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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin

Abstract Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout ( Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead ( O. mykiss ) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1 . We examined the distribution of genetic variation at 13 candidate markers spanning greb1L , intergenic, and rock1 regions versus 226 neutral markers for 113 populations ( n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.

Collins, Erin E.↗
DOE OSTI2023

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Narum, Shawn R.↗
NASA NTRS1987

Reverse time migration: A seismic processing application on the connection machine

The implementation of a reverse time migration algorithm on the Connection Machine, a massively parallel computer is described. Essential architectural features of this machine as well as programming concepts are presented. The data structures and parallel operations for the implementation of the reverse time migration algorithm are described. The algorithm matches the Connection Machine architecture closely and executes almost at the peak performance of this machine.

Fiebrich, Rolf-Dieter↗
NASA NTRSDate not supplied

Least Squares Reverse Time Migration (LSRTM) for Damage Imaging in Composite Laminates

A method for adapting least squares reverse time migration (LSRTM) for ultrasonic guided wave imaging of composite laminates is proposed in this paper. As composites become more widely used in fields such as the aerospace industry, the need for high-resolution imaging in structural health monitoring (SHM) and nondestructive evaluation (NDE) is also growing. For instance, delamination is a common problem in composite laminates, which has led to a certain degree of apprehension in the use of composite materials for load-bearing structures. Although the solver-based imaging techniques using conventional reverse time migration (RTM) methods illuminate damage with a wide range of damage-scattering effects, the resulting images do not fully define the damage regions due to the limited data acquisition aperture, sensor density, frequencies/wavelengths, and incompleteness of adjoint reconstruction. Previously, the LSRTM theory was derived by incorporating a least squares migration (LSM) algorithm into RTM, and benchmarked its high-resolution damage imaging performance for isotropic plates. To improve damage imaging in composite laminates, a process to create an ultrasonic guided wave-based LSRTM method for anisotropic materials is proposed in this paper. The derivation of the forward modeling operator and the adjoint operator is presented. Numerical case studies were conducted to show the improvement of LSRTM over RTM in mapping damage in composite plates. Multiple damage sites or damage with a complex shape were created in the numerical studies based on 1) Born approximation-based modeling or 2) reduction of the plate stiffness-based modeling. LSRTM begins by using a forward modeling process. The forward modeling accuracy for the flexural wave solver used in this study for LSRTM was also compared with the results from a three-dimensional rotated staggered grid (RSG) elastodynamic finite difference solver, previously open-sourced by NASA Langley Research Center. These benchmarking studies have shown that the LSRTM method is more effective in reducing artifacts, improving resolution, and enhancing damage model reconstruction compared to RTM in composite laminates.

Jiaze He↗
DOE OSTI2023

Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

Abstract Objective Salmonids with a complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding the viability of the natural populations. Methods We genotyped adult (n = 3108) and juvenile (n = 2624) samples of steelhead Oncorhynchus mykiss that were collected in the Klickitat River, Washington, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources, and variation in adult migration timing. Result Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%), as expected, since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Conclusion Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other subbasins, but genetic diversity remains high throughout the subbasin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations.

Collins, Erin E. (ORCID:0000000260978479)↗
DOE OSTI2024

Reverse Time Migration of Explosion-generated Infrasound and Ground-Coupled Airwaves

Accurately locating sources of seismic and infrasonic energy is integral to global monitoring of earthquakes and explosions. Infrasound arrivals times can be used to calculate the origins of events that generate acoustic energy. Picking times of emergent infrasound arrivals, however, can be difficult and prone to uncertainty. Reverse time migration (RTM) is a waveform based location method that does not rely on picked arrival times. Here we use RTM to locate a known chemical explosion that generated acoustic and acoustic-to-seismic signals on 26 and 108 receivers, respectively. All location predictions are less than 24 km from the known location with time errors of less than three minutes. We find strong overall agreement between our results and those of existing RTM and arrival time based methods. Our initial results suggest that RTM is a promising method of event location using acoustic arrivals recorded on both infrasound and seismic instrumentation.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2022

Quasielastic least-squares reverse time migration of PS reflections

Conventional analysis of amplitude variation with offset for elastic PS reflections is based on analytical reflection coefficients in a layered medium, and wave-equation-based PS migration is mainly used to produce a structural image. To overcome this problem, we have developed a least-squares reverse time migration (LSRTM) method for elastic PS reflections based on a quasielastic wave equation. Here, the quasielastic wave equation can accurately model PS reflections with elastic amplitudes under the first-order Born approximation. Our LSRTM method inverts for perturbations of the S-wave velocity and density by minimizing the L 2 norm of the difference between recorded and predicted PS reflections modeled using a quasielastic wave equation. We refer to our new method as quasielastic LSRTM of PS reflections. Numerical tests on synthetic and field data indicate that our method can properly handle the amplitudes of elastic PS reflections and provides an accurate estimate of the perturbations of S-wave velocity and density. Extending the method to the 3D case is not straightforward and might require incorporating certain PS data processing techniques into the inversion itself.

58 GEOSCIENCES↗
DOE OSTI2020

Steelhead ( Oncorhynchus mykiss ) lineages and sexes show variable patterns of association of adult migration timing and age‐at‐maturity traits with two genomic regions

Abstract As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age‐at‐maturity in steelhead ( Oncorhynchus mykiss ) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead ( R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139–0.170; females R 2 = 0.096–0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock‐specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Willis, Stuart C.↗
DOE OSTI2021

Shear reflectivity compensation in full-waveform inversion using least-squares reverse-time migration

SUMMARY The computational cost of elastic-waveform inversion is too high for inverting PP reflections, while using acoustic full-waveform inversion (FWI) is inaccurate because it does not depend on the shear modulus/velocity/impedance that affects elastic PP wavefield amplitudes. To solve this problem, we develop a waveform inversion method that uses acoustic least-squares reverse-time migration (LSRTM) to compensate the shear reflectivity for acoustic FWI. Our method is based on the quasi-elastic-wave equation developed by Chapman et al. (2014). The quasi-elastic-wave equation uses a linearized acoustic-wave equation with shear modulus μ as a virtual source to correct the acoustic PP wavefield amplitudes toward elastic ones. Our waveform inversion method inverts for elastic parameters by minimizing the L2 norm of the difference between recorded and predicted PP reflections modelled using the quasi-elastic-wave equation. Numerical tests on synthetic and field data show that our method can properly handle the amplitudes of elastic PP reflections and provides an accurate estimate of the P- and S-wave velocities/impedances and, in some cases, the density. The method does not need the computationally expensive numerical solution to the elastic-wave equation. It also gives a better estimate of elastic parameters than a pure LSRTM method for elastic PP reflections.

Feng, Zongcai↗
DOE OSTI2021

Local Explosion Detection and Infrasound Localization by Reverse Time Migration Using 3-D Finite-Difference Wave Propagation

Infrasound data are routinely used to detect and locate volcanic and other explosions, using both arrays and single sensor networks. However, at local distances (< km) topography often complicates acoustic propagation, resulting in inaccurate acoustic travel times leading to biased source locations when assuming straight-line propagation. Here we present a new method, termed Reverse Time Migration-Finite-Difference Time Domain (RTM-FDTD), that integrates numerical modeling into the standard RTM back-projection process. Travel time information is computed across the entire potential source grid via FDTD modeling to incorporate the effects of topography. The waveforms are then back-projected and stacked at each grid point, with the stack maximum corresponding to the likely source. We apply our method to three volcanoes with different network configurations, source-receiver distances, and topography. At Yasur Volcano, Vanuatu, RTM-FDTD locates explosions within ~20 m of the source and differentiates between multiple vents. RTM-FDTD produces a more accurate location for the two Yasur subcraters than standard RTM and doubles the number of detected events. At Sakurajima Volcano, Japan, RTM-FDTD locates the source within 50 m of the active vent despite notable topographic blocking. The RTM-FDTD location is similar to that from the Time Reversal Mirror method, but is more computationally efficient. Lastly, at Shishaldin Volcano, Alaska, RTM and RTM-FDTD both produce realistic source locations (<50 m) for ground-coupled airwaves recorded on a four-station seismic network. We show that RTM is an effective method to detect and locate infrasonic sources across a variety of scenarios, and by integrating numerical modeling, RTM-FDTD produces more accurate source locations and increases the detection capability.

58 GEOSCIENCES↗
DOE OSTI2024

Seismoacoustic Reverse Time Migration

Poster for AGU. Currently waiting HQ review - changes will be incorporated prior to final release.

Koch, Clinton [Sandia National Laboratories (SNL-N↗
DOE OSTI2023

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Abstract The distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high‐resolution portrait of genomic variation in Chinook salmon ( Oncorhynchus tshawytscha ) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered data set of ~13 million single nucleotide polymorphisms (SNPs) from low‐coverage whole genome resequencing of 53 populations (3566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine‐scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages ( r 2 = .58–.95; p < .001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream‐type) compared to the other two major lineages, which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Horn, Rebekah L.↗
DOE OSTI2021

Genomic region associated with run timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Abstract Conserving life‐history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early‐ and late‐migrating forms of Chinook salmon ( Oncorhynchus tshawytscha ) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high‐throughput genotyping (GT‐seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream‐type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream‐type and interior ocean‐type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River.

Willis, Stuart C.↗
DOE OSTI2021

Imaging Complex Subsurface Structures for Geothermal Exploration at Pirouette Mountain and Eleven-Mile Canyon in Nevada

Accurate imaging of subsurface complex structures with faults is crucial for geothermal exploration because faults are generally the primary conduit of hydrothermal flow. It is very challenging to image geothermal exploration areas because of complex geologic structures with various faults and noisy surface seismic data with strong and coherent ground-roll noise. In addition, fracture zones and most geologic formations behave as anisotropic media for seismic-wave propagation. Properly suppressing ground-roll noise and accounting for subsurface anisotropic properties are essential for high-resolution imaging of subsurface structures and faults for geothermal exploration. We develop a novel wavenumber-adaptive bandpass filter to suppress the ground-roll noise without affecting useful seismic signals. This filter adaptively exploits both characteristics of the lower frequency and the smaller velocity of the ground-roll noise than those of the signals. Consequently, this filter can effectively differentiate the ground-roll noise from the signal. We use our novel filter to attenuate the ground-roll noise in seismic data along five survey lines acquired by the U.S. Navy Geothermal Program Office at Pirouette Mountain and Eleven-Mile Canyon in Nevada, United States. We then apply our novel anisotropic least-squares reverse-time migration algorithm to the resulting data for imaging subsurface structures at the Pirouette Mountain and Eleven-Mile Canyon geothermal exploration areas. The migration method employs an efficient implicit wavefield-separation scheme to reduce image artifacts and improve the image quality. Our results demonstrate that our wavenumber-adaptive bandpass filtering method successfully suppresses the strong and coherent ground-roll noise in the land seismic data, and our anisotropic least-squares reverse-time migration produces high-resolution subsurface images of Pirouette Mountain and Eleven-Mile Canyon, facilitating accurate fault interpretation for geothermal exploration.

15 GEOTHERMAL ENERGY↗
NASA NTRS2004

On the Final Mass of Giant Planets

In the core accretion model of giant planet formation, when the core reaches critical mass, hydrostatic equilibrium is no longer possible and gas accretion ensues. If the envelope is radiative, the critical core mass is nearly independent of the boundary conditions and is roughly M(sub crit) ~ 10Mass of the Earth (with weak dependence on the rate of planetesimal accretion M(sub core) and the disk opacity k). Given that such a core may form at the present location of Jupiter in a time comparable to its Type I migration time (10(exp 5) - 10(exp 6) years) provided that the nebula was significantly enhanced in solids with respect to the MMSN and stall at this location in a weakly turbulent (alpha approximately less than 10(exp -4) disk, it may be appropriate to assume that such objects inevitably form and drive the evolution of late-phase T Tauri star disks. Here we investigate the final masses of giant planets in disks with one or more than one such cores. Although the presence of several planets would lead to Type II migration (due to the effective viscosity resulting from the planetary tidal torques), we ignore this complication for now and simply assume that each core has stalled at its location in the disk. Once a core has achieved critical mass, its gaseous accretion is governed by the given Kelvin-Helmholtz timescale.

Estrada, P. R.↗
DOE OSTI2019

Utah FORGE: Seismic Reflection Data

This is 2D and 3D seismic reflection data from Utah FORGE reprocessed during Phase 2c. The readme file containing an explanation of the data including data formats, software that can be used, processing, and projection and datum used. The Reprocessing document gives the rationale for reprocessing and shows examples of the improvements that were obtained. For all 3D and 2D data the following datasets were created and output in SEG-Y format: - Unmigrated Time - Prestack Time Migration (PSTM), Unenhanced (UnEnh) and Enhanced (Enh) - Prestack Depth Migration (PSDM), Unenhanced (UnEnh) and Enhanced (Enh) - Velocity Model used for Migration

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Vector elastic deconvolution migration with dual wavefield decomposition

Here, we report elastic-wave imaging using multicomponent data can provide more useful subsurface information than acoustic-wave imaging, but it is usually algorithmically challenging. We have developed a vector elastic deconvolution migration method for high-resolution imaging of subsurface structures in isotropic and anisotropic elastic media. Our new method uses a vector deconvolution imaging condition based on dual wavefield decomposition, including an explicit directional wavefield separation using the Hilbert transform and a P/S vector wavefield decomposition using the low-rank decomposition method. Using three elastic models, we numerically determine that our new method produces notably higher resolution and more amplitude-balanced elastic images compared with a crosscorrelation-based vector elastic reverse time migration method.

58 GEOSCIENCES↗