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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Detecting Coastal Wetland Degradation by Combining Remote Sensing and Hydrologic Modeling

Sea-level rise and climate change stresses pose increasing threats to coastal wetlands that are vital to wildlife habitats, carbon sequestration, water supply, and other ecosystem services with global significance. However, existing studies are limited in individual sites, and large-scale mapping of coastal wetland degradation patterns over a long period is rare. Our study developed a new framework to detect spatial and temporal patterns of coastal wetland degradation by analyzing fine-scale, long-term remotely sensed Normalized Difference Vegetation Index (NDVI) data. Then, this framework was tested to track the degradation of coastal wetlands at the Alligator River National Wildlife Refuge (ARNWR) in North Carolina, United States, during the period from 1995 to 2019. We identified six types of coastal wetland degradation in the study area. Most of the detected degradation was located within 2 km from the shoreline and occurred in the past five years. Further, we used a state-of-the-art coastal hydrologic model, PIHM-Wetland, to investigate key hydrologic processes/variables that control the coastal wetland degradation. The temporal and spatial distributions of simulated coastal flooding and saltwater intrusion confirmed the location and timing of wetland degradation detected by remote sensing. The combined method also quantified the possible critical thresholds of water tables for wetland degradation. The remote sensing–hydrologic model integrated scheme proposed in this study provides a new tool for detecting and understanding coastal wetland degradation mechanisms. Our study approach can also be extended to other coastal wetland regions to understand how climate change and sea-level rise impact wetland transformations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Drivers and ecological impacts of a wildfire outbreak in the southern Appalachian Mountains after decades of fire exclusion

During one of the warmest and driest droughts of the last century, the southern Appalachian Mountains experienced a regional outbreak of over a dozen large wildfires in late fall of 2016. We provide a synthesis of long-term forest changes leading up to the 2016 wildfires, examine the climatic setting and patterns of burn severity in relationship to topography, and discuss the ecological and management implications of these and future fires. During the pre- and post-European settlement periods, frequent low- and mixed-severity wildfires interacted with complex topographic gradients and maintained heterogenous landscapes dominated by several species of oak (Quercus spp.), pine (Pinus spp.), and the American chestnut (Castanea dentata). Land-use changes associated with European settlement, loss of the American chestnut, and 20th century fire exclusion resulted in large scale shifts towards mesic, fire-intolerant species (i.e. mesophication). Wildfire activity began increasing in the early 1980s, but most fires in the region are small (<1,000 ha). In Fall of 2016, deciduous tree leaf fall occurred concurrently with a period of anomalously dry and warm weather, creating ideal conditions for fire ignition and spread. Thousands of ignitions across the region strained suppression resources and eight fires grew to greater than 5,000 ha. The 2016 fires were larger and burned more area than in the previous three decades combined. In one unique landscape setting, the Chimney Tops 2 Fire, a synoptic wind event drove extreme fire behavior and burned large, high-severity patches resulting in devastating effects in the wildland urban interface. However, immediate post-fire burn severity mosaics for other fires were composed primarily of low- (73 %) and moderate-severity (21 %) fire effects. High-severity fire comprised only 6 % of the area burned, and occurred mostly on steep upper slopes and ridges on south-facing aspects, reflecting the importance of bottom-up topographic drivers in this region. Although the fires will likely enhance biodiversity by restoring fire-dependent species and creating early seral habitat, invasions of non-native plant species, delayed mortality of mature pines and oaks, and rapid re-sprouting of pyrophyllic shrubs pose significant management challenges. Although similar large fire outbreaks may become more common under future climatic conditions, they are unlikely to reverse the effects of mesophication and significantly alter forest dynamics at broad spatial scales. Furthermore, the 2016 fires exposed the vulnerability of the region to wildfire during acute fall drought and demonstrate the potential ecological effects of future wildfires in mixed pine-hardwood landscapes of the southern Appalachians.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Habitat fragmentation alters the distance of abiotic seed dispersal through edge effects and direction of dispersal

Habitat loss and fragmentation are leading causes of species declines, driven in part by reduced dispersal. Isolating the effects of fragmentation on dispersal, however, is daunting because the consequences of fragmentation are typically intertwined, such as reduced connectivity and increased prevalence of edge effects. We used a large-scale landscape experiment to separate consequences of fragmentation on seed dispersal, considering both distance and direction of local dispersal. We evaluated seed dispersal for five wind- or gravity-dispersed, herbaceous plant species that were planted at different distances from habitat edges, within fragments that varied in their connectivity and shape (edge-to-area ratio). Dispersal distance was affected by proximity and direction relative to the nearest edge. For four of five species, dispersal distances were greater further from habitat edges and when seeds dispersed in the direction of the nearest edge. Connectivity and patch edge-to-area ratio had minimal effects on local dispersal. Here our findings illustrate how some, but not all, landscape changes associated with fragmentation can affect the key population process of seed dispersal.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Disturbance and diversity: Lichen species richness decreases with increasing anthropogenic disturbance

Anthropogenic disturbance is rapidly increasing through habitat degradation, development, and deforestation. Gaps remain in understanding the effects of this disturbance on diverse and ecologically important organisms such as lichens. In North America, studies have focused on epiphytic macrolichens and catastrophic disturbance, largely ignoring microlichens and less severe disturbances. The Intermediate Disturbance Hypothesis predicts these moderate disturbances will lead to higher species richness. Here we examine the effects of anthropogenic disturbance in the form of land management on overall lichen richness, including microlichens, and on the species richness of eight lichen functional groups. The study draws on a comprehensive data set of 872 species, in 208 one-hectare plots throughout the Southern Appalachian Mountains, a global biodiversity hotspot in eastern North America. A habitat quality index based on an established forestry metric was used as a proxy for anthropogenic disturbance and was quantified using a 10-part score including categories such as percent native tree canopy cover and degree of fragmentation. Linear models were used to compare habitat quality scores to overall species richness and to species richness of functional groups. Rather than following the Intermediate Disturbance Hypothesis, all groups uniformly follow a negative linear relationship: as disturbance increases, species richness decreases. This pattern held even for widely variable functional groups such as morphotype. Effective conservation of lichen richness should prioritize the maintenance of existing older, less-disturbed stands within large, contiguously forested areas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

EVT 16s Data and Large Supplementary Files

Soil microorganisms often interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat has posed a challenge to elucidating such interactions between soil microorganisms. Here, we seek to address this challenge through analysis of a model soil consortium (MSC-2) of eight soil bacterial species. Our aim was to elucidate specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over three months. Multi-omics was used to understand how the community composition, transcripts, proteins and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles interactions between soil microorganisms.

McClure, Ryan [Pacific Northwest National Laborato↗
DOE OSTI2020

Risk Retirement—Decreasing Uncertainty and Informing Consenting Processes for Marine Renewable Energy Development

Marine renewable energy (MRE) is under development in many coastal nations, adding to the portfolio of low carbon energy sources that power national electricity grids as well as off-grid uses in isolated areas and at sea. Progress in establishing the MRE industry, largely wave and tidal energy, has been slowed in part due to uncertainty about environmental risks of these devices, including harm to marine animals and habitats, and the associated concerns of regulators and stakeholders. A process for risk retirement was developed to organize and apply knowledge in a strategic manner that considered whether specific environmental effects are likely to cause harm. The risk retirement process was tested against two key MRE stressors: effects of underwater noise from operational MRE devices on marine animals, and effects of electromagnetic fields from MRE electrical export cables on marine animals. The effects of installation of MRE devices were not accounted for in this analysis. Applying the risk retirement process could decrease the need for costly investigations of each potential effect at every new MRE project site and help move the industry beyond current barriers.

16 TIDAL AND WAVE POWER↗
DOE OSTI2020

Cropland expansion in the United States produces marginal yields at high costs to wildlife

Recent expansion of croplands in the United States has caused widespread conversion of grasslands and other ecosystems with largely unknown consequences for agricultural production and the environment. Here we assess annual land use change 2008–16 and its impacts on crop yields and wildlife habitat. We find that croplands have expanded at a rate of over one million acres per year, and that 69.5% of new cropland areas produced yields below the national average, with a mean yield deficit of 6.5%. Observed conversion infringed upon high-quality habitat that, relative to unconverted land, had provided over three times higher milkweed stem densities in the Monarch butterfly Midwest summer breeding range and 37% more nesting opportunities per acre for waterfowl in the Prairie Pothole Region of the Northern Great Plains. Our findings demonstrate a pervasive pattern of encroachment into areas that are increasingly marginal for production, but highly significant for wildlife, and suggest that such tradeoffs may be further amplified by future cropland expansion.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗
DOE OSTI2023

Climate Change Risks to Freshwater Subsistence Fisheries in Arctic Alaska: Insights and Uncertainty from Broad Whitefish Coregonus nasus

Arctic freshwater ecosystems and fish populations are largely shaped by seasonal and long-term watershed hydrology. In this paper, we hypothesize how changing air temperature and precipitation will alter freeze and thaw processes, hydrology, and instream habitat to assess potential indirect effects, such as the change to the foraging and behavioral ecology, on Arctic fishes, using Broad Whitefish Coregonus nasus as an indicator species. Climate change is expected to continue to alter hydrologic pathways, flow regimes, and, therefore, habitat suitability, connectivity, and availability for fishes. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories. We expect these changes to have mixed effects on Arctic subsistence fishes and fisheries. Management and conservation approaches focused on preserving the processes that create heterogeneity in aquatic habitats, genes, and communities will help maintain the resilience of Broad Whitefish and other important subsistence fisheries. Long-term effects are uncertain, so filling scientific knowledge gaps, such as identifying important habitats or increasing knowledge of abiotic variables in priority watersheds, is key to understanding and potentially mitigating likely impacts to Arctic fishes in a rapidly changing landscape.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Climate change will reduce North American inland wetland areas and disrupt their seasonal regimes

Abstract Climate change can alter wetland extent and function, but such impacts are perplexing. Here, changes in wetland characteristics over North America from 25° to 53° North are projected under two climate scenarios using a state-of-the-science Earth system model. At the continental scale, annual wetland area decreases by ~10% (6%-14%) under the high emission scenario, but spatiotemporal changes vary, reaching up to ±50%. As the dominant driver of these changes shifts from precipitation to temperature in the higher emission scenario, wetlands undergo substantial drying during summer season when biotic processes peak. The projected disruptions to wetland seasonality cycles imply further impacts on biodiversity in major wetland habitats of upper Mississippi, Southeast Canada, and the Everglades. Furthermore, wetlands are projected to significantly shrink in cold regions due to the increased infiltration as warmer temperature reduces soil ice. The large dependence of the projections on climate change scenarios underscores the importance of emission mitigation to sustaining wetland ecosystems in the future.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Outgassing behavior and heat treatment optimization of JSC-1A lunar regolith simulant

As NASA strives towards a long duration presence on the Moon, it has become increasingly important to learn how to better utilize resources from the lunar surface for everything from habitats, vehicle infrastructure, and chemical extraction. To that end, a variety of lunar simulants have been sourced from terrestrially available volcanic minerals and glass as Apollo regolith is unavailable for experimentation needing large masses. However, while mineralogy and chemical composition can approach that of lunar material in these simulants, there are still distinct non-lunar phases such as hydrates, carbonates, sulfates, and clays that can cause simulants to behave distinctly non-lunar in a variety of processing conditions that maybe applied in-situ to lunar material. Notably, severe glassy bubbling has been documented in a variety of vacuum sintering experiments on JSC-1A lunar mare simulant heated via microwaves. The origins of this outgassing have not been well understood but are normally attributed to the decomposition of non-lunar contaminates intrinsic to virtually all terrestrially sourced simulants. As such, a series of controlled environmental tests were performed to ascertain the origins of the high temperature outgassing and to develop heat treatments that can drive JSC-1A closer to lunar composition and behavior. It was found that in JSC-1A at elevated temperatures distinct gas evolutions of water, carbon dioxide, and sulfur dioxide occur in both inert gas and vacuum. Additionally, the presence of hydrogen during heat treatments was shown to dramatically change gas evolutions, leading to distinctly more lunar-like composition and behavior from JSC-1A simulant.

58 GEOSCIENCES↗
DOE OSTI2021

Studying drought-induced forest mortality using high spatiotemporal resolution evapotranspiration data from thermal satellite imaging

Drought can have pervasive and wide-spread impacts to forest health, as evidenced in several severe events occurring over the recent decades. Extensive forest die-off due to drought can impair the ecological functioning of forests, impacting habitat, water yield and quality from forested lands, and altering forest fire dynamics and intensity. Satellite remote sensing provides an effective means for detecting and monitoring spatial patterns of forest mortality over large areas, exploiting free and open long-term image archives available at a range in spatial and temporal resolutions. While remotely sensed surface reflectances and vegetation indices have been widely used to study optical response of forest canopies to drought events, retrievals of evapotranspiration (ET) derived from thermal satellite imagery – particularly at resolutions approaching crown scale - can provide insights into cumulative tree stresses that can incite disease and trigger mortality. In this study, we applied a multi-sensor satellite data fusion approach to estimate daily 30-m resolution ET and an associated Evaporative Stress Index (ESI) to study drought-induced mortality in a temperate forest at the Missouri Ozark AmeriFlux (MOFLUX) site, located in the central United States. The study covered the period from 2010 to 2014, including an exceptional drought year of 2012. Modeled ET agreed well with eddy flux measurements from the MOFLUX tower, with average monthly relative errors of 15%. Plot-scale ESI, describing temporal anomalies in the ratio of actual-to-reference ET, was used as an index of relative forest health to investigate relationships between forest mortality and drought severity. ESI showed good agreement with observed predawn leaf water potential, especially during the drought year. Furthermore, plot-scale ESI was also correlated with the subsequent year's tree mortality, suggesting the importance of considering the forest health condition prior to drought when studying drought-induced forest impacts. This study demonstrates the utility of multi-year ET remote sensing data at the stand or plot scale as an indicator of forest health and as a predictor of future mortality due to drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Comparison of fiber-optic distributed temperature sensing and high-sensitivity sensor spatial surveying of stream temperature

Measuring surface water temperature spatial variability is needed to estimate the interaction between surface water and groundwater, evaluate fish habitat and thermal inertia, and to estimate streamflow frequency and duration. Fiber optic distributed temperature sensing (FO-DTS) has been used in rivers and lakes, providing high-resolution and sensitive temperature monitoring over large temporal and spatial scales. However, in streams with cobbly or bedrock-lined streambeds and variable bathymetry, use of FO-DTS to measure temperature close to the surface water and groundwater interface can be challenging if even feasible. FO-DTS can also be costly, involve difficult installations, and require an advanced understanding of the technology, calibration, and data processing. In this study, we compared FO-DTS stream temperature survey results to an alternative temperature survey method employing a towed transect of high-resolution temperature loggers spaced at 1-m and transported in the stream along the study reach, to measure the spatial distribution of stream-water temperature in East Fork Poplar Creek near Oak Ridge, Tennessee, USA. We assessed the applicability and limitations of the two methods, and quantitatively compared in-situ temperature survey results measured simultaneously with each method. Regression results showed strong temporal and spatial correlation between the two methods. Differences were only elevated near the stream banks in areas that were coincident with correlation slope deviations from unity, which was attributed to shallower water and lower data density. Kriging standard errors were also low at channel center with minor increases near the stream banks. Furthermore, the results suggested that the array of the individual temperature sensors can provide a practical alternative to FO-DTS for thermal characterization of surface water, providing slightly lower spatial and temporal resolution, but with higher accuracy of temperature measurement, with greater simplicity, and with a broader range of conditions where it may be applied.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A heuristic tool to assess regional impacts of renewable energy infrastructure on conservation areas

Wind and hydropower are important renewable components of national energy portfolios, but their infrastructure negatively affects biodiversity. Regional development requires identification of scenarios that minimize the cumulative impacts of multiple facilities. We introduce the cumulative impact plot (CIP) to quantify cumulative impacts of renewable energy development within a region. Summed impacts of facilities are plotted as a function of the number of facilities, with facilities ranked by increasing (the best-case scenario) or decreasing (worst-case scenario) individual impact. These curves represent lower and upper bounds to which alternative development scenarios (e.g., facilities ranked by generating capacity) can be compared. We used CIPs to assess overlap of potential wind and hydropower facilities with two types of conservation area in the United States: (1) federally protected lands and (2) critical habitats of federally threatened and endangered species. Here, we evaluated two alternative scenarios: facilities ranked by (A) decreasing generating capacity and (B) increasing distance from urban centers. Differences between the best-case and worst-case scenarios were large, thus revealing opportunities to develop facilities with limited impact on conservation areas. Alternative scenarios maximizing energy density generally resulted in conservation area overlap intermediate to best-case and worst-case scenarios. CIPs can also identify the proportion of wind versus hydropower favored under alternative scenarios. Build-out scenarios aimed at minimizing conservation area overlap favor hydropower, whereas alternative scenarios favor wind power. We conclude that CIPs can (1) complement—but should not replace—project-level environmental impact assessment, (2) integrate strategic, cumulative, and scenario-based assessments, and (3) harness rapidly growing geospatial data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

ABSTRACT Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales) , respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 ( Hypocreales , Ascomycota ) was isolated from the sponge Stelletta normani . A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica . Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica . The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Continental-scale niche differentiation of dominant topsoil archaea in drylands

Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. Here, we hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e. deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Ocean-Powered Oyster Tumbling: A Review of Techniques and Opportunities for Emission Reductions

Oysters perform critical roles in shoreline ecosystems by improving water quality, providing habitat for species, and preventing erosion. These ecosystem functions are present even when oysters are farmed. Because of this, and the lack of need for nutrient inputs, oyster farming is often viewed as environmentally friendly. However, fossil fuels play a large part in oyster farming practices. Fossil fuels are used to power boats, tools, and farming equipment. Oyster tumbling machines, which are used to control biofouling and produce a desirable shape and size, use a significant amount of energy and are often powered by diesel generators. As the oyster farming industry grows and practices such as integrated multi-trophic aquaculture expand, decarbonization of the industry becomes more important. One solution may be “ocean-powered” tumbling, whereby oyster grow-out gear is designed to use a range of ocean movements to tumble oysters gradually as they grow. This solution eliminates the need for fossil fuel-powered tumblers and tends to be less labor intensive. A wide range of ocean-powered gear is used by farms across the United States. New approaches and designs are being explored, making ocean-powered oyster tumbling accessible in different environments. Water movements at oyster farms are primarily driven by tidal exchange, currents, wind waves, or a combination. This paper compares methods of ocean-powered tumbling, explores the transition from standard fossil fuel-powered tumbling techniques to ocean-powered tumbling, and estimates the emission reductions of decarbonizing oyster tumbling practices.

16 TIDAL AND WAVE POWER↗
DOE OSTI2026

The landscape of regulatory element evolution in a C4 perennial grass

Gene regulatory evolution is a well-known source of phenotypic diversity and adaptive evolution. Although cis-regulatory elements (CREs) play a vital role in gene expression evolution, the molecular evolution of CREs remains mostly unknown due to the difficulty in identifying and characterizing these functional elements. Comparative genomic analyses of noncoding DNA can be leveraged to identify conserved noncoding sequences (CNS), many of which may harbor functional CREs conserved by purifying selection. However, purely computational inference of CREs from putative CNS can be erroneous due to the complex genomic architecture in plants. One promising experimental approach to identify CREs is by profiling accessible chromatin regions (ACRs) that are often associated with the location of CREs. In this study, we use comparative genomics along with the profiling of ACRs to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses. We identified sets of CNS that varied in relationship to the degree of evolutionary divergence among the studied taxa, including identifying core-Panicoid-CNS. We augmented this analysis by profiling ACRs in Panicum hallii ecotypes using ATAC-seq. ACRs had low SNP density at the summit, harbored a high frequency of core-Panicoid-CNS, and were enriched with expression QTL. These data help to annotate the P. hallii genome for putative functional elements and suggest that a large proportion of these ACRs are evolving under purifying selection. Turnover in CNS and ACR between ecotypes of P. hallii identifies a small set of putatively divergent CREs that may underlie differences in gene regulation between genotypes from inland and coastal habitats. In summary, we profiled ACRs in Panicoid grasses and integrated this data with our putative CNS prediction framework, which provides unique insight into patterns of polymorphism and divergence in CREs in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗