Geology topics

Cody M. Kent

Publications and source records attributed to Cody M. Kent.

7 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↗

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

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↗

USGS2023

Waterfowl show spatiotemporal trends in influenza A H5 and H7 infections but limited taxonomic variation

Influenza A viruses in wild birds pose threats to the poultry industry, wild birds, and human health under certain conditions. Of particular importance are wild waterfowl, which are the primary reservoir of low pathogenicity influenza viruses that ultimately cause high pathogenicity outbreaks in poultry farms. Despite much work on the drivers of influenza A virus prevalence, the underlying viral subtype dynamics are still mostly unexplored. Nevertheless, understanding these dynamics, particularly for the agriculturally significant H5 and H7 subtypes, is important for mitigating the risk of outbreaks in domestic poultry farms. Here, using an expansive surveillance database, we take a large-scale look at the spatial, temporal, and taxonomic drivers in the prevalence of these two subtypes among influenza A positive wild waterfowl. We document spatiotemporal trends that are consistent with past work, particularly an uptick in H5 viruses in late autumn and H7 viruses in spring. Interestingly, despite large species differences in temporal trends in overall influenza A virus prevalence, we document only modest differences in the relative abundance of these two subtypes and little, if any, temporal differences among species. As such, it appears that differences in species' phenology, physiology, and behaviors that influence overall susceptibility to influenza A viruses play a much lesser role in relative susceptibility to different subtypes. Instead, species likely freely pass viruses among each other regardless of subtype. Importantly, despite the similarities among species documented here, individual species still may play important roles in moving viruses across large geographic areas or sustaining local outbreaks through their different migratory behaviors.

Ecological Applications↗

USGS2022

Spatiotemporal changes in influenza A virus prevalence among wild waterfowl inhabiting the continental United States throughout the annual cycle

Avian influenza viruses can pose serious risks to agricultural production, human health, and wildlife. An understanding of viruses in wild reservoir species across time and space is important to informing surveillance programs, risk models, and potential population impacts for vulnerable species. Although it is recognized that influenza A virus prevalence peaks in reservoir waterfowl in late summer through autumn, temporal and spatial variation across species has not been fully characterized. We combined two large influenza databases for North America and applied spatiotemporal models to explore patterns in prevalence throughout the annual cycle and across the continental United States for 30 waterfowl species. Peaks in prevalence in late summer through autumn were pronounced for dabbling ducks in the genera Anas and Spatula , but not Mareca . Spatially, areas of high prevalence appeared to be related to regional duck density, with highest predicted prevalence found across the upper Midwest during early fall, though further study is needed. We documented elevated prevalence in late winter and early spring, particularly in the Mississippi Alluvial Valley. Our results suggest that spatiotemporal variation in prevalence outside autumn staging areas may also represent a dynamic parameter to be considered in IAV ecology and associated risks.

Scientific Reports↗

USGS2021

A comparison of methods for the long-term harness-based attachment of radio-transmitters to juvenile Japanese quail (Coturnix japonica)

Background While the period from fledging through first breeding for waterbird species such as terns (e.g., genus Sterna, Sternula) is of great interest to researchers and conservationists, this period remains understudied due in large part to the difficulty of marking growing juveniles with radio transmitters that remain attached for extended periods. Methods In an effort to facilitate such research, we examined the impact of various combinations of harness types (backpack, leg-loop, and 3D-printed harnesses), harness materials (Automotive ribbon, Elastic cord, and PFTE ribbon), and transmitter types (center-weighted and rear-weighted) on a surrogate for juvenile terns, 28-day-old Japanese quail ( Coturnix japonica; selected due to similarities in adult mass and downy feathering of juveniles ), in a 30-day experiment. We monitored for abrasion at points of contact and tag gap issues via daily exams while also recording mass and wing cord as indices of growth. This study was designed to serve as an initial examination of the impacts of marking on the growth and development of young birds and does not account for any impacts of tags on movement or behavior. Results While we found that treatment (the specific combination of the transmitter type, harness type, and harness material) had no impact on bird growth relative to unmarked control birds ( P ≥ 0.05), we did observe differences in abrasion and tag gap between treatments ( P ≤ 0.05). Our results suggest that leg-loop harnesses constructed from elastic cord and backpack harnesses from PFTE ribbon are suitable options for long-term attachment to growing juveniles. Conversely, we found that automotive ribbon led to extensive abrasion with these small-bodied birds, and that elastic cord induced blisters when used to make a backpack harness. Conclusions While these results indicate that long-term tagging of juvenile birds is possible with limited impacts on growth, this work does not preclude the need for small-scale studies with individual species. Instead, we hope this provides an informed starting point for further exploration of this topic.

Animal Biotelemetry↗