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USGS2021

Evaluating the role of active management in mature Douglas-fir (Pseudotsuga menziesii) stands for songbird conservation

Forest birds, particularly those associated with late-successional forests, are of widespread conservation interest. Although birds are among the more widely studied taxa of forest wildlife, relatively few studies have examined the long-term effects of active management (i.e., intentional stand density reduction) on the forest bird assemblage. This is an important omission, as changes in stand structure and composition over the decades following harvesting may influence wildlife utilization of forest stands. We developed an observational study to evaluate forest bird response to stand structural development multiple decades following harvesting with differing levels of overstory density reduction, and in unmanaged stands. We focused, in particular, on songbirds and cavity excavating species associated with old-growth Douglas-fir forests, and the active management strategies that we examined – thinning and structural retention harvesting – were selected based on their potential to accelerate stand structural development. Our 18 mature stands (age range: 107–187 years) were located in the western hemlock zone of western Oregon, and bird surveys were conducted an average of 41 years and 22 years post-harvest in thinned and retention harvest stands, respectively. Poisson generalized linear models were formulated to evaluate the effects of management condition on forest birds. Although five species were associated with specific management conditions, relative abundance was not statistically different between unmanaged, thinned and retention harvest stands for a majority of the species in our analysis. Species richness was also relatively invariant across management conditions. Our results do suggest that retention harvesting adversely affects some songbird species associated with old-growth forests – Pacific-slope flycatcher ( Empidonax difficilis ) and Pacific wren ( Troglodytes pacificus ) for example - but our findings also indicate that retention harvesting has long-term benefits for birds associated with early-successional forests. This includes migrant species that have experienced significant population declines in Western North America over recent decades, such as Wilson’s and MacGillivray’s warblers ( Cardellina pusilla and Geothlypis tolmiei , respectively). Overall, our results imply that for many species of forest birds, including those associated with old-growth forests, managers have some flexibility in overstory density management where long-term species persistence is an objective. Equally significant, our results provide strong support for the application of variable retention harvesting as a tool for the conservation of bird species associated with early-successional forests, while also reinforcing the value of mature structural legacies for bird species associated with late-successional forests. While also reinforcing the value of mature structural legacies for birds associated with late-successional forests.

Oregon↗

USGS1979

Dispersal and migratory patterns of San Francisco Bay produced herons, egrets, and terns

San Francisco Bay, California, including its fringing marshes, supports a large and diverse water related avifauna (Grinnell and Wythe 19271 Sibley 1952, Gill 1973, 1977). Certain of man's alterations of the Bay's shallower wetlands have resulted in increased habitat diversity which has allowed colonization by several species of birds including some colonial nesting species. The extensive dikes associated with salt production and some areas of higher ground created by dredge spoils have provided increased tide-free substratum, some of it insular, suitable for nesting. The resulting numbers of Snowy Egrets ( Egretta thula) , Black-crowned Night Herons ( Nycticorax nycticorax ), Forster's Terns ( Sterna forsteri ), and Caspian Terns ( Sterna caspia ) using these areas now represent a significant portion of the northern California breeding populations of these species. In conjunction with a study of the breeding birds of the South San Francisco Bay Estuary (Gill 1973, 1977) from 1971 to 1973, we banded 187 Great Blue Herons ( Ardea herodias ), 1499 Snowy Egrets, 1615 Black-crowned Night Herons, 2943 Forster's Terns, and 743 Caspian Terns; often this represented a substantial portion of these species banded in the western states during these years (Table 1). Recoveries from these bandings through 1977 plus additional recoveries from a few earlier and some more recent bandings provide the data for this report on dispersal patterns and migration of San Francisco Bay produced herons, egrets, and terns.

California↗

USGS2009

Molecular Population Genetic Structure in the Piping Plover

The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect differences in spatiotemporal stability of Piping Plover nesting habitat between regions.

Open-File Report↗

USGS2020

High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California

Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment efforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, Salt Marsh Bird’s Beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration efforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the species range in Southern California, and three additional occurrences from Baja California, Mexico. We used flow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found four to five distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These findings can bolster management and restoration efforts by identifying potentially isolated occurrences and areas that are rich sources of allelic diversity, and by providing insight into the amount of genetic differentiation across the species range.

California↗

USGS2012

Influence of space use on fitness and the reintroduction success of the Laysan teal

Translocation is an important tool for wildlife conservation and biodiversity restoration, but an inefficient one because of the unpredictability of success. Predictors of success such as habitat quality of the release site and number of individuals released have been identified, but the dynamics of successful translocations remain poorly understood. In particular, little is known about the relationship of individual post-release movements to population establishment. In 2004, Laysan teal Anas laysanensis were reintroduced by translocating 20 wild birds from Laysan Island to Midway Atoll. Twenty-two additional wild founders were brought the next year. We monitored the survival, reproductive success and movements of the 42 translocated individuals and their offspring for 4 years. Additionally, we monitored population size from 2004 to 2010. Unlike most translocations, we did not observe elevated post-release mortality despite flight-feather trimming to prevent immediate dispersal off-island: first year survival was > 90% and survival rates until 2009 were 0.65±0.08 for founding adults. Laysan teal flew between the two main islands of Midway Atoll, and offspring had significantly larger maximum movement distances than founders. We monitored 84 nests and observed a significant, negative relationship of home range size to productivity for founding females. Flightless founders did not show fidelity to their release sites, but had strong fidelity to annual home ranges after attaining flight. Although we observed a component Allee effect on mate-finding, this did not translate into a demographic Allee effect, and generally, the high fitness of founders contributed substantially to successful population establishment. Laysan teal abundance increased linearly until 2009, but showed evidence of population regulation afterwards. The population estimate was 473 (95% confidence interval 439–508) in 2010. On the much larger main Hawaiian Islands, we expect greater post-release movement, a stronger component Allee effect, lower survival and lower reproductive rates because of predation to preclude successful reintroductions of this species to sites without predator management.

Laysan Island;Midway Atoll↗

USGS1988

Post-epizootic surveys of waterfowl for duck plague (duck virus enteritis)

Surviving birds from nine duck plague outbreaks in urban and confined waterfowl were sampled for duck plague (DP) virus and DP antibody during 1979-86. Duck plague virus was found in combined oral and cloacal swabs of birds from three outbreaks, and DP-neutralizing antibody was demonstrated in some birds from all nine outbreaks. Greater prevalence of DP antibody and higher titers were found in survivors from confined populations than from free-flying urban populations. Free-flying waterfowl from within 52 km of four DP outbreak sites were also sampled; virus was not found in any birds, but DP antibody was found in urban waterfowl in the vicinity of an outbreak in Potterville, Michigan. No evidence of exposure to or shedding of DP virus in migratory waterfowl was found in two regions where DP appears enzootic in urban and confined waterfowl (Eastern Shore of Maryland and the vicinity of Sacramento, California).

Avian Diseases↗

USGS2005

Life-history variation of a neotropical thrush challenges food limitation theory

Since David Lack first proposed that birds rear as many young as they can nourish, food limitation has been accepted as the primary explanation for variation in clutch size and other life-history traits in birds. The importance of food limitation in life-history variation, however, was recently questioned on theoretical grounds. Here, we show that clutch size differences between two populations of a neotropical thrush were contrary to expectations under Lack's food limitation hypothesis. Larger clutch sizes were found in a population with higher nestling starvation rate (i.e. greater food limitation). We experimentally equalized clutches between populations to verify this difference in food limitation. Our experiment confirmed greater food limitation in the population with larger mean clutch size. In addition, incubation bout length and nestling growth rate were also contrary to predictions of food limitation theory. Our results demonstrate the inability of food limitation to explain differences in several life-history traits: clutch size, incubation behaviour, parental feeding rate and nestling growth rate. These life-history traits were better explained by inter-population differences in nest predation rates. Food limitation may be less important to life history evolution in birds than suggested by traditional theory. ?? 2005 The Royal Society.

Proceedings of the Royal Society B: Biological Sci↗

USGS2004

Redistribution and growth of the Caspian Tern population in the Pacific Coast region of North America, 1981-2000

We examined nesting distribution and demography of the Pacific Coast population of Caspian Terns ( Sterna caspia ) using breeding records and band recoveries spanning two decades since the first population assessment. Since 1980, population size has more than doubled to about 12 900 pairs, yet the proportion of the population nesting at inland (18%) versus coastal sites (82%) has remained constant. Although the breeding range of the Pacific Coast population has expanded northward into Alaska and farther south in Mexico, there was no net latitudinal shift in the distribution of breeding pairs or new colonies. The distribution of breeding birds among areas changed dramatically, however, with 69% of breeding terns now nesting in Oregon (primarily in the Columbia River estuary) versus 4% during the late 1970s. During the past 20 years, there has continued to be a greater proportion of Caspian Terns breeding at anthropogenic sites compared to natural sites. Estimated annual survival rates for hatch-year and after-third-year birds during 1981-1998 were greater than during 1955-1980, consistent with the higher rate of population increase in recent decades. Fecundity required to maintain a stable population ( λ = 1 ) was estimated at 0.32–0.74 fledglings pair −1 , depending on band recovery probabilities for sub-adults. Caspian Terns readily moved among breeding sites and rapidly colonized new areas; however, a greater concentration of breeding Caspian Terns among fewer colonies in response to anthropogenic factors is an important conservation concern for this species.

Condor↗

USGS2020

Identifying sustainable winter habitat for whooping cranes

The only self-sustaining population of endangered whooping cranes ( Grus americana ) requires a network of conservation lands for wintering along the Texas Gulf Coast (USA), so that this increasing population can reach downlisting under the Endangered Species Act (1,000 birds). We identify locations providing the highest quality and most sustainable wintering habitat for these whooping cranes through 2100 by predicting future habitats under three projections of sea level rise (0.6, 1.0 and 2.0 m by 2100), while incorporating two scenarios of future urban development. Our method combines predictions of future habitat quality with current whooping crane density estimates to calculate the potential carrying capacity of whooping cranes for each 10 m pixel within this 17,725 km 2 area. We found whooping cranes used locations with salt marsh at twice the rate of places lacking marsh. Areas > 15 km from development or < 2 km from estuarine water had increased crane use. Predicted area of salt marsh habitat oscillated across time given different rates of sea level rise. One urbanization scenario predicted 3% and the other 1% of the area converting to development by 2100. We estimated the study area can support 4414 (95% CI: 4096-4789) whooping cranes currently, 4795 (95% CI: 4402-5269) with 0.6 m sea level rise, 3559 (95% CI: 3352-3791) with 1 m sea level rise, and 2480 (95% CI: 2375-2592) with 2 m sea level rise by 2100, under the more aggressive urban development scenario. By anticipating climate-induced habitat loss with species population expansion we provide the requisite spatial information for conservation planners to build a sustainable conservation estate for downlisting whooping cranes. By coupling wildlife biology with conservation planning and on-the-ground implementation, our work exemplifies a proactive approach to recover endangered species.

Texas↗

USGS2016

Encounters with Pinyon-Juniper influence riskier movements in Greater Sage-Grouse across the Great Basin

Fine-scale spatiotemporal studies can better identify relationships between individual survival and habitat fragmentation so that mechanistic interpretations can be made at the population level. Recent advances in Global Positioning System (GPS) technology and statistical models capable of deconstructing high-frequency location data have facilitated interpretation of animal movement within a behaviorally mechanistic framework. Habitat fragmentation due to singleleaf pinyon (Pinus monophylla; hereafter pinyon) and Utah juniper (Juniperus osteosperma; hereafter juniper) encroachment into sagebrush (Artemisia spp.) communities is a commonly implicated perturbation that can adversely influence greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) demographic rates. Using an extensive GPS data set (233 birds and 282,954 locations) across 12 study sites within the Great Basin, we conducted a behavioral change point analysis and subsequently constructed Brownian bridge movement models from each behaviorally homogenous section. We found a positive relationship between modeled movement rate and probability of encountering pinyon-juniper with significant variation among age classes. The probability of encountering pinyon-juniper among adults was two and three times greater than that of yearlings and juveniles, respectively. However, the movement rate in response to the probability of encountering pinyon-juniper trees was 1.5 times greater for juveniles. We then assessed the risk of mortality associated with an interaction between movement rate and the probability of encountering pinyon-juniper using shared frailty models. During pinyon-juniper encounters, on average, juvenile, yearling, and adult birds experienced a 10.4%, 0.2%, and 0.3% reduction in annual survival probabilities. Populations that used pinyon-juniper habitats with a frequency ≥ 3.8 times the overall mean experienced decreases in annual survival probabilities of 71.1%, 0.9%, and 0.9%. This analytical framework identifies a likely behavioral mechanism behind how pinyon-juniper encroachment decreases habitat suitability for sage-grouse, whereby encountering pinyon-juniper stimulates faster yet riskier movements that may make sage-grouse more vulnerable to visually acute predators.

Rangeland Ecology and Management↗

USGS2024

Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination

The ongoing panzootic of highly pathogenic H5 clade 2.3.4.4b avian influenza (HPAI) spread to North America in late 2021, with detections of HPAI viruses in Alaska beginning in April 2022. HPAI viruses have since spread across the state, affecting many species of wild birds as well as domestic poultry and wild mammals. To better understand the dissemination of HPAI viruses spatiotemporally and among hosts in Alaska and adjacent regions, we compared the genomes of 177 confirmed HPAI viruses detected in Alaska during April – December 2022. Results suggest multiple viral introductions into Alaska between November 2021 and August or September 2022, as well as dissemination to areas within and outside of the state. Viral genotypes differed in their spatiotemporal spread, likely influenced by timing of introductions relative to population immunity. We found evidence for dissemination of HPAI viruses between wild bird species, wild birds and domestic poultry, as well as wild birds and wild mammals. Continued monitoring for and genomic characterization of HPAI viruses in Alaska can improve our understanding of the evolution and dispersal of these economically costly and ecologically relevant pathogens.

Emerging Microbes & Infections↗

USGS2020

Black oystercatcher (Haematopus bachmani) population size, use of marine reserve complexes, and spatial distribution in Oregon

The Black Oystercatcher is a large shorebird found along the west coast of North America. Because of their small global population size, low reproductive rate, and dependence on rocky intertidal habitats, they are considered a “species of high conservation concern” and may act as an indicator of intertidal ecosystem health. In 2015, the Audubon Society of Portland initiated a 3-year shore-based population survey in Oregon building upon long-term monitoring previously conducted by the U.S. Geological Survey (USGS) and others. The objectives were to 1) Estimate the current minimum population of breeding Black Oystercatchers in Oregon and to compare that to previous estimates to better understand the population trend; 2) Document oystercatcher abundance adjacent to the Oregon’s system of Marine Reserves and Marine Protected Areas; and 3) Describe spatial distribution of breeding oystercatchers along the coast. We targeted all rocky shoreline habitats along Oregon’s coastline to perform abundance surveys each spring. A total of 75 survey routes were sampled using a standardized protocol. Trained volunteer community scientists conducted the majority of the surveys. We used N-mixture statistical models to estimate oystercatcher population size and probability of detection. Population estimates from the best fitting models were consistent, with estimates ranging from 506 oystercatchers in 2016 (95% credible interval, 463-560) to 629 (548-743) in 2015. These estimates indicated a small but stable population. Probability of detection remained consistent across years (ranging from 0.51 to 0.53). The effect of geographic region corresponded with greater bird density in the southern region of Oregon. Oystercatcher abundance adjacent to MR/MPAs accounted for between 12.4-18.3% of the total population estimate which was lower than expected (~25%). We recommend that subsequent conservation efforts directed on Black Oystercatchers in Oregon balance limiting human disturbance, particularly on the north and central coasts, with ensuring protection of core habitats on the south coast where much of the population resides.

Oregon↗

USGS1976

Determining population size of territorial red-winged blackbirds

Population sizes of territorial male red-winged blackbirds ( Agelaius phoeniceus ) were determined with counts of territorial males (area count) and a Petersen-Lincoln Index method for roadsides (roadside estimate). Weather conditions and time of day did not influence either method. Combined roadside estimates had smaller error bounds than the individual transect estimates and were not hindered by the problem of zero recaptures. Roadside estimates were usually one-half as large as the area counts, presumably due to an observer bias for marked birds. The roadside estimate provides only an index of major changes in populations of territorial male redwings. When the roadside estimate is employed, the area count should be used to determine the amount and nature of observer bias. For small population surveys, the area count is probably more reliable and accurate than the roadside estimate.

Journal of Wildlife Management↗

USGS2003

Short-term bird response to harvesting switchgrass for biomass in Iowa

The Conservation Reserve Program (CRP) provides habitat for grassland birds, but as contracts expire, some CRP fields might be returned to rowcrop production. One alternative to returning CRP fields to rowcrops is to produce switchgrass ( Panicum virgatum ) for use as a biomass fuel. Because the biomass is harvested during the fall and winter, breeding birds would not be directly affected by mowing the fields bur might be influenced by changes in vegetation structure resulting from the harvest. We evaluated bird abundances and nest success in totally harvested, partially harvested (alternating cut and uncut strips), and nonharvested CRP switchgrass fields in southern Iowa, USA, in 1999 and 2000. Species richness did not differ among harvest treatments. Abundances of most species (16 of 18) were not affected by the harvesting of switchgrass fields, and strip width did not affect bird numbers in strip-harvested fields. Grasshopper sparrows ( Ammodramus savannarum ) were more abundant in harvested portions of fields, and more sedge wrens ( Cistothorus platensis ) were recorded in nonharvested areas. The residual vegetation in nonharvested areas provided nest cover for species that begin nesting early in the season (e.g., northern harrier [Circus cyaneus] and ring-necked pheasant [ Phasianus colchicus ]). Nest success rates of grasshopper sparrows and common yellowthroats ( Geothlypis trichas ) were similar to those reported by other studies in switchgrass fields and might be sufficient to maintain stable populations. In general, switchgrass biomass fields create breeding habitat for some grassland birds, and a mixture of harvested and nonharvested fields would be more beneficial to grassland birds than totally harvesting or partially harvesting all switchgrass fields.

Iowa↗

USGS2018

Allowable take of black vultures in the eastern United States

Black vultures ( Coragyps atratus ) have been increasing in density and expanding their range in the eastern United States since at least the 1960s. In many areas, their densities have increased to the level where they are causing damage to property and livestock and the number of requests for allowable take permits has increased throughout these areas. The United States Fish and Wildlife Service (USFWS) requires updated information to help inform the number of take permits that could reduce conflicts while meeting obligations under the Migratory Bird Treaty Act. We expanded analyses used to estimate allowable take in Virginia to cover the range of black vultures in the eastern United States. We used the prescribed take level approach, which integrates demographic rates, population size estimates, and management objectives into an estimate of allowable take. We provide estimates of allowable take at 4 different scales: individual states, Bird Conservation Regions, USFWS administrative regions, and flyways. Our updated population time series provides evidence of rapidly increasing black vulture populations in many regions of the eastern United States, with an overall population estimate of approximately 4.26 million in 2015 in the Atlantic and Mississippi Flyways. Estimated allowable take ranged from a few hundred individuals per year in states at the northern end of the species range to approximately 287,000/year over the entire eastern United States. The USFWS has no legal mandate regarding the spatial scale at which take should be managed and we found little biological evidence of subpopulation structure for black vultures in the eastern United States. We suggest that allowable take for the species be implemented at a scale that meets stakeholder objectives (e.g., reducing conflict, and ensuring that black vultures are not extirpated from local areas) and is efficient for administrative and monitoring purposes.

Journal of Wildlife Management↗

USGS2019

Coastal marsh bird habitat selection and responses to Hurricane Sandy

Wetlands provide numerous ecosystem functions such as water purification, nutrient cycling, and wildlife habitat. Avian populations are indicators of wetland health, and understanding their responses to extreme events can aid in targeting restoration efforts following disturbance. Here, we assessed the habitat selection of six coastal wetland bird species (American Bittern, Black-crowned Night Heron, Great Egret, Glossy Ibis, Snowy Egret, Yellow-crowned Night Heron) related to an extreme weather event, Hurricane Sandy. We used Discrete Choice Resource Selection Functions to estimate habitat selection. Results showed species probability of use increased with lower elevation and slope, and closer proximity to marsh, salt marsh, Phragmites , and protected areas. Estimates of marsh dieback from Hurricane Sandy occurred disproportionately in areas with higher probability of species use. Species were observed farther from the coast and at higher elevations in the four breeding seasons after (2013–2016) compared to before (2000–2012) Hurricane Sandy. Our results indicate that although high suitability areas were affected by the storm, these six wetland bird species may have responded by moving inland and to higher elevation. Understanding how coastal wetland birds respond to storm events is important for conservation planning, particularly as storm frequency is projected to increase in the future.

New Jersey↗

USGS2012

Evidence for population bottlenecks and subtle genetic structure in the yellow rail

The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

The Condor↗

USGS2013

Estimating transmission of avian influenza in wild birds from incomplete epizootic data: implications for surveillance and disease spreac

Estimating disease transmission in wildlife populations is critical to understand host–pathogen dynamics, predict disease risks and prioritize surveillance activities. However, obtaining reliable estimates for free-ranging populations is extremely challenging. In particular, disease surveillance programs may routinely miss the onset or end of epizootics and peak prevalence, limiting the ability to evaluate infectious processes. We used profile likelihood to estimate the force of infection (FOI) in a low pathogenic avian influenza virus (LPAIv) epizootic model from censored time series of LPAIv prevalence in hatch-year waterfowl (order Anseriformes) at postbreeding and migration sites in North America. We found a mean LPAIv FOI of 0·12 day −1 [95% CI, 0·00–0·39], corresponding to an incidence rate of 0·11 day −1 , with geographic heterogeneity (min–max: 0·02–0·23 day −1 ) among study sites. These high infection rates indicate that most hatch-year waterfowl are likely infected with LPAIv early in the fall migration. Comparison of model-predicted and observed immunity confirmed our assumption of naïve hatch-year waterfowl and suggested long-term immunity (>6 months) for adults. Using the mean LPAIv incidence rate, we predict a shorter and lower epizootic curve for highly pathogenic avian influenza virus (HPAIv; 5 weeks with peak prevalence of 28% and 30% mortality) than LPAIv (8 weeks with peak prevalence of 50%). These findings indicate it is harder to detect HPAIv than LPAIv with swabs from live birds, which are commonly used during disease surveillance. Synthesis and applications . Our study highlights the potential of integrating incomplete surveillance data with epizootic models to quantify disease transmission and immunity. This modelling approach provides an important tool to understand spatial and temporal epizootic dynamics and inform disease surveillance. Our findings suggest focusing highly pathogenic avian influenza virus (HPAIv) surveillance on postbreeding areas where mortality of immunologically naïve hatch-year birds is most likely to occur, and collecting serology to enhance HPAIv detection. Our modelling approach can integrate various types of disease data facilitating its use with data from other surveillance programs (as illustrated by the estimation of infection rate during an HPAIv outbreak in mute swans Cygnus olor in Europe).

Journal of Applied Ecology↗