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Geology topics

Jeffery D. Sullivan

Publications and source records attributed to Jeffery D. Sullivan.

At least 19 recordsLinked to original sources
USGS2026

Improved estimates of relative occurrence and abundance using opportunistic surveys and presence-only observations: A zero-inflated integrated species distribution model

Modeling tools for estimating and forecasting shifts in species distributions are becoming increasingly valuable for conservation planning and response. This is especially true for wild bird populations, which have been declining across habitats and regions. Species distribution models (SDM) represent a diverse set of tools with options for addressing various sources of bias. Complex spatial processes associated with rare or clustered species can be accounted for using zero-inflated SDMs, whereas biased survey data can be integrated with additional data sources to improve estimates. Each option addresses an important and common source of bias, but the two SDM frameworks have not been implemented together previously. We present a novel zero-inflated extension of an integrated SDM framework for a Poisson regression (ZI-iSDM), allowing for the estimation of independent occurrence and abundance processes by integrating opportunistic survey and presence-only data. We validated performance of this ZI-iSDM using simulated datasets under different degrees of species rarity and density on the landscape as well as sampling bias in opportunistic datasets. We additionally applied this model to real survey data for multiple wild bird species using publicly available observation data combined with open-access environmental information to describe habitat associations. We found that integrating presence-only data, such as banding or harvest events, can compensate for potential deficiencies in opportunistic surveys by expanding sampling to be more representative of available and used habitat. Additionally, models that first differentiated occurrence and abundance using a ZI term were better suited for approximating distributions of spatially clustered species.

Ecological Modeling↗
USGS2026

Feathers and flu: Identifying data gaps in avian influenza host dynamics to prioritize wildlife conservation

Highly pathogenic avian influenza viruses (HPAIV) have had disastrous, worldwide effects on wild birds and domestic poultry since the emergence of the A/goose/Guangdong/1/1996 (Gs/GD/96) lineage. The currently circulating H5N1 clade 2.3.4.4b has an expanded set of susceptible hosts, including many migratory wild birds, and is associated with higher transmission rates, increased susceptibility among wild bird hosts, and a greater number of wildlife reservoirs. Certain wild bird life-history strategies and behaviors have been suggested to explain avian hosts’ susceptibility and exposure to HPAIV. These biological traits include gregariousness, such as colonial nesting and mixed flock foraging, predation or scavenging on wild birds, and association with aquatic habitats. Variation in host infection responses (e.g., infectability, shedding rates and duration, mortality rate, antibody development) informs the overall infection risk across avian species, yet the specific role of biological traits is often inconsistent and unclear across taxa. Moreover, the interactions and potential compounding effects among these biological traits remain largely unknown. To develop a more holistic understanding of cumulative risk across bird species, we integrate existing information on infection risk factors (i.e., susceptibility, immunological response, and behavioral traits) into a qualitative multivariate analysis. This approach enabled us to examine how infection risk factors relate to biological traits (e.g., phylogeny, physiology, behavior, species range) and to begin disentangling their complex interactions. We quantified and summarized these risk factors across host species and qualitatively ranked species by their viral responses along a proposed HPAIV response continuum, guided by expectations of traits and metrics associated with competence or vulnerability to HPAIV. In doing so, we aimed to better understand how viral responses and biological traits synergistically interact to influence cumulative risk across wild bird species. This work broadly expands on the previous avian influenza literature, which has focused on Anseriformes and Charadriiformes as primary viral reservoirs. We tie our findings to effective disease management responses with links to risk components, including descriptions of potential surveillance strategies applied to research and One Health goals, as well as a fuller understanding of how resources may be better deployed for rapid response when spillovers do inevitably occur. Additionally, we identified numerous areas where vital epidemiological information is lacking to best characterize the spread of these viruses. Ultimately, this improved understanding will help identify and inform disease management needs and decision making.

Wildlife Monographs↗
USGS2026

Waterfowl move less in heterogeneous and human-populated landscapes, with implications for spread of avian influenza viruses

Animal movements contribute to the spread of infectious diseases and are driven in part by environmental conditions. We investigated the links among the environment, animal movement, and infectious disease dynamics in waterfowl, which are among the primary wildlife hosts of avian influenza viruses. By combining telemetry data on 4606 individuals from 26 waterfowl species with data on land cover, weather, and vegetation, we found that waterfowl moved less in areas of higher land cover heterogeneity and higher human population density. Moreover, predicted waterfowl movement distances were weakly but positively correlated with distances between detections of H5N1 highly pathogenic avian influenza in wild waterfowl, suggesting that environmental conditions might contribute to the spread of this disease via their effects on bird movements. By considering wildlife movements alongside other drivers of infectious disease dynamics, such as livestock production and human mobility, we move closer to predicting outbreaks and informing interventions.

Ecology Letters↗
USGS2025

Rapid increase in antibodies to influenza A virus H5 and N1 in Lesser Scaup (Aythya affinis) following the introduction of 2.3.4.4B H5N1 into North America

Clade 2.3.4.4b Eurasian-origin H5N1 entered North America in late 2021 and spread across the continent. While studies have characterized the antibody response mounted by dabbling ducks following exposure, little data are available for diving ducks. This study sought to identify influenza A virus (IAV) infection and antibodies in Lesser and Greater Scaup captured in Maryland, Illinois, and Rhode Island. In Maryland, IAV seroprevalence increased from the 2021/2022 to 2022/2023 sampling season, with IAV antibody prevalence increasing for juvenile (38% to 80%) and adult (82% to 90%) Lesser Scaup. While adult Lesser Scaup sampled in Illinois in 2021/2022 had IAV antibody prevalence comparable to those sampled in Maryland (76% and 82%, respectively), they had higher antibody prevalence to both H5 (48% and 18%) and N1 (68% and 35%), potentially due to being sampled in March versus December and January. Our data suggest that Lesser Scaup had limited antibodies to highly pathogenic H5 IAV prior to the introduction of clade 2.3.4.4b H5N1 to North America, but relevant antibodies were widely observed in the months and year following. Our more limited data suggest similar trends may have occurred in Greater Scaup as well.

Canadian Journal of Microbiology↗
USGS2025

Potential impacts of 2.3.4.4b highly pathogenic H5N1 avian influenza virus infection on Snow Goose (Anser caerulescens) movement ecology

While wild waterfowl are known reservoirs of avian influenza viruses and facilitate the movement of these viruses, there are notable differences in the response to infection across species. This study explored differential responses to infection with highly pathogenic avian influenza in Snow Geese ( Anser caerulescens ) located in the California Central Valley. Though H5 antibody prevalence was high across years among birds sampled in the winter (75% in both years via hemagglutination inhibition), these values were even higher among birds sampled in summer that failed to migrate (i.e., August 2023 = 100% and August 2024 = 93% via hemagglutination inhibition). Birds that failed to migrate were also generally lighter than birds sampled in the winter and presented notable damage to cerebrum and cerebellum. In December 2022, a single individual positive for infection with H5N1 at the time of sampling indicated reduced movement during the 14 days following sampling but completed spring migration comparably with uninfected conspecifics. However, while no birds were actively infected during sampling and marking in 2023, two marked geese departed for migration late and one did not migrate at all. Additional banded birds marked in August have been reencountered in scenarios ranging from hunter harvest at a different site over a year later to found dead shortly after banding. Our data indicate that Snow Geese infected with HPAI have the potential to express variable outcomes following infection with highly pathogenic H5N1, ranging from rapid recovery within a migratory season to death. These data also suggest that the abnormal failure of some Snow Geese to migrate from the Central Valley is likely driven by HPAI infection.

California↗
USGS2025

Perpetuation of avian influenza from molt to fall migration in wild Swan Geese (Anser cygnoides): An agent-based modeling approach

Wild waterfowl are considered to be the reservoir of avian influenza, but their distinct annual life cycle stages and their contribution to disease dynamics are not well understood. Studies of the highly pathogenic avian influenza (HPAI) virus have primarily focused on wintering grounds, where human and poultry densities are high year-round, compared with breeding grounds, where migratory waterfowl are more isolated. Few if any studies of avian influenza have focused on the molting stage where wild waterfowl congregate in a few selected wetlands and undergo the simultaneous molt of wing and tail feathers during a vulnerable flightless period. The molting stage may be one of the most important periods for the perpetuation of the disease in waterfowl, since during this stage, immunologically naïve young birds and adults freely intermix prior to the fall migration. Our study incorporated empirical data from virological field samplings and markings of Swan Geese ( Anser cygnoides ) on their breeding grounds in Mongolia in an integrated agent-based model (ABM) that included susceptible–exposed–infectious–recovered (SEIR) states. Our ABM results provided unique insights and indicated that individual movements between different molting wetlands and the transmission rate were the key predictors of HPAI perpetuation. While wetland extent was not a significant predictor of HPAI perpetuation, it had a large effect on the number of infections and associated death toll. Our results indicate that conserving undisturbed habitats for wild waterfowl during the molting stage of the breeding season could reduce the risk of HPAI transmission.

Viruses↗
USGS2025

Spatiotemporal overlap of mallards with poultry farms is associated with greater risk of avian influenza wild bird spillover events

Animal movement influences local transmission and geographic spread of pathogens. Waterfowl are known reservoirs of pathogens, including H5 goose/Guangdong lineage (H5 GsGd) highly pathogenic avian influenza (HPAI). This HPAI virus lineage causes high rates of morbidity and mortality in domestic poultry and many wild bird species. Mallards ( Anas platyrhynchos ) are a generalist waterfowl species whose habitat largely overlaps with many other waterfowl and are considered effective spillover vectors of HPAI. To investigate the potential contribution of waterfowl to HPAI spillover, we used mallards as a proxy and measured the spatiotemporal overlap of 183 GPS-tagged mallards during 2021–2022 with respect to confirmed wild bird spillover events in United States (U.S.) poultry farms. Additionally, we estimated the probability of HPAI spillover events as a function of mallard overlap and poultry farm type. We found infrequent overlap instances between mallards and poultry farms; however, several of these overlap instances lasted > 5 days and up to 19 days. Population-level overlap with poultry farms was greatest during pre-breeding migration, followed by the breeding season. The probability of HPAI spillover was predicted to be greatest for commercial turkey farms, followed by backyard poultry farms. Importantly, farms overlapped by mallards were more than twice as likely to experience a spillover (i.e., increased risk probability), even in the absence of known mallard infection status at the time of overlap. These findings suggest that mallards (and/or other waterfowl) may be important contributors to HPAI spillover into poultry farms and that additional biosecurity measures may be needed. Because few instances of overlap occurred between mallards and farms with reported spillover events, tagged mallards are likely a proxy for other untagged waterfowl. Further studies of wild waterfowl interactions with poultry farms could improve understanding of how landscape characteristics influence spatial overlap, potentially informing which premises may require enhanced biosecurity measures.

Tennessee↗
USGS2025

Avian influenza spillover into poultry: Environmental influences and biosecurity protections

With the continued spread of highly pathogenic avian influenza (HPAI), understanding the complex dynamics of virus transfer at the wild – agriculture interface is paramount. Spillover events (i.e., virus transfer from wild birds into poultry) are related to proximity to infected wild bird populations and environmental conditions. By accounting for such dynamics, we can take a combined approach to assess the impacts of biosecurity measures implemented at poultry farms while simultaneously accounting for their local risk levels. We implemented a Bayesian joint-likelihood logistic regression for the Continental U.S. comparing models of spatiotemporal risk according to land use, weather, and predicted waterfowl distributions followed by integrating a farm-level case-control questionnaire dataset focused on identifying trends in HPAI spillover risk associated with a farm's biosecurity practices. We found that estimates of waterfowl abundance, along with mean precipitation and temperature during winter, were most correlated with spatiotemporal HPAI risk. Additionally, we identified multiple biosecurity practices associated with reduced risk to HPAI, where the strongest relationships were related to litter decontamination treatments, vehicle wash stations, and avoiding shared dead-bird disposal sites with other farms. This model broadly guides surveillance of HPAI in wild and domestic populations, identifying when and where we are most likely to see increased instances of the virus while also providing insights into how poultry farms can better protect themselves from risk.

contiguous United States↗
USGS2025

Avian influenza infection and antibodies not identified in eastern wild turkeys (Meleagris gallopavo silvestris) sampled on the Delmarva Peninsula

Although highly pathogenic avian influenza presents a notable threat to domestic turkeys ( Meleagris gallopavo domesticus ), there have been minimal infections identified in wild turkeys ( Meleagris gallopavo ) across the United States. Indeed, recent infections in wild turkeys have either been linked back to or suspected to be the result of spillback from nearby infected domestic turkeys. This study presents avian influenza sampling data for Eastern wild turkeys ( Meleagris gallopavo silvestris ) across the Maryland portion of the Delmarva Peninsula, in the winter of 2023–2024, with an objective of identifying any circulating influenza A viruses (IAVs), as well as determining the extent of previous exposure to IAVs in this population. We collected swab samples from 36 female wild turkeys. No IAV viral RNA was detected in any sample, based on real-time reverse transcriptase PCR. We collected sera from 31 of the 36 sampled individuals, all of which had biomimetic enzyme-linked immunosorbent assay (bELISA) S/N values >0.7 (range: 0.79–1.29) indicating a lack of antibodies to IAVs. Although our sample size is limited, these results indicate no evidence of current or recent previous IAV infection in sampled birds.

Maryland↗
USGS2025

Common Terns (Sterna hirundo) use of a staging site in the Chesapeake Bay

In 2021, we initiated fieldwork to assess the relative importance of a staging area for Sterna hirundo (Common Tern) at a pier at the confluence of the Patuxent River and Chesapeake Bay, MD. During the post-breeding periods of 2021 through 2023, we resighted 378 banded Common Terns at this staging area, with individuals originating from 6 breeding colonies. Most banded individuals were from Poplar Island, a major nesting site 50 km north of the pier, with up to 37% of that island's annual hatch-year population observed at this staging area. Additionally, biologists have previously observed staging terns at this site, suggesting these observations do not reflect a change in the species' behavior within the region. Cumulatively, our data suggest that this habitat acts as an important staging area for the Chesapeake Bay's Common Tern population, particularly for those nesting on Poplar Island.

Maryland↗
USGS2024

Identifying the forage base and critical forage taxa for Chesapeake waterbirds

To effectively maximize the conservation value of management plans intended to capture ecosystem-wide health, it is essential to obtain an understanding of emergent patterns in dietary dynamics spanning many species. Chesapeake Bay, USA, is a critical ecosystem used annually by a diverse assortment of waterbird species, including several of conservation concern. However, the ecosystem is threatened by many ecological pressures driven largely by the dense human population of the surrounding region. These issues necessitate proactive monitoring and management efforts to track the health of ecosystems like the Chesapeake Bay. Such monitoring efforts of population dynamics require adequate data on the connections between trophic levels to understand how changes to the forage base might influence higher trophic levels, such as these diverse avian predators. However, we have historically lacked standardized quantitative data drawing these connections at the community level, as well as the relative importance of these taxa in the diet of such predators. We collated existing quantitative data on avian dietary composition to construct a database on the diets of 58 waterbird species that make use of the Chesapeake Bay. From this database, we quantified the relative importance of forage taxa to the diet of each waterbird species. Such data can enable managers to develop a comprehensive suite of forage taxa indicators whose abundance and distributions can be monitored as a proxy for ecosystem health. It is our goal that this database be harnessed as a tool to enable conservation practitioners to prioritize indicator taxa for monitoring purposes, contributing towards conservation plans that best address the health of the ecosystem at large.

Delaware, Maryland, Virginia↗
USGS2024

A systematic review of laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America

The lack of consolidated information regarding the response of wild bird species to infection with avian influenza virus (AIV) is a challenge to both conservation managers and researchers alike, with related sectors also impacted, such as public health and commercial poultry. Using two independent searches, we reviewed published literature for studies describing wild bird species experimentally infected with avian influenza to assess host species’ relative susceptibility to AIVs. Additionally, we summarize broad-scale parameters for elements such as shedding duration and minimum infectious dose that can be used in transmission modelling efforts. Our synthesis shows that waterfowl (i.e. Anatidae) compose the vast majority of published AIV pathobiology studies, whereas gulls and passerines are less represented in research despite evidence that they also are susceptible and contribute to highly pathogenic avian influenza disease dynamics. This study represents the first comprehensive effort to compile available literature regarding the pathobiology of AIVs in all wild birds in over a decade. This database can now serve as a tool to all researchers, providing generalized estimates of pathobiology parameters for a variety of wild avian families and an opportunity to critically examine and assess what is known and identify where further insight is needed.

Proceeding of the Royal Society B↗
USGS2024

Using an adaptive modeling framework to identify avian influenza spillover risk at the wild-domestic interface

The wild to domestic bird interface is an important nexus for emergence and transmission of highly pathogenic avian influenza (HPAI) viruses. Although the recent incursion of HPAI H5N1 Clade 2.3.4.4b into North America calls for emergency response and planning given the unprecedented scale, readily available data-driven models are lacking. Here, we provide high resolution spatial and temporal transmission risk models for the contiguous United States. Considering virus host ecology, we included weekly species-level wild waterfowl (Anatidae) abundance and endemic low pathogenic avian influenza virus prevalence metrics in combination with number of poultry farms per commodity type and relative biosecurity risks at two spatial scales: 3 km and county-level. Spillover risk varied across the annual cycle of waterfowl migration and some locations exhibited persistent risk throughout the year given higher poultry production. Validation using wild bird introduction events identified by phylogenetic analysis from 2022 to 2023 HPAI poultry outbreaks indicate strong model performance. The modular nature of our approach lends itself to building upon updated datasets under evolving conditions, testing hypothetical scenarios, or customizing results with proprietary data. This research demonstrates an adaptive approach for developing models to inform preparedness and response as novel outbreaks occur, viruses evolve, and additional data become available.

contiguous United States↗
USGS2024

Identifying an understudied interface: Preliminary evaluation of the use of retention ponds on commercial poultry farms by wild waterfowl

While the recent incursion of highly pathogenic avian influenza into North America has resulted in notable losses to the commercial poultry industry, the mechanism by which virus enters commercial poultry houses is still not understood. One theorized mechanism is that waterfowl shed virus into the environment surrounding poultry farms, such as into retention ponds, and is then transmitted into poultry houses via bridge species. Little is known about if and when wild waterfowl use these retention ponds, leading to uncertainty regarding the potential significance of this interface. To quantify the use of retention ponds on commercial poultry farms by wild waterfowl, we surveyed 12 such ponds across Somerset and Dorchester counties, Maryland, USA. This region was chosen due to the high level of poultry production and its importance for migratory waterfowl. Surveys consisted of recording waterfowl visible on the retention ponds from public roadways at least once per week from 20 September 2022–31 March 2023. Throughout the course of this study, we observed a total of nine species of waterfowl using retention ponds on commercial poultry farms at nine of 12 sites. The number of waterfowl observed at retention ponds varied notably throughout the course of our survey period, with values generally following trends of fall migration within each species indicating that resident birds were not the only individuals to utilize these habitats. Additionally, waterfowl use was highest at sites with little vegetation immediately surrounding the pond, and lowest when ponds were surrounded by trees. Our data suggest that retention ponds on commercial poultry farms present a notable interface for waterfowl to introduce avian influenza viruses to farm sites. However, additional testing and surveys could provide further insight into whether it may be possible to reduce the use of these habitats by wild waterfowl through vegetative management as preliminarily reported here.

Transboundary and Emerging Diseases↗
USGS2024

Potential use of poultry farms by wild waterfowl in California's Central Valley varies across space, times of day, and species: implications for influenza transmission risk

Interactions between wildlife and livestock can lead to cross-species disease transmission, which incurs economic costs and threatens wildlife conservation. Wild waterfowl are natural hosts of avian influenza viruses (AIVs), are often abundant near poultry farms, and have been linked to outbreaks of AIVs in poultry. Interspecific and seasonal variation in waterfowl movement and habitat use means that the risk of disease transmission between wild birds and poultry inevitably varies across species, space, and time. Here, we used GPS telemetry data from 10 waterfowl species in and near California's Central Valley, a region where both wild waterfowl and domestic poultry are abundant, to study selection of poultry farms by waterfowl across diel, seasonal, and annual cycles. We found that waterfowl selected for wetlands, open water, protected areas, and croplands, which meant that they generally avoided habitats that were likely to be used for poultry farming. These selection patterns were linked to species' ecology and diel behavioral patterns, such that avoidance of poultry habitats was stronger for local or partial migrants than for long-distance migrants, and stronger during daytime than at night. We then combined these habitat selection results with data on poultry farm locations to map risk of waterfowl–poultry contact across the Central Valley. Average selection strength at poultry farms was low, suggesting that current placement of poultry farms is generally effective for limiting risk of contact with wild birds. When we combined these habitat selection results with data on species' abundances and AIV infection prevalence, we found dramatic variation in potential AIV transmission risk among species. These results could be used to prioritize surveillance and biosecurity efforts for regions and times of relatively high risk. More generally, these results highlight that fine-scale movement data can help identify interspecific, seasonal, and diel patterns in animal behaviors that affect wildlife and poultry health.

California↗
USGS2024

Dust management at an active construction area impacts monarch distribution

The North American population of monarch butterflies ( Danaus plexippus) is experiencing dramatic declines, necessitating investigations into challenges facing this species that can be resolved through management actions. For instance, dust made airborne by heavy equipment driving along a dirt road can settle on roadside vegetation, resulting in reduced use by monarchs. Dust accumulation on areas where floral nectaries such as leaves, stems, and flowers may be present could reduce the ability of pollinators, such as monarchs, to access nectar from flowering plants needed during migration. One such challenge was observed on Poplar Island, an island restoration project located in the Maryland portion of the Chesapeake Bay, USA. To determine if road watering would result in notable reductions of dust accumulation on adjacent roadside vegetation, and if such a reduction in dust would affect monarch use of treated habitat, water was applied via spraying to sections of the roadway during the 2022 fall migration period. Treatment areas where water was applied to the road were found to have significant reductions in dust accumulation ( P ≤0.001) as well as significantly higher use by monarchs ( P = 0.002), relative to non-watered control areas. While these results indicate potential utility of road watering to support monarchs at sites with high dust accumulation, numerous additional elements such as water usage and logistical constraints must also be considered. While limited in scope, these data do provide a notable proof-of-concept for managing this issue at other sites and can be built upon with further research.

Maryland↗
USGS2024

Antibodies to influenza A virus in Lesser (Aythya affinis) and Greater Scaup (Aythya marila) in the USA

Scaup, including both Lesser and Greater ( Aythya affinis and Aythya marila , respectively), are a grouping of populous and widespread North American diving ducks. Few influenza type A viruses (IAV) have been reported from these species despite a high prevalence of antibodies to IAV being reported. Existing virologic and serologic data indicate that IAV infection routinely occurs in scaup, yet it is unknown which IAV subtypes are linked to these infections. In this study, we aimed to gain a more complete picture of IAV natural history in Lesser and Greater Scaup from two coastal flyways in North America in 2015–18 (302 samples from California in the Pacific Flyway and 471 samples from Maryland in the Atlantic Flyway). Low prevalence of active IAV infection was detected by real-time reverse-transcription PCR in Lesser Scaup sampled in Maryland and California (2.8% and 8.1%, respectively). A single IAV (H1N1) was isolated in embryonated chicken eggs from a bird sampled in California. Similarly low levels were observed in Greater Scaup in California (3.3%). Antibodies to the nucleoprotein as detected with a commercial blocking ELISA were observed in all species and flyway combinations. Antibody seroprevalence estimates were higher in adult Lesser Scaup than in juveniles at both the ≤0.5 ( P <0.001, z=–3.582) and ≤0.7 serum-sample-to-negative-control absorbance thresholds ( P =0.003, z=–2.996). Neutralizing antibodies to H1–H12, H14, and H15 were detected using a microtiter virus neutralization assay, with the highest prevalence of antibodies against H1 (38%), H6 (36%), and H11 (35%). The high prevalence of antibodies to IAV and evidence of previous exposure to numerous subtypes are consistent with a high level of population immunity and a low prevalence of infection. These results must be interpreted in the context of season (winter sampling), as results may vary with the annual influx of naïve juvenile birds.

California, Maryland↗