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USGS2015

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2014 through December 2014

Executive Summary The Wind River subbasin in southwest Washington State provides habitat for a population of wild Lower Columbia River steelhead Oncorhynchus mykiss , which are listed as threatened under the Endangered Species Act. No hatchery steelhead have been planted in the Wind River subbasin since 1994, and hatchery adults are estimated to be less than one percent of adults in any year (Thomas Buehrens, Washington Department of Fish and Wildlife, personal communication). Numerous restoration actions have been implemented in the subbasin, including the removal of Hemlock Dam on Trout Creek in 2009. We used Passive Integrated Transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTIS) to investigate life-histories, populations, and efficacy of habitat restoration actions for these steelhead. Data from our study, and companion work by Washington Department of Fish and Wildlife (WDFW), will contribute to Bonneville Power Administration’s (BPA) Research Monitoring and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring ( www.cbfish.org/ProgramStrategy.mvc/ViewProgramStrategySummary/1 ), specifically the sub-strategies of: 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and to Uncertainties Research regarding differing life histories of a wild steelhead population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer 2014, we PIT-tagged steelhead parr in headwater areas of the Wind River subbasin to investigate life-history diversity, specifically to compare fate of those juvenile steelhead that move downstream prior to smolting with those that remain in their natal areas until smolting. A series of instream PTISs monitored movement of these fish. We added a new multi-antenna PTIS on Trout Creek and made improvements to two of our smaller tributary PTISs during 2014. Detections at the instream PTISs showed trends of parr emigration during summer and fall, in addition to the expected movement of parr and smolts in spring. Long-term monitoring of PIT-tagged fish will provide information on contribution of various life-history strategies to smolt production and adult returns, as well as helping to identify factors influencing parr movement. Movements of PIT-tagged adult steelhead were tracked with our instream PTISs. These data will contribute to a better understanding of timing and distribution of spawning by this population of wild steelhead within the Wind River subbasin. Additionally, these data have provided information on timing of adult movements to various parts of the watershed, which is allowing us to assess adult use of tributary watersheds within the Wind River subbasin. These data are contributing to evaluating steelhead response to the removal of Hemlock Dam from Trout Creek. Hemlock Dam, which was located at rkm 2.0 of Trout Creek, was removed in summer 2009 and had contributed to hydrologic impairment of Trout Creek and potentially caused some deterrent to upstream adult steelhead migration. Evaluating restoration efforts is of interest to many managers and agencies so that funding and time are allocated for best results. The evaluation of various life-histories of Lower Columbia River steelhead within the Wind River subbasin provides information to better track populations, and more effectively direct habitat restoration and water allocation planning. Increasingly detailed Viable Salmonid Population information (Crawford and Rumsey 2009), such as that provided by PIT-tagging and instream PTISs networks like those we build and operate in the Wind River subbasin, provide data to better inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

Washington↗

USGS2023

Coproduction and modeling spatial contact networks prevent bias about infectious hematopoietic necrosis virus transmission for Snake River Basin salmonids

Much remains unknown about variation in pathogen transmission across the geographic range of a free-ranging fish or animal species and about the influence of movement (associated with husbandry practices or animal behavior) on pathogen transmission. Salmonid hatcheries are an ideal system in which to study these processes. Salmonid hatcheries are managed for endangered species recovery, supplementation of threatened or at-risk fish stocks, support of fisheries, and ecosystem stability. Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus of significant concern to salmon aquaculture. Landscape IHNV transmission dynamics previously had been estimated only for salmonid hatcheries in the Lower Columbia River Basin (LCRB). The objectives of this study were to estimate IHNV transmission dynamics in a unique geographic region, the Snake River Basin (SRB), and to quantitatively estimate the effect of model coproduction on inference because previous assessments of coproduction have been qualitative. In contrast to the LCRB, the SRB has hatchery complexes consisting of a main hatchery and ≥1 satellite facility. Knowledge about hatchery complexes was held by a subset of project researchers but would not have been available to project modelers without coproduction. Project modelers generated and tested multiple versions of Bayesian susceptible-exposedinfected models to realistically represent the SRB and estimate the effect of coproduction. Models estimated the frequency of transmission routes, route-specific infection probabilities, and infection probabilities for combinations of salmonid hosts and IHNV lineages. Model results indicated that in the SRB, avoiding exposure to IHNV-positive adult salmonids is the most important action to prevent juvenile infections. Migrating adult salmonids exposed juvenile cohort-sites most frequently, and the infection probability was greatest following exposure to migrating adults. Without coproduction, the frequency of exposure by migrating adults would have been overestimated by 70 cohort-sites, and the infection probability following exposure to migrating adults would have been underestimated by∼0.09. The coproduced model had less uncertainty in the infection probability if no transmission route could be identified (Bayesian credible interval (BCI) width = 0.12) compared to the model without coproduction (BCI width = 0.34). Evidence for virus lineage MD specialization on steelhead and rainbow trout (both Oncorhynchus mykiss) was apparent without model coproduction. In the SRB, we found a greater probability of virus lineage UC infection in Chinook salmon (Oncorhynchus tshawytscha) compared to in O. mykiss, whereas in the LCRB, UC more clearly exhibited a generalist approach. Coproduction influenced estimates that depended on transmission routes, which operated differently at main hatcheries and satellite sites within hatchery complexes. Hatchery complexes are found outside of the SRB and are not specific to salmonid hatcheries alone. There is great potential for coproduction and modeling spatial contact networks to advance understanding about infectious disease transmission in complex production systems and surrounding free-ranging animal populations.

Idaho, Oregon, Washington↗

USGS2023

Historical DNA reveals climate adaptation in an endangered songbird

To cope with climate change, species may shift their distributions or adapt in situ to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher ( Empidonax traillii extimus ) through whole-genome comparisons between historical specimens, collected from 1888 to 1909 near San Diego, California, United States, and contemporary individuals from across the breeding range. Genomic analyses revealed that introgression into San Diego increased adaptive potential over time and shifted genome-wide population structure towards that of neighbouring populations. In contrast, loci linked to climate (dew point temperature and precipitation) shifted away from neighbouring populations and in a direction consistent with adaptation to climate change in southern California. This research highlights the role of admixture in facilitating adaptive shifts through its impact on genome-wide genetic variation and represents one of the few studies to document climate adaptation in a wild population.

Nature Climate Change↗

USGS2016

Model description and evaluation of the mark-recapture survival model used to parameterize the 2012 status and threats analysis for the Florida manatee ( Trichechus manatus latirostris )

This report provides supporting details and evidence for the rationale, validity and efficacy of a new mark-recapture model, the Barker Robust Design, to estimate regional manatee survival rates used to parameterize several components of the 2012 version of the Manatee Core Biological Model (CBM) and Threats Analysis (TA). The CBM and TA provide scientific analyses on population viability of the Florida manatee subspecies ( Trichechus manatus latirostris ) for U.S. Fish and Wildlife Service’s 5-year reviews of the status of the species as listed under the Endangered Species Act. The model evaluation is presented in a standardized reporting framework, modified from the TRACE (TRAnsparent and Comprehensive model Evaluation) protocol first introduced for environmental threat analyses. We identify this new protocol as TRACE-MANATEE SURVIVAL and this model evaluation specifically as TRACE-MANATEE SURVIVAL, Barker RD version 1. The longer-term objectives of the manatee standard reporting format are to (1) communicate to resource managers consistent evaluation information over sequential modeling efforts; (2) build understanding and expertise on the structure and function of the models; (3) document changes in model structures and applications in response to evolving management objectives, new biological and ecological knowledge, and new statistical advances; and (4) provide greater transparency for management and research review.

Open-File Report↗

USGS2017

Status of White Sturgeon (Acipenser transmontanus Richardson, 1863) throughout the species range, threats to survival, and prognosis for the future

White Sturgeon, Acipenser transmontanus (WS), are distributed throughout three major river basins on the West Coast of North America: the Sacramento-San Joaquin, Columbia, and Fraser River drainages. Considered the largest North American freshwater fish, some WS use estuarine habitat and make limited marine movements between river basins. Some populations are listed by the United States or Canada as threatened or endangered (upper Columbia River above Grand Coulee Dam; Kootenai River; lower, middle and, upper Fraser River and Nechako River), while others do not warrant federal listing at this time (Sacramento-San Joaquin Rivers; Columbia River below Grand Coulee Dam; Snake River). Threats that impact WS throughout the species’ range include fishing effects and habitat alteration and degradation. Several populations suffer from recruitment limitations or collapse due to high early life mortality associated with these threats. Efforts to preserve WS populations include annual monitoring, harvest restrictions, habitat restoration, and conservation aquaculture. This paper provides a review of current knowledge on WS life history, ecology, physiology, behavior, and genetics and presents the status of WS in each drainage. Ongoing management and conservation efforts and additional research needs are identified to address present and future risks to the species.

Journal of Applied Ichthyology↗

USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗

USGS2012

Is science in danger of sanctifying the wolf?

Historically the wolf ( Canis lupus ) was hated and extirpated from most of the contiguous United States. The federal Endangered Species Act fostered wolf protection and reintroduction which improved the species' image. Wolf populations reached biological recovery in the Northern Rocky Mountains and upper Midwest, and the animal has been delisted from the Endangered Species List in those areas. Numerous studies in National Parks suggest that wolves, through trophic cascades, have caused ecosystems to change in ways many people consider positive. Several studies have been conducted in Yellowstone National Park where wolf interactions with their prey, primarily elk ( Cervus elaphus ), are thought to have caused reduction of numbers or changes in movements and behavior. Some workers consider the latter changes to have led to a behaviorally-mediated trophic cascade. Either the elk reduction or the behavioral changes are hypothesized to have fostered growth in browse, primarily willows ( Salix spp.) and aspen ( Populus spp.), and that growth has resulted in increased beavers ( Castor Canadensis ), songbirds, and hydrologic changes. The wolf's image thus has gained an iconic cachet. However, later research challenges several earlier studies' findings such that earlier conclusions are now controversial; especially those related to causes of browse regrowth. In any case, any such cascading effects of wolves found in National Parks would have little relevance to most of the wolf range because of overriding anthropogenic influences there on wolves, prey, vegetation, and other parts of the food web. The wolf is neither a saint nor a sinner except to those who want to make it so.

Biological Conservation↗

USGS2015

Literature review of giant gartersnake ( Thamnophis gigas ) biology and conservation

This report reviews the available literature on giant gartersnakes ( Thamnophis gigas ) to compile existing information on this species and identify knowledge gaps that, if addressed, would help to inform conservation efforts for giant gartersnakes. Giant gartersnakes comprise a species of semi-aquatic snake precinctive to wetlands in the Central Valley of California. The diversion of surface water and conversion of wetlands to agricultural and other land uses resulted in the loss of more than 90 percent of natural giant gartersnake habitats. Because of this habitat loss, giant gartersnakes are now listed by the United States and California Endangered Species Acts as Threatened. Most extant populations occur in the rice-growing regions of the Sacramento Valley, which comprises the northern portion of the giant gartersnake’s former range. The huge demand for water in California for agriculture, industry, recreation, and other human consumption, combined with periodic severe drought, places remaining giant gartersnake habitats at increased risk of degradation and loss. This literature review summarizes the available information on giant gartersnake distribution, habitat relations, behavior, demography, and other aspects of its biology relevant to conservation. This information is then compiled into a graphical conceptual model that indicates the importance of different aspects of giant gartersnake biology for maintaining positive population growth, and identifies those areas for which important information relevant for conservation is lacking. Directing research efforts toward these aspects of giant gartersnake ecology will likely result in improvements to conserving this unique species while meeting the high demands for water in California.

Open-File Report↗

USGS2010

Legal mechanisms for protecting riparian resource values

Riparian resources include the borders of rivers, lakes, ponds, and potholes. These border areas are very important for a number of reasons, including stream channel maintenance, flood control, aesthetics, erosion control, fish and wildlife habitat, recreation, and water quality maintenance. These diverse functions are not well protected by law or policy. We reviewed law and policies regarding endangered species habitat designation, land use planning, grazing management, water allocation, takings, and federal permits and licenses, along with the roles of federal, state, and local governments. We discuss the politics of implementing these policies, focusing on the difficulties in changing entrenched water and land use practices. Our review indicates a lack of direct attention to riparian ecosystem issues in almost all environmental and land use programs at every level of government. Protection of riparian resource values requires a means to integrate existing programs to focus on riparian zones.

Water Resources Research↗

USGS2023

A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus).

The Lesser Prairie-Chicken ( Tympanuchus pallidicinctus ; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays. Unfortunately, the species has disappeared across much of its historical range, with corresponding precipitous declines in contemporary population abundance, largely due to climatic and anthropogenic factors. These declines led to a 2022 US Fish and Wildlife decision to identify and list two distinct population segments (DPSs; i.e., northern and southern DPSs) as threatened or endangered under the 1973 Endangered Species Act. Herein, we describe an annotated reference genome that was generated from a LEPC sample collected from the southern DPS. We chose a representative from the southern DPS because of the potential for introgression in the northern DPS, where some populations hybridize with the Greater Prairie-Chicken ( Tympanuchus cupido ). This new LEPC reference assembly consists of 206 scaffolds, an N50 of 45 Mb, and 15,563 predicted protein-coding genes. We demonstrate the utility of this new genome assembly by estimating genome-wide heterozygosity in a representative LEPC and in related species. Heterozygosity in a LEPC sample was 0.0024, near the middle of the range (0.0003–0.0050) of related species. Overall, this new assembly provides a valuable resource that will enhance evolutionary and conservation genetic research in prairie grouse.

Genome Biology and Evolution↗

USGS2007

Vascular Plant and Vertebrate Inventory of Organ Pipe Cactus National Monument

Executive Summary We summarized inventory and monitoring efforts for plants and vertebrates at Organ Pipe Cactus National Monument (NM) in Arizona. We used data from previous research to compile complete species lists for the monument and to assess inventory completeness. There have been 1,031 species of plants and vertebrates observed at the monument. Most of the species on the list are documented by voucher specimens. There are 59 non-native species established in the monument: one mammal, three birds, and 55 non-native plants. Most non-native plant species were first recorded along roads. In each taxon-specific chapter, we highlight areas that contribute disproportionately to species richness or that have unique species for the monument. Of particular importance are Quitobaquito Springs and Pond, which are responsible for the monument having one of the highest number of bird species in the Sonoran Desert Network of parks. Quitobaquito also contains the only fish in the monument, the endangered Quitobaquito pupfish (Cyprinodon eremus). Other important resources for the plants and vertebrates include the xeroriparian washes (e.g., Alamo Canyon) and the Ajo Mountains. Based on the review of past studies, we believe the inventories of vascular plants and vertebrates are nearly complete and that the monument has one of the most complete inventories of any unit in the Sonoran Desert Network.

Open-File Report↗

USGS2012

Use of a storm water retention system for conservation of regionally endangered fishes

Maintaining aquatic biodiversity in urban or suburban areas can be problematic because urban landscapes can be nearly devoid of aquatic habitats other than engineered basins for storm water management. These areas are usually of questionable value for fish, but we examined a case study in which five regionally imperiled fish species were reintroduced into an artificial storm water detention pond and subsequently thrived. Although not a formal experiment, postintroduction survey data suggested that three of the five species maintained high population densities for 10 years after initial stocking, and two persisted in lower numbers. Success was likely due to a combination of unique design features and prior habitat preparation that resulted in clear water conditions that supported dense vegetation. Stocked fish persisted despite occasional bouts of low dissolved oxygen and increased chloride levels resulting from road salt application within the watershed. Transplanted fish served as a source population for both research and further reintroduction experiments. We suggest that, for some fish species, habitat preservation has a middle ground between natural habitats and completely artificial environments that require constant husbandry and that storm water systems could be used to create engineered sanctuaries within the human landscape that have many potential benefits for both humans and fish.

Fisheries↗

USGS1986

Use of an inactivated eastern equine encephalitis virus vaccine in cranes

An unprecedented outbreak of fatal eastern equine encephalitis (EEE) virus occurred during the late summer and fall of 1984 in endangered whooping cranes (Grus americana) at the Patuxent Wildlife Research Center, Laurel, Maryland. As part of efforts to prevent future epizootics of EEE. studies were conducted to evaluate the antibody response of cranes following vaccination with a formalin-inactivated EEE virus vaccine. Viral specific neutralizing antibody was elicited in sandhill cranes (Grus canadensis) and whooping cranes following 1M inoculation with the vaccine. Among the 1M-inoculated cranes, peak antibody titers of 1:80 on days 30 to 60 had waned to undetectable levels by days 90 to 120. Although the initial titers were not increased by the first booster dose, the duration of the antibody was extended considerably. Whooping cranes, receiving vaccine 6 months after their first vaccination, developed titers of 1:80 to 1:320 by day 30. At 45 days after the final vaccination, these titers had dropped to 1:10 to 1:160. Cranes with preexisting EEE virus antibody, apparently reflecting natural infection, exhibited an anamnestic response indicated by a rapid increase and sustained high antibody titer. Even though EEE virus vaccine induced neutralizing antibody and produced no adverse side effects, further studies will be required to assess the significance of this response as a strategy for protecting whooping cranes against natural EEE virus infection. The loss of captive whooping cranes to the EEE virus presented a previously unrecognized risk and obstacle to recovery of this species. Not only was, there a setback in the captive breeding and reintroduction program for the whooping crane, but, because of the susceptibility of the species to the EEE virus. establishment of additional crane populations may be more complicated than initially envisioned. However, through continued surveillance, serological monitoring, and vaccination activities, we are confident that the impact of EEE virus on whooping crane recovery can be overcome to the ultimate benefit of this endangered species.

American Association of Zoo Veterinarians, Annual ↗

USGS2006

Assessing recreation impacts to cliffs in Shenandoah National Park: Integrating visitor observation with trail and recreation site measurements

The rock outcrops and cliffs of Shenandoah National Park provide habitat for several rare and endangered plant and animal species, including the federally endangered Shenandoah Salamander (Plethodon shenandoah; Ludwig et al., 1993). The location of the well-known park tour road, Skyline Drive, along the ridgeline provides exceptional access to many outcrops and cliffs throughout the park for a large number of the park?s 1.2 million annual visitors. Consequently, visitor use of cliff areas has led to natural resource impacts, including marked decreases in size and vigor of known rare plant populations. Despite the clear ecological value and potential threats to the natural resources at cliff areas, managers possess little information on visitor use of cliff sites and presently have no formal planning document to guide management. Thus, a park wide study of cliff sites was initiated during the 2005 visitor use season. As part of this research effort, our study used an integrative approach to study recreational use and visitor-caused resource impacts at one of the more heavily visited cliff sites in the park: Little Stony Man Cliffs (LSMC). In particular, this study integrated data from resource impact measurements and visitor use observation to help assess the effects of recreational use on the natural resources of LSMC. Procedures derived from campsite and trail impact studies were used to measure and characterize the amount of visitor-caused resource impacts on LSMC (Marion & Leung, 2001; Marion, 1995). Visitor use observations were conducted on top of LSMC to document and characterize the type and amount of recreational use the cliffs receive and the behaviors of recreationists that may contribute to cliff-top resource impacts. Resource impact measurement data show trampling disturbance present at LSMC, characterized by vegetation loss, exposed soil, and root exposure. Documentation of informal trails, soil erosion, tree damage, and tree stumps provide further indicators of resource damage at LSMC. Results of visitor use observation offer several insights into contributory factors of cliff-top resource damage by showing differences in use and behavior between visitor types. The findings from this study suggest that a management approach characterized by visitor education, some site hardening, and concentration of visitor use on durable surfaces, along with the installation of fixed anchors at the top of popular climbing routes is likely to have the greatest success at balancing visitor enjoyment with resource protection at LSMC.

Journal of Park and Recreation Administration↗

USGS2010

The persistence of endangered Florida Salt Marsh Voles in salt marshes of the central Florida Gulf Coast

Two endangered Microtus pennsylvanicus dukecampbelli (Florida Salt Marsh Vole) were captured at a new location, in February of 2009, at Lower Suwannee National Wildlife Refuge. Since the species discovery in 1979, only 43 Florida Salt Marsh Voles (hereafter FSM Vole) have been captured. Outside of the type locality, this is only the second documented location for the FSM Vole. Given the difficulty in trapping this species and the lack of information about its life history, its discovery in a new location lends itself to the possibility that it is more widespread in the Central Florida Gulf Coast than previously thought. Although much of the salt marsh in the area is in public ownership, a good deal of it has already been altered by logging or development and is threatened by global climate change. More research is needed to adequately protect and manage the habitat for the FSM Vole. A study of FSM Vole coastal salt marsh habitat could also serve as a valuable monitoring tool for subtle changes in salt marsh habitats as global climate change progresses.

Southeastern Naturalist↗

USGS2014

Habitat prioritization across large landscapes, multiple seasons, and novel areas: an example using greater sage-grouse in Wyoming

Animal habitat selection is an important and expansive area of research in ecology. In particular, the study of habitat selection is critical in habitat prioritization efforts for species of conservation concern. Landscape planning for species is happening at ever-increasing extents because of the appreciation for the role of landscape-scale patterns in species persistence coupled to improved datasets for species and habitats, and the expanding and intensifying footprint of human land uses on the landscape. We present a large-scale collaborative effort to develop habitat selection models across large landscapes and multiple seasons for prioritizing habitat for a species of conservation concern. Greater sage-grouse ( Centrocercus urophasianus , hereafter sage-grouse) occur in western semi-arid landscapes in North America. Range-wide population declines of this species have been documented, and it is currently considered as “warranted but precluded” from listing under the United States Endangered Species Act. Wyoming is predicted to remain a stronghold for sage-grouse populations and contains approximately 37% of remaining birds. We compiled location data from 14 unique radiotelemetry studies (data collected 1994–2010) and habitat data from high-quality, biologically relevant, geographic information system (GIS) layers across Wyoming. We developed habitat selection models for greater sage-grouse across Wyoming for 3 distinct life stages: 1) nesting, 2) summer, and 3) winter. We developed patch and landscape models across 4 extents, producing statewide and regional (southwest, central, northeast) models for Wyoming. Habitat selection varied among regions and seasons, yet preferred habitat attributes generally matched the extensive literature on sage-grouse seasonal habitat requirements. Across seasons and regions, birds preferred areas with greater percentage sagebrush cover and avoided paved roads, agriculture, and forested areas. Birds consistently preferred areas with higher precipitation in the summer and avoided rugged terrain in the winter. Selection for sagebrush cover varied regionally with stronger selection in the Northeast region, likely because of limited availability, whereas avoidance of paved roads was fairly consistent across regions. We chose resource selection function (RSF) thresholds for each model set (seasonal × regional combination) that delineated important seasonal habitats for sage-grouse. Each model set showed good validation and discriminatory capabilities within study-site boundaries. We applied the nesting-season models to a novel area not included in model development. The percentage of independent nest locations that fell directly within identified important habitat was not overly impressive in the novel area (49%); however, including a 500-m buffer around important habitat captured 98% of independent nest locations within the novel area. We also used leks and associated peak male counts as a proxy for nesting habitat outside of the study sites used to develop the models. A 1.5-km buffer around the important nesting habitat boundaries included 77% of males counted at leks in Wyoming outside of the study sites. Data were not available to quantitatively test the performance of the summer and winter models outside our study sites. The collection of models presented here represents large-scale resource-management planning tools that are a significant advancement to previous tools in terms of spatial and temporal resolution.

Wyoming↗

USGS2018

Population viability analyses for three Macrhybopsis spp. of the Lower Missouri River

Recent declines in three species of chubs that inhabit the lower Missouri River (shoal chub M. hyostoma , sicklefin chub M. meeki and sturgeon chub M. gelida ) have become a concern in the management of their own populations and the endangered pallid sturgeon ( Scaphirhynchus albus ) that feeds on them. These chub populations encounter threats from fish predation and habitat loss. With the recent advancements in the understanding of the reproductive life history of these species, their declines have prompted development of population models and population viability analyses. For each species, we developed an age‐structured population matrix model with hierarchical stochasticity, which partitions parameter total variance into sampling and temporal components. Using these models, we found population growth rate of all three chub species decreased when stochasticity was added to the model. While examining sensitivity, we found individual fish growth, as measured by length‐at‐age, to impact population growth rate and depending on the species, could be up to four times more influential than overall survival, the next most sensitive parameter. Current survival rates have large temporal variance; more research into accuracy and factors that influence survival rates is needed.

Journal of Applied Ichthyology↗

USGS2001

Microsatellite DNA markers for the study of Allegheny woodrat (Neotoma magister) populations and cross-species amplification the genus Neotoma

The Allegheny woodrat ( Neotoma magister ) is a colony-forming murid rodent inhabiting rock outcrops, cliff and talus slopes, and caves within the Central and Southern Appalachians of North America ( Hall 1981 ). The species is currently considered threatened, endangered, or at risk throughout its range purportedly due to the direct or indirect effects of human-fragmented landscapes. Currently, Allegheny woodrat management units are arbitrarily defined as metapopulations that roughly constitute contiguous rock outcrops interconnected by forested habitat. To strengthen long-term population stability and reduce the need for further protection through the regulatory process, an effective conservation programme for this at-risk species will require unambiguous, objectively defined units of management that discern evolutionarily important lineages ( Avise 1994 ). A prerequisite in the development of management strategies that recognize and maintain significant woodrat lineages is a thorough understanding of the levels of gene exchange among geographically proximate and distal populations. However, no information exists on population structure, levels of gene flow, or relatedness among Allegheny woodrat populations or colonies. As an initial step towards addressing this research need, we have developed a suite of polymorphic microsatellite DNA markers for this species. In this paper, we describe the isolation and characterization of these markers and demonstrate their suitability in amplifying putatively homologous products in seven additional Neotoma species.

Alabama, Georgia, Kentucky, Mississippi, North Car↗