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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS2019

Air Pollution Inputs to the Mojave Desert By Fusing Surface Mobile and Airborne in Situ and Airborne and Satellite Remote Sensing: A Case Study of Interbasin Transport With Numerical Model Validation

Deserts are fragile and highly sensitive ecosystems that increasingly are affected by upwind urban areas and industrial activities. The Los Angeles Basin (LAB) contributes to poor air quality in downwind deserts including the Mojave Desert. Few studies have investigated potential air pollution inputs to the Mojave, whose fragile ecosystem includes endangered plant and animal species. Data were collected on 19 August 2015 by a mobile air quality laboratory, AMOG (AutoMObile trace Gas) Surveyor, that observed inputs can arise from the LAB as well as the San Joaquin Valley (SJV), California. The campaign used a strong methane (CH4) plume as a tracer for the downwind fate of emissions from Bakersfield area petroleum production and also measured ozone (O3). Additional in situ concurrent airborne GHG and O3 data were collected by AJAX - Alpha Jet Atmospheric eXperiment. Both AMOG and AJAX measure winds. Mojave Desert air quality was very poor (visibility ~4 km). Based on the winds, an additional source was inferred beyond the LAB and SJV Basins. Numerical transport modeling and analysis of aerosol lidar data collected the same day by the Cloud Profiling LiDAR onboard the Earth Research-2 stratospheric airplane demonstrated that fires in Northern California were responsible, with prevailing winds transporting air southwards along the eastern Sierra Nevada Range (Bishop Valley) to the Mojave. Whereas the southern and eastern Mojave are impacted by SJV and LAB outflow, the north Mojave generally avoids these inputs. This study shows it can be affected by even distant wildfires, which likely will increase in occurrence and intensity from climate change. Thus, regulatory efforts to reduce air quality impacts on the endangered Mojave ecosystem must include wildfires and also account for the significant differences between different regions of the Mojave. Currently, there is a paucity of studies, highlighting the critical need for field research.

Ira Leifer↗
DOE OSTI2022

The avoidance of unwanted catch and cooperation: the case of the British Columbia groundfish trawl fishery

Abstract This paper focuses on a particularly successful avoidance of unwanted catch of protected, endangered, and threatened (PET) species in the form of ecologically important sponge and coral, to be found off Canada's Pacific coast. The fishery causing the unwanted catch—the British Columbia groundfish trawl fishery. A campaign to protect the sponge/coral led by environmental NGOs (ENGOs) resulted in the industry's access to the key California market being threatened. For reasons explained, the national resource manager's ability to take effective direct action had become severely compromised. The groundfish trawl fishing industry responded to the economic threat with a bottom up approach to the unwanted catch problem, by negotiating a habitat agreement with a consortium of ENGOs, with the blessing and full support of the national resource manager. The agreement, now in its tenth year of operation, has proved to be a remarkable success in avoidance of unwanted catch. The paper argues that the success rests fundamentally upon the fact that the fishers have been and are playing a stand alone stable cooperative game, which has led them in turn to play stable cooperative games with both the national resource manager and the ENGO consortium. The paper analyses the factors leading to the stand alone stable cooperative fisher game, doing so by necessity through the lens of game theory.

Grønbæk, L.↗
DOE OSTI2021

AmeriFlux US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM)

This is the AmeriFlux version of the carbon flux data for the site US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM). Site Description - NEON's PUUM field site is located in the Pu'u Maka'ala Natural Area Reserve (NAR) on the eastern side of Hawaii’s “Big Island,” managed by the Hawaii Division of Forestry and Wildlife (DOFAW). More than 18,000 acres in size, the NAR is home to a rainforest with many native species, some of them endangered. It was established to protect some of the Big Island’s best wet native forest and unique geologic features.

Network), NEON (National Ecological Observatory↗
DOE OSTI2025

AmeriFlux FLUXNET-1F US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM). This is the FLUXNET version of the carbon flux data for the site US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM) produced by applying the standard ONEFlux (1F) software. Site Description - NEON's PUUM field site is located in the Pu'u Maka'ala Natural Area Reserve (NAR) on the eastern side of Hawaii’s “Big Island,” managed by the Hawaii Division of Forestry and Wildlife (DOFAW). More than 18,000 acres in size, the NAR is home to a rainforest with many native species, some of them endangered. It was established to protect some of the Big Island’s best wet native forest and unique geologic features.

Network), NEON (National Ecological Observatory [N↗
DOE OSTI2020

Critical habitat identification of peripheral Sage Thrashers under climate change

Abstract The Sage Thrasher ( Oreoscoptes montanus ) has been assessed as “Endangered” in Canada since 1992. Like other species with a geographic range that barely extends into Canada, Sage Thrashers are rare. Thirty‐one percent of Canada's bird species listed for recovery under the Canadian Species at Risk Act (SARA) are at the periphery of their range. A listing of “endangered” under SARA requires identification of critical habitat for the species. With anticipated climate change, recovery of species requires a more proactive intervention than relying on historical occurrence to locate suitable habitat. We synthesized 19 years of Sage Thrasher occurrence and related habitat data across the species' northern range in British Columbia (BC) and Washington (WA) to define critical habitat characteristics. We found Sage Thrashers selected less leaf litter and less grass cover in flat or low‐slope regions farther from anthropogenic or natural habitat breaks; habitat sensitive to the expected climate change impacts of fire, changes in precipitation, and invasive species establishment. By augmenting the BC data collected in the species' peripheral range with data from their core distribution in WA, we identified key habitat elements of an otherwise data‐poor species that do not breed in sufficient numbers in Canada to reliably characterize their habitat. These methods improve the identification of “critical habitat” for peripheral species like Sage Thrashers in preparation for climate‐induced range expansion northward. The framework developed demonstrates a useful template for conservation strategies for data‐limited peripheral populations in other regions. Focusing on the landscape‐level variables that indicate good habitat, and not the locations of habitat, can identify suitable future areas for conservation.

Millikin, Rhonda L.↗
DOE OSTI2021

Towards Resolving the Risk of Turbine Collision on Fish: FY21-22 Seedling Report Phase I

The most important concern for permitting tidal and river turbines is the collision risk of marine animals with the turbine blades. Our understanding of the risk to individual fish from colliding with turbine blades is poor; if these collisions were to occur, it is unknown whether fish will sustain recoverable injuries or be killed. Equally unknown is the impact these collisions might have on populations, particularly for threatened, endangered, or commercially managed fish species. In addition to observations of interactions of fish with turbines, numerical models need to be developed or expanded to predict impacts on fish populations. These models could replace expensive and technically challenging monitoring programs in high energy, often murky, tidal or river waters. In this project, a multi-pronged approach was taken to understand the state of knowledge for collision risk of fish with turbines and build a pathway forward. This approach included a workshop with experts, a literature review of modeling and empirical studies, the development of a research framework, and the identification of case studies to address through future work. This project is a first step towards the future development of effective and robust numerical models for assessing the collision risk of fish around turbines. This will achieve a balanced and improved estimate of the severity of collision risk to fish at the population scale.

Garavelli, Lysel↗
DOE OSTI2022

Conflicts of Greens’ in Renewable Energy Landscapes: Case Studies and a Planning Framework

Reducing greenhouse gas emissions (GHG) through renewable energy deployment is a goal for many cities and nations to mitigate the effects of a rapidly changing climate while securing energy needs. Given national and state level policies on green energy to achieve GHG reduction targets, localities are considering utility-scale renewable energy (USRE) facilities on remote lands, rural areas, oceans, coastal waters and large rivers to meet the energy needs for urban residents and industries. Although these USRE facilities generate much “greener” electricity than fossil fuel power plants, locating them can pose conflicts with wildlife, including endangered, threatened and/or special status species, and the habitats that support wildlife populations (Brunette et al., 2013; Gasparatos et al. 2016; Mulvaney 2017), which lead to a “Conflict of Greens” (Ko et al., 2011). In addition to ecological impacts, conflicts over social and cultural resources in local communities lead to concerns over environmental justice, in this context “energy justice,” where negative environmental, social, and economic impacts of energy projects fall more heavily upon marginalized, vulnerable, or indigenous communities. The Pacific Rim region is a center of major and growing economies, and it has become a battlefield for competing “green” objectives. In addition to progressive renewable energy goals, such as in California, Hawaii, and Taiwan, countries around the Pacific Rim have the majority of the growth in manufacturing of wind and solar energy devices and also some of the highest levels of renewables deployment with China, India, and the US leading the way in wind and solar installations. Developing renewable energy source in the ocean such as offshore wind, tidal, and wave energy, are beginning to add to this mix. Given this challenge, the APRU SCL energy working group provides six case studies that address questions about the “Conflict of Greens” across the Pacific Rim including South Korea, Taiwan, and the United States (California, Hawaii, and Massachusetts). The literature review highlights the emerging ecological, social, and economic aspects of conflicts over siting renewables on the landscape. Using case studies, we examine the trial and errors in least-conflict spatial planning, data collection and analysis, public participation in decision-making, mitigation, social planning for energy transitions, and multi-scalar approaches. Lastly, we recommend interdisciplinary policy, planning, and design actions for sustainable energy landscapes across the Pacific Rim and beyond.

green versus green, renewable energy↗
DOE OSTI2021

Group size mediates effects of intraspecific competition and forest structure on productivity in a recovering social woodpecker population

Conservation of endangered social wildlife in disturbance-prone forests is challenging because direct and indirect effects of management strategies developed at the time of species’ listing when population density is low may change under high-density conditions in locally recovered populations. Here, we used piecewise structural equation modeling to evaluate direct and indirect drivers of productivity in the federally endangered cooperatively breeding red-cockaded woodpecker Dryobates borealis (RCW) on Savannah River Site, South Carolina, USA. We estimated direct and indirect relationships among group size, neighboring group sizes, fledgling production, density of cavity tree clusters occupied by RCWs, area satisfying threshold criteria of ≥22 stems ha –1 of pines ≥35.6 cm diameter at breast height (dbh), <1.4 m 2 ha –1 basal area (BA) of hardwoods 7.6–22.9 cm dbh, and <6% hardwood canopy cover, and area treated with prescribed fire, and tested whether group size mediated indirect effects of area satisfying threshold criteria on fledgling production. Increases in area with ≥22 stems ha –1 of pines ≥35.6 cm dbh and <1.4 m 2 ha –1 BA of hardwoods 7.6–22.9 cm dbh, and area treated with prescribed fire, but not area with <6% hardwood canopy cover, had direct positive effects on group size. Group size and area treated with prescribed fire, but not area satisfying threshold criteria, had direct positive effects on fledgling production. The direct effect of neighboring group sizes on fledgling production was negative and smaller relative to the direct positive effect of group size on fledgling production. Overall, our results indicate positive direct effects of group size on fledgling production outweighed negative direct effects of neighboring group sizes, and that group size mediated positive indirect effects of area satisfying structural threshold criteria on fledgling production. These findings indicate that ongoing forest management aimed to increase area with ≥22 pines ha –1 ≥35.6 cm dbh and <1.4 m 2 ha –1 BA of hardwoods 7.6–22.9 cm dbh will promote large group sizes, which in turn improve fledgling production and offset costs of heightened competition with neighboring groups under high-density conditions. Additionally, positive effects of area treated with prescribed fire on RCW group size and fledgling production indicate prescribed fire has unique contributions to woodpecker productivity, likely via direct effects on forest structure and potentially indirect effects on arthropod prey available to foraging RCWs. Furthermore, by simultaneously accounting for multiple drivers of productivity in social wildlife, our study contributes to the understanding of how increases in social wildlife population sizes can alter previously documented habitat-fitness relationships.

prescribed fire↗
DOE OSTI2022

Modeling the distribution of the endangered Jemez Mountains salamander (Plethodon neomexicanus) in relation to geology, topography, and climate

The Jemez Mountains salamander (Plethodon neomexicanus; hereafter JMS) is an endangered salamander restricted to the Jemez Mountains in north-central New Mexico, United States. This strictly terrestrial and lungless species requires moist surface conditions for activities such as mating and foraging. Threats to its current habitat include fire suppression and ensuing severe fires, changes in forest composition, habitat fragmentation, and climate change. Forest composition changes resulting from reduced fire frequency and increased tree density suggest that its current aboveground habitat does not mirror its historically successful habitat regime. However, because of its limited habitat area and underground behavior, we hypothesized that geology and topography might play a significant role in the current distribution of the salamander. We modeled the distribution of the JMS using a machine learning algorithm to assess how geology, topography, and climate variables influence its distribution. The best habitat suitability model indicates that geology type and maximum winter temperature (November to March) were most important in predicting the distribution of the salamander (23.5% and 50.3% permutation importance, respectively). Minimum winter temperature was also an important variable (21.4%), suggesting this also plays a role in salamander habitat. Our habitat suitability map reveals low uncertainty in model predictions, and we found slight discrepancies between the designated critical habitat and the most suitable areas for the JMS. Because geological features are important to its distribution, we recommend that geological and topographical data are considered, both during survey design and in the description of localities of JMS records once detected.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2021

Maine Ecological Forecasting: Using NASA Earth Observations to Assess Federally Endangered Atlantic Salmon Habitat in Maine

Atlantic salmon (Salmo salar) is a species of anadromous fish that was historically prevalent throughout the New England region. Overfishing and habitat loss caused a severe decline in the salmon population, restricting North America’s remaining wild Atlantic salmon to rivers in Maine. Land use and land cover (LULC) change and factors associated with temperature and precipitation are important for understanding the suitability of freshwater habitat for juvenile salmon. In collaboration with the Maine Department of Marine Resources and the Downeast Salmon Federation, the team utilized NASA Earth observations to aid partners in understanding how these factors change in relation to critical salmon habitat. Landsat 5 Thematic Mapper (TM) and Landsat 8 Operational Land Imager (OLI) imagery was analyzed to assess changes in LULC between 1985 and 2021. Terra Moderate Resolution Imaging Spectroradiometer (MODIS) and Integrated Multi-satellite Retrievals for Global Precipitation Measurement (GPM IMERG) data were used to determine land surface temperature and precipitation, respectively; between 2000 and 2020. Lastly, temperature and precipitation anomaly maps visualized deviation from the 20-year climatic average for each pixel. LULC analysis for 1985 to 2020 showed a loss of forest cover throughout critical salmon habitat although gains in forested area were also observed. Assessment of mean summer land surface temperature revealed an increase in temperature from 2000 to 2020 and anomaly maps highlighted areas experiencing abnormally high or low summer precipitation and temperature. These results and the underlying data were packaged for the partner organizations to inform future conservation efforts.

Michael Corley↗
DOE OSTI2021

Small Mammal Trapping Survey for the Lawrence Livermore National Laboratory Site 300 and Corral Hollow Ecological Reserve

ECORP Consulting, Inc. conducted a nocturnal small mammal trapping survey within Lawrence Livermore National Laboratory’s (LLNL) Site 300 and the adjacent California Department of Fish and Wildlife (CDFW) Corral Hollow Ecological Reserve. Both sites are located east of the City of Livermore and southwest of the City of Tracy, Alameda and San Joaquin Counties, California (Figure 1-1). A small mammal trapping survey of the project site was conducted in 2002 in preparation for the 2005 LLNL Site-Wide Environmental Impact Statement (SWEIS; Jones & Stokes 2003). The San Joaquin pocket mouse (Perognathus inornatus) was the only special-status species (federal species of concern) captured on Site 300 during the study (West and Woollett 2003). However, since then P. inornatus was taxonomically split into separate subspecies and the pocket mouse species identified on Site 300 in 2002 is no longer considered a special-status species. The 2002 survey also captured woodrats, but identification of the subspecies was not possible. Further investigation was necessary to determine if the woodrat species on the project site was the federally listed (endangered) riparian (San Joaquin Valley) woodrat (Neotoma macrotis riparia [Formerly described as Neotoma fuscipes riparia]), the common Diablo Range woodrat (N. f. perplexa), or another form.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Burrowing Owl Conservation Report: 2020

The Western Burrowing Owl (Athene cunicularia) is a small migratory species of owl found throughout the Western United States. Burrowing Owls are found throughout a variety of habitats including shrubsteppe; and during the breeding season the Hanford Site is situated at the center of the predicted distribution of Burrowing Owls in Washington State (Smith et al. 1997). The Western Burrowing Owl is declining over much of its range, including on the Hanford Site and throughout the Columbia Basin (HNF-59375, Conway 2006). These declines have been attributed to habitat loss and a subsequent loss in burrowing mammals that the owls depend on for nesting habitat (Conway et al. 2006, Johnson et al. 2010). The Washington State Department of Fish and Wildlife lists Western Burrowing Owls as a Candidate Species, meaning the species is a candidate for listing as Sensitive, Threatened, or Endangered in Washington (WDFW 2020). Without intervention, continued declines may result in the extirpation of Burrowing Owls from the Hanford Site and the Columbia Basin.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Financial Analysis of the Smallmouth Bass Flows implemented at the Glen Canyon Dam during Water Year 2024

The Glen Canyon Dam (GCD) is a Colorado River Storage Project (CRSP) power resource that is a component of the Salt Lake City Area Integrated Projects (SLCA/IP). The 2016 record of decision (ROD) for the GCD long-term experimental and management plan (LTEMP) final Environmental Impact Statement (EIS) specifies criteria for GCD monthly water releases, daily and hourly operating limits, and experimental releases. This report presents a financial analysis of the Smallmouth bass (Micropterus dolomieu) (SMB) flows implemented at GCD during Water Year (WY) 2024. These bypass flows were introduced by the U.S. Bureau of Reclamation (USBR) as an emergency response to the growing threat posed by invasive SMB in the Colorado River ecosystem downstream of the dam. SMB are a non-native predatory species that pose a significant threat to native fish populations, including the endangered humpback chub (Gila cypha). The thermal regime below GCD, typically cold due to hypolimnetic releases from Lake Powell, has historically served as a thermal barrier limiting SMB establishment. However, persistently low reservoir levels in recent years have reduced stratification in Lake Powell, allowing warmer water to be released downstream. This has enabled SMB to spawn successfully below the dam, prompting urgent ecological concerns. To mitigate the risk of SMB proliferation, the USBR implemented a series of bypass flows in WY 2024. Drawn from a lower elevation than the penstocks, the bypass structures released cooler water downstream. These short-duration bypass flows aimed to keep temperatures cool enough to prevent SMB from spawning, thereby reducing the ecological threat posed by this invasive species. Although motivated by ecological objectives, these bypass flows came with financial tradeoffs. Releasing water through the bypass structures instead of the turbines at GCD reduced hydropower generation, resulting in a significantly lower financial position for Western Area Power Administration (WAPA), which is responsible for marketing the electricity produced by the GCD Powerplant. This report analyzes the financial impact of the SMB flows implemented from July to November 2024. These experimental releases led to an estimated financial cost of approximately $18.9 million, primarily driven by the substantial volume of water diverted through the bypass structures. This study applies an integrated set of tools to estimate WAPA financial impacts by simulating GCD under two types of cases; namely, (1) a “With Experiment” case that mimics the water operations that actually occurred, including the SMB bypass flows, and (2) a “Without Experiment” case that simulates operations under the assumption that the SMB flows did not occur. Both cases comply with LTEMP hourly and daily operating criteria, and the monthly water release volumes are assumed to be identical under both cases. The Colorado River Storage Project Python-based model (CRiSPPy) model was the main modeling tool used to simulate the dispatch of the GCD hydropower plant and associated water releases from Lake Powell. In the modeling process, the research team used extensive data sets and historical information on SLCA/IP power plant characteristics, hydrologic conditions, and WAPA’s power purchases and sales prices.

13 HYDRO ENERGY↗
NASA NTRS2015

50-Year Window to Establish a Space Faring Civilization

Humankind may only have a short window of 50 years to become a space-faring civilization, after which time the opportunity to do so may become too difficult or impractical to pursue. Current policies for space exploration and infrastructure development implicitly assume a gradualistic approach to technology, budgets, and mission execution -- the common thought has been that there will be plenty of time in humankind's future to become a space-based species, and whatever we are unable to accomplish will be borne by the generations that follow. However, considering natural events, available energy, and human tendencies, the timing to make the most effective effort to achieve multi-planet status might be now, before momentum is lost and we become distracted by Peak Oil and changing energy economies -- restarting a space program after such turmoil may be more difficult than would be practical without cheap, storable, high-energy density petroleum. "Space-faring civilization" is defined as an economically profitable space-based economy that demands the presence of humans off-world in order to sustain a high level of prosperity. An initial foothold for a space-based economy that would fit within the 50-year window might include Earth dependence on rare-earth elements or other hard-to-obtain minerals mined from moons or asteroids, or a permanent settlement on another planet. Using published sources, notional mass and energy requirements for a minimal self-sustaining Mars settlement is calculated, and the number of launch vehicles discussed. Setting the launch schedule to match that of current NASA projections, it could take more than 26 years of semi-annual launches to build up such a self-sustaining human settlement -- a cost and commitment that has not been acknowledged nor planned for. Considering the time required to establish a multi-planet species, this paper frames the required window of decision that, if not taken, could condemn the species to Earth subject to whatever natural or human-made calamities that endanger single-planet civilizations.

human exploration↗
DOE OSTI2021

Chemical compositions, pharmacological activities, quality control studies of Erycibes plants, and the development of their substitutes

Erycibes are members of the Convolvulaceae family, including more than 10 species worldwide that are distributed in tropical Asia. Some Erycibes species have long been used as traditional remedies for rheumatoid arthritis, fever, hepatitis, and liver injury in China and Thailand. A total of 152 compounds from Erycibes plants have been isolated and identified, categorized as flavonoids, coumarins, quinic acid derivatives, lignans, and alkaloids. Coumarins are the characteristic and active constituents of this species, including scopoletin and scopolin. Modern pharmacological studies have shown that the extracts and bioactive components of Erycibes plants exhibit several biological activities, including antiinflammatory, analgesic, hepatoprotective, anti‐gout, antitumor, antioxidation, and other therapeutic effects. However, in recent years, due to destructive exploitation and utilization, some Erycibes plants' natural resources have become rare or endangered. Developing substitutes is a strategy to alleviate the pressure on those endangered medicinal plant resources. To provide a scientific basis for the development and protection of those threatened Erycibes species, this review summarized the current status of the chemical compositions, pharmacological activities, quality control studies, and the development of substitutes for Erycibes plants. In particular, the rationale for use of Porana sinensis currently on the market is discussed.

Peng, Yu↗
NASA NTRS1996

A Conservation Strategy for the Florida Scrub-Jay on John F. Kennedy Space Center/Merritt Island National Wildlife Refuge: An Initial Scientific Basis for Recovery

The Florida Scrub-Jay (Aphelocoma coerulescens) is an indicator of ecosystem integrity of Florida scrub, an endangered ecosystem that requires frequent fire. One of the largest populations of this federally threatened species occurs on John F. Kennedy Space Center/Merritt Island National Wildlife Refuge. Population trends were predicted using population modeling and field data on reproduction and survival of Florida Scrub-Jays collected from 1988 - 1995. Analyses of historical photography indicated that habitat suitability has been declining for 30 years. Field data and computer simulations suggested that the population declined by at least 40% and will decline by another 40% in 1 0 years, if habitat management is not greatly intensified. Data and computer simulations suggest that habitat suitability cannot deviate greatly from optimal for the jay population to persist. Landscape trajectories of vegetation structure, responsible for declining habitat suitability, are associated with the disruption of natural fire regimes. Prescribed fire alone can not reverse the trajectories. A recovery strategy was developed, based on studies of Florida Scrub-Jays and scrub vegetation. A reserve design was formulated based on conservation science principles for scrub ecosystems. The strategy emphasizes frequent fire to restore habitat, but includes mechanical tree cutting for severely degraded areas. Pine thinning across large areas can produce rapid increases in habitat quality. Site-specific strategies will need to be developed, monitored, and modified to achieve conditions suitable for population persistence.

Breininger, D. R.↗
DOE OSTI2024

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids,Acropora palmataandA. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genusAcroporaexhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from oneA. palmatafamily and 16A. cervicornisfamilies using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM forA. palmataandA. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the AtlanticAcropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Biotechnology & Applied Microbiology↗
DOE OSTI2021

Estimating carrying capacity for juvenile salmon using quantile random forest models

Abstract Establishing robust methods and metrics to evaluate habitat quality is critical for the recovery of endangered Pacific salmonids ( Oncorhynchus spp.). A variety of modeling approaches are used for status and trend monitoring of anadromous species throughout the Pacific Northwest, USA, but current methods may fail to capture the complex relationship between fish and habitat and are often limited in predictive power beyond specific watersheds. Further, the focus on species distribution and abundance is not easily manipulated to predict carrying capacity and traditional stock‐recruitment analyses are reliant on long‐term data which are not always available. In this study, we developed a quantile random forest model to provide estimates of habitat carrying capacity for Chinook salmon ( O. tshawytscha ) parr during the summer months, at both the site and watershed scale. Quantile random forest models allow for the consideration of noisy data, correlated variables, and non‐linear relationships: common features in fish–habitat datasets. We leveraged Columbia Habitat Monitoring Program data to select habitat co‐variates and predict capacity at those sites. We also identified a set of globally available attributes to extrapolate capacity estimate predictions throughout wadeable streams within the Columbia River basin. Total capacity estimates for watersheds closely matched estimates from alternative fish productivity models. Carrying capacity estimates based on quantile random forest models, like those presented here, provide managers a framework to guide the identification, prioritization, and development of habitat rehabilitation actions to recover salmon populations.

See, Kevin E.↗