The size-category sampling scheme ensured subsamples of fish from all size-categories within a site-day, and achieved data on catch-at-age that are fit-for purpose at 24% of the total cost for the standard concurrent sampling. The effect of sampling designs and sample sizes on horse mackerel stock assessment outputs showed that the onshore biological sampling to estimate catch-at-age compositions for stock assessment is optimized with the size-category sampling scheme. Pilot field experiments should be carried out for selected species that evidence consistent size grading among commercial categories.
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  • 97
    Publication Date: 2021-08-23
    Description: In 2020, the developing COVID-19 pandemic disrupted fisheries surveys to an unprecedented extent. Many surveys were cancelled, including those for walleye pollock (Gadus chalcogrammus) in the eastern Bering Sea (EBS), the largest fishery in the United States. To partially mitigate the loss of survey information, we deployed three uncrewed surface vehicles (USVs) equipped with echosounders to extend the ship-based acoustic-trawl time series of pollock abundance. Trawling was not possible from USVs, so an empirical relationship between pollock backscatter and biomass established from previous surveys was developed to convert USV backscatter observations into pollock abundance. The EBS is well suited for this approach since pollock dominate midwater fishes in the survey area. Acoustic data from the USVs were combined with historical surveys to provide a consistent fishery-independent index in 2020. This application demonstrates the unique capabilities of USVs and how they could be rapidly deployed to collect information on pollock abundance and distribution when a ship-based survey was not feasible. We note the limitations of this approach (e.g. higher uncertainty relative to previous ship-based surveys), but found the USV survey to be useful in informing the stock assessment in a situation where ship-based surveys were not possible.
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  • 98
    Publication Date: 2021-07-29
    Description: Sexually dimorphic development is responsible for some of the most remarkable phenotypic variation found in nature. Alternative splicing of the transcription factor gene doublesex (dsx) is a highly conserved developmental switch controlling the expression of sex-specific pathways. Here, we leverage sex-specific differences in butterfly wing color pattern to characterize the genetic basis of sexually dimorphic development. We use RNA-seq, immunolocalization, and motif binding site analysis to test specific predictions about the role of dsx in the development of structurally based ultraviolet (UV) wing patterns in Zerene cesonia (Southern Dogface). Unexpectedly, we discover a novel duplication of dsx that shows a sex-specific burst of expression associated with the sexually dimorphic UV coloration. The derived copy consists of a single exon that encodes a DNA binding but no protein-binding domain and has experienced rapid amino-acid divergence. We propose the novel dsx paralog may suppress UV scale differentiation in females, which is supported by an excess of Dsx-binding sites at cytoskeletal and chitin-related genes with sex-biased expression. These findings illustrate the molecular flexibility of the dsx gene in mediating the differentiation of secondary sexual characteristics.
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  • 99
    Publication Date: 2021-07-29
    Description: The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects. We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that—unlike APOL2—APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 100
    Publication Date: 2021-07-21
    Description: Understanding how genetic variation is maintained within species is a major goal of evolutionary genetics that can shed light on the preservation of biodiversity. Here, we examined the maintenance of a regulatory single-nucleotide polymorphism (SNP) of the X-linked Drosophila melanogaster gene fezzik. The derived variant at this site is at intermediate frequency in many worldwide populations but absent in populations from the ancestral species range in sub-Saharan Africa. We collected and genotyped wild-caught individuals from a single European population biannually over a period of 5 years, which revealed an overall difference in allele frequency between the sexes and a consistent change in allele frequency across seasons in females but not in males. Modeling based on the observed allele and genotype frequencies suggested that both sexually antagonistic and temporally fluctuating selection may help maintain variation at this site. The derived variant is predicted to be female-beneficial and mostly recessive; however, there was uncertainty surrounding our dominance estimates and long-term modeling projections suggest that it is more likely to be dominant. By examining gene expression phenotypes, we found that phenotypic dominance was variable and dependent upon developmental stage and genetic background, suggesting that dominance may be variable at this locus. We further determined that fezzik expression and genotype are associated with starvation resistance in a sex-dependent manner, suggesting a potential phenotypic target of selection. By characterizing the mechanisms of selection acting on this SNP, our results improve our understanding of how selection maintains genetic and phenotypic variation in natural populations.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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