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DOE OSTI2022

High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa

Abstract Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

DVMDOSTEM v0.8.3: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics

The impacts of climate change on natural ecosystems are the result of complex physical and ecological processes operating and interacting at a variety of spatio-temporal scales, that can be represented in process-based ecosystem models. DVMDOSTEM is an advanced process-based terrestrial ecosystem model (TEM) designed to study ecosystem responses to climate changes and disturbances. It has a particular focus on permafrost regions (i.e. regions characterized by soils that stay partially frozen all year round for at least two consecutive years), encompassing boreal, arctic, and alpine landscapes. The model couples two previous versions of the Terrestrial Ecosystem Model (TEM) (McGuire et al., 1992): DVMTEM that includes a dynamic vegetation module (DVM) (E. S. Euskirchen et al., 2009), and DOSTEM that includes a dynamic organic soil module (DOS) (H. Genet et al., 2013; Yi et al., 2010). DVMDOSTEM simulates processes at yearly and monthly scales, with some physical processes operating at an even finer temporal resolution. Its versatility allows for site-specific to regional simulations, making it valuable for predicting shifts in permafrost, vegetation, and carbon (C) and nitrogen (N) dynamics. While DVMDOSTEM has been described in the methods sections of many manuscripts, this paper is the first stand alone description of DVMDOSTEM, independent of a particular scientific investigation.

Carman, Tobey B. [Univ. of Alaska, Fairbanks, AK (↗

DOE OSTI2020

Litter Production of Oak-Hickory Forest at Missouri Ozark (MOFLUX) Site: 2003-2022

This dataset contains measurements of litter production at the second-growth upland oak-hickory forest at the Missouri Ozark AmeriFlux (MOFLUX) site. The MOFLUX site is located in the University of Missouri Baskett Forest situated in the Ozark Border Region of central Missouri, USA, and is part of the AmeriFlux network (site ID: US-MOz). During 2003, 24 circular vegetation plots (each 0.08 hectares) were established in the MOFLUX forest. The plots were situated 50 meters apart on 5 linear transects radiating out from the flux tower base in southeast, south, southwest, west, and northwest directions—there were 5 plots per transect except for the northwest one, which had only 4 due to the presence of a small pond at the terminus (Fig. 1). Litter measurements were initiated in October 2003 and continue to the present. Data through 2022 are reported in this dataset. On each plot, two subplots were established for the collection of litter. Subplots were setup using a stratified random design to ensure the collectors were not immediately adjacent to one another. Litter collectors were usually emptied at monthly intervals, or less during the autumn leaf drop. Samples were dried to constant mass and then sorted before determining the dry mass of leaf, vegetative and woody litter. These litter data have been valuable in modeling efforts to examine the impacts of intensifying moisture extremes (i.e., moisture excess and deficit conditions) on soil carbon cycling. More recent data will be added periodically with no changes to previously released data or the format and structure of the data file. This dataset contains one data file in comma separate (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1983

Atmospheric effects on radiometry from zenith of a plane with dark vertical protrusions

Effects of an optically thin plane-parallel scattering atmosphere on radiometric imaging from the zenith of a specific surface-type are analyzed. The surface model was previously developed to describe arid steppe, where the sparse vegetation forms dark vertical protrusions from the bright soil-plane. The analysis is in terms of the surface reflectivity to the zenith r sub p for the direct beam, which is formulated as r sub p = r sub i exp (-s tan theta sub 0), where v sub i is the Lambert law reflectivity of the soil, the protrusions parameters s is the projection on a vertical plane of protrusions per unit area and theta sub 0 is the zenith angle. The surface reflectivity r sub p is approximately equal to that for the global irradiance (which is directly measured in the field) only for a narrow range of the solar zenith angles. The effects of the atmosphere when imaging large uniform areas of this type are comparable to those in imaging a Lambert surface with a reflectivity r sub p. Thus, the effects can be approximated by those in the case of a dark Lambert surface (analyzed previously), inasmuch as r sub p is smaller than the soil reflectivity r sub i for any off-zenith illumination. The surface becomes effectively darker with increasing solar zenith angle. Adjacency effects of a reflection from one area and scattering in the instantaneous field of view (object pixel) are analyzed as cross radiance and cross irradiance.

Otterman, J.↗

NASA NTRS1983

Evaluation of spatial, radiometric and spectral Thematic Mapper performance for coastal studies

A series of experiments were initiated to determine the feasibility of using thematic mapper spectral data to estimate wetlands biomass. The experiments were conducted using hand-held radiometers simulating thematic mapper wavebands 3, 4 and 5. Spectral radiance data were collected from the ground and from a low altitude aircraft in an attempt to gain some insight into the potential utility of actual thematic mapper data for biomass estimation in wetland plant communities. In addition, radiative transfer models describing volume reflectance of eight water column containing submerged aquatic vegetation were refined.

Klemas, V.↗

NASA NTRS1987

Correlation between aircraft MSS and lidar remotely sensed data on a forested wetland

Inland wetland in a portion of the Savannah River swamp forest were mapped with an overall accuracy of 88.5 percent on April 26,l985 using high resolution aircraft Daedalus AADS-1268 MSS data. In addition, data were acquired using a NASA sensor system flown along two flight lines over the Steel Creek Delta. The data were significantly correlated with in situ tree height measurements. The data were registered to the wetland classification map and correlated. Statistical analyses demonstrated that the laser derived canopy height information was significantly associated with the Steel Creek Delta wetland classes encountered along the transect (an F-value of 58.46 at the 0.0001 level of confidence). The relationship between vegetation height and vegetation type was then used to produce a three-dimensional model of the landscape which can be of value when computing biomass or canopy density in this forested wetland environment.

Jensen, John R.↗

NASA NTRS1988

An approach for detecting post-launch spectral changes in satellite multispectral sensors

An approach for testing whether or not post-launch changes have occurred in sensor spectral responses is described. The approach uses field measurements of ground targets having differing spectral reflectance properties as well as calculations based on the original spectral response characteristics. As an example, a shift in band location was modeled and evaluated through the simulation of signals from soil and vegetation targets in the spectral bands of five satellite systems.

Suits, G. H.↗

NASA NTRS2000

Baseline Calibration of the GeoSAR Interferometric Mapping Instrument

GeoSAR is a dual frequency, X-Band and P-Band, interferometric mapping radar flown on a Gulfstream II with a nominal flying altitude of 10000 and a swath width of 10 km on both left and right sides of the aircraft. The radar is designed to generate high resolution and high accuracy digital elevation maps both above and below the vegetation canopy. In order to generate the high accuracy digital elevations models it is necessary to have extremely precise knowledge of the interferometric baseline, approximately .1 mm for the X-band system and 3 mm for the P-band system. Baseline knowledge to this level of accuracy is achieved through a combination of active baseline measurement using a Laser Baseline Metrology System (LBMS) and baseline calibration using an accurately surveyed array of corner reflectors. In this paper, we describe the LBMS system used to measure the dynamic component of the interferometric baseline and the least squares procedure used to estimate all three components of the interferometric baseline based on differences between calculated and surveyed corner reflector locations.

Hensley, Scott↗

NASA NTRS2019

Downscaling and Validation of SMAP Radiometer Soil Moisture in CONUS

The SMAP (Soil Moisture Active/Passive) satellite provides global soil moisture (SM) estimates that can be used for scientific research and applications (such as the hydrological cycle, agriculture, ecology, and land atmosphere interactions). Currently, SMAP provides the enhanced radiometer-only SM product (L2SMP) at 9 km grid resolution. However, this spatial resolution is still not enough to satisfy the needs of some studies that require a finer spatial resolution SM product, particularly in agricultural and watershed applications. This study applied a downscaling algorithm to the SMAP 9 km SM product to produce a 1 km resolution over the CONUS (Contiguous United States). The downscaling algorithm is based on the relationship between temperature change and SM modulated by Normalized Difference Vegetation Index (NDVI) of a given time period. This relationship was modeled using variables derived from NLDAS (North America Land Data Assimilation System) and NASA's LTDR (Land Long Term Data Record) between 1981-2018. The algorithm was implemented uses the 1 km MODIS Aqua LST (Land Surface Temperature) product. The downscaled SMAP 1 km SM was validated using in situ SM measurements from the ISMN (International Soil Moisture Network). The validation metrics show an improved overall accuracy of the downscaled SM.

downscaling↗

NASA NTRS2024

Assessing the effects of landcover and land use change on wildfire exposure and risk to communities and olive orchards in Mediterranean landscapes

A growing concern in the Mediterranean region is that recent landcover and land use change is increasing wildfire risk, or the exposure and impacts of wildfire to valued resources. However, the magnitude of these effects is not well understood given the widely diverse landscapes of communities, natural vegetation, and agricultural land. In this study, we use wildfire simulation modeling to assess how landcover and land use changes in three areas of southern Greece have affected exposure of- and fire risk to- communities and economically important permanent agriculture such as Olea europaea (European olive) orchards. We mapped agricultural and wildland fuel change from 2000 to 2020 and simulated fuel scenarios in agricultural land to assess the impacts of agricultural land practices, such as understory clearing, on fire risk. We show that wildfire exposure and risk to communities and permanent agriculture has increased in some areas due to natural fuel densification and decreased in other areas, mainly due to agricultural land expansion. These results highlight that wildfire exposure and risk are driven by local conditions including density and location of communities, spatial arrangement of natural fuels and agricultural land, and agricultural land use practices. Human settlement burn probability and modeled permanent crop loss increased with greater unmaintained agricultural area in all study areas, emphasizing the importance of agricultural land maintenance practices, such as understory clearing, to reduce fuel continuity and fire intensity. Ultimately, quantitative fire risk analyses such as this study provide a useful framework to identify areas of concern where either fuel mitigation or landowner incentives to maintain agricultural land in a less-burnable condition could be applied.

Aaron M Sparks↗

DOE OSTI2025

Multiple RGB ortho-mosaics and digital surface models in 2017 and 2018 across the Lower Montane site in the East River Watershed, Colorado

Aerial imagery was collected at the Lower Montane site (Pumphouse) in the East River Watershed, Colorado during the spring, summer, and fall seasons of 2017 and 2018 to improve the understanding of seasonal vegetation dynamics and their drivers. The datasets include Red-Green-Blue (RGB) ortho-mosaics and digital surface models (DSMs) inferred from the Unoccupied Aerial System (UAS) acquired aerial RGB imagery for June 3, June 19, July 7, and August 14, 2017, and for March 14, April 26, June 1, June 18, July 6, and August 7, 2018. Real-Time Kinematic Global Positioning System (RTK-GPS) surveyed Ground control points (GCPs) were used to increase the reconstruction accuracy. The reconstructed RGB mosaics and DSMs have been trimmed to cover a similar spatial domain. The accuracy of the RGB mosaics is considered high (~10 cm). DSM accuracy is highest (~10 cm) where sufficient GCPS are available, and more difficult to assess elsewhere (see reconstruction reports for uncertainty estimates). The dataset includes a total of 20 GeoTIFF (.tif) files, 10 PDF (.pdf) files, 3 data CSV (.csv) files, and 2 metadata CSV (.csv) files. Feel free to contact the authors with any questions or collaboration interests.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2012

View Angle Effects on MODIS Snow Mapping in Forests

Binary snow maps and fractional snow cover data are provided routinely from MODIS (Moderate Resolution Imaging Spectroradiometer). This paper investigates how the wide observation angles of MODIS influence the current snow mapping algorithm in forested areas. Theoretical modeling results indicate that large view zenith angles (VZA) can lead to underestimation of fractional snow cover (FSC) by reducing the amount of the ground surface that is viewable through forest canopies, and by increasing uncertainties during the gridding of MODIS data. At the end of the MODIS scan line, the total modeled error can be as much as 50% for FSC. Empirical analysis of MODIS/Terra snow products in four forest sites shows high fluctuation in FSC estimates on consecutive days. In addition, the normalized difference snow index (NDSI) values, which are the primary input to the MODIS snow mapping algorithms, decrease as VZA increases at the site level. At the pixel level, NDSI values have higher variances, and are correlated with the normalized difference vegetation index (NDVI) in snow covered forests. These findings are consistent with our modeled results, and imply that consideration of view angle effects could improve MODIS snow monitoring in forested areas.

MODIS↗

DOE OSTI2022

Estimation of Corn Latent Heat Flux from High Resolution Thermal Imagery

Crop evapotranspiration (ET), which is directly related to latent heat flux, is also a key indicator in determining the water status of crops. In order to estimate the latent heat flux, two-source energy balance (TSEB) models have been developed for thermal imagery from satellite platforms. However, because of the coarse resolution of thermal sensors on the satellite, distinguishing soil and vegetation is difficult which complicates the calculation process and introduces errors in latent heat estimates. In this research, high-resolution thermal datasets (0.05 m) and corresponding RGB datasets (0.03 m) were used for calculating crop latent heat flux using an adapted TSEB model. The RGB datasets were used for supervised classification of soil and vegetation, and the classification results were then used to filter the thermal mosaics to separate vegetation and soil temperatures. The vegetation temperature is used for calculating latent heat flux and the results are validated against the ground reference measurements of latent heat using a handheld porometer. The objective of this research is to introduce a workflow including an adapted TSEB model which is customized for high resolution thermal images from unmanned aircraft systems (UAS) to estimate the latent heat flux of row crops in agricultural fields. Nine dates of data collection in 2018 and 2020 have been evaluated and the root mean square error (RMSE) varies between 16 to 106 W/m2 depending on the days after planting (DAP) and the time of measurement for each day. The results indicate that the workflow introduced here is able to provide estimates of instantaneous latent heat flux (evapotranspiration) measurements for row crops in agricultural fields which will enable people to make reliable decisions related to irrigation scheduling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

A Greening Future Elevates Flash Drought Risk in Northern Mid‐to‐High Latitudes

Flash droughts have become a growing concern, as they can emerge rapidly and increase the risk of crop failure. Although past studies have investigated the meteorological drivers and future changes of flash drought, why flash drought is more frequent over humid and vegetated regions remains underexplored. This study delves further into the mechanism by which vegetation regulates flash drought and its future change using observations from multiple data sets and large ensemble simulations from three Earth system models. On an interannual timescale, both observations and simulations show robust increases in flash drought frequency and a higher flash-to-sub-seasonal drought ratio during spring or antecedent conditions with dense vegetation, supporting the important role of vegetation in flash drought occurrence, especially in the northern mid-to-high latitudes. In the latter regions, the large ensemble simulations show robust increases in flash drought (e.g., 67% and 46% increases in Eastern U.S. and North Asia in 2050–2100 relative to 1950–2000 under the high emission scenario), where the growing season is lengthening. Although greening might suggest reduced drought stress, it drives precipitation-soil moisture-evapotranspiration decoupling by increasing evapotranspiration partitioning to transpiration. As transpiration can access deep soil water through the plant root system, its increased portion can weaken the constraints of concurrent precipitation on evapotranspiration, thus accelerating soil moisture depletion under high evaporative demand, driving a slow-to-rapid drought transition. How vegetation regulates flash drought by regulating surface moisture budget is supported by observations and simulations. Although warming supports early planting, agriculture may increasingly be threatened by surging flash drought risk.

Drought↗

NASA NTRS2013

Daily MODIS 500 m Reflectance Anisotropy Direct Broadcast (DB) Products for Monitoring Vegetation Phenology Dynamics

Land surface vegetation phenology is an efficient bio-indicator for monitoring ecosystem variation in response to changes in climatic factors. The primary objective of the current article is to examine the utility of the daily MODIS 500 m reflectance anisotropy direct broadcast (DB) product for monitoring the evolution of vegetation phenological trends over selected crop, orchard, and forest regions. Although numerous model-fitted satellite data have been widely used to assess the spatio-temporal distribution of land surface phenological patterns to understand phenological process and phenomena, current efforts to investigate the details of phenological trends, especially for natural phenological variations that occur on short time scales, are less well served by remote sensing challenges and lack of anisotropy correction in satellite data sources. The daily MODIS 500 m reflectance anisotropy product is employed to retrieve daily vegetation indices (VI) of a 1 year period for an almond orchard in California and for a winter wheat field in northeast China, as well as a 2 year period for a deciduous forest region in New Hampshire, USA. Compared with the ground records from these regions, the VI trajectories derived from the cloud-free and atmospherically corrected MODIS Nadir BRDF (bidirectional reflectance distribution function) adjusted reflectance (NBAR) capture not only the detailed footprint and principal attributes of the phenological events (such as flowering and blooming) but also the substantial inter-annual variability. This study demonstrates the utility of the daily 500 m MODIS reflectance anisotropy DB product to provide daily VI for monitoring and detecting changes of the natural vegetation phenology as exemplified by study regions comprising winter wheat, almond trees, and deciduous forest.

Vegetation↗

NASA NTRS2019

The Arctic-Boreal vulnerability experiment model benchmarking system

NASA's Arctic-Boreal Vulnerability Experiment (ABoVE) integrates field and airborne data into modeling and synthesis activities for understanding Arctic and Boreal ecosystem dynamics. The ABoVE Benchmarking System (ABS) is an operational software package to evaluate terrestrial biosphere models against key indicators of Arctic and Boreal ecosystem dynamics, i.e.: carbon biogeochemistry, vegetation, permafrost, hydrology, and disturbance. The ABS utilizes satellite remote sensing data, airborne data, and field data from ABoVE as well as collaborating research networks in the region, e.g.: the Permafrost Carbon Network, the International Soil Carbon Network, the Northern Circumpolar Soil Carbon Database, AmeriFlux sites, the Moderate Resolution Imaging Spectroradiometer, the Orbiting Carbon Observatory 2, and the Soil Moisture Active Passive mission. The ABS is designed to be interactive for researchers interested in having their models accurately represent observations of key Arctic indicators: a user submits model results to the system, the system evaluates the model results against a set of Arctic-Boreal benchmarks outlined in the ABoVE Concise Experiment Plan, and the user then receives a quantitative scoring of model strengths and deficiencies through a web interface. This interactivity allows model developers to iteratively improve their model for the Arctic-Boreal Region by evaluating results from successive model versions. We show here, for illustration, the improvement of the Lund–Potsdam–Jena-Wald Schnee und Landschaft (LPJwsl) version model through the ABoVE ABS as a new permafrost module is coupled to the existing model framework. The ABS will continue to incorporate new benchmarks that address indicators of Arctic-Boreal ecosystem dynamics as they become available.

ABoVE↗

DOE OSTI2023

Understanding How Reservoir Operations Influence Methane Emissions: A Conceptual Model

Because methane is a potent greenhouse gas (GHG), understanding controls on methane emissions from reservoirs is an important goal. Yet, reservoirs are complex ecosystems, and mechanisms by which reservoir operations influence methane emissions are poorly understood. In part, this is because emissions occur in ‘hot spots’ and ‘hot moments’. In this study, we address three research questions, ‘What are the causal pathways through which reservoir operations and resulting water level fluctuations (WLF) influence methane emissions?’; ‘How do influences from WLF differ for seasonal drawdown and diurnal hydropeaking operations?’; and ‘How does understanding causal pathways inform practical options for mitigation?’. A graphical conceptual model is presented that links WLF in reservoirs to methane emissions via four causal pathways: (1) water-column mixing (2) drying–rewetting cycles, (3) sediment delivery and redistribution, and (4) littoral vegetation. We review what is known about linkages for WLF at seasonal and diurnal resolutions generate research questions, and hypothesize strategies for moderating methane emissions by interrupting each causal pathway. Those related to flow management involve basin-scale management of tributary flows, seasonal timing of hydropeaking (pathway #1), timing and rates of drawdown (pathway #2). In addition, we describe how sediment (pathway #3) and vegetation management (pathway #4) could interrupt linkages between WLF and emissions. We demonstrate the strength of conceptual modeling as a tool for generating plausible hypotheses and suggesting mitigation strategies. Future research is needed to develop simpler models at appropriate timescales that can be validated and used to manage flow releases from reservoirs.

13 HYDRO ENERGY↗

NASA NTRS1987

Relationships between vegetation indices, radiation absorption, and net photosynthesis evaluated by a sensitivity analysis

A two-stream approximation to the radiative-transfer equation is used to calculate the vegetation indices (simple ratio and normalized difference), the fraction of incident photosynthetically active radiation (PAR) absorbed by the canopy, and the daily mean canopy net photosynthesis under clear-sky conditions. The model calculations are tested against field observations over wheat, cotton, corn, and soybean. The relationships between the vegetation indices and radiation absorption or net photosynthesis are generally found to be curvilinear, and changes in the soil reflectance affected these relationships. The curvilinearity of the relationship between normalized differences and PAR absorption decreases as the magnitude of soil reflectance increases. The vegetation indices might provide the fractional radiation absorption with some a priori knowledge about soil reflectance. The relationship between the vegetation indices and net photosynthesis must be distinguished for C3 and C4 crops. Effects of spatial heterogeneity are discussed.

Choudhury, Bhaskar J.↗