Spectral Analysis of Absorption Features for Mapping Vegetation Cover and Microbial Communities in Yellowstone National Park Using AVIRIS Data

This report summarizes the application of imaging spectroscopy to the study of biotic components of Yellowstone National Park ecosystems. Maps of vegetation cover and hot-spring microorganisms were generated using spectral-feature analysis of data from the airborne visible and infrared imaging spectrometer (AVIRIS). AVIRIS data were calibrated to surface reflectance using a radiative-transfer model and a ground-calibration target. A spectral library of canopy-reflectance signatures was created by averaging pixels of reflectance data over known occurrences of 27 vegetation cover types in Yellowstone. Distributions of these vegetation types were determined by comparing absorption features of the vegetation in the spectral library with every pixel of the AVIRIS data using continuum removal and spectral analysis in the U.S. Geological Survey’s Tetracorder expert system. Analysis of the chlorophyll- and leaf-water-absorption features (centered near 0.68, 0.98, and 1.20 μm, respectively) allowed accurate identification of vegetation cover types. Conifer cover types of lodgepole pine, whitebark pine, Douglas fir, and a mixed Engelmann spruce/subalpine fir class were spectrally identified and their distributions were mapped in AVIRIS images. Field-reflectance measurements revealed a distinct spectral signature of hot-spring microorganisms. These field measurements were added to the vegetation spectral library, and maps showing the distributions of microbial mats in the geyser basins of Yellowstone were produced

Calibration and evaluation of AVIRIS data: Cripple Creek in October 1987

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data were obtained over Cripple Creek and Canon City Colorado on October 19, 1987 at local noon. Multiple ground calibration sites were measured within both areas with a field spectrometer and samples were returned to the laboratory for more detailed spectral characterization. The data were used to calibrate the AVIRIS data to ground reflectance. Once calibrated, selected spectra in the image were extracted and examined, and the signal to noise performance was computed. Images of band depth selected to be diagnostic of the presence of certain minerals and vegetation were computed. The AVIRIS data were extremely noisy, but images showing the presence of goethite, kaolinite and lodgepole pine trees agree with ground checks of the area

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Mapping vegetation in Yellowstone National Park using spectral feature analysis of AVIRIS data

Knowledge of the distribution of vegetation on the landscape can be used to investigate ecosystem functioning. The sizes and movements of animal populations can be linked to resources provided by different plant species. This paper demonstrates the application of imaging spectroscopy to the study of vegetation in Yellowstone National Park (Yellowstone) using spectral feature analysis of data from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). AVIRIS data, acquired on August 7, 1996, were calibrated to surface reflectance using a radiative transfer model and field reflectance measurements of a ground calibration site. A spectral library of canopy reflectance signatures was created by averaging pixels of the calibrated AVIRIS data over areas of known forest and nonforest vegetation cover types in Yellowstone. Using continuum removal and least squares fitting algorithms in the US Geological Survey’s Tetracorder expert system, the distributions of these vegetation types were determined by comparing the absorption features of vegetation in the spectral library with the spectra from the AVIRIS data. The 0.68 μm chlorophyll absorption feature and leaf water absorption features, centered near 0.98 and 1.20 μm, were analyzed. Nonforest cover types of sagebrush, grasslands, willows, sedges, and other wetland vegetation were mapped in the Lamar Valley of Yellowstone. Conifer cover types of lodgepole pine, whitebark pine, Douglas fir, and mixed Engelmann spruce/subalpine fir forests were spectrally discriminated and their distributions mapped in the AVIRIS images. In the Mount Washburn area of Yellowstone, a comparison of the AVIRIS map of forest cover types to a map derived from air photos resulted in an overall agreement of 74.1% (kappa statistic = 0.62)

Hydrothermally Altered Rock and Hot-Spring Deposits at Yellowstone National Park—Characterized Using Airborne Visible- and Infrared-Spectroscopy Data

The hydrothermal system in Yellowstone National Park has created altered rock and hot-spring deposits that were mapped using AVIRIS (airborne visible and infrared imaging spectrometer) data. The mapped minerals are indicative of the geologic processes and environments that controlled their formation. Ongoing volcanic activity is expressed at the surface by geothermal features, earthquakes, and geologically recent caldera formation. Precipitated minerals such as siliceous sinter and travertine on the surface are derived from chloride-rich alkaline solutions that are leaching silica and calcite from the underlying country rock. Siliceous sinter and montmorillonite are associated with hydrothermal systems abundant in hot water, whereas kaolinite and alunite are associated with acidic-vapor-dominated hydrothermal systems

The surface composition of Iapetus: Mapping results from Cassini VIMS

Cassini VIMS has obtained spatially resolved imaging spectroscopy data on numerous satellites of Saturn. A very close fly-by of Iapetus on September 10, 2007 provided the best data on the spectral signature and spatial extent of dark material on Iapetus. This Cassini Rev 49 Iapetus fly-by provided spatially resolved imaging spectroscopy data of the dark material and the leading/trailing side transition from the dark material to visually bright ice on the trailing side. Compositional mapping and radiative transfer modeling shows that the dark material is composed of metallic iron, nano-size iron oxide (hematite), CO2, H2O ice, and possible signatures of ammonia, bound water, H2 or OH-bearing minerals, trace organics, and as yet unidentified materials. CO2 indicates a pattern of increasing CO2 strength from the leading side apex to the transition zone to the icy trailing side. A Rayleigh scattering peak in the visible part of the spectrum indicates the dark material has a large component of fine, sub-0.5-μm diameter particles consistent with nanophase hematite and nanophase iron. Spectral signatures of ice also indicate that sub-0.5-μm diameter particles are present in the icy regions. Multiple lines of evidence point to an external origin for the dark material on Iapetus, including the global spatial pattern of dark material, local patterns including crater and cliff walls shielding implantation on slopes facing away from the leading side, exposing clean ice, and slopes facing the leading direction which show higher abundances of dark material. Multiple spectral features and overall spectral shape of the dark material on Iapetus match those seen on Phoebe, Hyperion, Dione, Epimetheus, Saturn's rings Cassini Division, and the F-ring implying the material has a common composition throughout the Saturn system. The dark material appears to have significant components of nanophase metallic iron and nanophase hematite contributing to the observed UV absorption. The blue scattering peak with a strong UV-visible absorption is observed in spectra of all satellites that contain dark material, again pointing to a common origin of contamination by metallic iron that is partially oxidized