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USGS2024

Population genetics of museum specimens indicate decreasing genetic resiliency: The case of two bumble bees of conservation concern

Genetic resiliency is the likelihood that populations retain sufficient genetic diversity to respond to environmental change. It is rarely examined through time in conservation genetic studies due to challenges of acquiring and sequencing historical specimens. Focusing on populations of two sibling bumble bee species of conservation concern with different recent patterns of decline, we used museum specimens collected between 1960 and 2020 and 15 microsatellite markers to assess genetic resiliency (allelic richness, expected heterozygosity, and inbreeding) through time and across geographic space. We find evidence of decreasing allelic richness through time, starting at least 30 years before observed abundance declines in one species and at least 20 years before present in a species with apparently stable abundance. We also found increasing expected heterozygosity through time, indicating increased inbreeding, in the putatively stable species. We demonstrate that genetic measurements taken from specimens collected through time can be used to detect population decline in imperiled species before decreases in abundance are detected. We also demonstrate the importance of interpreting population genetic metrics within the context of historical patterns to assess species' conservation statuses. Finally, we discuss the limitations of currently available population genetic methods, including the influence of isolation by distance and sampling density on measurements of genetic structure, and the influence of demographic characteristics and choice of genetic markers on estimates of genetic diversity and structure. We call for further development of individual-based modeling methods to measure genetic structure, as opposed to commonly applied population-based metrics, to overcome these limitations.

Biological Conservation↗

USGS2013

Next generation of global land cover characterization, mapping, and monitoring

Land cover change is increasingly affecting the biophysics, biogeochemistry, and biogeography of the Earth's surface and the atmosphere, with far-reaching consequences to human well-being. However, our scientific understanding of the distribution and dynamics of land cover and land cover change (LCLCC) is limited. Previous global land cover assessments performed using coarse spatial resolution (300 m–1 km) satellite data did not provide enough thematic detail or change information for global change studies and for resource management. High resolution (∼30 m) land cover characterization and monitoring is needed that permits detection of land change at the scale of most human activity and offers the increased flexibility of environmental model parameterization needed for global change studies. However, there are a number of challenges to overcome before producing such data sets including unavailability of consistent global coverage of satellite data, sheer volume of data, unavailability of timely and accurate training and validation data, difficulties in preparing image mosaics, and high performance computing requirements. Integration of remote sensing and information technology is needed for process automation and high-performance computing needs. Recent developments in these areas have created an opportunity for operational high resolution land cover mapping, and monitoring of the world. Here, we report and discuss these advancements and opportunities in producing the next generations of global land cover characterization, mapping, and monitoring at 30-m spatial resolution primarily in the context of United States, Group on Earth Observations Global 30 m land cover initiative (UGLC).

International Journal of Applied Earth Observation↗

USGS2020

What processes must we understand to forecast regional-scale population dynamics?

An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools.

Proceedings of the Royal Society B: Biological Sci↗

USGS2018

Assessment of Alaska rain-on-snow events using dynamical downscaling

The ice formed by cold-season rainfall or rain on snow (ROS) has striking impacts on the economy and ecology of Alaska. An understanding of the atmospheric drivers of ROS events is required to better predict them and plan for environmental change. The spatially/temporally sparse network of stations in Alaska makes studying such events challenging, and gridded reanalysis or remote sensing products are necessary to fill the gaps. Recently developed dynamically downscaled climate data provide a new suite of high-resolution variables for investigating historical and projected ROS events across all of Alaska from 1979 to 2100. The dynamically downscaled reanalysis data of ERA-Interim replicated the seasonal patterns of ROS events but tended to produce more rain events than in station observations. However, dynamical downscaling reduced the bias toward more rain events in the coarse reanalysis. ROS occurred most frequently over southwestern and southern coastal regions. Extreme events with the heaviest rainfall generally coincided with anomalous high pressure centered to the south/southeast of the locations receiving the event and warm-air advection from the resulting southwesterly wind flow. ROS events were projected to increase in frequency overall and for extremes across most of the region but were expected to decline over southwestern/southern Alaska. Increases in frequency were projected as a result of more frequent winter rainfall, but the number of ROS events may ultimately decline in some areas as a result of temperatures rising above the freezing threshold. These projected changes in ROS can significantly affect wildlife, vegetation, and human activities across the Alaska landscape.

Alaska↗

USGS2022

Human populations in the world’s mountains: Spatio-temporal patterns and potential controls

Changing climate and human demographics in the world's mountains will have increasingly profound environmental and societal consequences across all elevations. Quantifying current human populations in and near mountains is crucial to ensure that any interventions in these complex social-ecological systems are appropriately resourced, and that valuable ecosystems are effectively protected. However, comprehensive and reproducible analyses on this subject are lacking. Here, we develop and implement an open workflow to quantify the sensitivity of mountain population estimates over recent decades, both globally and for several sets of relevant reporting regions, to alternative input dataset combinations. Relationships between mean population density and several potential environmental covariates are also explored across elevational bands within individual mountain regions (i.e. sub-mountain range scale). Globally, mountain population estimates vary greatly from 0.344 billion (<5% of the corresponding global total) to 2.289 billion (>31%) in 2015. A more detailed analysis using one of the population datasets (GHS-POP) revealed that in 35% of mountain sub-regions, population increased at least twofold over the 40-year period 19752015. The urban proportion of the total mountain population in 2015 ranged from 6% to 39%, depending on the combination of population and urban extent datasets used. At sub-mountain range scale, population density was found to be more strongly associated with climatic than with topographic and protected-area variables, and these relationships appear to have strengthened slightly over time. Such insights may contribute to improved predictions of future mountain population distributions under scenarios of future climatic and demographic change. Overall, our work emphasizes that irrespective of data choices, substantial human populations are likely to be directly affected by and themselves affect mountainous environmental and ecological change. It thereby further underlines the urgency with which the multitudinous challenges concerning the interactions between mountain climate and human societies under change must be tackled.

PLoS ONE↗

USGS2017

Local adaptation in Trinidadian guppies alters stream ecosystem structure at landscape scales despite high environmental variability

While previous studies have shown that evolutionary divergence alters ecological processes in small-scale experiments, a major challenge is to assess whether such evolutionary effects are important in natural ecosystems at larger spatial scales. At the landscape scale, across eight streams in the Caroni drainage, we found that the presence of locally adapted populations of guppies ( Poecilia reticulata ) is associated with reduced algal biomass and increased invertebrate biomass, while the opposite trends were true in streams with experimentally introduced populations of non-locally adapted guppies. Exclusion experiments conducted in two separate reaches of a single stream showed that guppies with locally adapted phenotypes significantly reduced algae with no effect on invertebrates, while non-adapted guppies had no effect on algae but significantly reduced invertebrates. These divergent effects of phenotype on stream ecosystems are comparable in strength to the effects of abiotic factors (e.g., light) known to be important drivers of ecosystem condition. They also corroborate the results of previous experiments conducted in artificial streams. Our results demonstrate that local adaptation can produce phenotypes with significantly different effects in natural ecosystems at a landscape scale, within a tropical watershed, despite high variability in abiotic factors: five of the seven physical and chemical parameters measured across the eight study streams varied by more than one order of magnitude. Our findings suggest that ecosystem structure is, in part, an evolutionary product and not simply an ecological pattern.

Copeia↗

USGS2019

Characteristics of feeding sites of California Condors (Gymnogyps californianus) in the human-dominated landscape of Southern California

Wildlife conservation is often improved by understanding the movement ecology of species and adapting management strategies to dynamic conditions associated with movement. Despite a remarkable recovery over the past 30 year, the establishment of self-sustaining populations of California Condors (Gymnogyps californianus) has been challenging in the human-dominated landscapes of southern California. Among these challenges are those imposed by condor ground-foraging behavior that exposes them to environmental contamination. These include lead poisoning from the ingestion of spent ammunition and micro-trash ingestion and, during takeoff and landing, collisions with human structures. We tracked 28 California Condors for 24 months with patagially mounted GPS telemetry units to investigate the characteristics of ground sites condors visited and to identify spatiotemporal trends that might aid in conservation of this critically endangered species. Ground sites occurred on a wide variety of land cover types, primarily on steep slopes, and those more frequently used were associated with open cover. Condors concentrated their visits to ground sites around a 3 h period near midday, and usage increased from winter to late summer. Our study is the first to use remotely sensed telemetry data to describe fine-scale ecological correlates of condor ground-foraging ecology and therefore has important relevance for ongoing conservation and management strategies for this species. The descriptions of ground sites we provide can be used to target conservation or management actions.

California↗

USGS2011

An adaptive approach to invasive plant management on U.S. Fish and Wildlife Service-owned native prairies in the Prairie Pothole Region: decision support under uncertainity

Much of the native prairie managed by the U.S. Fish and Wildlife Service (Service) in the Prairie Pothole Region (PPR) is extensively invaded by the introduced cool-season grasses smooth brome (Bromus inermis) and Kentucky bluegrass (Poa pratensis). The central challenge to managers is selecting appropriate management actions in the face of biological and environmental uncertainties. We describe the technical components of a USGS management project, and explain how the components integrate and inform each other, how data feedback from individual cooperators serves to reduce uncertainty across the whole region, and how a successful adaptive management project is coordinated and maintained on a large scale. In partnership with the Service, the U.S. Geological Survey is developing an adaptive decision support framework to assist managers in selecting management actions under uncertainty and maximizing learning from management outcomes. The framework is built around practical constraints faced by refuge managers and includes identification of the management objective and strategies, analysis of uncertainty and construction of competing decision models, monitoring, and mechanisms for model feedback and decision selection. Nineteen Service field stations, spanning four states of the PPR, are participating in the project. They share a common management objective, available management strategies, and biological uncertainties. While the scope is broad, the project interfaces with individual land managers who provide refuge-specific information and receive updated decision guidance that incorporates understanding gained from the collective experience of all cooperators.

Prairie Pothole Region↗

USGS2014

Partners in amphibian and reptile conservation 2013 annual report

Partners in Amphibian and Reptile Conservation (PARC) was established in 1999 to address the widespread declines, extinctions, and range reductions of amphibians and reptiles, with a focus on conservation of taxa and habitats in North America. Amphibians and reptiles are affected by a broad range of human activities, both as incidental effects of habitat alteration and direct effect from overexploitation; these animals are also challenged by the perception that amphibians and reptiles are either dangerous or of little environmental or economic value. However, PARC members understand these taxa are important parts of our natural an cultural heritage and they serve important roles in ecosystems throughout the world. With many amphibians and reptiles classified as threatened with extinction, conservation of these animals has never been more important.

Annual Report↗

USGS2014

To understand coral disease, look at coral cells

Diseases threaten corals globally, but 40 years on their causes remain mostly unknown. We hypothesize that inconsistent application of a complete diagnostic approach to coral disease has contributed to this slow progress. We quantified methods used to investigate coral disease in 492 papers published between 1965 and 2013. Field surveys were used in 65% of the papers, followed by biodetection (43%), laboratory trials (20%), microscopic pathology (21%), and field trials (9%). Of the microscopic pathology efforts, 57% involved standard histopathology at the light microscopic level (12% of the total investigations), with the remainder dedicated to electron or fluorescence microscopy. Most (74%) biodetection efforts focused on culture or molecular characterization of bacteria or fungi from corals. Molecular and immunological tools have been used to incriminate infectious agents (mainly bacteria) as the cause of coral diseases without relating the agent to specific changes in cell and tissue pathology. Of 19 papers that declared an infectious agent as a cause of disease in corals, only one (5%) used microscopic pathology, and none fulfilled all of the criteria required to satisfy Koch’s postulates as applied to animal diseases currently. Vertebrate diseases of skin and mucosal surfaces present challenges similar to corals when trying to identify a pathogen from a vast array of environmental microbes, and diagnostic approaches regularly used in these cases might provide a model for investigating coral diseases. We hope this review will encourage specialists of disease in domestic animals, wildlife, fish, shellfish, and humans to contribute to the emerging field of coral disease.

EcoHealth↗

USGS2018

Occupancy modeling of autonomously recorded vocalizations to predict distribution of rallids in tidal wetlands

Conservation and management for a species requires reliable information on its status, distribution, and habitat use. We identified occupancy and distributions of king ( Rallus elegans ) and clapper ( R. crepitans ) rail populations in marsh complexes along the Pamunkey and Mattaponi Rivers in Virginia, USA by modeling data on vocalizations recorded from autonomous recording units (ARUs). Occupancy probability for both species combined was 0.64 (95% CI: 0.53, 0.75) in marshes along the Pamunkey and 0.59 (0.45, 0.72) in marshes along the Mattaponi. Occupancy probability along the Pamunkey was strongly influenced by salinity, increasing logistically by a factor of 1.62 (0.6, 2.65) per parts per thousand of salinity. In contrast, there was not a strong salinity gradient on the Mattaponi and therefore vegetative community structure determined occupancy probability on that river. Estimated detection probability across both marshes was 0.63 (0.62, 0.65), but detection rates decreased as the season progressed. Monitoring wildlife within wetlands presents unique challenges for conservation managers. Our findings provide insight not only into how rails responded to environmental variation but also into the general utility of ARUs for occupancy modeling of the distribution and habitat associations of rails within tidal marsh systems.

Virginia↗

USGS2006

Overview of the Opportunity Mars Exploration Rover Mission to Meridiani Planum: Eagle Crater to Purgatory Ripple

The Mars Exploration Rover Opportunity touched down at Meridiani Planum in January 2004 and since then has been conducting observations with the Athena science payload. The rover has traversed more than 5 km, carrying out the first outcrop‐scale investigation of sedimentary rocks on Mars. The rocks of Meridiani Planum are sandstones formed by eolian and aqueous reworking of sand grains that are composed of mixed fine‐grained siliciclastics and sulfates. The siliciclastic fraction was produced by chemical alteration of a precursor basalt. The sulfates are dominantly Mg‐sulfates and also include Ca‐sulfates and jarosite. The stratigraphic section observed to date is dominated by eolian bedforms, with subaqueous current ripples exposed near the top of the section. After deposition, interaction with groundwater produced a range of diagenetic features, notably the hematite‐rich concretions known as “blueberries.” The bedrock at Meridiani is highly friable and has undergone substantial erosion by wind‐transported basaltic sand. This sand, along with concretions and concretion fragments eroded from the rock, makes up a soil cover that thinly and discontinuously buries the bedrock. The soil surface exhibits both ancient and active wind ripples that record past and present wind directions. Loose rocks on the soil surface are rare and include both impact ejecta and meteorites. While Opportunity's results show that liquid water was once present at Meridiani Planum below and occasionally at the surface, the environmental conditions recorded were dominantly arid, acidic, and oxidizing and would have posed some significant challenges to the origin of life.

Journal of Geophysical Research E: Planets↗

USGS2021

Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed)

The rapid invasion of the non-native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native wetland ecosystems in North America and elsewhere. We describe the first reference genome for P . australis and compare invasive (ssp. australis ) and native (ssp. americanus ) genotypes collected from replicated populations across the Laurentian Great Lakes to deduce genomic bases driving its invasive success. Here, we report novel genomic features including a Phragmites lineage-specific whole genome duplication, followed by gene loss and preferential retention of genes associated with transcription factors and regulatory functions in the remaining duplicates. Comparative transcriptomic analyses revealed that genes associated with biotic stress and defence responses were expressed at a higher basal level in invasive genotypes, but native genotypes showed a stronger induction of defence responses when challenged by a fungal endophyte. The reference genome and transcriptomes, combined with previous ecological and environmental data, add to our understanding of mechanisms leading to invasiveness and support the development of novel, genomics-assisted management approaches for invasive Phragmites .

Michigan, Ohio↗

USGS2014

The changing role of history in restoration ecology

In the face of rapid environmental and cultural change, orthodox concepts in restoration ecology such as historical fidelity are being challenged. Here we re-examine the diverse roles played by historical knowledge in restoration, and argue that these roles remain vitally important. As such, historical knowledge will be critical in shaping restoration ecology in the future. Perhaps the most crucial role in shifting from the present version of restoration ecology (“v1.0”) to a newer formulation (“v2.0”) is the value of historical knowledge in guiding scientific interpretation, recognizing key ecological legacies, and influencing the choices available to practitioners of ecosystem intervention under conditions of open-ended and rapid change.

Frontiers in Ecology and the Environment↗

USGS2003

Infectivity and pathogenicity of the oomycete Aphanomyces invadans in Atlantic menhaden Brevoortia tyrannus

Atlantic menhaden Brevoortia tyrannus develop characteristic skin ulcers in response to infection by the oomycete Aphanomyces invadans . To investigate pathogenicity , we conducted a dose response study. Juvenile menhaden were inoculated subcutaneously with 0, 1, 5, 10, 100, and 500 secondary zoospores per fish and monitored for 37 d post-injection (p.i.). Survival rates declined with increasing zoospore dose, with significantly different survivorship curves for the different doses. Moribund and dead fish exhibited characteristic ulcerous lesions at the injection site starting at 13 d p.i. None of the sham-injected control fish (0 zoospore treatment) died. The LD 50 (lethal dose killing 50% of exposed menhaden ) for inoculated fish was estimated at 9.7 zoospores; however, some fish receiving an estimated single zoospore developed infections that resulted in death. Menhaden were also challenged by aqueous exposure and confirmed that A. invadans was highly pathogenic by this more environmentally realistic route. Fish that were acclimated to culture conditions for 30 d, and presumably free of skin damage, then aqueously exposed to 100 zoospores ml -1 , exhibited 14% lesion prevalence with 11% mortality. Net-handled fish that were similarly infected had a significantly higher lesion prevalence (64%) and mortality (64%). Control fish developed no lesions and did not die. Scanning electron microscopy of fish skin indicated that zoospores adhered to intact epidermis, germinated and penetrated the epithelium with a germ tube. Our results indicate that A. invadans is a primary pathogen of menhaden and is able to cause disease at very low zoospore concentrations.

Diseases of Aquatic Organisms↗

USGS2013

Counting at low concentrations: the statistical challenges of verifying ballast water discharge standards

Discharge from the ballast tanks of ships is one of the primary vectors of nonindigenous species in marine environments. To mitigate this environmental and economic threat, international, national, and state entities are establishing regulations to limit the concentration of living organisms that may be discharged from the ballast tanks of ships. The proposed discharge standards have ranged from zero detectable organisms to <10 organisms/m 3 . If standard sampling methods are used, verifying whether ballast discharge complies with these stringent standards will be challenging due to the inherent stochasticity of sampling. Furthermore, at low concentrations, very large volumes of water must be sampled to find enough organisms to accurately estimate concentration. Despite these challenges, adequate sampling protocols comprise a critical aspect of establishing standards because they help define the actual risk level associated with a standard. A standard that appears very stringent may be effectively lax if it is paired with an inadequate sampling protocol. We describe some of the statistical issues associated with sampling at low concentrations to help regulators understand the uncertainties of sampling as well as to inform the development of sampling protocols that ensure discharge standards are adequately implemented.

Ecological Applications↗

USGS2013

In situ spectrophotometric measurement of dissolved inorganic carbon in seawater

Autonomous in situ sensors are needed to document the effects of today’s rapid ocean uptake of atmospheric carbon dioxide (e.g., ocean acidification). General environmental conditions (e.g., biofouling, turbidity) and carbon-specific conditions (e.g., wide diel variations) present significant challenges to acquiring long-term measurements of dissolved inorganic carbon (DIC) with satisfactory accuracy and resolution. SEAS-DIC is a new in situ instrument designed to provide calibrated, high-frequency, long-term measurements of DIC in marine and fresh waters. Sample water is first acidified to convert all DIC to carbon dioxide (CO 2 ). The sample and a known reagent solution are then equilibrated across a gas-permeable membrane. Spectrophotometric measurement of reagent pH can thereby determine the sample DIC over a wide dynamic range, with inherent calibration provided by the pH indicator’s molecular characteristics. Field trials indicate that SEAS-DIC performs well in biofouling and turbid waters, with a DIC accuracy and precision of &sim;2 μmol kg –1 and a measurement rate of approximately once per minute. The acidic reagent protects the sensor cell from biofouling, and the gas-permeable membrane excludes particulates from the optical path. This instrument, the first spectrophotometric system capable of automated in situ DIC measurements, positions DIC to become a key parameter for in situ CO 2 -system characterizations.

Environmental Science & Technology↗

USGS2018

Harnessing big data to rethink land heterogeneity in Earth system models

The continual growth in the availability, detail, and wealth of environmental data provides an invaluable asset to improve the characterization of land heterogeneity in Earth system models – a persistent challenge in macroscale models. However, due to the nature of these data (volume and complexity) and computational constraints, these data are underused for global applications. As a proof of concept, this study explores how to effectively and efficiently harness these data in Earth system models over a 1/4° ( ∼ 25 km) grid cell in the western foothills of the Sierra Nevada in central California. First, a novel hierarchical multivariate clustering approach (HMC) is introduced that summarizes the high-dimensional environmental data space into hydrologically interconnected representative clusters (i.e., tiles). These tiles and their associated properties are then used to parameterize the sub-grid heterogeneity of the Geophysical Fluid Dynamics Laboratory (GFDL) LM4-HB land model. To assess how this clustering approach impacts the simulated water, energy, and carbon cycles, model experiments are run using a series of different tile configurations assembled using HMC. The results over the test domain show that (1) the observed similarity over the landscape makes it possible to converge on the macroscale response of the fully distributed model with around 300 sub-grid land model tiles; (2) assembling the sub-grid tile configuration from available environmental data can have a large impact on the macroscale states and fluxes of the water, energy, and carbon cycles; for example, the defined subsurface connections between the tiles lead to a dampening of macroscale extremes; (3) connecting the fine-scale grid to the model tiles via HMC enables circumvention of the classic scale discrepancies between the macroscale and field-scale estimates; this has potentially significant implications for the evaluation and application of Earth system models.

Hydrology and Earth System Sciences↗