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USGS2008

Yellow-billed Cuckoo Distribution, Abundance, and Habitat Use Along the Lower Colorado River and Its Tributaries, 2007 Annual Report

This 2007 annual report details the second season of a 2-year study documenting western yellow-billed cuckoo (Coccyzus americanus occidentalis) distribution, abundance, and habitat use throughout the Lower Colorado River Multi-Species Conservation Program boundary area. We conducted cuckoo surveys at 40 sites within 14 areas, between 11 June and 9 September 2007. The 169 surveys across all sites yielded 163 yellow-billed cuckoo detections. Cuckoos were detected at 25 of the 40 sites, primarily at the Bill Williams River National Wildlife Refuge (NWR) study area (n = 139 detections; 85 percent of all detections). Detections declined slightly through the cuckoo breeding season, with most detections occurring in the first and second survey periods (n = 92; 54 percent). We detected breeding activity only at the Bill Williams River NWR, where we confirmed 27 breeding events, including two nesting observations. However, the breeding status of most detected birds was unknown. We used playback broadcast recordings to survey for yellow-billed cuckoos. Compared to simple point counts or surveys, this method increases the number of detections of this secretive, elusive species. It has long been suspected that cuckoos have a fairly low response rate, and that the standard survey method of using broadcast recordings might fail to detect all birds present in an area. In 2007, we found that the majority (84 percent) of cuckoo detections were solicited through broadcast at all study sites. The number of solicited detections was highest during the first survey period and declined as the breeding season progressed, while the number of unsolicited detections (cuckoos heard calling before broadcast was initiated) remained fairly constant through the first, second, and third survey periods. The majority (66 percent) of cuckoo detections, solicited or unsolicited, were aural, 23 percent were both heard and seen, and 11 percent were visual detections only. We also found that 50 percent of all responses by cuckoos were evenly split between the first and second broadcasts at sites with >10 detections, while 45 percent of responses occurred after a single broadcast at the sites with <10 detections. We refined our collection of vegetation data in 2007 and found that across the entire study area the dominant tree species were tamarisk (Tamarix spp.), willow (Salix spp.), and cottonwood (Populus spp.). The smallest size class (<8 cm diameter at breast height) trees were the most common and were dominated by tamarisk, but cottonwood and willows were well represented in the larger size classes. Sites that were occupied by yellow-billed cuckoos generally had higher canopies, denser cover in the upper layers of the canopy, and sparse shrub layers compared to unoccupied sites that consistently had higher densities of woody species. As most occupied sites were within the Bill Williams River NWR and most unoccupied sites were at Grand Canyon National Park/Lake Mead National Recreation Area, vegetation characteristics at these study areas drove the cuckoo distribution patterns we observed in 2007. However, there was a range of habitat conditions in locations that were used by yellow-billed cuckoos across the entire lower Colorado River Multi-Species Conservation Program study area. We measured microclimate variables (temperature, relative humidity, soil moisture) at occupied and unoccupied sites, and found that, across the entire study area, occupied sites were consistently cooler during the day and more humid during the day and night compared to unoccupied sites, but that soil moisture did not differ between occupied and unoccupied sites. While most cuckoo detections occurred at Bill Williams River NWR, with generally cooler and more humid conditions, cuckoos were also detected at study areas that had hotter and dryer microclimate conditions. We did not find any relationship of canopy cover characteristics to temperature or soil moisture, suggesting

Open-File Report↗

USGS2020

Terrestrial wildlife in the post-mined Appalachian landscape: Status and opportunities

Coal mining is an anthropogenic stressor that has impacted terrestrial and semi-aquatic wildlife in the Appalachian Plateau since European settlement. Creation of grassland and early-successional habitats resulting from mining in a forested landscape has resulted in novel, non-analog habitat conditions. Depending on the taxa, the extent of mining on the landscape, and reclamation practices, effects have ranged across a gradient of negative to positive. Forest-obligate species such as woodland salamanders and forest-interior birds or those that depend on aquatic systems in their life cycle have been most impacted. Others, such as grassland and early-successional bird species have responded favorably. Some bat species, as an unintended consequence, use legacy deep mines as winter hibernacula in a region with limited karst geology. Recolonization of impacted wildlife often depends on life strategies and species’ vagility, but also on altered or arrested successional processes on the post-surface mine landscape. Many wildlife species will benefit from Forest Reclamation Approach practices going forward. In the future, managers will be faced with decisions about reforestation versus maintaining open habitats depending on the conservation need of species. Lastly, the post-mined landscape currently is the focal point for a regional effort to restore elk ( Cervus canadensis ) in the Appalachians.

Appalachian Plateau↗

USGS2014

Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

Journal of Virological Methods↗

USGS2008

Inference methods for spatial variation in species richness and community composition when not all species are detected

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species in surveyed areas are not detected. Thus, counts of species detected underestimate the number of species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (and associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larger number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on these methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species richness and community composition.

Conservation Biology↗

USGS2024

Developing a range-wide sampling framework for endangered species: A case study with light-footed Ridgway’s rail

Monitoring provides the foundation for evaluating recovery of endangered species, yet many species lack monitoring programs designed to integrate a species’ unique attributes, specific monitoring objectives, and principles of statistical sampling theory. We developed a framework for monitoring and assessment of endangered light-footed Ridgway’s rails ( Rallus obsoletus levipes ) across their U.S. range, relative to multi-scale recovery goals. We created spatially explicit sample units and a sampling frame covering all potential habitat to facilitate range-wide probability sampling, and also built a model of the call-broadcast process commonly used to survey marsh birds that included heterogeneity in availability for detection and conditional detectability for each bird during each survey. We used the model to simulate 96 sampling strategies that included different levels of replication, multiple approaches for sample allocation amongst strata, and both simple random and weighted probability sampling (i.e., weights proportional to local rail abundance) of sample units within strata. Effective monitoring surveyed ≥20–30% of the sampling frame on ≥3 occasions, with weighted sample selection and more targeted sampling (50% of units) for strata that are key to species recovery. We also tested Bayesian N-mixture models for estimating abundance and show that multiple models provide reasonable estimates. This work lays the foundation for statistical sampling and multi-scale population estimation for an endangered bird, and for refinement of abundance estimation models. Moreover, this work provides a replicable process for building customized and statistically defensible sampling frameworks to assess recovery of endangered species that can used for other sensitive species.

California↗

USGS2024

Polar bear energetic and behavioral strategies on land with implications for surviving the ice-free period

Declining Arctic sea ice is increasing polar bear land use. Polar bears on land are thought to minimize activity to conserve energy. Here, we measure the daily energy expenditure (DEE), diet, behavior, movement, and body composition changes of 20 different polar bears on land over 19–23 days from August to September (2019–2022) in Manitoba, Canada. Polar bears on land exhibited a 5.2-fold range in DEE and 19-fold range in activity, from hibernation-like DEEs to levels approaching active bears on the sea ice, including three individuals that made energetically demanding swims totaling 54–175 km. Bears consumed berries, vegetation, birds, bones, antlers, seal, and beluga. Beyond compensating for elevated DEE, there was little benefit from terrestrial foraging toward prolonging the predicted time to starvation, as 19 of 20 bears lost mass (0.4–1.7 kg•day −1 ). Although polar bears on land exhibit remarkable behavioral plasticity, our findings reinforce the risk of starvation, particularly in subadults, with forecasted increases in the onshore period.

Manitoba↗

USGS2003

Science support for managing migratory waterfowl.

Migratory birds in North America are an international resource shared by Canada, the United States, and Mexico. Ultimate population management authority in the U.S. lies with the U.S. Fish and Wildlife Service (FWS), but states participate in development of management decisions through the Flyway system. The FWS, state wildlife agencies, and nongovernmental organizations participate through independent actions and cooperative Joint Ventures under the North American Waterfowl Management Plan (NAWMP) to acquire, protect, restore, and enhance wetlands and other habitats critical to the long-term conservation of breeding, migrating, and wintering waterfowl. A thorough base of scientific information is required to support and evaluate waterfowl populations and habitat management in North America.

WERC Fact Sheet↗

USGS2026

King Rails in southeastern Arkansas are majority resident

King Rails ( Rallus elegans ), a declining species of secretive marsh bird, have a mixed migratory strategy, with some individuals migrating and some being year-round residents. Determining the distribution of migratory versus resident King Rails is critical to guiding habitat management and assessing risks to populations. We examined the migratory status of adult King Rails at the Choctaw West Wildlife Management Area in southeastern Arkansas, the only known site in Arkansas with multiple breeding pairs. Of the 23 adult King Rails we tagged in 2022 and 2023, two birds migrated away from the local area, one in each year. One migrated 145 km, and the other 450 km. Our findings suggest that the line between the migratory and resident range of Arkansas King Rails could be north of our site.

Arkansas↗

USGS2026

Exploring trip preference heterogeneity in away-from-home birdwatchers using a discrete choice experiment

Birdwatching has grown in popularity worldwide and birdwatchers have emerged as an important constituency for wildlife and habitat conservation. To help promote wetland conservation, agencies and managers need to understand birdwatchers' desired trip experiences. We conducted national web-based surveys of American and Canadian birdwatchers by employing a discrete choice experiment to explore birdwatching trip preferences. We also collected information about participation in birdwatching and recreation specialization. We used latent class analysis to identify groups of birdwatchers with similar preferences. Our analysis indicated that birdwatchers were not homogeneous in their preferences. The seven attributes and associated attribute levels that were presented to participants (travel distance, site naturalness, bird rarity, the presence of waterfowl and wetlands, ease of access, species diversity and the number of birds seen) were all relevant, to varying degrees, in decisions about whether to take a birdwatching trip. We identified five latent classes of birdwatchers in the United States and Canada. ‘Nature seekers’ prioritised setting naturalness; ‘local birdwatchers’ strongly preferred shorter travel distances; ‘list-focused birdwatchers’ prioritised bird rarity and diversity; whereas ‘site-focused birdwatchers’ prioritised on-site characteristics above bird-related characteristics; and ‘casual birdwatchers’ were most likely to opt out of taking a trip. We found variation in recreation specialization and avidity levels across all the classes. Some classes ( e.g. list-focused birdwatchers) tend to be more specialised and more avid than others ( e.g. casual and local birdwatchers). Recognising the diversity of birdwatcher trip preferences can help outdoor recreation and wildlife managers provide a variety of suitable settings, services, and experiences.

Journal of Outdoor Recreation and Tourism↗

USGS2026

Estimating greater sage-grouse population sizes within Oregon, 2017–24

We fit a binomial mixture ( N -mixture) model to lek (breeding area) count data to estimate annual population sizes of greater sage-grouse ( Centrocercus urophasianus ; sage-grouse) within Oregon between 2017 and 2024. Population estimates were delineated among 24 priority areas for conservation, and additional sources of information were considered, including male-to-female sex ratios, lek attendance rates, numbers of unmodeled leks, and the existence of unsampled/unknown leks. In 2024, Oregon was estimated to contain approximately 41,875 sage-grouse (95-percent credible interval [CRI=38,980–54,634]), which was down from a high of 50,869 (95-percent CRI=41,794–66,238) in 2017. A nadir (low point) was identified during 2019, when the median statewide population estimate was 30,644 birds. A complete population oscillation was not evident during the inferential period based on local maxima that were observed during the start (2017) and stop (2024) years of analysis. In addition to estimating population sizes, we evaluated N -mixture model estimates for precision and accuracy after randomly removing single and repeat counts in 10-percent increments (relative to total sample size). We estimated an increase in absolute bias of approximately 1.6 percent for every 10-percent reduction in effort.

Oregon↗

USGS2020

Standardized guide to the examination and necropsy of the horseshoe crab using Limulus polyphemus as Limulidae prototype

The Atlantic, or American, horseshoe crab (L imulus polyphemus ) has existed largely unchanged for over 100 million years. Millions of individuals are commonly observed ashore in spring and summer months during spawning events along the entire North American coastline expanding from the East to the Gulf coasts of the United States and Mexico. Other species can be found in the Indian and Pacific Ocean. The massive deposit of eggs in nearshore sand provides a critical source of food for endangered migrating birds, especially the Red Knot ( Calidruis canutus rufa ) in the Delaware Bay. Horseshoe crabs are also an important component of the sea turtle diet. In addition to the ecological importance, horseshoe crabs are used commercially for bait in eel and conch fisheries and for biomedical purposes in the production of Limulus Amebocyte Lysate (LAL) to detect bacterial toxins in injectable drugs and implantable devices. Commercial demands have led to population declines in some regions. Fisheries are regulated by state and the current International Union for Conservation of Nature (IUCN) listing for L. polyphemus is vulnerable. A small number of individuals are housed in public aquaria for educational purposes. With growing interest in animal welfare, the health and stability of populations, and potential stressors that can contribute to decline , it is important to have clear and detailed descriptions of horseshoe crab anatomy and necropsy techniques. The purpose of this guide is to illustrate the normal anatomy and the step-by-step technique for dissection of horseshoe crabs. The contents are largely excerpts of the master’s thesis of artist, Katie (Bergdale) Roorda, which was based on photographs from C. Meteyer documenting the sequence and procedure used for necropsy dissection.

Cooperator Report↗

USGS2026

Incorporating data sets with multiple sources of uncertainty in integrated species distribution models

Data integration methods aim to improve species distribution estimates by incorporating multiple sources of uncertainty across datasets. Two major sources of uncertainty are: (1) variation in sampling effort across space and within datasets, and (2) variation in reliability associated with data collection protocols or timing among datasets. Our goal was to evaluate how different approaches to address these uncertainties influence predictive performance of integrated models. We modeled distributions of four bird species using three datasets that differed in sampling design. We examined three strategies to reduce uncertainty: (1) filtering data, (2) incorporating functions that account for uncertainty in observation models, and (3) varying how datasets are integrated into a single estimate. We first examine methods to account for variable effort in observations, focusing on both spatial differences in sampling intensity and effort given to a single observation record. We then examine approaches to account for data sets with differing reliability. Sampling effort was best addressed through conservative filtering, including spatial thinning and excluding observations with highly variable effort. Next, we considered how to account for potential false positive detections—due to either misidentification or changes in distributions. We found that treating less reliable data as a covariate, an approach previously suggested for data integration that can greatly speed up model fitting, performed well. Other effective approaches included directly modeling false positive rates and complete exclusion of less reliable data sets. Our results provide insights into best practices in integrated modeling for handling uncertainty in integrated models. We demonstrate the flexible options available when using integrated models to address uncertainty.

Pennsylvania↗

USGS2004

The relationship between species detection probability and local extinction probability

In community-level ecological studies, generally not all species present in sampled areas are detected. Many authors have proposed the use of estimation methods that allow detection probabilities that are < 1 and that are heterogeneous among species. These methods can also be used to estimate community-dynamic parameters such as species local extinction probability and turnover rates (Nichols et al. Ecol Appl 8:1213-1225; Conserv Biol 12:1390-1398). Here, we present an ad hoc approach to estimating community-level vital rates in the presence of joint heterogeneity of detection probabilities and vital rates. The method consists of partitioning the number of species into two groups using the detection frequencies and then estimating vital rates (e.g., local extinction probabilities) for each group. Estimators from each group are combined in a weighted estimator of vital rates that accounts for the effect of heterogeneity. Using data from the North American Breeding Bird Survey, we computed such estimates and tested the hypothesis that detection probabilities and local extinction probabilities were negatively related. Our analyses support the hypothesis that species detection probability covaries negatively with local probability of extinction and turnover rates. A simulation study was conducted to assess the performance of vital parameter estimators as well as other estimators relevant to questions about heterogeneity, such as coefficient of variation of detection probabilities and proportion of species in each group. Both the weighted estimator suggested in this paper and the original unweighted estimator for local extinction probability performed fairly well and provided no basis for preferring one to the other.

Oecologia↗

USGS2026

Estimating greater sage-grouse population sizes within the state of Oregon, USA 2017–2024

We fit an N -mixture model to lek (breeding area) count data to estimate annual population sizes of greater sage-grouse ( Centrocercus urophasianus ; sage-grouse) within the state of Oregon, USA between 2017–2024. Population estimates were delineated among 24 Priority Areas for Conservation (PACs) and considered additional sources of information including male-to-female sex ratios, lek attendance rates, numbers of unmodeled leks, and the existence of unsampled/unknown leks. In 2024, the state of Oregon was estimated to contain approximately 41,875 sage-grouse (95% credible interval [CRI] = 38,980–54,634), which was down from a high of 50,869 (95% CRI = 41,794–66,238) in 2017. A nadir (low point) was identified during 2019, when the median statewide population estimate was 30,644 birds. A complete population oscillation was not evident during the inferential period based on local maxima that were observed during the start (2017) and stop (2024) years of analysis. In addition to estimating population sizes, we evaluated N -mixture model estimates for precision and accuracy after randomly removing single and repeat counts in 10% increments (relative to total sample size). We estimated an increase in absolute bias of approximately 1.6% for every 10% reduction in effort.

BioRxiv↗

USGS2017

No evidence of critical slowing down in two endangered Hawaiian honeycreepers

There is debate about the current population trends and predicted short-term fates of the endangered forest birds, Hawai`i Creeper ( Loxops mana ) and Hawai`i `Ākepa ( L . coccineus ). Using long-term population size estimates, some studies report forest bird populations as stable or increasing, while other studies report signs of population decline or impending extinction associated with introduced Japanese White-eye ( Zosterops japonicus ) increase. Reliable predictors of impending population collapse, well before the collapse begins, have been reported in simulations and microcosm experiments. In these studies, statistical indicators of critical slowing down, a phenomenon characterized by longer recovery rates after population size perturbation, are reported to be early warning signals of an impending regime shift observable prior to the tipping point. While the conservation applications of these metrics are commonly discussed, early warning signal detection methods are rarely applied to population size data from natural populations, so their efficacy and utility in species management remain unclear. We evaluated two time series of state-space abundance estimates (1987–2012) from Hakalau Forest National Wildlife Refuge, Hawai`i to test for evidence of early warning signals of impending population collapse for the Hawai`i Creeper and Hawai`i `Ākepa. We looked for signals throughout the time series, and prior to 2000, when white-eye abundance began increasing. We found no evidence for either species of increasing variance, autocorrelation, or skewness, which are commonly reported early warning signals. We calculated linear rather than ordinary skewness because the latter is biased, particularly for small sample sizes. Furthermore, we identified break-points in trends over time for both endangered species, indicating shifts in slopes away from strongly increasing trends, but they were only weakly supported by Bayesian change-point analyses (i.e., no step-wise changes in abundance). The break-point and change-point test results, in addition to the early warning signal analyses, support that the two populations do not appear to show signs of critical slowing down or decline.

Hawai'i↗

USGS2015

Aerial-broadcast application of diphacinone bait for rodent control in Hawai`i: Efficacy and non-target species risk assessment

Introduced rats ( Rattus rattus, R. exulans , and R. norvegicus ) have been implicated in the decline or extinction of numerous species of plants and animals in Hawai‘i. This study investigated the efficacy of aerial-broadcast application of Ramik® Green baits containing 50 ppm (0.005%) diphacinone in reducing rat and mouse populations and the risk to non-target species. The study was undertaken in paired 45.56-ha treatment and non-treatment plots in Hawai‘i Volcanoes National Park. All 21 radio-collared rats in the treatment plot died within nine days of bait application, whereas none of the 18 radio-collared rats in the non-treatment plot died. There was a 99% drop in both the rat capture rate and percentage of non-toxic census bait blocks gnawed by rats in the treatment plot relative to the non-treatment plot three weeks after bait application. The only rat captured in the treatment plot three weeks after bait application was not ear-tagged (i.e., it was not a recapture), whereas 44% of the 52 rats captured in the non-treatment plot were ear-tagged. Most of the bait had disappeared from the forest floor within about one month of application. No birds likely to have eaten bait were found dead, although residues of diphacinone were found in the livers of three species of introduced seed-eating/omnivorous birds captured alive after bait application. No predatory birds were found dead one month or three months after bait application. The remains of a Hawaiian hawk (Buteo solitarius) were found six months after bait application, but it was not possible to determine the cause of death. This study demonstrated the efficacy of aerially broadcast diphacinone bait for control of rats and mice in Hawaiian montane forests, and was part of the dataset submitted to the U.S. Environmental Protection Agency for the national registration of a diphacinone bait for the control of rat populations in conservation areas.

Hawaii↗

USGS2024

Dynamics of the nesting group of the steppe eagle in Aktobe region in 2018-2023

Kazakhstan is a key area for the conservation of the steppe eagle, which is classified as an endangered species by the IUCN. Systematic work on monitoring changes in its number and reproductive success is carried out in protected areas. The remaining steppe spaces are explored sporadically. Our work partially fills this gap. Over 5 years of monitoring the nesting group in the north of the Aktobe region, 85 successful nests of the steppe eagle were identified. 160 fledglings were counted. Data have been collected on the spatial distribution and population dynamics of this bird.

Aktobe region↗

USGS1997

Effects of the landscape on shorebird movements at spring migration stopovers

We monitored the inter-wetland movements of 115 radio-tagged Pectoral Sandpipers (Calidris melanotos) at three migration stopovers in the Great Plains of North America during April and May from 1992 to 1995. While resident at a stopover, individuals were very localized in their movements. Over 40% of the birds made no inter, wetland movements, and over 90% of individuals moved less than 10 km from their original release site. Characteristics of wetlands where birds were released did not affect bird movements. However, the structure of the surrounding landscape explained up to 46% of variation in individual bird movements. As the distance between wetlands decreased, and the proportion of the landscape composed of wetlands increased, individual birds moved between wetlands more frequently and moved longer distances from their release site. These movement patterns indicate that a more connected landscape allows shorebirds to exploit more feeding sites with reduced searching costs; a result consistent with foraging theory. We estimate a degree of landscape connectivity at which a wetland complex functions as a single large wetland as measured by sandpiper feeding patterns. Our data provide support for the idea that complexes of small, closely spaced wetlands can be important migration stopovers and may have significant conservation value.

Condor↗