Geology topics

John Y. Takekawa

Publications and source records attributed to John Y. Takekawa.

At least 19 recordsLinked to original sources

USGS2026

A systematic review of avian influenza virus transmission models: Gaps and opportunities

Highly pathogenic avian influenza virus (HPAIV) increasingly threatens wild birds, poultry, non-human mammals and humans, yet gaps and opportunities in avian influenza virus (AIV) transmission modelling have not been comprehensively synthesized. We reviewed 182 articles published through 2025, categorized dimensions, including modelling approaches, data, host types, biological levels, spatial scales, temporal scales and model objectives, examined associations among these dimensions, and synthesized author-stated limitations and recommendations. Statistical and mechanistic models dominated. Model data centred on population dynamics and demography, disease surveillance, host epidemiology and competence, meteorology and land use and land cover. Most studies focused on poultry or wild birds at regional spatial scales, seasonal/annual and multi-year temporal scales, population or multi-population levels, and were retrospective. Machine learning and decision- making models were less common. Immunity, behaviour and life history, community composition, morphology, viral genetics and viral persistence received less attention. Non-human mammals, individual and community biological levels, local and broader spatial scales, daily temporal scales and prospective modelling were also less frequently modelled. The authors frequently reported limitations related to data availability, surveillance sampling and reporting bias, and model simplification, while commonly recommending improved data quality and greater model complexity and realism.

Methods in Ecology and Evolution↗

USGS2026

Seasonal and decadal changes in winter body condition of four sympatric diving ducks

Winter body condition is an important driver of survival, reproductive output, and overall population health in waterfowl. Diving duck species use distinct habitats, exploit unique resources, and can collectively provide an integrated index of winter habitat quality. The San Francisco Bay (SFB) is the largest estuary on the west coast of North America, serving as critical wintering habitat for diving ducks in the Pacific Flyway. To evaluate the body condition of diving ducks after multiple decades of tidal habitat restoration in SFB, we compared structurally corrected measurements (annual and decadal) of total carcass lipid among canvasback ( Aythya valisineria ), greater scaup ( Aythya marila ), lesser scaup ( Aythya affinis ), and ruddy duck ( Oxyura jamaicensis ). We found greater and lesser scaup gained lipid reserves within the estuary prior to spring migration; however, canvasback and ruddy duck lipid levels declined throughout the winter and into the spring. Lipid loss over the wintering period could indicate a reduction in foraging resource availability, dietary shifts, or metabolic changes. These deficiencies could have negative cross-seasonal implications, as these species must accumulate resources outside of their wintering areas to fuel migration and reproduction. Lipid levels were elevated in lesser scaup collected in 2017-2019 compared to 1998-2000, while we found no decadal differences in lipid levels for canvasback or greater scaup. Our findings suggest tidal restoration in SFB, among other factors, may benefit some diving duck species.

California↗

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↗

USGS2026

Global change and threats to waterbirds in the Asian flyways

Avian migration represents one of nature’s most spectacular phenomena, providing critical ecological services and acting as an indicator of environmental change. Flyways are geographical ranges through which migrating bird species move, and the flyway concept has been used to identify countries that share species to highlight their collective responsibility for conservation. Of the nine recognized global waterbird flyways, the Central Asian Flyway (CAF) and the East Asian–Australasian Flyway (EAAF) are among the most important areas in Eurasia, supporting millions of waterbirds across a vast network of habitats. We proposed this special issue in Avian Research entitled “Global Change and Threats to Waterbirds in the Asian Flyways” to synthesize recent findings from 12 papers covering a wide range of topics. The CAF stretches from the Siberian tundra through Central Asia including Mongolia, the Qinghai-Tibet Plateau, the Trans-Caucasus, and the Himalayas, extending south to the Indian subcontinent and parts of the Middle East. The EAAF spans eastern Siberia and Alaska to Southeast Asia, Australia, and New Zealand, including China, Japan, the Korean Peninsula, and the Russian Far East. These two flyways include 47 countries comprising critical wetlands, river basins, and coastal areas, which are vital breeding, stopover, and wintering grounds for waterbirds. Seasonal migration in these flyways is fundamentally influenced by climate and weather conditions, land cover dynamics, and anthropogenic activities, and contributes significantly to ecological processes such as pest control, nutrient cycling, and organism dispersal. However, migratory waterbirds and their habitats are undergoing enormous challenges. Changes in climate, habitat availability and connectivity, and human activities are altering the phenology, distribution, population dynamics, and health of the migratory bird populations. As migratory waterbirds travel across international boundaries, understanding their movements and responses to environmental change requires collaborative, cross-border research efforts that promote knowledge sharing and interdisciplinary approaches.

Avian Research↗

USGS2025

Landscape changes elevate the risk of avian influenza virus diversification and emergence in the East Asian–Australasian Flyway

Highly pathogenic avian influenza viruses (HPAIV) persistently threaten wild waterfowl, domestic poultry, and public health. The East Asian–Australasian Flyway plays a crucial role in HPAIV dynamics due to its large populations of migratory waterfowl and poultry. Over recent decades, this flyway has undergone substantial landscape changes, including both losses and gains of waterfowl habitats. These changes can affect waterfowl distributions, increase contact with poultry, and consequently alter ecological conditions that favor avian influenza virus (AIV) evolution. However, limited research has assessed these likely impacts. Here, we integrated empirical data and an individual-based model to simulate AIV transmission in migratory waterfowl and domestic poultry, including wild-to-poultry spillover and reassortment dynamics in poultry, across landscapes representing the years 2000 and 2015. We used the reassortment incidence as a proxy for ecological and transmission conditions that support viral diversification and the emergence of novel subtypes. Our simulations show that landscape change reshaped the waterfowl distribution, facilitated bird aggregation at improved habitats, increased coinfection, and raised reassortment rate by 1,593%, indicating a substantially higher potential for viral diversification and emergence. Model-generated risk maps show expanded and increased reassortment risk in southeastern China, the Yellow River Basin, and northeastern China. These findings suggest the importance of landscape change as a driver of potential AIV diversification and subtype emergence. This underscores the need for interdisciplinary approaches that integrate landscape dynamics, host movement, and viral evolution to better assess and mitigate future risk.

East Asian–Australasian Flyway↗

USGS2025

Trait-based selection of seeds ingested and dispersed by North American waterfowl

There are few studies on the extent to which waterfowl select plant food compared with what is available in wetland ecosystems. We used a new dataset on the presence of seeds in the alimentary canal or feces to identify flowering plant species whose seeds are ingested by North American ducks or geese. These data are a proxy for dispersal interactions because an important fraction of ingested seeds survives gut passage and is dispersed by endozoochory. We compared the plant traits of species whose seeds were ingested with those of species on the U.S. Department of Agriculture National Wetland Plants List (NWPL). Using a global dataset on plant form and function and chi-squared tests, we compared four categorical traits (moisture requirements, growth form, plant height, and seed mass) between species whose seeds are ingested by North American ducks and geese with the NWPL. Our analyses identified significant differences between the trait distributions of plants whose seeds were ingested by waterfowl guilds and those of the NWPL. Geese and ducks (except whistling ducks) ingested more aquatic and semiaquatic plant species than expected from the NWPL. All guilds except sea ducks ingested more herbaceous graminoids and fewer shrubs or trees than expected. Diving ducks interacted with fewer of the taller plants (>5 m) than expected, but otherwise plant height distributions did not differ from those expected. All waterfowl guilds ingested more species of intermediate seed size (1–10 mg) and fewer species of the smallest (<0.1 mg) or largest (>100 mg) size categories than expected. These results help to explain the role of the long-distance dispersal of seeds by migratory waterfowl in plant biogeography and how plant distributions are likely to respond to global change.

North America↗

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↗

USGS2024

Mitigating risk: Predicting H5N1 avian influenza spread with an empirical model of bird movement

Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (Dec 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted non-migratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multi-species tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.

Transboundary and Emerging Diseases↗

USGS2024

Benthic macroinvertebrate response to estuarine emergent marsh restoration across a delta-wide environmental gradient

Benthic invertebrates play vital roles in estuarine ecosystems, but like other taxa they have been excluded from former marshlands by diking and land use conversion. Dike removal is one way of restoring marsh, but the response of benthic invertebrates has been little studied. Also understudied is variation in benthic invertebrate communities across entire deltas, particularly in the Pacific Northwest of North America where deltas receive high flows and sediment loads for their size. Our goals were to evaluate invertebrate response to large-scale dike removal on the Nisqually River Delta in Puget Sound, Washington, U.S.A., characterize delta-wide invertebrate community variation, and relate invertebrate response and spatial variation to environmental conditions. We sampled invertebrates annually from one year before to three years after dike removal in restoring marsh, previously restored marsh, undisturbed reference marsh, and adjacent tidal flats. Marine taxa immediately colonized the area recently restored to tidal inundation and population size grew exponentially thereafter for several of them. Community composition and diversity recovered completely, and density and biomass were approaching recovery three years later. Invertebrate communities converged between restoring and pre-existing marsh (previously restored and reference), suggesting an influence of reestablished connectivity. Just offshore from the dike line, invertebrates declined one year after dike removal but then rebounded indicating resilience to short-term disturbance. Dike removal effects were not detected farther offshore. Near the offshore edge of the delta, invertebrate biomass and body size were greater than elsewhere and a diverse assemblage of crustaceans, polychaetes, and bivalves was present. Farther inshore, tidal flats were dominated by a few species of small-bodied polychaetes and had higher density but lower biomass and diversity. Facultative detritivores, which can also filter feed, were the dominant feeding guild everywhere on the tidal flats. Density, biomass, diversity, and community composition on the marsh were more similar to the inner than outer tidal flats. Environmental variables most associated with invertebrate community variation were elevation, salinity, and sediment grain size and organic content. Our results are relevant to assessing performance and setting expectations for future restorations and have broad implications for the role of benthic invertebrates in estuarine ecosystems.

Washington↗

USGS2024

Evaluating conservation units using network analysis: A sea duck case study

Conserving migratory wildlife requires understanding how groups of individuals interact across seasons and landscapes. Telemetry reveals individual movements at large spatiotemporal scales; however, using movement data to define conservation units requires scaling up from individual movements to species- and community-level patterns. We developed a framework to define flyways and identify important sites from telemetry data and applied it to long-term, range-wide tracking data from three species (640 individuals) of sea ducks: namely, North American scoters ( Melanitta spp). Our network of 88 nodes included both multispecies hotspots and areas uniquely important to individual species. We found limited spatial overlap between scoters wintering on the Atlantic and Pacific coasts of North America, with differing connectivity patterns between coasts. Finally, we identified four multispecies conservation units that did not correspond to traditional management flyways. From this approach, we show how individual movements can be used to quantify range-wide connectivity of migratory species and reveal gaps in conservation strategies.

Frontiers in Ecology and the Environment↗

USGS2024

Contrasting migratory chronology and routes of Lesser Scaup: Implications of different migration strategies in a broadly distributed species

Migration allows birds to improve fitness by exploiting seasonal resource peaks and avoiding limitations. Migration strategies may differ among individuals within a species, but for all strategies, the benefit of increased fitness should outweigh the costs of migration. These costs can include increased mortality risk, time constraints in the annual cycle, and metabolic energy loss. We compared migratory chronology and routes of individuals from a broadly distributed species of waterfowl, the Lesser Scaup ( Aythya affinis ; hereafter Scaup), marked at the northern (66.51000° N, 145.98556° W) and southern (44.63778° N, 111.73694° W) extents of its breeding distribution in North America. Scaup breeding farther north in interior Alaska, USA migrated greater distances and had protracted migrations, especially in fall, compared to Scaup breeding farther south in southwest Montana, USA. During migration, Scaup breeding in Alaska used more staging and stopover areas compared to Scaup breeding in Montana. Scaup breeding in Alaska also spent less time at their breeding area and more time at their wintering areas compared to Scaup breeding in Montana. In addition, Scaup breeding in Alaska were largely absent from wintering areas in the Intermountain West that were used by Scaup breeding in Montana. These differences could have important effects on Scaup fitness and could contribute to differences in fecundity and recruitment observed across the Scaup’s broad latitudinal distribution. Understanding the fitness implications of intraspecific variation in migration strategies of broadly distributed species can assist resource managers by focusing conservation efforts on specific breeding populations, informing models of disease transmission, and improving projections of species’ responses to environmental change.

Journal of Field Ornithology↗

USGS2023

Linking meso-scale spatial variation in methylmercury production to bioaccumulation in tidal marsh food webs

Differences in sediment biogeochemistry among tidal marsh features with different hydrological and geomorphological characteristics, including marsh interiors, marsh edges, first-order channels, and third-order channels, can result in spatial variation in MeHg production and availability. To better understand the link between MeHg production in sediments and bioaccumulation in primary and secondary consumer invertebrates and fish, we characterized mesoscale spatial variation in sediment biogeochemistry and MeHg concentrations of sediments, water, and consumer tissues among marsh features. Our results indicated that marsh interiors had biogeochemical conditions, including greater concentrations of organic matter and sulfate reduction rates, that resulted in greater MeHg concentrations in sediments and surface water particulates from marsh interiors compared to other features. Tissue MeHg concentrations of consumers also differed among features, with greater concentrations from marsh edges and interiors compared to channels. This spatial mismatch of MeHg concentrations in sediments and water compared to those in consumers may have resulted from differences in behavior and physiology among consumers that influenced the spatial scale over which MeHg was integrated into tissues. Our results highlight the importance of sampling across a suite of marsh features and considering the behavioral and physiological traits of sentinel taxa for contaminant monitoring studies.

Environmental Science and Technology↗

USGS2023

Evaluation of breeding distribution and chronology of North American scoters

North America's scoter species are poorly monitored relative to other waterfowl. Black Melanitta americana , surf M. perspicillata , and white-winged M. deglandi scoter abundance and trend estimates are thus uncertain in many parts of these species' ranges. The most extensive source of waterfowl abundance and distribution data in North America is the Waterfowl breeding population and habitat survey (WBPHS). Although the WBPHS effectively monitors most species, both its timing and geographic coverage may preclude accurate scoter monitoring. Therefore, our goal was to better define when and where scoters breed to help interpret survey results and optimize potential supplemental survey efforts for scoters. We integrated satellite telemetry tracking data from scoters marked at multiple molting, staging, breeding, and wintering areas along the Atlantic and Pacific coasts to quantify continent-wide breeding chronology and distribution. We also examined possible drivers of variation in timing of arrival, length of stay, and departure at nesting locations. We documented a northwest to southeast distribution of estimated breeding sites across Alaska and Canada. On average, scoters arrived at nest sites on 1 June. Surf scoters and Pacific black scoters arrived earliest and departed earliest. Pacific-wintering black and white-winged scoters began breeding earlier than Atlantic-wintering birds. Additionally, birds arrived at nesting locations earlier in years with earlier snowmelt, and later snowmelt reduced lengths of stay for males. Breeding chronology also varied by age group, with adults arriving earlier than subadults. Our study is the first to comprehensively describe spatial variation in timing of breeding of both Atlantic and Pacific populations of all three scoter species across North America. Our results increase our understanding of how current surveys enumerate scoters and will inform possible supplemental efforts to improve continental monitoring of scoter populations.

Wildlife Biology↗

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↗

USGS2022

Pathways for avian influenza virus spread: GPS reveals wild waterfowl in commercial livestock facilities and connectivity with the natural wetland landscape

Zoonotic diseases are of considerable concern to the human population and viruses such as avian influenza (AIV) threaten food security, wildlife conservation and human health. Wild waterfowl and the natural wetlands they use are known AIV reservoirs, with birds capable of virus transmission to domestic poultry populations. While infection risk models have linked migration routes and AIV outbreaks, there is a limited understanding of wild waterfowl presence on commercial livestock facilities, and movement patterns linked to natural wetlands. We documented 11 wild waterfowl (three Anatidae species) in or near eight commercial livestock facilities in Washington and California with GPS telemetry data. Wild ducks used dairy and beef cattle feed lots and facility retention ponds during both day and night suggesting use for roosting and foraging. Two individuals (single locations) were observed inside poultry facility boundaries while using nearby wetlands. Ducks demonstrated high site fidelity, returning to the same areas of habitats (at livestock facilities and nearby wetlands), across months or years, showed strong connectivity with surrounding wetlands, and arrived from wetlands up to 1251 km away in the week prior. Telemetry data provides substantial advantages over observational data, allowing assessment of individual movement behaviour and wetland connectivity that has significant implications for outbreak management. Telemetry improves our understanding of risk factors for waterfowl–livestock virus transmission and helps identify factors associated with coincident space use at the wild waterfowl–domestic livestock interface. Our research suggests that even relatively small or isolated natural and artificial water or food sources in/near facilities increases the likelihood of attracting waterfowl, which has important consequences for managers attempting to minimize or prevent AIV outbreaks. Use and interpretation of telemetry data, especially in near-real-time, could provide key information for reducing virus transmission risk between waterfowl and livestock, improving protective barriers between wild and domestic species, and abating outbreaks.

Transboundary and Emerging Diseases↗

USGS2021

Small shorebirds feast on green slime to fuel their long migration

Shorebirds wade in shallow waters along shorelines searching for food. More than a million shorebirds visit the San Francisco Estuary each year during their migration to feast on the insects, worms, clams, and crabs that live on or under the surface of the sand or mud. The abundant food in the Estuary provides shorebirds with the energy they need to migrate thousands of kilometers, between their breeding areas in the Arctic and their wintering areas along the Pacific coast of North and South America. Scientists have discovered that, during migration, small species of shorebirds eat a green slime called biofilm that grows on the surface of the mud. Larger shorebirds do not eat biofilm. This article describes how the bills and tongues of small shorebirds help them eat biofilm, what biofilm is, and why biofilm is an important food for those birds during migration.

Frontiers for Young Minds↗

USGS2021

Do contrasting patterns of migration movements and disease outbreaks between congeneric waterfowl species reflect differing immunity?

Long-distance migrations influence the dynamics of hostpathogen interactions and understanding the role of migratory waterfowl in the spread of the highly pathogenic avian influenza viruses (HPAIV) is important. While wild geese have been associated with outbreak events, disease ecology of closely related species has not been studied to the same extent. The swan goose ( Anser cygnoides ) and the bar-headed goose ( Anser indicus ) are congeneric species with distinctly different HPAIV infection records; the former with few and the latter with numerous records. We compared movements of these species, as well as the more distantly related whooper swan ( Cygnus cygnus ) through their annual migratory cycle to better understand exposure to HPAIV events and how this compares within and between congeneric and noncongeneric species. In spite of their record of fewer infections, swan geese were more likely to come in contact with disease outbreaks than bar-headed geese. We propose two possible explanations: i) frequent prolonged contact with domestic ducks increases innate immunity in swan geese, and/or ii) the stress of high-elevation migration reduces immunity of bar-headed geese. Continued efforts to improve our understanding of species-level pathogen response is critical to assessing disease transmission risk.

Geospatial Health↗

USGS2021

Seasonal impoundment alters patterns of tidal wetland plant diversity across spatial scales

Understanding patterns of biodiversity is a key goal of ecology and is especially pressing in the current human‐caused biodiversity crisis. In wetland ecosystems, human impacts are centered around hydrologic manipulation including the common practice of wetland diking and impoundment. Constraining how wetland management influences plant biodiversity patterns across spatial scales will provide information on how best to modify actions to preserve biodiversity and ecosystem function in managed wetlands. Here, we compare patterns of plant diversity and species presence, abundance, and community composition at several spatial scales among tidal wetlands along an estuarine salinity gradient and managed wetlands that were formerly tidal. Managed impounded wetlands had decreased alpha and gamma diversity of rare species, with less than 60% of the species richness found in tidal brackish wetlands at several spatial scales. There was little change in the overall pattern of alpha, beta, and gamma diversity for common species in impounded wetlands; however, dominant tidal brackish species, primarily perennial rhizomatous graminoids, were replaced with management target plants and non‐native annual grasses in impounded wetlands. This species replacement led to over 60% of impounded sites being classified as containing novel plant assemblages. An additional 25% of impounded sites were classified as containing tidal saline plant assemblages, suggesting potential soil salinization. Along the estuarine gradient, patchiness and codominance of common plant species drove high diversity and turnover in tidal brackish wetlands, while it remains unclear whether tidal fresh or brackish wetlands maximize rare plant diversity. With reduced species richness, altered functional dominants, and novel or saline assemblages, impounded brackish wetlands may require careful water management to balance native plant biodiversity, associated ecosystem processes, and waterfowl requirements.

California↗