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USGS2021

Sexual dimorphism in morphology and plumage of endangered Yuma Ridgway’s Rails: A model for documenting sex

Many applications in wildlife management require knowledge of the sex of individual animals. The Yuma Ridgway's rail Rallus obsoletus yumanensis is an endangered marsh bird with monomorphic plumage and secretive behaviors, thereby complicating sex determination in field studies. We collected morphometric measurements from 270 adult Yuma Ridgway's rails and quantified the plumage and mandible color of 91 of those individuals throughout their geographic range to evaluate intersexual differences in morphology and coloration. We genetically sexed a subset of adult Yuma Ridgway's rails ( n = 101) and used these individuals to determine the optimal combination of measurements (based on discriminant function analyses) to distinguish between sexes. Males averaged significantly larger than females in all measurements, and the optimal discriminant function contained whole leg, culmen, and tail measurements and classified correctly 97.8% (95% CI: 92.5–100.0%) of genetically sexed individuals. We used two additional functions that classified correctly ≥ 95.6% of genetically sexed Yuma Ridgway's rails to assign sex to individuals with missing measurements. These simple models provide managers and researchers with a practical tool to determine the sex of Yuma Ridgway's rails based on morphometric measurements. Although color measurements were not in the most accurate discriminant functions, we quantified subtle intersexual differences in the color of mandibles and greater coverts of Yuma Ridgway's rails. These results document sex-specific patterns in coloration that allow future researchers to test hypotheses to determine the mechanisms underlying sex-based differences in plumage coloration.

Arizona, California, Nevada↗

USGS2013

Mortality of Palmetto bass following catch-and-release angling

Palmetto bass (Striped Bass Morone saxatilis x White Bass M. chrysops ) have been stocked into reservoirs in the southeastern USA since the late 1960s and have gained widespread acceptance as a sport fish. These fisheries are growing in popularity and catch-and-release (CR) fishing is commonplace; however, there is a dearth of information on CR mortality of palmetto bass. We experimentally angled palmetto bass ( n = 56; >373-mm TL) in a Tennessee reservoir using traditional angling gear in water temperatures ranging from 13 °C to 32 °C. Ultrasonic transmitters equipped with floats were externally attached to fish, which were released immediately and tracked multiple times within 10 d of release. Mortality was negligible (3.6%) in fall and spring at cool water temperatures but was high (39.3%) in summer when water temperatures exceeded 26 °C. The best logistic regression model based on Akaike's information criterion for small sample sizes scores relied on water temperature alone to predict CR mortality of palmetto bass; there was little support for other models that included all possible combinations of the six other predictor variables we tested. Palmetto bass in our study experienced lower CR mortality than Striped Bass in other systems, but CR mortality rates for palmetto bass that approach or exceed 40% during summer are still problematic if the goal is to maintain fishing quality.

North American Journal of Fisheries Management↗

USGS2025

Carbon and nitrogen isotopes of different native fish tissues from the Santa Ana River, California

Objective Stable isotopes are commonly used to understand the role of fishes in aquatic food webs. However, variability in species- and tissue-specific isotopic values can affect the inference that is drawn from a stable isotope study. We evaluated differences in stable isotopes of carbon (δ 13 C) and nitrogen (δ 15 N) among three tissue types (white muscle, caudal fin rays, and eye lenses) for Santa Ana Sucker Pantosteus santaanae and Arroyo Chub Gila orcuttii to inform the design of a stable isotope study in the Santa Ana River, an urban river that is located in southern California. Methods We used multivariate analyses to test for differences in the stable isotopes of carbon (δ 13 C) and nitrogen (δ 15 N) among the three tissue types that were collected from Santa Ana Sucker and Arroyo Chub. We also summarized the variability in isotopic values that was recorded over time in fish eye lenses and interpreted this variability in reference to the spatial patterns in isotopic values that have been previously reported throughout the Santa Ana River. Results We found that fin ray tissue and white muscle tissue were not significantly different for either isotope or fish species. Fish eye lenses were significantly higher in δ 13 C than muscle tissue, and eye lenses were significantly higher in δ 15 N than fin ray tissue for both fishes. We also found a greater range in δ 13 C and δ 15 N across eye lens layers for Santa Ana Sucker (δ 13 C = 2.01 ± 0.96‰, δ 15 N = 4.93 ± 4.18‰) than for Arroyo Chub (δ 13 C = 0.96 ± 0.65‰, δ 15 N = 4.63 ± 1.45‰). Conclusion Our results indicate that fin rays may be a viable nonlethal alternative to white muscle tissue for use in a stable isotope study of native fish of the Santa Ana River. Additionally, eye lenses could provide a chemical history of fishes within the river, but species-specific correction factors may be needed if stable isotope values for eye lenses are to be compared with more conventional tissue types (e.g., white muscle).

California↗

USGS2022

Redear Sunfish occurrence, abundance, growth, and size structure as related to abiotic and biotic factors in Florida lakes

Panfish support popular, socioeconomically valuable fisheries across the United States. Whereas Bluegill Lepomis macrochirus and Black Crappie Pomoxis nigromaculatus receive considerable research attention, Redear Sunfish L . microlophus are seldom studied despite their wide distribution, large size, socioeconomic contributions, and invasion potential in parts of their introduced range. We evaluated Redear Sunfish occurrence, density, relative abundance, growth, and size structure in 60 Florida lakes with varied surface area (2–12,412 ha), trophic state (oligotrophic to hypereutrophic), and macrophyte abundance (0.3–100% of lake volume inhabited), a range of environmental conditions over which Redear Sunfish populations have scarcely been investigated. Lake surface area, chlorophyll- a concentration, and macrophyte abundance explained 98% of variation in Redear Sunfish occurrence. Redear Sunfish density increased asymptotically with calcium concentration, whereas relative abundance (electrofishing fish/h) peaked at intermediate surface area (50–100 ha) and chlorophyll a (20 μg/L). Mean length at age 3 declined with increasing macrophyte abundance and was parabolically related to Redear Sunfish density, peaking at approximately 450 fish/ha. The proportional size distribution (PSD) and PSD of preferred-length fish were also negatively related to macrophyte abundance, and PSD declined with increasing Redear Sunfish density. Our results suggest that Redear Sunfish fisheries with abundant individuals of quality size (≥180 mm) require large (>100 ha), fertile (>20 μg/L chlorophyll a ) lakes with calcium concentrations >5 mg/L, moderate macrophyte abundance (0–25% of lake volume inhabited), and Redear Sunfish densities between 200 and 700 fish/ha. Our modeling approach can help managers predict Redear Sunfish occurrence, density, relative abundance, growth, and size structure based on a suite of abiotic and biotic variables.

Florida↗

USGS2019

Modeling connectivity of non‐floodplain wetlands: Insights, approaches, and recommendations

Representing hydrologic connectivity of non‐floodplain wetlands (NFWs) to downstream waters in process‐based models is an emerging challenge relevant to many research, regulatory, and management activities. We review four case studies that utilize process‐based models developed to simulate NFW hydrology. Models range from a simple, lumped parameter model to a highly complex, fully distributed model. Across case studies, we highlight appropriate application of each model, emphasizing spatial scale, computational demands, process representation, and model limitations. We end with a synthesis of recommended “best modeling practices” to guide model application. These recommendations include: (1) clearly articulate modeling objectives, and revisit and adjust those objectives regularly; (2) develop a conceptualization of NFW connectivity using qualitative observations, empirical data, and process‐based modeling; (3) select a model to represent NFW connectivity by balancing both modeling objectives and available resources; (4) use innovative techniques and data sources to validate and calibrate NFW connectivity simulations; and (5) clearly articulate the limits of the resulting NFW connectivity representation. Our review and synthesis of these case studies highlights modeling approaches that incorporate NFW connectivity, demonstrates tradeoffs in model selection, and ultimately provides actionable guidance for future model application and development.

Journal of the American Water Resources Associatio↗

USGS2014

Daily survival rates for nests of Black Skimmers from a core breeding area of the Southeastern USA

Little is known about the reproductive success of Black Skimmers ( Rynchops niger ) throughout the southeastern USA where availability of undisturbed beaches for nesting is limited. Daily survival rates (DSR) of nests were examined at three nesting sites in Cape Romain National Wildlife Refuge (CRNWR), South Carolina, USA, 2009–2010. The percent of successful nests ( n = 346 nests) ranged from 42–69% among colony sites when data were pooled across both years. The DSR of nests was primarily related to colony site, predation risk, height of high tide, and clutch size. Predation and overwash were the principal causes of identifiable nest loss, each accounting for &sim;33% of nest failures during the two study years. Because of the challenges of resighting skimmer chicks, we were not able to measure chick survival effectively and therefore accurate measures of productivity remain elusive. High variability in nest success among sites within close proximity to each other (<20 km) suggests factors at local scales such as disturbance, predation, and overwash events strongly influenced nest success of Black Skimmers during these 2 years as opposed to more region-wide stressors such as tropical storms or food availability. Although time-intensive techniques to control predators do exist, management options to limit flooding and overwash are far more limited. Conservation of Black Skimmers in the southeastern USA would benefit from coordinated, multi-state efforts to measure nest and chick survival.

South Carolina↗

USGS2019

Variation in Bluegill catch rates and total length distributions among four sampling gears used in two Wisconsin lakes dominated by small Ffsh

Many Bluegill Lepomis macrochirus populations are dominated by fish ≤125 mm total length (TL) that may be underrepresented when using standard sampling gears. To identify efficient sampling methods for these populations, we compared catch per unit effort (CPUE) and TL frequency distributions of Bluegill captured in cloverleaf traps, boat electrofishing, mini-fyke nets, and beach seine hauls from two northern Wisconsin lakes supporting populations dominated by fish ≤125 mm TL. Mean Bluegill CPUE ranged from 41 (SE = 11) fish per cloverleaf trap lift to 16 (SE = 8) fish per beach seine haul. Cloverleaf traps generally captured smaller Bluegill relative to other gears and were the only gear to consistently capture Bluegill ≤80 mm TL. Conversely, boat electrofishing captured the widest TL range of Bluegill, and fish ≥80 mm TL composed a greater proportion of catch (37%) relative to other gears. With few exceptions, the effort required to detect 10% or 25% changes in Bluegill CPUE was >100 units of effort regardless of lake, sampling gear, or month. Furthermore, there was no consistency between lakes or months in terms of which sampling gear required the fewest number of samples to detect a 50% change in CPUE. Estimated units of effort needed to detect 10% or 25% changes in mean Bluegill TL were ≤16 for all sampling gears on the lake with consistently higher CPUE (i.e., more fish to measure per unit). In the lake with lower CPUE, cloverleaf traps consistently required less effort to detect changes in mean TL. We note that comparing sample size requirements among gears is not straightforward because gears are sampling differing segments of the Bluegill population. Our study emphasizes the importance of evaluating gear biases and sampling efficiency so that fisheries managers can develop suitable sampling protocols.

Wisconsin↗

USGS2015

Wildlife, urban inputs, and landscape configuration are responsible for degraded swimming water quality at an embayed beach

Jeorse Park Beach, on southern Lake Michigan, experiences frequent closures due to high Escherichia coli ( E. coli ) levels since regular monitoring was implemented in 2005. During the summer of 2010, contaminant source tracking techniques, such as the conventional microbial and physical surveys and hydrodynamic models, were used to determine the reasons for poor water quality at Jeorse Park. Fecal indicator bacteria ( E. coli , enterococci) were high throughout the season, with densities ranging from 12–2419 (culturable E. coli ) and 1–2550 and < 1–5831 (culturable and qPCR enterococci, respectively). Genetic markers for human ( Bacteroides HF183) and gull ( Catellicoccus marimammalium ) fecal contamination were found in 15% and 37% of the samples indicating multiple sources contributing to poor water quality. Nesting colonies of double-crested cormorants ( Phalacrocorax auritus ) have steadily increased since 2005, coinciding with high E. coli levels. A hydrodynamic model indicated that limited circulation allows bacteria entering the embayed area to be retained in nearshore areas; and bacterial resuspension from sand and stranded beach wrack during storm events compounds the problem. The integration of hydrodynamics, expanded use of chemical and biological markers, as well as more complex statistical multivariate techniques can improve microbial source tracking, informing management actions to improve recreational water quality. Alterations to embayed structures to improve circulation and reduce nuisance algae as well as growing native plants to retain sand to improve beach morphometry are among some of the restoration strategies under consideration in ongoing multi-agency collaborations.

Indiana↗

USGS2025

Weather, habitat area, connectivity, and number of patches influence breeding ecology of ring-necked pheasants

Understanding habitat selection is critical in habitat prioritization for species of conservation and management concern. Information on habitat selection is particularly important for grassland bird species whose populations have suffered steep declines over the last few decades. We assessed ring-necked pheasants' ( Phasianus colchicus ) habitat selection in a dynamic agricultural landscape. The population dynamics of pheasants are partially related to nest survival, which may be influenced by the quality of nesting habitat. Consequently, knowledge of vegetation composition and structural characteristics associated with the selection and survival of nests would help inform management decisions to improve nest success. We monitored nests from 103 radio-collared pheasants inhabiting an agricultural landscape in South Dakota, USA, from 2017–2019 to determine the effect of landscape composition and configuration on nest-site selection and nest survival. We explored nesting behavior at 2 orders of selection: resource selection within the home range (third order) and selection of specific resource items from a resource patch (fourth order). Proportion of row crop and connectivity of row crop was negatively associated with nest-site selection at the third order. At the fourth order, pheasants tended to select for taller vegetation and greater percent grass cover than at paired random sites. Pheasants also selected areas with more grasslands. A 1% increase in grass cover and proportion of grassland increased the odds of nest-site selection by 1% and 2%, respectively. Connectivity of row crop patches was negatively associated with daily nest survival. We also evaluated factors affecting pheasant brood-site selection. A 1-unit increase in grass cover and Hemiptera biomass increased the odds of brood-site selection by 4%. The probability of brood-site selection also increased with fewer row crop patches. Weather played a crucial role in driving nest survival. The consideration of local weather trends and regional variation in habitat can inform habitat management for pheasants. Pheasant populations may benefit from research that identifies thermal landscapes and land management techniques that promote cooler microclimates for nesting and brood-rearing activities.

South Dakota↗

USGS1972

The future of salmonid communities in the Laurentian Great Lakes

The effects of human population growth, industrialization, and the introduction of marine fishes have reduced the suitability of each of the Great Lakes for oligotrophic fish communities. The ultimate consequence has been a reduction of fishery productivity that has ranged from extreme in Lake Ontario to moderate in Lake Superior. If measures are not taken to alleviate the adverse effects of marine invaders and trends in environmental quality, a major reduction in fishery productivity can eventually be expected throughout the Great Lakes.Prospects for the next century will be improved if the lakes can be intensively managed. More stringent control of the sea lamprey ( Petromyzon marinus ), and subsequent reduction of the alewife ( Alosa pseudoharengus ), by the reestablishment of populations of large piscivores, should permit the recovery of some of the previous predator and prey species, or the development of populations of new species that are more compatible with a reduced number of lampreys. Even if marine species can be reduced greatly, the full restoration of the former fishery productivity remains uncertain and will require a high degree of coordination among all management and research agencies that have responsibilities on the Great Lakes.Unfavorable trends toward progressive degradation of water quality pose the greatest threat to restoration of the fishery resources of the Great Lakes. Where changes in water quality have been the greatest, oligotrophic species have become scarce or absent, and in the deepwater regions no other species have reoccupied the vacated niches.

Journal of the Fisheries Research Board of Canada↗

USGS2024

Use of Doppler velocity radars to monitor and predict debris and flood wave velocities and travel times in post-wildfire basins

The magnitude and timing of extreme events such as debris and floodflows (collectively referred to as floodflows) in post-wildfire basins are difficult to measure and are even more difficult to predict. To address this challenge, a sensor ensemble consisting of noncontact, ground-based (near-field), Doppler velocity (velocity) and pulsed (stage or gage height) radars, rain gages, and a redundant radio communication network was leveraged to monitor flood wave velocities, to validate travel times, and to compliment observations from NEXRAD weather radar. The sensor ensemble (DEbris and Floodflow Early warNing System, DEFENS) was deployed in Waldo Canyon, Pike National Forest, Colorado, USA, which was burned entirely (100 percent burned) by the Waldo Canyon fire during the summer of 2012 ( MTBS, 2020 ). Surface velocity, stage, and precipitation time series collected during the DEFENS deployment on 10 August 2015 were used to monitor and predict flood wave velocities and travel times as a function of stream discharge (discharge; streamflow). The 10 August 2015 event exhibited spatial and temporal variations in rainfall intensity and duration that resulted in a discharge equal to 5.01 cubic meters per second (m 3 /s). Discharge was estimated post-event using a slope-conveyance indirect discharge method and was verified using velocity radars and the probability concept algorithm. Mean flood wave velocities – represented by the kinematic celerity ( c k = 2.619 m e t e r s p e r s e c o n d , m / s ± 0.556 p e r c e n t "> 𝑐 𝑘 = 2.619 𝑚𝑒𝑡𝑒𝑟𝑠 𝑝𝑒𝑟 𝑠𝑒𝑐𝑜𝑛𝑑, m/s ± 0.556 𝑝𝑒𝑟𝑐𝑒𝑛𝑡) and dynamic celerity ( c d = 3.533 m / s ± 0.181 p e r c e n t a n d t h e i r u n c e r t a i n t i e s "> 𝑐 𝑑 = 3.533 m/s ± 0.181 𝑝𝑒𝑟𝑐𝑒𝑛𝑡) and their uncertainties were computed. L-moments were computed to establish probability density functions (PDFs) and associated statistics for each of the at-a-section hydraulic parameters to serve as a workflow for implementing alert networks in hydrologically similar basins that lack data. Measured flood wave velocities and travel times agreed well with predicted values. Absolute percent differences between predicted and measured flood wave velocities ranged from 1.6 percent to 49 percent and varied with water slope, hydraulic radius, and depth. The kinematic celerity was a better predictor for steep slopes and wide flood plains associated with the Upper Waldo and Middle Waldo radar streamgages; whereas, the dynamic celerity was a better surrogate for shallow slopes and incised channels such as the Lower Waldo radar streamgage. The method demonstrates the potential extensibility of a post-wildfire warning system by (1) leveraging multiple systems (i.e., weather radar, near-field velocity and stage radars, and rain gages) for accurate and timely warnings of debris and floodflows, (2) establishing an order of operations to site, install, and operate near-field radars and conventional rain gages to record floodflows, forecast travel times, and document geomorphic change in this basin and hydrologically similar basins that lack data, and (3) communicating data operationally with the Colorado Department of Transportation engineering staff, National Weather Service forecasters, and emergency managers.

Colorado↗

USGS2023

Providing a framework for seagrass mapping in United States coastal ecosystems using high spatial resolution satellite imagery

Seagrasses have been widely recognized for their ecosystem services, but traditional seagrass monitoring approaches emphasizing ground and aerial observations are costly, time-consuming, and lack standardization across datasets. This study leveraged satellite imagery from Maxar's WorldView-2 and WorldView-3 high spatial resolution, commercial satellite platforms to provide a consistent classification approach for monitoring seagrass at eleven study areas across the continental United States, representing geographically, ecologically, and climatically diverse regions. A single satellite image was selected at each of the eleven study areas to correspond temporally to reference data representing seagrass coverage and was classified into four general classes: land, seagrass, no seagrass, and no data. Satellite-derived seagrass coverage was then compared to reference data using either balanced agreement, the Mann-Whitney U test, or the Kruskal-Wallis test, depending on the format of the reference data used for comparison. Balanced agreement ranged from 58% to 86%, with better agreement between reference- and satellite-indicated seagrass absence (specificity ranged from 88% to 100%) than between reference- and satellite-indicated seagrass presence (sensitivity ranged from 17% to 73%). Results of the Mann-Whitney U and Kruskal-Wallis tests demonstrated that satellite-indicated seagrass percentage cover had moderate to large correlations with reference-indicated seagrass percentage cover, indicative of moderate to strong agreement between datasets. Satellite classification performed best in areas of dense, continuous seagrass compared to areas of sparse, discontinuous seagrass and provided a suitable spatial representation of seagrass distribution within each study area. This study demonstrates that the same methods can be applied across scenes spanning varying seagrass bioregions, atmospheric conditions, and optical water types, which is a significant step toward developing a consistent, operational approach for mapping seagrass coverage at the national and global scales. Accompanying this manuscript are instructional videos describing the processing workflow, including data acquisition, data processing, and satellite image classification. These instructional videos may serve as a management tool to complement field- and aerial-based mapping efforts for monitoring seagrass ecosystems.

Alaska, California, Delaware, Florida, Maine, Mary↗

USGS2011

Nest success of northern bobwhite on managed and unmanaged landscapes in southeast Iowa

Range‐wide declines in northern bobwhite populations ( Colinus virginianus ) have been attributed to concomitant loss of breeding habitat. Bobwhite management efforts to restore this habitat resource can be informed by empirical studies of associations between breeding success and multi‐scale habitat attributes. We compared bobwhite nest success in 2 southern Iowa landscapes as a function of microhabitat and landscape composition. Lake Sugema Fish and Wildlife Area (LSWA) was managed to promote bobwhite recruitment, and Harrisburg Township (HT) was an adjacent landscape dominated by private agricultural production. Survival rate modeling based on telemetry data provided evidence for age‐specific daily nest survival rate. Daily survival rates decreased as nest age increased, but the decline was more severe at HT. Nest survival at LSWA ( S = 0.495, SE = 0.103) was nearly twice that on HT ( S = 0.277, SE = 0.072). We found no evidence that habitat composition or spatial attributes within 210 m of a nest site significantly influenced nest success. Forb canopy at the nest site had a positive influence on nest success at HT but not at LSWA. We suggest nesting habitat with greater forb canopy cover will increase the opportunity for nesting success in landscapes with limited nesting habitat.

Iowa↗

USGS2010

Importance of coastal change variables in determining vulnerability to sea- and lake-level change

In 2001, the U.S. Geological Survey began conducting scientific assessments of coastal vulnerability to potential future sea- and lake-level changes in 22 National Park Service sea- and lakeshore units. Coastal park units chosen for the assessment included a variety of geological and physical settings along the U.S. Atlantic, Pacific, Gulf of Mexico, Gulf of Alaska, Caribbean, and Great Lakes shorelines. This research is motivated by the need to understand and anticipate coastal changes caused by accelerating sea-level rise, as well as lake-level changes caused by climate change, over the next century. The goal of these assessments is to provide information that can be used to make long-term (decade to century) management decisions. Here we analyze the results of coastal vulnerability assessments for several coastal national park units. Index-based assessments quantify the likelihood that physical changes may occur based on analysis of the following variables: tidal range, ice cover, wave height, coastal slope, historical shoreline change rate, geomorphology, and historical rate of relative sea- or lake-level change. This approach seeks to combine a coastal system's susceptibility to change with its natural ability to adapt to changing environmental conditions, and it provides a measure of the system's potential vulnerability to the effects of sea- or lake-level change. Assessments for 22 park units are combined to evaluate relationships among the variables used to derive the index. Results indicate that Atlantic and Gulf of Mexico parks have the highest vulnerability rankings relative to other park regions. A principal component analysis reveals that 99% of the index variability can be explained by four variables: geomorphology, regional coastal slope, water-level change rate, and mean significant wave height. Tidal range, ice cover, and historical shoreline change are not as important when the index is evaluated at large spatial scales (thousands of kilometers). ?? 2010 Coastal Education and Research Foundation.

Journal of Coastal Research↗

USGS1985

An aerial photographic census of Chesapeake Bay and North Carolina canvasbacks

We used conventional 35-mm photography to conduct an aerial photographic census of canvasbacks ( Aythya valisineria ) throughout Chesapeake Bay (tidal Maryland and Virginia) and coastal North Carolina, 26-30 January 1981. Flock size and sex ratio characteristics were determined from examination of color transparencies of 165 canvasback flocks totaling over 95,000 birds. A sex ratio of 2.91 males/female was determined from 68,769 birds, 80% of the birds in 150 flocks. Sex ratio for the Atlantic Flyway was projected as 2.90 males/female. We recorded the greatest number of canvasbacks and the widest range of flock size in Maryland waters; the fewest canvasbacks and the smallest average flock size in Virginia; and the fewest but on average the largest flocks of canvasbacks in North Carolina. Sex ratio varied latitudinally in the flyway with a tendency for males to occupy more northern and females more southern latitudes in winter. Sex ratio (males/female) was highest in Maryland (3.98), slightly lower in Virginia (3.71), and lowest in North Carolina (1.70). Locally, sex ratio varied with flock size. In Chesapeake Bay, small flocks (<100 birds) had lower sex ratio (P < 0.05) than medium (100-1,000) or large (>1,000) flocks. By providing large- sample sex ratio information, as well as exact counts of birds, we conclude that low-level 35-mm aerial photography is the most efficient and accurate means of determining canvasback population status in eastern coastal habitats.

Maryland, North Carolina, Virginia↗

USGS2023

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake ( Crotalus oreganus ) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus , in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

California↗

USGS2020

Northern Goshawk (Accipiter gentilis) home range, movement and forays revealed by GPS-tracking

The Northern Goshawk ( Accipiter gentilis ) is an apex predator occurring across North America and Eurasia. The species has received considerable conservation focus in late-seral conifer forests of western North America, where its habitat has been substantially reduced and altered by timber harvest and is increasingly at risk from high severity fire, drought, and forest pathogens. In the Sierra Nevada range of California, management and conservation of goshawks are hampered by a lack of knowledge of their basic space use and movement ecology. We used global positioning system (GPS) loggers to investigate space use of 20 resident, adult Northern Goshawks over 3 yr (2015–2018) in the Plumas National Forest, California. Median home range sizes of male goshawks were more than twice as large as those of females, and nonbreeding-season home ranges were three times larger than breeding-season home ranges. High resolution GPS data (location interval 1–6 min) allowed quantification of daily transit distances up to 60 km for individual goshawks and revealed long-distance forays into adjacent territories and surrounding areas. Four goshawks (three males, one female) undertook forays >8 km from their nest locations, with forays lasting up to 6 d; these forays occurred during both breeding and nonbreeding seasons for both sexes. Comparing our results to current conservation approaches, we determined that USDA Forest Service goshawk Protected Activity Centers protected <25% of both the roost locations and the area used during the daytime. Conservation efforts for Northern Goshawks in the Sierra Nevada would benefit from consideration of year-round habitat needs at larger scales than previously thought.

California↗

USGS2002

Yellowstone grizzly bear investigations: Annual report of the Interagency Grizzly Bear Study Team, 2001

The contents of this Annual Report summarize results of monitoring and research from the 2001 field season. The report also contains a summary of nuisance grizzly bear ( Ursus arctos horribilis ) management actions. In addition to our normal monitoring, we completed an array of studies addressing the potential impacts of winter recreation on denning grizzly bears. This research was in response to a lawsuit filed against the Gallatin National Forest and subsequent need to develop a biological assessment addressing effects of snowmobile use on grizzly bears (Chemy 2001). Research results were also used by the National Park Service for a biological assessment and winter use plan (U.S. Department of the Interior 2001). The Interagency Grizzly Bear Study Team (IGBST) was able to use existing data collected from collared bears to address several issues and data needs for both agencies. Denning chronology (Haroldson et al. 2002), denning areas (Podruzny et al. 2002), and grizzly distribution (Schwartz et al. 2002) were all addressed. Information from these studies was presented at the International Association for Bear Research and Management (IBA) in Jackson Hole, Wyoming in 2001, and all 3 manuscripts have been officially accepted for publication in the journal Ursus . Abstracts are attached to this report (Appendices A, B. and C). Additionally, members of the study team participated in a workshop held by the National Park Service to develop monitoring protocols addressing the impacts of snowmobiles on wildlife (Graves and Reams 2001). The study team has also been working on issues associated with counts of unduplicated females with cubs-of-the-year (COY). These counts are used to establisha minimum population size, which is then used to establish mortality thresholds for the Recovery Plan (U.S. Fish and Wildlife Service [USFWS) 1993). Efforts by the Study Team to calculate more statistically sound estimates of population size have been underway for sometime. Eberhardt and Knight (1996) applied a Peterson-type capturemark-recapture estimator to unduplicated counts, and Boyce et al. (1999) recommended a maximum likelihood method. These methods assumed equal sightability of families, which was unrealistic for the Yellowstone population. Consequently, Boyce et al. (2001) recommended using a negative binomial distribution but found that they obtained reasonable results only when the coefficient of variation among sightings was assumed to be constant overtime. This assumption is also difficult to justify. Recent work by the study team (Keating et al. 2002) evaluated the application of 7 nonparametric estimators to assess their performance in determining the number of females with COY in a given year. This work identified 2 estimators that performed well using Monte Carlo simulations over a range of sampling conditions deemed plausible for the Yellowstone population: Chao's estimator (Chao 1984) and the sample coverage estimator (Chao and Lee 1992, Lee and Chao 1994). This work was presented at the IBA meeting in Jackson and the manuscript has been accepted in the journal Ursus . An abstract of this work is attached to this annual report (Appendix D). We are currently refining the application of these techniques to expand the predicted number of females with COY into a total population estimate. We anticipate completion of that work in 2002 or 2003.

Idaho, Montana, Wyoming↗