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USGS2002

Genetic characterization of infectious hematopoietic necrosis virus of coastal salmonid stocks in Washington State

Infectious hematopoietic necrosis virus (IHNV) is a pathogen that infects many Pacific salmonid stocks from the watersheds of North America. Previous studies have thoroughly characterized the genetic diversity of IHNV isolates from Alaska and the Hagerman Valley in Idaho. To enhance understanding of the evolution and viral transmission patterns of IHNV within the Pacific Northwest geographic range, we analyzed the G gene of IHNV isolates from the coastal watersheds of Washington State by ribonuclease protection assay (RPA) and nucleotide sequencing. The RPA analysis of 23 isolates indicated that the Skagit basin IHNV isolates were relatively homogeneous as a result of the dominance of one G gene haplotype (S). Sequence analysis of 303 bases in the middle of the G gene (midG region) of 61 isolates confirmed the high frequency of a Skagit River basin sequence and identified another sequence commonly found in isolates from the Lake Washington basin. Overall, both the RPA and sequence analysis showed that the Washington coastal IHNV isolates are genetically homogeneous and have little genetic diversity. This is similar to the genetic diversity pattern of IHNV from Alaska and contrasts sharply with the high genetic diversity demonstrated for IHNV isolates from fish farms along the Snake River in Idaho. The high degree of sequence and haplotype similarity between the Washington coastal IHNV isolates and those from Alaska and British Columbia suggests that they have a common viral ancestor. Phylogenetic analyses of the isolates we studied and those from different regions throughout the virus's geographic range confirms a conserved pattern of evolution of the virus in salmonid stocks north of the Columbia River, which forms Washington's southern border.

Washington↗

USGS2013

Animal migration amid shifting patterns of phenology and predation: Lessons from a Yellowstone elk herd

Migration is a striking behavioral strategy by which many animals enhance resource acquisition while reducing predation risk. Historically, the demographic benefits of such movements made migration common, but in many taxa the phenomenon is considered globally threatened. Here we describe a long-term decline in the productivity of elk ( Cervus elaphus ) that migrate through intact wilderness areas to protected summer ranges inside Yellowstone National Park, USA. We attribute this decline to a long-term reduction in the demographic benefits that ungulates typically gain from migration. Among migratory elk, we observed a 21-year, 70% reduction in recruitment and a 4-year, 19% depression in their pregnancy rate largely caused by infrequent reproduction of females that were young or lactating. In contrast, among resident elk, we have recently observed increasing recruitment and a high rate of pregnancy. Landscape-level changes in habitat quality and predation appear to be responsible for the declining productivity of Yellowstone migrants. From 1989 to 2009, migratory elk experienced an increasing rate and shorter duration of green-up coincident with warmer spring–summer temperatures and reduced spring precipitation, also consistent with observations of an unusually severe drought in the region. Migrants are also now exposed to four times as many grizzly bears ( Ursus arctos ) and wolves ( Canis lupus ) as resident elk. Both of these restored predators consume migratory elk calves at high rates in the Yellowstone wilderness but are maintained at low densities via lethal management and human disturbance in the year-round habitats of resident elk. Our findings suggest that large-carnivore recovery and drought, operating simultaneously along an elevation gradient, have disproportionately influenced the demography of migratory elk. Many migratory animals travel large geographic distances between their seasonal ranges. Changes in land use and climate that disparately influence such seasonal ranges may alter the ecological basis of migratory behavior, representing an important challenge for, and a powerful lens into, the ecology and conservation of migratory taxa.

Idaho, Montana, Wyoming↗

USGS2002

Toxicological assessment of aquatic ecosystems: application to watercraft contaminants in shallow water environments

Recreational boating and personal watercraft use have the potential to adversely impact shallow water systems through contaminant release and physical disturbance of bottom sediments. These nearshore areas are often already degraded by surface runoff, municipal and industrial effluents, and other anthropogenic activities. For proper management, information is needed on the level of contamination and environmental quality of these systems. A number of field and laboratory procedures can be used to provide this much needed information. Contaminants, such as metals, pesticides, polychlorinated biphenyls and polycyclic aromatic hydrocarbons, entering aquatic environments generally attach to particulate matter that eventually settles and becomes incorporated into the bottom sediments. Because bottom sediments serve as a sink and as a source for contaminants, environmental assessments generally focus on this matrix. While contaminant residues in sediments and sediment pore waters can reflect environmental quality, characteristics of sediment (redox potential, sediment/pore-water chemistry, acid volatile sulfides, percent organic matter, and sediment particle size) influence their bioavailability and make interpretation of environmental significance difficult. Comparisons of contaminant concentrations in pore water (interstitial water) and sediment with water quality criteria and sediment quality guidelines, respectively, can provide insight into potential biological effects. Laboratory bioaccumulation studies and residue concentrations in resident or caged biota also yield information on potential biological impacts. The usefulness of these measurements may increase as data are developed relating in-situ concentrations, tissue residue levels, and biological responses. Exposure of test organisms in situ or to field-collected sediment and pore water are additional procedures that can be used to assess the biological effects of contaminants. A battery of tests using multi-species and/or various life stages with different sensitivities to contaminants may offer a more conservative assessment of toxicity than single species testing. Using a ?weight of evidence? approach, the Sediment Quality Trial produces a robust evaluation of habitat quality and includes a measure of contaminant concentrations in the sediment, an assessment of sediment/pore-water toxicity to laboratory animals, and an evaluation of in situ biological assemblages. Field and laboratory procedures are available that can be used to ascertain habitat quality, identify contaminants causing environmental degradation and delineate aquatic systems requiring mitigation of protective efforts. These studies provide the scientific data that are integral to developing an environmental risk assessment of contaminants from watercraft use in shallow water systems.

Book chapter↗

USGS2018

River otter distribution in Nebraska

The river otter ( Lontra canadensis ) was extirpated from Nebraska, USA, in the early 1900s and reintroduced starting in 1986. Information is needed regarding the distribution of river otters in Nebraska before decisions can be made regarding its conservation status. Understanding distribution of a species is critically important for effective management. We investigated river otter distribution in Nebraska with occupancy modeling and maximum entropy (Maxent) modeling using 190 otter sign observations on Nebraska's navigable rivers and 380 historical otter records from November 1977 to April 2014. Both methods identified the Platte River, Elkhorn River, central and eastern Niobrara River, and southern Loup River system as core areas within the distribution of otters in Nebraska. The Maxent model provided more liberal estimates of site occupancy and identified some smaller rivers as being within the distribution of otters in Nebraska, which were not identified using occupancy modeling. We recommend that multiple data sets and analysis methods be used to estimate species distribution because this allows for the broadest geographical coverage and decreases the likelihood of overlooking areas with fewer animal records. If further reintroduction efforts or translocation efforts are to take place in the future, we recommend focusing on areas with high modeled occupancy but few historical and survey records

Nebraska↗

USGS2023

Host vs. pathogen evolutionary arms race: Effects of exposure history on individual response to a genetically diverse pathogen

Introduction: Throughout their range, bighorn sheep ( Ovis canadensis ) populations have seen significant disease-associated declines. Unfortunately, understanding of the underlying epidemiological processes driving the disease dynamics in this species has hindered conservation efforts aimed at improving the health and long-term viability of these populations. Individual response to pathogen exposure emerges from dynamic interactions between competing evolutionary processes within the host and pathogen. The host’s adaptive immune system recognizes pathogens and mounts a defensive response. Pathogens have evolved strategies to overcome adaptive immune defenses including maintaining high genetic diversity through rapid evolution. The outcomes of this evolutionary warfare determine the success of pathogen invasion of the host and ultimately the success of conservation efforts. Methods: During an epizootic dominated by a single strain, we explore these host-pathogen dynamics by examining the variation in effects of pathogen invasion on captive bighorn sheep with differing histories of exposure to genetically diverse strains of Mycoplasma ovipneumoniae (Movi). We monitored clinical signs of disease and sampled animals and their environment to detect spread of Movi among 37 bighorn sheep separated into nine pens based on known exposure Results: We documented Movi transmission within and across pens and we detected Movi DNA in air, water, and invertebrate samples. Higher levels of antibody to Movi prior to the epizootic were associated with a lower likelihood of presenting clinical signs of pneumonia. Nonetheless, higher antibody levels in symptomatic individuals were associated with more severe progressive disease, increased probability and speed of pneumonia-induced mortality, and reduced likelihood of returning to a healthy state. Bighorn sheep with previous exposure to a strain other than the predominant epizootic strain were more likely to recover. Discussion: Our results indicate that Movi-strain variability was sufficient to overwhelm the adaptive host immunological defenses. This outcome indicates, in free-ranging herds, past exposure is likely insufficient to protect bighorn sheep from infection by new Movi strains, although it influences the progression of disease and recovery within the herd. Therefore, given Movi-strain variability and the lack of immunological protection from past exposure, focusing management efforts on minimizing the introduction of Movi into bighorn herds, through separation of domestic and bighorn sheep and avoidance of management activities that create commingling of bighorn sheep carrying differing Movi strains, will likely be the most effective approach for reducing the effects of disease and achieving bighorn sheep conservation goals.

Idaho, Oregon, South Dakota, Washington↗

USGS2020

Assessing population-level consequences of anthropogenic stressors for terrestrial wildlife

Human activity influences wildlife. However, the ecological and conservation significances of these influences are difficult to predict and depend on their population‐level consequences. This difficulty arises partly because of information gaps, and partly because the data on stressors are usually collected in a count‐based manner (e.g., number of dead animals) that is difficult to translate into rate‐based estimates important to infer population‐level consequences (e.g., changes in mortality or population growth rates). However, ongoing methodological developments can provide information to make this transition. Here, we synthesize tools from multiple fields of study to propose an overarching, spatially explicit framework to assess population‐level consequences of anthropogenic stressors on terrestrial wildlife. A key component of this process is using ecological information from affected animals to upscale from count‐based field data on individuals to rate‐based demographic inference. The five steps to this framework are (1) framing the problem to identify species, populations, and assessment parameters; (2) field‐based measurement of the effect of the stressor on individuals; (3) characterizing the location and size of the populations of interest; (4) demographic modeling for those populations; and (5) assessing the significance of stressor‐induced changes in demographic rates. The tools required for each of these steps are well developed, and some have been used in conjunction with each other, but the entire group has not previously been unified together as we do in this framework. We detail these steps and then illustrate their application for two species affected by different anthropogenic stressors. In our examples, we use stable hydrogen isotope data to infer a catchment area describing the geographic origins of affected individuals, as the basis to estimate population size for that area. These examples reveal unexpectedly greater potential risks from stressors for the more common and widely distributed species. This work illustrates key strengths of the framework but also important areas for subsequent theoretical and technical development to make it still more broadly applicable.

Ecosphere↗

USGS2017

Multinomial N-mixture models improve the applicability of electrofishing for developing population estimates of stream-dwelling Smallmouth Bass

Failure to account for variable detection across survey conditions constrains progressive stream ecology and can lead to erroneous stream fish management and conservation decisions. In addition to variable detection’s confounding long-term stream fish population trends, reliable abundance estimates across a wide range of survey conditions are fundamental to establishing species–environment relationships. Despite major advancements in accounting for variable detection when surveying animal populations, these approaches remain largely ignored by stream fish scientists, and CPUE remains the most common metric used by researchers and managers. One notable advancement for addressing the challenges of variable detection is the multinomial N -mixture model. Multinomial N -mixture models use a flexible hierarchical framework to model the detection process across sites as a function of covariates; they also accommodate common fisheries survey methods, such as removal and capture–recapture. Effective monitoring of stream-dwelling Smallmouth Bass Micropterus dolomieu populations has long been challenging; therefore, our objective was to examine the use of multinomial N -mixture models to improve the applicability of electrofishing for estimating absolute abundance. We sampled Smallmouth Bass populations by using tow-barge electrofishing across a range of environmental conditions in streams of the Ozark Highlands ecoregion. Using an information-theoretic approach, we identified effort, water clarity, wetted channel width, and water depth as covariates that were related to variable Smallmouth Bass electrofishing detection. Smallmouth Bass abundance estimates derived from our top model consistently agreed with baseline estimates obtained via snorkel surveys. Additionally, confidence intervals from the multinomial N -mixture models were consistently more precise than those of unbiased Petersen capture–recapture estimates due to the dependency among data sets in the hierarchical framework. We demonstrate the application of this contemporary population estimation method to address a longstanding stream fish management issue. We also detail the advantages and trade-offs of hierarchical population estimation methods relative to CPUE and estimation methods that model each site separately.

Missouri, Oklahoma↗

USGS2001

Evaluation of the major histocompatibility complex (Mhc) in cranes: applications to conservation efforts

Although there have been heated discussions concerning the relative importance of using Mhc diversity as a basis for selecting breeders in conservation projects, most parties agree that the genetic variability residual in an endangered species should be maintained through genetic management, if at all possible. Substantial evidence exists (particularly in birds) documenting the influences of specific Mhc haplotypes on disease outcome and also that those individuals which are heterozygous for Mhc alleles appear to have an advantage for survival over those that are homozygous. Thus, conservation of genetic variability of the Mhc is likely important for the preservation of fitness, especially in small breeding populations. More than half of the world's crane species are listed as endangered. Members of all 15 known species are represented among breeding animals for captive propagation at the International Crane Foundation (Wisconsin) and the USGS Patuxent Wildlife Research Center (Maryland). Collaborative multi-organization efforts and the availability of extensive pedigree records have allowed the study of Mhc variability in several species of cranes. We have found, for example, that Mhc diversity in the captive Florida sandhill crane (Grus canadensis pratensis) population appears high, whereas in the captive whooping crane (Grus americana), which has undergone a severe 'genetic bottleneck,? both the number of alleles and the levels of heterozygosity appear to be substantially reduced.

Book chapter↗

USGS2013

Developing an outcome-based biodiversity metric in support of the field to market project: Final report

Our objective was to create a metric that would calculate the relative impact of common commercial agricultural practices on terrestrial vertebrate richness. We sought to define impacts in fields (including field borders) of the southeastern region’s commercial production of corn, wheat, soy, and cotton. The metric is intended to serve as an educational tool, allowing producers to see how operational decisions made at the field level impact overall vertebrate species richness and to explore decision impacts to targeted species groups (e.g. game, pest, or beneficial species). Agricultural landscapes are often mistakenly thought to be unsuitable habitat for most species. However, as demonstrated by results reported here, even large-scale, conventional agricultural producers are potentially important partners in biodiversity conservation. Many vertebrate species do inhabit agricultural landscapes, benefitting from the provision of water, food, or shelter within cultivated fields and their immediate borders (e.g., Holland et al. 2012). In the Southeastern US, of the 613 terrestrial vertebrate species modeled by the Southeast Gap Analysis Program (SEGAP) (http://www.basic.ncsu.edu/segap/index.html), 263 utilize row crop and associated agricultural land cover classes as potential habitat (Box 1). While some species may be sensitive to certain operational practices (e.g., tillage, pest management, or field border management practices), others are generally tolerant, and some may benefit either directly or indirectly. For example, field margins and ditches often serve as semi-natural habitats providing foraging resources and shelter for vertebrates and are shown to positively influence species richness and abundance (Billeter et al. 2007; Herzon & Helenius 2008; Marshall & Moonen 2002; Shore et al. 2005; Weibull et al. 2003; Wuczyńskia et al. 2011). Biodiversity responses are, therefore, complex, as an individual species’ responses to agricultural production practices depends on that animal’s resource specialization, mobility, and life history strategies (Jeanneret et al. 2003a, b; Jennings & Pocock 2009). The knowledge necessary to define the biodiversity contribution of agricultural lands is specialized, dispersed, and nuanced, and thus not readily accessible. Given access to clearly defined biodiversity tradeoffs between alternative agricultural practices, landowners, land managers and farm operators could collectively enhance the conservation and economic value of agricultural landscapes. Therefore, Field to Market: The Keystone Alliance for Sustainable Agriculture and The Nature Conservancy jointly funded a pilot project to develop a biodiversity metric to integrate into Field to Market’s existing sustainability calculator, The Fieldprint Calculator (http://www. fieldtomarket.org/). Field to Market: The Keystone Alliance for Sustainable Agriculture is an alliance among producers, agribusinesses, food companies, and conservation organizations seeking to create sustainable outcomes for agriculture. The Fieldprint Calculator supports the Keystone Alliance’s vision to achieve safe, accessible, and nutritious food, fiber and fuel in thriving ecosystems to meet the needs of 9 billion people in 2050. In support of this same vision, our project provides proof-of-concept for an outcome-based biodiversity metric for Field to Market to quantify biodiversity impacts of commercial row crop production on terrestrial vertebrate richness. Little research exists examining the impacts of alternative commercial agricultural practices on overall terrestrial biodiversity (McLaughlin & Mineau 1995). Instead, most studies compare organic versus conventional practices (e.g. Freemark & Kirk 2001; Wickramasinghe et al. 2004), and most studies focus on flora, avian, or invertebrate communities (Jeanneret et al. 2003a; Maes et al. 2008; Pollard & Relton 1970). Therefore, we used an expert-knowledge-based approach to develop a metric that predicts expected impacts to shelter and forage resources, individual species, and overall biodiversity (species richness). This approach is modeled after an ecosystems services concept (WRI 2005), except that we examine services (i.e., resources) provided to vertebrate wildlife rather than service provided to the human population. SEGAP predicts species that are potentially present in an area given landscape-scale habitat availability, configuration, and context (e.g., patch size, proximity to resources, connectivity, potential for disturbance). Based on the prediction of species that may be potentially present, the impacts of management decisions within fields and around their borders can be analyzed based on the impact of those practices to the availability of species’ resources. The final metric provides an index of a producer’s relative impact, but perhaps even more importantly, the underlying database allows producers to explore details such as which species are most impacted or how alternative decisions would impact their score.

Technical Bulletin↗

USGS2026

Genetic structure in a previously extirpated population of gray wolves following reintroduction and natural recolonization

Genetic structuring in wildlife populations is driven by barriers that restrict gene flow as well as the history of population demography. Mechanisms driving genetic structuring can be nuanced in group-living species, such as gray wolves ( Canis lupus ). Behavioral factors, such as social affiliation and resistance, natal habitat imprinting, and trade-offs between dispersal from natal packs and territorial biding, affect habitat selection of wolves despite landscape barriers providing little resistance to their extensive dispersal capabilities. Wolves were previously extirpated from Idaho, USA, and current populations are the result of both reintroductions in 1995 and 1996 and natural dispersal from Canada. In this context we examined genetic structure of wolves in Idaho using 101 individuals genotyped at 18 nuclear DNA microsatellite loci and a subset of 38 individuals genotyped at 1019 single nucleotide polymorphism markers. We hypothesized panmictic (i.e., random mating) genetic structure in Idaho due to the long-distance dispersal abilities of gray wolves. Contrary to our hypothesis, we found three genetic clusters of gray wolves in Idaho, primarily supported by SNP markers. Microsatellite data suggested similar patterns, but permutation tests indicated these differences were not statistically significant. The extent of differentiation and evidence of gene flow, however, suggests that the three genetic clusters are not wholly isolated from one another. The distinctions between clusters spatially align with areas of reintroduction into central Idaho and Yellowstone National Park, as well ongoing natural recolonization from adjacent populations in Canada and Montana. Wolves at the periphery of analysis areas showed more admixture than those in the core, consistent with territoriality and mating behaviors contributing to genetic structuring. We demonstrate how management history, including reintroduction efforts, and animal behavior may interact and contribute to patterns of genetic structure in wild populations.

Idaho, Montana, Wyoming↗

USGS2017

Life histories and conservation of long-lived reptiles, an illustration with the American crocodile (Crocodylus acutus)

Successful species conservation is dependent on adequate estimates of population dynamics, but age-specific demographics are generally lacking for many long-lived iteroparous species such as large reptiles. Accurate demographic information allows estimation of population growth rate, as well as projection of future population sizes and quantitative analyses of fitness trade-offs involved in the evolution of life-history strategies. Here, a long-term capture–recapture study was conducted from 1978 to 2014 on the American crocodile ( Crocodylus acutus ) in southern Florida. Over the study period, 7,427 hatchlings were marked and 380 individuals were recaptured for as many as 25 years. We estimated survival to be strongly age dependent with hatchlings having the lowest survival rates (16%) but increasing to nearly 90% at adulthood based on mark–recapture models. More than 5% of the female population were predicted to be reproductive by age 8 years; the age-specific proportion of reproductive females steadily increased until age 18 when more than 95% of females were predicted to be reproductive. Population growth rate, estimated from a Leslie–Lefkovitch stage-class model, showed a positive annual growth rate of 4% over the study period. Using a prospective sensitivity analysis, we revealed that the adult stage, as expected, was the most critical stage for population growth rate; however, the survival of younger crocodiles before they became reproductive also had a surprisingly high elasticity. We found that variation in age-specific fecundity has very limited impact on population growth rate in American crocodiles. We used a comparative approach to show that the original life-history strategy of American crocodiles is actually shared by other large, long-lived reptiles: while adult survival rates always have a large impact on population growth, this decreases with declining increasing growth rates, in favour of a higher elasticity of the juvenile stage. Crocodiles, as a long-lived and highly fecund species, deviate from the usual association of life histories of “slow” species. Current management practices are focused on nests and hatchling survival; however, protection efforts that extend to juvenile crocodiles would be most effective for conservation of the species, especially in an ever-developing landscape.

Journal of Animal Ecology↗

USGS1996

Measuring and monitoring biological diversity: Standard methods for mammals

Measuring and Monitoring Biological Diversity: Standard Methods for Mammals provides a comprehensive manual for designing and implementing inventories of mammalian biodiversity anywhere in the world and for any group, from rodents to open-country grazers. The book emphasizes formal estimation approaches, which supply data that can be compared across habitats and over time. Beginning with brief natural histories of the twenty-six orders of living mammals, the book details the field techniques—observation, capture, and sign interpretation—appropriate to different species. The contributors provide guidelines for study design, discuss survey planning, describe statistical techniques, and outline methods of translating field data into electronic formats. Extensive appendixes address such issues as the ethical treatment of animals in research, human health concerns, preserving voucher specimens, and assessing age, sex, and reproductive condition in mammals. Useful in both developed and developing countries, this volume and the Biological Diversity Handbook Series as a whole establish essential standards for a key aspect of conservation biology and resource management.

Book↗

USGS2007

Historic distribution and challenges to bison recovery in the northern Chihuahuan Desert

Ecologists and conservationists have long assumed that large grazers, including bison ( Bison bison ), did not occur in post-Pleistocene southwestern North America. This perception has been influential in framing the debate over conservation and land use in the northern Chihuahuan Desert. The lack of an evolutionary history of large grazers is being used to challenge the validity of ranching as a conservation strategy and to limit the protection and reintroduction of bison as a significant component of desert grassland ecosystems. Archeological records and historical accounts from Mexican archives from AD 700 to the 19th century document that the historic range of the bison included northern Mexico and adjoining areas in the United States. The Janos-Hidalgo bison herd, one of the few free-ranging bison herds in North America, has moved between Chihuahua, Mexico, and New Mexico, United States, since at least the 1920s. The persistence of this cross-border bison herd in Chihuahuan Desert grasslands and shrublands demonstrates that the species can persist in desert landscapes. Additional lines of evidence include the existence of grazing-adapted grasslands and the results of experimental studies that document declines in vegetation density and diversity following the removal of large grazers. The Janos-Hidalgo herd was formed with animals from various sources at the turn of the 19th century. Yet the future of the herd is compromised by differing perceptions of the ecological and evolutionary role of bison in the Desert Grasslands of North America. In Mexico they are considered native and are protected by federal law, whereas in New Mexico, they are considered non-native livestock and therefore lack conservation status or federal protection. Evidence written in Spanish of the presence of bison south of the accepted range and evidence from the disciplines of archaeology and history illustrate how differences in language and academic disciplines, in addition to international boundaries, have acted as barriers in shaping comprehensive approaches to conservation. Bison recovery in the region depends on binational cooperation.

Arizona, Chihuahua, Coahuila, Durango, New Mexico,↗

USGS2025

A 21st Century butterfly net: Using eDNA to detect the imperiled Dakota skipper

The development of environmental DNA (eDNA) methods for terrestrial arthropods could be transformative for the difficult task of assessing the status of species of conservation concern. The primary goal of this study was to investigate the efficacy of detecting the Dakota skipper ( Hesperia dacotae ) from its DNA left behind on inflorescences as a means of inferring species presence. We developed and tested a novel qPCR assay and validated the assay in both controlled and field contexts. Using captive animals at the Minnesota Zoo, we found that the number of skippers in an enclosure increased the probability of skipper DNA detection. In the field, Dakota skipper DNA was found on 14% (11 of 81) of inflorescences collected. All detections were from narrowleaf purple coneflower ( Echinacea angustifolia ). Known visitation of an inflorescence by Dakota skipper prior to sample collection was not a strong predictor of either skipper DNA presence or amount of DNA, but skipper eDNA was detected at 60% (3 of 5) of sites where skippers were observed and 33% (1 of 3) of sites where skippers were not observed. These findings demonstrate successful application of a targeted-species approach to eDNA sampling for butterflies in the field. Taken together, our findings indicate that this method could provide a novel and useful source of data for assessing occupancy trends of butterflies without capturing or even observing them in the wild.

Minnesota, North Dakota, South Dakota↗

USGS2012

Translocation as a conservation tool for Agassiz's desert tortoises: survivorship, reproduction, and movements

We translocated 120 Agassiz's desert tortoises to 5 sites in Nevada and Utah to evaluate the effects of translocation on tortoise survivorship, reproduction, and habitat use. Translocation sites included several elevations, and extended to sites with vegetation assemblages not typically associated with desert tortoises in order to explore the possibility of moving animals to upper elevation areas. We measured survivorship, reproduction, and movements of translocated and resident animals at each site. Survivorship was not significantly different between translocated and resident animals within and among sites, and survivorship was greater overall during non-drought years. The number of eggs produced by tortoises was similar for translocated and resident females, but differed among sites. Animals translocated to atypical habitat generally moved until they reached vegetation communities more typical of desert tortoise habitat. Even within typical tortoise habitat, tortoises tended to move greater distances in the first year after translocation than did residents, but their movements in the second or third year after translocation were indistinguishable from those of resident tortoises. Our data show that tortoises translocated into typical Mojave desert scrub habitats perform well; however, the large first-year movements of translocated tortoises have important management implications. Projects that employ translocations must consider how much area will be needed to contain translocated tortoises and whether roads need fencing to prevent the loss of animals.

Journal of Wildlife Management↗

USGS2024

Joint spatial modeling bridges the gap between disparate disease surveillance and population monitoring efforts informing conservation of at-risk bat species

White-Nose Syndrome (WNS) is a wildlife disease that has decimated hibernating bats since its introduction in North America in 2006. As the disease spreads westward, assessing the potentially differential impact of the disease on western bat species is an urgent conservation need. The statistical challenge is that the disease surveillance and species response monitoring data are not co-located, available at different spatial resolutions, non-Gaussian, and subject to observation error requiring a novel extension to spatially misaligned regression models for analysis. Previous work motivated by epidemiology applications has proposed two-step approaches that overcome the spatial misalignment while intentionally preventing the human health outcome from informing estimation of exposure. In our application, the impacted animals contribute to spreading the fungus that causes WNS, motivating development of a joint framework that exploits the known biological relationship. We introduce a Bayesian, joint spatial modeling framework that provides inferences about the impact of WNS on measures of relative bat activity and accounts for the uncertainty in estimation of WNS presence at non-surveyed locations. Our simulations demonstrate that the joint model produced more precise estimates of disease occurrence and unbiased estimates of the association between disease presence and the count response relative to competing two-step approaches. Our statistical framework provides a solution that leverages disparate monitoring activities and informs species conservation across large landscapes. Stan code and documentation are provided to facilitate access and adaptation for other wildlife disease applications.

Journal of Agricultural, Biological and Environmen↗

USGS2017

Coupling gene-based and classic veterinary diagnostics improves interpretation of health and immune function in the Agassiz’s desert tortoise (Gopherus agassizii)

The analysis of blood constituents is a widely used tool to aid in monitoring of animal health and disease. However, classic blood diagnostics (i.e. hematologic and plasma biochemical values) often do not provide sufficient information to determine the state of an animal’s health. Field studies on wild tortoises and other reptiles have had limited success in drawing significant inferences between blood diagnostics and physiological and immunological condition. However, recent research using gene transcription profiling in the threatened Mojave desert tortoise ( Gopherus agassizii ) has proved useful in identifying immune or physiologic responses and overall health. To improve our understanding of health and immune function in tortoises, we evaluated both standard blood diagnostic (body condition, hematologic, plasma biochemistry values, trace elements, plasma proteins, vitamin A levels) and gene transcription profiles in 21 adult tortoises (11 clinically abnormal; 10 clinically normal) from Clark County, NV, USA. Necropsy and histology evaluations from clinically abnormal tortoises revealed multiple physiological complications, with moderate to severe rhinitis or pneumonia being the primary cause of morbidity in all but one of the examined animals. Clinically abnormal tortoises had increased transcription for four genes (SOD, MyD88, CL and Lep), increased lymphocyte production, biochemical enzymes and organics, trace elements of copper, and decreased numbers of leukocytes. We found significant positive correlations between increased transcription for SOD and increased trace elements for copper, as well as genes MyD88 and Lep with increased inflammation and microbial insults. Improved methods for health assessments are an important element of monitoring tortoise population recovery and can support the development of more robust diagnostic measures for ill animals, or individuals directly impacted by disturbance.

Conservation Physiology↗

USGS2000

2nd interface between ecology and land development in California

The 2nd Interface Between Ecology and Land Development Conference was held in association with Earth Day 1997, five years after the first Interface Conference. Rapid population growth in California has intensified the inevitable conflict between land development and preservation of natural ecosystems. Sustainable development requires wise use of diminishing natural resources and, where possible, restoration of damaged landscapes. These Earth Week Celebrations brought together resource managers, scientists, politicians, environmental consultants, and concerned citizens in an effort to improve the communication necessary to maintain our natural biodiversity, ecosystem processes and general quality of life. As discussed by our keynote speaker, Michael Soule, the best predictor of habitat loss is population growth and nowhere is this better illustrated than in California. As urban perimeters expand, the interface between wildlands and urban areas increases. Few problems are more vexing than how to manage the fire prone ecosystems indigenous to California at this urban interface. Today resource managers face increasing challenges of dealing with this problem and the lead-off section of the proceedings considers both the theoretical basis for making decisions related to prescribed burning and the practical application. Habitat fragmentation is an inevitable consequence of development patterns with significant impacts on animal and plant populations. Managers must be increasingly resourceful in dealing with problems of fragmentation and the often inevitable consequences, including susceptibility to invasive oganisms. One approach to dealing with fragmentation problems is through careful landplanning. California is the national leader in the integration of conservation and economics. On Earth Day 1991, Governor Pete Wilson presented an environmental agenda that promised to create between land owners and environmentalists, agreements that would guarantee the protection of -endangered species and out of this grew the pioneering initiative, known as the Natural Communities Conservation Planning (NCCP) program. California's vast expanse of seemingly endless resources has traditionally been viewed as justification for abusive land use practices. The modem day recognition that resources are finite has led to greater concern, not only for conserving what is left, but for restoring abused landscapes. Ecological restoration is a new science devoted to returning disturbed environments to a semblance of their 'pristine' state. Based on principles of 'revegetation,' restoration goes far beyond simple replanting, rather the ambition of ecological restoration is to return landscapes to functioning ecosystems and is the focus of the last section.

Open-File Report↗