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A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat‐specific behaviors.Here we use behavioral change point analysis to identify behavioral states of golden eagles (Aquila chrysaetos) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation‐relevant habitat associations.We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, with two clusters of short‐distance movement behaviors characterized by low AGL (state 1 AGL = 14 m (median); state 2 AGL = 11 m) and two associated with longer‐distance movement behaviors and characterized by higher AGL (state 3 AGL = 108 m; state 4 AGL = 450 m).Behaviors such as perching and low‐altitude hunting were associated with short‐distance movements in updraft‐poor environments, at higher elevations, and over steeper and more north‐facing terrain. In contrast, medium‐distance movements such as hunting and transiting were over gentle and south‐facing slopes. Long‐distance transiting occurred over the desert habitats that generate the best updraft.This information can guide management of this species, and our approach provides a template for behavior‐specific habitat associations for other species of management concern., Despite the importance of linking habitat use to specific behaviors, this is almost never done, in part because of the many challenges in understanding where and when individual behaviors occur. Here, we use long‐term, short‐interval, and highly precise GPS data as input to recently developed models to interpret animal behavior from telemetry data to identify where and when behavioral states occur. Subsequently, we link these behavioral states to habitat, as a mechanism to identify the environmental correlates of each behavior, and to infer potential threats to these animals based on those behavior‐specific habitat associations.

The ‘bet hedging’ life history strategy of long-lived iteroparous species reduces short-term reproductive output to minimize the risk of reproductive failure over a lifetime. For desert-dwelling ectotherms living in variable and unpredictable environments, reproductive output is further influenced by precipitation and temperature via effects on food availability and limits on activity. We assembled multiple (n = 12) data sets on egg production for the threatened Agassiz’s desert tortoise Gopherus agassizii across its range and used these data to build a range-wide predictive model of annual reproductive output as a function of annual weather variation and individual-level attributes (body size and prior-year reproductive status). Climate variables were more robust predictors of reproductive output than individual-level attributes, with overall reproductive output positively related to prior-year precipitation and an earlier start to the spring activity season, and negatively related to spring temperature extremes (monthly temperature range in March-April). Reproductive output was highest for individuals with larger body sizes that reproduced in the previous year. Expected annual reproductive output from 1990-2018 varied from 2-5 to 6-12 eggs female-1 yr-1 , with a weak decline in expected reproductive output over this time (p = 0.02). Climate-driven environmental variation in expected reproductive output was highly correlated across all 5 Recovery Units for this species (Pearson’s r > 0.9). Overall, our model suggests that climate change could strongly impact the reproductive output of Agassiz’s desert tortoise, and could have a negative population-level effect if precipitation is significantly reduced across the species’ range as predicted under some climate models.

Two tortoise species native to the American southwest have experienced significant habitat loss from development and are vulnerable to ongoing threats associated with continued development. Mojave desert tortoises Gopherus agassizii are listed as threatened under the US Endangered Species Act, and Sonoran desert tortoises G. morafkai are protected in Arizona (USA) and Mexico. Substantial habitat for both species occurs on multiple-use public lands, where development associated with traditional and renewable energy production, recreation, and other activities is likely to continue. Our goal was to quantify development to inform and evaluate actions implemented to protect and manage desert tortoise habitat. We quantified a landscape-level index of development across the Mojave and Sonoran desert tortoise ranges using models of potential habitat for each species (152485 total observations). We used 13 years of Mojave desert tortoise monitoring data (4732 observations) to inform the levels and spatial scales at which tortoises may be affected by development. Most (66-70%) desert tortoise habitat has some development within 1 km. Development levels on desert tortoise habitat are lower inside versus outside areas protected by actions at national, state, and local levels, suggesting that protection efforts may be having the desired effects and providing a needed baseline for future effectiveness evaluations. Of the relatively undeveloped desert tortoise habitat, 43% (74030 km2) occurs outside of existing protections. These lands are managed by multiple federal, state, and local entities and private landowners, and may provide opportunities for future land acquisition or protection, including as mitigation for energy development on public lands.

Habitat loss and fragmentation in the Mojave desert have been increasing, which can create barriers to movement and gene flow in populations of native species. Disturbance and degradation of Mojave desert tortoise habitat includes linear features (e.g. highways, railways, a network of dirt roads), urbanized areas, mining activities, and most recently, utility-scale solar facilities. To evaluate the spatial genetic structure of tortoises in an area experiencing rapid habitat loss, we genotyped 299 tortoises at 20 microsatellite loci from the Ivanpah valley region along the California/Nevada border. We used a Bayesian clustering analysis to quantify population genetic structure across valley and mountain pass habitats. A spatial principal components analysis was used to further investigate patterns with isolation-by-distance. To explicitly consider landscape features (e.g. habitat and anthropogenic linear barriers), we used maximum likelihood population effects analyses. We quantified recent gene flow through relatedness using a maximum likelihood pedigree approach. We detected three genetic clusters that generally corresponded to valleys separated by mountains, with one genetically distinguishable population in a mountain pass. Pedigree analyses showed second order relationships up to 60 km apart suggesting a greater range of interactions and inter-relatedness than previously suspected. Our results support historical gene flow with isolation-by-resistance and reveal reduced genetic connectivity across two parallel linear features bisecting our study area (a railway and a highway). Our work demonstrates the potential for tortoises to use a range of habitats, spanning valleys to mountain passes, but also indicates habitat fragmentation limits connectivity with relatively rapid genetic consequences.

We examined Red-tailed Hawk (Buteo jamaicensis) nestling diets in Reno and Sparks, NV, USA during the 2015 and 2016 breeding seasons. Field researchers and nest cameras recorded 1348 prey items spanning 28 species at 88 nests. Prey consisted of 86% mammalia, 10% aves and 4% reptilia. Differential prey selection occurred among the population and at individual nests relative to an expected diet. Diet breadth differed between nests and increased with urban density. Avian prey consumption increased relative to mammalian and reptilian prey in impervious areas. When prey items were plotted on a continuous urban density spectrum, mammalian prey increased in the suburban areas and decreased toward the urban core and was inversely correlated with avian prey. Mammalian prey consumption increased and decreased at the end of April and in mid-May before increasing through the remainder of the breeding season (mid-June). Avian prey consumption peaked in May and increased through the season, and reptilian prey varied little. The geographic patterns of prey species consumed in our study reflect those in cities elsewhere. As the urban area changes, we predict that the densest populations of Red-tailed Hawks will continue to reside in the suburban areas where prey diversity and abundance are highest. This was one of the first studies to record urban Red-tailed Hawk diet and revealed patterns in how an urban population used food resources.

Using data from six wild Mojave Desert Tortoise (Gopherus agassizii (Cooper, 1861)) populations, we quantified seasonal differences in immune system measurements and microbial load in the respiratory tract, pertinent to this species’ susceptibility to upper respiratory tract disease. We quantified bacteria-killing activity of blood plasma and differential leukocyte counts to detect trends in temporal variation in immune function. We used centered log-ratio (clr) transformations of leukocyte counts and stress that such transformations are necessary for compositional data. We tested animals for the potential pathogen Pasteurella testudinis Snipes and Biberstein, 1982 with a newly created quantitative polymerase chain reaction (qPCR) assay, as well as for the known respiratory pathogens Mycoplasma agassizii Brown et al., 2001 and Mycoplasma testudineum Brown et al., 2004. We found very little disease and suggest that P. testudinis is a prevalent, commensal microbe in these Mojave Desert Tortoise populations, and its quantification may be a tool to study natural fluctuations in microbe levels in Mojave Desert Tortoise respiratory tracts. Our analyses showed that both the potential for inflammatory responses and microbe levels are highest in the spring for healthy Mojave Desert Tortoises, when lymphocyte levels are lowest. The genetic and statistical tools that we used are easily applicable to other wildlife systems and provide the necessary data to quantify species-wide trends in health and test hypotheses pertinent to host–microbe dynamics.

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises (Gopherus agassizii), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30–60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420–595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

The Mojave Desert tortoise (Gopherus agassizii), federally listed as threatened, has suffered habitat loss and fragmentation due to human activities. Upper respiratory tract disease (URTD), a documented health threat to desert tortoises, has been detected at the Large-Scale Translocation Study Site (LSTS) in southwestern Nevada, US, a fenced recipient site for translocated animals. Our study aimed to 1) estimate prevalence of URTD and Mycoplasma infection at LSTS and three nearby unfenced sites; 2) assess whether Mycoplasma infection status was associated with developing clinical signs of URTD; and 3) determine whether such an association differed between LSTS and unfenced areas. We sampled 421 tortoises in 2016 to describe the current status of these populations. We evaluated three clinical signs of URTD (nasal discharge, ocular discharge, nasal erosions) and determined individual infection status for Mycoplasma agassizii and Mycoplasma testudineum by quantitative PCR and enzyme-linked immunosorbent assay. In 2016, LSTS had the highest prevalence of M. agassizii (25.0%; 33/132), M. testudineum (3.0%; 4/132), and URTD clinical signs (18.9%; 25/132). Controlling for other factors, clinical sign(s) were positively associated with M. agassizii infection (odds ratio [OR]=7.7, P=0.001), and this effect was similar among study sites (P>0.99). There was no association with M. testudineum status (P=0.360). Of the 196 tortoises in a longitudinal comparison of 2011-14 with 2016, an estimated 3.2% converted from M. agassizii-negative to positive during the study period, and incidence was greater at LSTS (P=0.002). Conversion to positive M. agassizii status was associated with increased incidence of clinical signs in subsequent years (OR=11.1, P=0.018). While M. agassizii and URTD are present outside the LSTS, there is a possibility that incidence of Mycoplasma infection and URTD would increase outside LSTS if these populations were to reconnect. Population-level significance of this risk appears low, and any risk must be evaluated against the potential long-term benefits to population viability through increased connectivity.

Mojave Desert shrublands are home to unique plants and wildlife and are experiencing rapid habitat change due to unprecedented large-scale disturbances; yet, established practices to effectively restore disturbed landscapes are not well developed. A priority species list of native plant taxa was developed to guide seed collectors, commercial growers, resource managers, and restoration practitioners in support of the Bureau of Land Management's Mojave Desert Native Plant Program. We identify focal plant taxa that are important for habitats of the threatened Mojave desert tortoise (Gopherus agassizii), a widely distributed herbivore in low and middle elevations, and pollinator taxa, including mostly Lepidopterans and Apoidean bees, some of whose populations are in decline. We identified 201 unique plant taxa in the diets of tortoises, and 49 taxa that provide thermal cover for tortoises with some overlapping taxa that provide both diet and cover. We discuss 134 native pollinators associated with plants used for nectaring, larval hosts, or cover and nesting materials. Detailed plant species accounts describing the status-of-knowledge for 57 plant taxonomic groups including detailed information on life history, ecology, and pollinator syndrome relevant to restoration success, methods of seed harvesting, propagation, and historical use in restoration. Our approach for developing a priority plant species list for the Mojave Desert provides a data-guided listing of species for restoration practitioners and identifies knowledge gaps for future investigation.

A key assumption in species distribution modeling (SDM) with presence‐background (PB) methods is that sampling of occurrence localities is unbiased and that any sampling bias is proportional to the background distribution of environmental covariates. This assumption is rarely met when SDM practitioners rely on federated museum records from natural history collections for geo‐located occurrences due to inherent sampling bias found in these collections. We use a simulation approach to explore the effectiveness of three methods developed to account for sampling bias in SDM with PB frameworks. Two of the methods rely on careful filtering of observation data—geographic thinning (G‐Filter) and environmental thinning (E‐Filter)—while a third, FactorBiasOut, creates selection weights for background data to bias locations toward areas where the observation dataset was sampled. While these methods have been assessed previously, evaluation has emphasized spatial predictions of habitat potential. Here, we dig deeper into the effectiveness of these methods by exploring how sampling bias not only affects predictions of habitat potential, but also our understanding of niche characteristics such as which explanatory variables and response curves best represent species–environment relationships. We simulate 100 virtual species ranging from generalist to specialist in their habitat preferences and introduce geographic and environmental bias at three intensity levels to measure the effectiveness of each correction method to (1) predict true probability of occurrence across a study area, (2) recover true species–environment relationships, and (3) identify true explanatory variables. We find that the FactorBiasOut most often showed the greatest improvement in recreating known distributions but did no better at correctly identifying environmental covariates or recreating species–environment relationships than G‐Filter or E‐Filter methods. Narrow niche species are most problematic for biased calibration datasets, such that correction methods can, in some cases, make predictions worse.

Interactions between wildlife hosts act as transmission routes for directly transmitted pathogens and vary in ways that affect transmission efficiency. Identifying drivers of contact variation can allow both contact inference and estimation of transmission dynamics despite limited data. In desert tortoises, mating strategy, burrow use and seasonal change influence numerous behaviours and likely shape contact patterns. In this study, we ask to what extent tortoise contact behaviour varies between sexes and seasons, and whether space or burrow-use data can be used to infer contact characteristics consistent with those recorded by proximity loggers. We identified sex and season-biased contact behaviour in both wild and captive populations indicative of female-female avoidance and seasonal male mate-seeking behaviour. Space and burrow-use patterns were informative, but did not always predict the extent of sex or seasonal biases on contact. We discuss the implications these findings have for transmission patterns and disease mitigation in tortoise populations.

Spatial demographic models can help guide monitoring and management activities targeting at-risk species, even in cases where baseline data are lacking. Here, we provide an example of how site-specific changes in land use and anthropogenic stressors can be incorporated into a spatial demographic model to investigate effects on population dynamics of Golden Eagles (Aquila chrysaetos). Our study focused on a population of Golden Eagles exposed to risks associated with rapid increases in renewable energy development in southern California, U.S.A. We developed a spatially explicit, individual-based simulation model that integrated empirical data on demography of Golden Eagles with spatial data on the arrangement of nesting habitats, prey resources, and planned renewable energy development sites. Our model permitted simulated eagles of different stage-classes to disperse, establish home ranges, acquire prey resources, prospect for breeding sites, and reproduce. The distribution of nesting habitats, prey resources, and threats within each individual's home range influenced movement, reproduction, and survival. We used our model to explore potential effects of alternative disturbance scenarios, and proposed conservation strategies, on the future distribution and abundance of Golden Eagles in the study region. Results from our simulations suggest that probable increases in mortality associated with renewable energy infrastructure (e.g., collisions with wind turbines and vehicles, electrocution on power poles) could have negative consequences for population trajectories, but that site-specific conservation actions could reduce the magnitude of negative effects. Our study demonstrates the use of a flexible and expandable modeling framework to incorporate spatially dependent processes when determining relative effects of proposed management options to Golden Eagles and their habitats.

— The Common Raven (Corvus corax) is a ubiquitous species in the Mojave Desert of southern Nevada and California. From 5 to 24 May 2014, using remote trail cameras, we observed ravens repeatedly kleptoparasitizing food resources from the nest of a pair of Golden Eagles (Aquila chyrsaetos) in the Spring Mountains of southern Nevada. The ravens fed on nine (30%) of the 30 prey items delivered to the nest during the chick rearing period. Kleptoparasitic behavior by the ravens decreased as the eagle nestling matured to seven weeks of age, suggesting a narrow temporal window in which ravens can successfully engage in kleptoparasitic behavior at eagle nests. The observation of kleptoparasitism by Common Ravens at the nest suggests potential risks to young Golden Eagles from Common Ravens.

The Mojave Desert is a vast and diverse landscape in the southwestern United States, encompassing 127,689 km2. This ecoregion is bordered by the colder and wetter Great Basin desert to the north, and the warmer and wetter Sonoran and Chihuahuan deserts to the south. Spanning from 86 m below sea level at Badwater Basin in Death Valley, California, to 3632 m at its highest mountains near Las Vegas, Nevada, the Mojave is the driest of the four North American deserts, in part due to the rain-shadow caused by the Transverse Ranges on its western edge. Extremes of moisture availability, temperature, physiographic variety, and soil diversity all are key in the formation of this unique landscape, and the divergence of its inhabitants over time. While the Mojave is often considered an intermediary with respect to the plants and animals that occupy the Great Basin and Sonoran Deserts, there are many species unique to the Mojave that aid in highlighting its unique characteristics. The Joshua Tree, Mojave Desert Tortoise, Mohave ground squirrel, and several species of fringe-toed lizards are all endemics to this ecoregion that have adapted to this austere environment. There is also a wide array of fishes and aquatic invertebrates that occupy the Mojave's sparse and discontinuous waterways and springs. Nearly all of these Mojave endemics are the subjects of conservation concern facing a rapidly changing environment driven by increasing human populations and land use, and a changing climate.

AIMS: To investigate spatial congruence between ecological niches and genotype in two allopatric species of desert tortoise that are species of conservation concern. LOCATION: Mojave and Sonoran Desert ecoregions; California, Nevada, Arizona, Utah, USA. METHODS: We compare ecological niches of Gopherus agassizii and Gopherus morafkai using species distribution modelling (SDM) and then calibrate a pooled‐taxa distribution model to explore local differences in species–environment relationships based on the spatial residuals of the pooled‐taxa model. We use multiscale geographically weighted regression (MGWR) applied to those residuals to estimate local species–environment relationships that can vary across the landscape. We identify multivariate clusters in these local species–environment relationships and compare them against models of (a) a geographically based taxonomic designation for two sister species and (b) an environmental ecoregion designation, with respect to their ability to predict a genotype association index for these two species. RESULTS: We find non‐identical niches for these species, with differences that span physiographic and vegetation niche dimensions. We find evidence for two distinct clusters of local species–environment relationships that when mapped, predict an index of genotype association for the two sister taxa better than did either the geographically based taxonomic designation or an environmental ecoregion designation. MAIN CONCLUSIONS: Exploring local species–environment relationships by coupling SDM and MGWR can benefit studies of biogeography and conservation. We find that niche separation in habitat selection conforms to genotypic differences between sister taxa of tortoise in a recent secondary contact zone. This result may inform decision making by agencies with regulatory or land management authority for the two sister taxa addressed here.

Summary 1.In spite of growing reliance on translocations in wildlife conservation, translocation efficacy remains inconsistent. One factor that can contribute to failed translocations is releasing animals into poor quality or otherwise inadequate habitat. 2.Here we used a targeted approach to test the relationship of habitat features to post-translocation dispersal and survival of juvenile Mojave desert tortoises Gopherus agassizii. 3.We selected three habitat characteristics—rodent burrows, substrate texture (prevalence and size of rocks), and washes (ephemeral river beds)–that are tied to desert tortoise ecology. At the point of release, we documented rodent burrow abundance, substrate texture, and wash presence and analysed their relationship to maximum dispersal. We also documented relative use by each individual for each habitat characteristic and analysed their relationships with survival and fatal encounters with a predator in the first year after release. 4.In general, the presence of refugia or other areas that enabled animals to avoid detection, such as burrows and substrate, decreased overall mortality as well as predator-mediated mortality. The presence of washes and substrate that enhanced the tortoises’ ability to avoid detection also associated with reduced dispersal away from the release site. These results indicate an important role for all three measured habitat characteristics in driving dispersal, survival, or fatal encounters with a predator in the first year after translocation. 5.Synthesis and applications. Resource managers using translocations as a conservation tool should prioritize acquiring data linking habitat to fitness. In particular, for species that depend on avoiding detection, refuges such as burrows and habitat that improved concealment had notable ability to improve survival and dispersal. Our study on juvenile Mojave desert tortoises showed that refuge availability or the distributions of habitat appropriate for concealment are important considerations for identifying translocation sites for species highly dependent on crypsis, camouflage, or other forms of habitat matching. This article is protected by copyright. All rights reserved.

Predicting changes in species distributions under a changing climate is becoming widespread with the use of species distribution models (SDMs). The resulting predictions of future potential habitat can be cast in light of planned land use changes, such as urban expansion and energy development to identify areas with potential conflict. However, SDMs rarely incorporate an understanding of dispersal capacity, and therefore assume unlimited dispersal in potential range shifts under uncertain climate futures. We use SDMs to predict future distributions of the Mojave ground squirrel, Xerospermophilus mohavensis Merriam, and incorporate partial dispersal models informed by field data on juvenile dispersal to assess projected impact of climate change and energy development on future distributions of X. mohavensis. Our models predict loss of extant habitat, but also concurrent gains of new habitat under two scenarios of future climate change. Under the B1 emissions scenario- a storyline describing a convergent world with emphasis on curbing greenhouse gas emissions- our models predicted losses of up to 64% of extant habitat by 2080, while under the increased greenhouse gas emissions of the A2 scenario, we suggest losses of 56%. New potential habitat may become available to X. mohavensis, thereby offsetting as much as 6330 km2 (50%) of the current habitat lost. Habitat lost due to planned energy development was marginal compared to habitat lost from changing climates, but disproportionately affected current habitat. Future areas of overlap in potential habitat between the two climate change scenarios are identified and discussed in context of proposed energy development.

The distribution and abundance of human-caused disturbances vary greatly through space and time and are cause for concern among land stewards in natural areas of the southwestern border-lands between the USA and Mexico. Human migration and border protection along the international boundary create Unauthorized Trail and Road (UTR) networks across National Park Service lands and other natural areas. UTRs may cause soil erosion and compaction, damage to vegetation and cultural resources, and may stress wildlife or impede their movements. We quantify the density and severity of UTR disturbances in relation to soils, and compare the use of previously established targeted trail assessments (hereafter — targeted assessments) against randomly placed transects to detect trail densities at Coronado National Memorial in Arizona in 2011. While trail distributions were similar between methods, targeted assessments estimated a large portion of the park to have the lowest density category (0–5 trail encounters...

Conservation planning and biodiversity management require information on landscape connectivity across a range of spatial scales from individual home ranges to large regions. Reduction in landscape connectivity due changes in land use or development is expected to act synergistically with alterations to habitat mosaic configuration arising from climate change. We illustrate a multiscale connectivity framework to aid habitat conservation prioritization in the context of changing land use and climate. Our approach, which builds upon the strengths of multiple landscape connectivity methods, including graph theory, circuit theory, and least-cost path analysis, is here applied to the conservation planning requirements of the Mohave ground squirrel. The distribution of this threatened Californian species, as for numerous other desert species, overlaps with the proposed placement of several utility-scale renewable energy developments in the American southwest. Our approach uses information derived at three spatial scales to forecast potential changes in habitat connectivity under various scenarios of energy development and climate change. By disentangling the potential effects of habitat loss and fragmentation across multiple scales, we identify priority conservation areas for both core habitat and critical corridor or stepping stone habitats. This approach is a first step toward applying graph theory to analyze habitat connectivity for species with continuously distributed habitat and should be applicable across a broad range of taxa.

For several species, refuges (such as burrows, dens, roosts, nests) are an essential resource for protection from predators and extreme environmental conditions. Refuges also serve as focal sites for social interactions, including mating, courtship, and aggression. Knowledge of refuge use patterns can therefore provide information about social structure, mating, and foraging success, as well as the robustness and health of wildlife populations, especially for species considered to be relatively solitary. In this study, we construct networks of burrow use to infer social associations in a threatened wildlife species typically considered solitary—the desert tortoise. We show that tortoise social networks are significantly different than null networks of random associations, and have moderate spatial constraints. We next use statistical models to identify major mechanisms behind individual-level variation in tortoise burrow use, popularity of burrows in desert tortoise habitat, and test for stressor-driven changes in refuge use patterns. We show that seasonal variation has a strong impact on tortoise burrow switching behavior. On the other hand, burrow age and topographical condition influence the number of tortoises visiting a burrow in desert tortoise habitat. Of three major population stressors affecting this species (translocation, drought, disease), translocation alters tortoise burrow switching behavior, with translocated animals visiting fewer unique burrows than residents. In a species that is not social, our study highlights the importance of leveraging refuge use behavior to study the presence of and mechanisms behind non-random social structure and individual-level variation. Our analysis of the impact of stressors on refuge-based social structure further emphasizes the potential of this method to detect environmental or anthropogenic disturbances. Adaptive and social behavior that affects fitness is now being increasingly incorporated in the conservation and management of wildlife species. However, direct observations of social interactions in species considered to be solitary are difficult, and therefore integration of behavior in conservation and management decisions in such species has been infrequent. For such species, we propose quantifying refuge use behavior as it can provide insights towards their (hidden) social structure, establish relevant contact patterns of infectious disease spread, and provide early warning signals of population stressors. Our study highlights this approach in a long-lived and threatened species, the desert tortoise. We provide evidence toward the presence of and identify mechanisms behind the social structure in desert tortoises formed by their burrow use preferences. We also show how individuals burrow use behavior responds to the presence of population stressors.

Across the western United States, Leporidae are the most important prey item in the diet of Golden Eagles (Aquila chrysaetos). Leporids inhabiting the western United States include black-tailed (Lepus californicus) and white-tailed jackrabbits (Lepus townsendii) and various species of cottontail rabbit (Sylvilagus spp.). Jackrabbits (Lepus spp.) are particularly important components of the ecological and economic landscape of western North America because their abundance influences the reproductive success and population trends of predators such as coyotes (Canis latrans), bobcats (Lynx rufus), and a number of raptor species. Here, we review literature pertaining to black-tailed and white-tailed jackrabbits comprising over 170 published journal articles, notes, technical reports, conference proceedings, academic theses and dissertations, and other sources dating from the late 19th century to the present. Our goal is to present information to assist those in research and management, particularly ...

In the Mojave Desert of the southwestern United States, adult Agassiz's desert tor- toises Gopherus agassizii typically experience high survival, but population declines associated with anthropogenic impacts led to their listing as a threatened Species under the US Endangered Species Act in 1990. Predation of adult tortoises is not often considered a significant threat as they are adapted to deter most predation attempts. Despite these adaptations, some populations have experienced elevated mortality attributed to predators, suggesting that predation pressure may occasionally increase. During the tortoise activity seasons of 2012 and 2013, we observed unsus- tainably high mortality in 1 of 4 populations of adult desert tortoises (22 and 84%, respectively) in the western Mojave Desert in the vicinity of Barstow, CA. Photographic evidence from trail cam- eras and examination of carcass condition suggest that American badgers Taxidea taxus —a sometimes cited but unconfirmed predator of adult tortoises — may have been responsible for some of the mortality observed. We discuss the American badger as a plausible predator of a local tortoise population, but recommend further investigation into these events and the impacts such mortality can have on tortoise persistence.

Wildfires burned 24,254 ha of critical habitat designated for the recovery of the threatened Mojave desert tortoise (Gopherus agassizii) in southern Nevada during 2005. The proliferation of non-native annual grasses has increased wildfire frequency and extent in recent decades and continues to accelerate the conversion of tortoise habitat across the Mojave Desert. Immediate changes to vegetation are expected to reduce quality of critical habitat, yet whether tortoises will use burned and recovering habitat differently from intact unburned habitat is unknown. We compared movement patterns, home-range size, behavior, microhabitat use, reproduction, and survival for adult desert tortoises located in, and adjacent to, burned habitat to understand how tortoises respond to recovering burned habitat. Approximately 45% of home ranges in the post-fire environment contained burned habitat, and numerous observations (n = 12,223) corroborated tortoise use of both habitat types (52% unburned, 48% burned). Tortoises moved progressively deeper into burned habitat during the first 5 years following the fire, frequently foraging in burned habitats that had abundant annual plants, and returning to adjacent unburned habitat for cover provided by intact perennial vegetation. However, by years 6 and 7, the live cover of the short-lived herbaceous perennial desert globemallow (Sphaeralcea ambigua) that typically re-colonizes burned areas declined, resulting in a contraction of tortoise movements from the burned areas. Health and egg production were similar between burned and unburned areas indicating that tortoises were able to acquire necessary resources using both areas. This study documents that adult Mojave desert tortoises continue to use habitat burned once by wildfire. Thus, continued management of this burned habitat may contribute toward the recovery of the species in the face of many sources of habitat loss. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Summary 1. Recent elevated temperatures and prolonged droughts in many already water-limited regions throughout the world, including the southwestern United States, are likely to intensify according to future climate-model projections. This warming and drying can negatively affect perennial vegetation and lead to the degradation of ecosystem properties. 2. To better understand these detrimental effects, we formulate a conceptual model of dryland ecosystem vulnerability to climate change that integrates hypotheses on how plant species will respond to increases in temperature and drought, including how plant responses to climate are modified by landscape, soil and plant attributes that are integral to water availability and use. We test the model through a synthesis of fifty years of repeat measurements of perennial plant species cover in large permanent plots across the Mojave Desert, one of the most water-limited ecosystems in North America. 3. Plant species ranged in their sensitivity to precipitation in different seasons, capacity to increase in cover with high precipitation and resistance to decrease in cover with low precipitation. 4. Our model successfully explains how plant responses to climate are modified by biophysical attributes in the Mojave Desert. For example, deep-rooted plants were not as vulnerable to drought on soils that allowed for deep-water percolation, whereas shallow-rooted plants were better buffered from drought on soils that promoted water retention near the surface. 5. Synthesis. Our results emphasize the importance of understanding climate–vegetation relationships in the context of biophysical attributes that influence water availability and provide an important forecast of climate-change effects, including plant mortality and land degradation in dryland regions throughout the world.

Wildlife managers consider animal translocation a means of increasing the viability of a local population. However, augmentation may disrupt existing resident disease dynamics and initiate an outbreak that would effectively offset any advantages the translocation may have achieved. This paper examines fundamental concepts of disease ecology and identifies the conditions that will increase the likelihood of a disease outbreak following translocation. We highlight the importance of susceptibility to infection, population size and population connectivity ‐ a characteristic likely affected by translocation but not often considered in risk assessments ‐ in estimating outbreak risk due to translocation. We then explore these features in a species of conservation concern often translocated in the presence of infectious disease, the Mojave Desert tortoise, and use data from experimental tortoise translocations to detect changes in population connectivity that may influence pathogen transmission. Preliminary analyses comparing contact networks inferred from spatial data at control and translocation plots and infection simulation results through these networks suggest increased outbreak risk following translocation due to dispersal-driven changes in contact frequency and network structure. We outline future research goals to test these concepts and aid managers in designing effective risk assessment and intervention strategies that will improve translocation success.

Rates of soil disruption from hikers and vehicle traffic are poorly known, particularly for arid landscapes. We conducted an experiment in Organ Pipe Cactus National Monument (ORPI) in western Arizona, USA, on an air-dry very fine sandy loam that is considered to be vulnerable to disruption. We created variable-pass tracks using hikers, an all-terrain vehicle (ATV), and a four-wheel drive vehicle (4WD) and measured changes in cross-track topography, penetration depth, and bulk density. Hikers (one pass = 5 hikers) increased bulk density and altered penetration depth but caused minimal surface disruption up to 100 passes; a minimum of 10 passes were required to overcome surface strength of this dry soil. Both ATV and 4WD traffic significantly disrupted the soil with one pass, creating deep ruts with increasing passes that rendered the 4WD trail impassable after 20 passes. Despite considerable soil loosening (dilation), bulk density increased in the vehicle trails, and lateral displacement created berms of loosened soil. This soil type, when dry, can sustain up to 10 passes of hikers but only one vehicle pass before significant soil disruption occurs; greater disruption is expected when soils are wet. Bulk density increased logarithmically with applied pressure from hikers, ATV, and 4WD.

Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

Mohave ground squirrels Xerosper- mophilus mohavensis Merriam are small ground- dwelling rodents that have a highly restricted range in the northwest Mojave Desert, California, USA. Their small natural range is further reduced by habitat loss from agriculture, urban develop- ment, military training and recreational activities. Development of wind and solar resources for re - newable energy has the potential to further re - duce existing habitat. We used maximum entropy habitat models with observation data to describe current potential habitat in the context of future renewable energy development in the region. While 16% of historic habitat has been impacted by, or lost to, urbanization at present, an additional 10% may be affected by renewable energy devel- opment in the near future. Our models show that X. moha vensis habitat suitability is higher in areas slated for renewable energy development than in surrounding areas. We provide habitat maps that can be used to develop sampling designs, evaluate conservation corridors and inform development planning in the region.

Habitat disturbance from development, resource extraction, off-road vehicle use, and energy development ranks highly among threats to desert systems worldwide. In the Mojave Desert, United States, these disturbances have promoted the establishment of nonnative plants, so that native grasses and forbs are now intermixed with, or have been replaced by invasive, nonnative Mediterranean grasses. This shift in plant composition has altered food availability for Mojave Desert tortoises (Gopherus agassizii), a federally listed species. We hypothesized that this change in forage would negatively influence the physiological ecology, immune competence, and health of neonatal and yearling tortoises. To test this, we monitored the effects of diet on growth, body condition, immunological responses (measured by gene transcription), and survival for 100 captive Mojave tortoises. Tortoises were assigned to one of five diets: native forbs, native grass, invasive grass, and native forbs combined with either the native or invasive grass. Tortoises eating native forbs had better body condition and immune functions, grew more, and had higher survival rates (>95%) than tortoises consuming any other diet. At the end of the experiment, 32% of individuals fed only native grass and 37% fed only invasive grass were found dead or removed from the experiment due to poor body conditions. In contrast, all tortoises fed either the native forb or combined native forb and native grass diets survived and were in good condition. Health and body condition quickly declined for tortoises fed only the native grass (Festuca octoflora) or invasive grass (Bromus rubens) with notable loss of fat and muscle mass and increased muscular atrophy. Bromus rubens seeds were found embedded in the oral mucosa and tongue in most individuals eating that diet, which led to mucosal inflammation. Genes indicative of physiological, immune, and metabolic functions were transcribed at lower levels for individuals fed B. rubens, indicating potential greater susceptibility to disease or other health-related problems. This study highlights the negative indirect effects of invasive grasses, such as red brome, in desert ecosystems, and provides definitive evidence of a larger negative consequence to health, survival, and ultimately population recruitment for Mojave Desert tortoises than previously understood.

Aim We explored lineage diversification within desert-dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre-Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location Mojave, Colorado, and Sonoran Deserts, USA. Methods We analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra-population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results In seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions Most of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long-term preservation of species-level biodiversity would entail selecting areas for protection in Mojave and Sonoran Deserts to retain divergent genetic diversity and ensure connectedness across environmental gradients.

Wildlife translocation is increasingly used to mitigate disturbances to animals or habitat due to human activities, yet little is known about the extent to which translocating animals causes stress. To understand the relationship between physiological stress and translocation, we conducted a multiyear study (2007–2009) using a population of desert tortoises (Gopherus agassizii) near Fort Irwin, California. Blood samples were collected from adult tortoises in three treatment groups (resident, translocated and control) for 1 year prior to and 2 years after translocation. Samples were analyzed by radioimmunoassay for plasma total corticosterone (CORT), a glucocorticoid hormone commonly associated with stress responses in reptiles. CORT values were analyzed in relation to potential covariates (animal sex, date, behavior, treatment, handling time, air temperature, home-range size, precipitation and annual plant production) among seasons and years. CORT values in males were higher than in females, and values for both varied monthly throughout the activity season and among years. Year and sex were strong predictors of CORT, and translocation explained little in terms of CORT. Based on these results, we conclude that translocation does not elicit a physiological stress response in desert tortoises.

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. 2012 The Wildlife Society.

Heterogeneity in habitat often influences how organisms traverse the landscape matrix that connects populations. Understanding landscape connectivity is important to determine the ecological processes that influence those movements, which lead to evolutionary change due to gene flow. Here, we used landscape genetics and statistical models to evaluate hypotheses that could explain isolation among locations of the threatened Mojave desert tortoise (Gopherus agassizii). Within a causal modeling framework, we investigated three factors that can influence landscape connectivity: geographic distance, barriers to dispersal, and landscape friction. A statistical model of habitat suitability for the Mojave desert tortoise, based on topography, vegetation, and climate variables, was used as a proxy for landscape friction and barriers to dispersal. We quantified landscape friction with least-cost distances and with resistance distances among sampling locations. A set of diagnostic partial Mantel tests statistically separated the hypotheses of potential causes of genetic isolation. The best-supported model varied depending upon how landscape friction was quantified. Patterns of genetic structure were related to a combination of geographic distance and barriers as defined by least-cost distances, suggesting that mountain ranges and extremely low-elevation valleys influence connectivity at the regional scale beyond the tortoises’ ability to disperse. However, geographic distance was the only influence detected using resistance distances, which we attributed to fundamental differences between the two ways of quantifying friction. Landscape friction, as we measured it, did not influence the observed patterns of genetic distances using either quantification. Barriers and distance may be more valuable predictors of observed population structure for species like the desert tortoise, which has high dispersal capability and a long generation time.

Understanding predator-prey relationships can be pivotal in the conservation of spe- cies. For 2 decades, desert tortoise Gopherus agassizii populations have declined, yet quantitative evidence regarding the causes of declines is scarce. In 2005, Ft. Irwin National Training Center, California, USA, implemented a translocation project including 2 yr of baseline monitoring of desert tortoises. Unusually high predation on tortoises was observed after translocation occurred. We conducted a retrospective analysis of predation and found that translocation did not affect the proba- bility of predation: translocated, resident, and control tortoises all had similar levels of predation. However, predation rates were higher near human population concentrations, at lower elevation sites, and for smaller tortoises and females. Furthermore, high mortality rates were not limited to the National Training Center. In 2008, elevated mortality (as high as 43%) occurred throughout the listed range of the desert tortoise. Although no temporal prey base data are available for analysis from any of the study sites, we hypothesize that low population levels of typical coyote Canis latrans prey (i.e. jackrabbits Lepus californicus and other small animals) due to drought conditions influenced high predation rates in previous years. Predation may have been exacerbated in areas with high levels of subsidized predators. Many historical reports of increased predation, and our observation of a range- wide pattern, may indicate that high predation rates are more common than generally considered and may impact recovery of the desert tortoise throughout its range.

Hypolithic microbes, primarily cyanobacteria, inhabit the highly specialized microhabitats under translucent rocks in extreme environments. Here we report findings from hypolithic cyanobacteria found under three types of translucent rocks (quartz, prehnite, agate) in a semiarid region of tropical Australia. We investigated the photosynthetic responses of the cyanobacterial communities to light, temperature and moisture in the laboratory, and we measured the microclimatic variables of temperature and soil moisture under rocks in the field over an annual cycle. We also used molecular techniques to explore the diversity of hypolithic cyanobacteria in this community and their phylogenetic relationships within the context of hypolithic cyanobacteria from other continents. Based on the laboratory experiments, photosynthetic activity required a minimum soil moisture of 15% (by mass). Peak photosynthetic activity occurred between approximately 8 degrees C and 42 degrees C, though some photosynthesis occurred between -1 degrees C and 51 degrees C. Maximum photosynthesis rates also occurred at light levels of approximately 150-550 micromol m(-2) s(-1). We used the field microclimatic data in conjunction with these measurements of photosynthetic efficiency to estimate the amount of time the hypolithic cyanobacteria could be photosynthetically active in the field. Based on these data, we estimated that conditions were appropriate for photosynthetic activity for approximately 942 h (approximately 75 days) during the year. The hypolithic cyanobacteria community under quartz, prehnite and agate rocks was quite diverse both within and between rock types. We identified 115 operational taxonomic units (OTUs), with each rock hosting 8-24 OTUs. A third of the cyanobacteria OTUs from northern Australia grouped with Chroococcidiopsis, a genus that has been identified from hypolithic and endolithic communities from the Gobi, Mojave, Atacama and Antarctic deserts. Several OTUs identified from northern Australia have not been reported to be associated with hypolithic communities previously.

Assessing the recovery of the federally listed Mojave population of desert tortoises Gopherus agassizii requires detecting subtle changes in population size over a period of many years. The methods that have been employed by the US Fish and Wildlife Service to estimate population density of desert tortoises are inadequate for detecting modest trends in population density, partly due to a hidden variance in a parameter (g0) that corrects for the proportion of tortoises that are inactive and thus unavailable for sampling when population density is being assessed. We used small dataloggers to record the activity of tortoises throughout their active season, and derived daily esti- mates of g0, which we compared with the 2004 estimate published by the US Fish and Wildlife Ser- vice. Due to the substantial variation in animal activity that we found within and among days during the active season, we used a daily method to estimate density. We found that this method, while pro- viding a more accurate assessment of g0, translates into estimates of density with coefficients of vari- ation that are 4" larger than previously reported due to the variation in g0 and n (number of animals encountered). This discrepancy could adversely influence managers' perceptions of population recovery for desert tortoises, and could undermine any ability to monitor the efficacy of recovery actions for populations.

The use of dogs (Canis lupus familiaris) trained to locate wildlife under natural conditions may increase the risk of attracting potential predators or alter behavior of target species. These potentially negative effects become even more problematic when dealing with threatened or endangered species, such as the Mojave Desert tortoise (Gopherus agassizii). We addressed three concerns regarding use of dogs trained to locate desert tortoises in the wild. First, we looked at the potential for dogs to attract native and non-native predators to sites at a greater rate than with human visitation alone by comparing presence of predator sign before and after visitation by dogs and by humans. We found no significant difference in predator sign based upon type of surveyor. Second, we looked at the difference in risk of predation to desert tortoises that were located in the wild by humans versus humans with wildlife-detector dogs. Over a 5-week period, during which tortoises were extensively monitored and a subsequent period of 1 year during which tortoises were monitored monthly, there was no predation on, nor sign of predator-inflicted trauma to tortoises initially encountered either by humans or wildlife-detector dogs. Third, we looked at movement patterns of tortoises after encounter by either humans or wildlife-detector dogs. Movement of desert tortoises was not significantly different after being found by a human versus being found by a wildlife-detector dog. Based upon these initial results we conclude that use of trained wildlife-detector dogs to survey for desert tortoises in the wild does not appear to increase attraction of predators, increase risk of predation, or alter movement patterns of desert tortoises more than surveys conducted by humans alone.

This research examined the onset, duration, and termination of hibernation in Desert Tortoises (Gopherus agassizii) over several years at multiple sites in the northeastern part of their geographic range, and recorded the temperatures experienced by tortoises during winter hibernation. The timing of hibernation by Desert Tortoises differed among sites and years. Environmental cues acting over the short-term did not appear to influence the timing of the hibernation period. Different individual tortoises entered hibernation over as many as 44 days in the fall and emerged from hibernation over as many as 49 days in the spring. This range of variation in the timing of hibernation indicates a weak influence at best of exogenous cues hypothesized to trigger and terminate hibernation. There do appear to be regional trends in hibernation behavior as hibernation tended to begin earlier and continue longer at sites that were higher in elevation and generally cooler. The emergence date was generally more similar among study sites than the date of onset. While the climate and the subsequent timing of hibernation differed among sites, the average temperatures experienced by tortoises while hibernating differed by only about five degrees from the coldest site to the warmest site.

The federally listed desert tortoise (Gopherus agassizii) is currently monitored using distance sampling to estimate population densities. Distance sampling, as with many other techniques for estimating population density, assumes that it is possible to quantify the proportion of animals available to be counted in any census. Because desert tortoises spend much of their life in burrows, and the proportion of tortoises in burrows at any time can be extremely variable, this assumption is difficult to meet. This proportion of animals available to be counted is used as a correction factor (g0) in distance sampling and has been estimated from daily censuses of small populations of tortoises (6-12 individuals). These censuses are costly and produce imprecise estimates of g0 due to small sample sizes. We used data on tortoise activity from a large (N = 1 50) experimental population to model activity as a function of the biophysical attributes of the environment, but these models did not improve the precision of estimates from the focal populations. Thus, to evaluate how much of the variance in tortoise activity is apparently not predictable, we assessed whether activity on any particular day can predict activity on subsequent days with essentially identical environmental conditions. Tortoise activity was only weakly correlated on consecutive days, indicating that behavior was not repeatable or consistent among days with similar physical environments.

For several species, refuges (such as burrows, dens, roosts, nests) are an essential resource for protection from predators and extreme environmental conditions. Refuges also serve as focal sites for social interactions including mating, courtship and aggression. Knowledge of refuge use patterns can therefore provide information about social structure, mating and foraging success, as well as the robustness and health of wildlife populations, especially for species considered to be relatively solitary. In this study, we construct networks of burrow use to infer social associations in a threatened wildlife species typically considered solitary - the desert tortoise. We show that tortoise social networks are significantly different than null networks of random associations, and have moderate spatial constraints. We next use statistical models to identify major mechanisms behind individual-level variation in tortoise burrow use, popularity of burrows in desert tortoise habitat and test for stressor-driven changes in refuge use patterns. We show that seasonal variation has a strong impact on tortoise burrow switching behavior. On the other hand, burrow age and topographical condition influence the number of tortoises visiting a burrow in desert tortoise habitat. Of three major population stressors affecting this species (translocation, drought, disease), translocation alters tortoise burrow switching behavior, with translocated animals visiting fewer unique burrows than residents. In a species that is not social, our study highlights the importance of leveraging refuge use behavior to study the presence of and mechanisms behind non-random social structure and individual-level variation. Our analysis of the impact of stressors on refuge-based social structure further emphasizes the potential of this method to detect environmental or anthropogenic disturbances.Significance statement: Adaptive and social behavior that affects fitness is now being increasingly incorporated in the conservation and management of wildlife species. However, direct observations of social interactions in species considered to be solitary are difficult, and therefore integration of behavior in conservation and management decisions in such species has been infrequent. For such species, we propose quantifying refuge use behavior as it can provide insights towards their (hidden) social structure, establish relevant contact patterns of infectious disease spread, and provide early warning signals of population stressors. Our study highlights this approach in a long-lived and threatened species, the desert tortoise. We provide evidence towards the presence of and identify mechanisms behind the social structure in desert tortoises formed by their burrow use preferences. We also show how individuals burrow use behavior responds to the presence of population stressors.

Most directly transmitted infections require some form of close contact between infectious and susceptible hosts to spread. Often disease models assume contacts are equal and use mean field estimates of transmission probability for all interactions with infectious hosts. Such methods may inaccurately describe transmission when interactions differ substantially in their ability to cause infection. Understanding this variation in transmission risk may be critical to properly model and manage some infectious diseases. In this study, we investigate how varying exposure and transmission may be key to understanding disease dynamics in the threatened desert tortoise Gopherus agassizii. We created heterogeneity in Mycoplasma agassizii exposure (the putative bacterial agent of a respiratory disease) by varying the duration of interactions between naturally infected and uninfected captive desert tortoises. Using qPCR, we identified new infections and compared models of transmission probability as a function of contact duration and pathogen load. We then examined the contact patterns of a wild tortoise population using proximity loggers to identify heterogeneity in contact duration. The top-ranked model predicting M. agassizii transmission included a dose term defined as the product of the number of days in proximity to an infected host and the infection level of that host. Models predicted low transmission probability for short interactions, unless the infectious host had a high load of M. agassizii: such hosts were predicted to transmit infection at higher rates with any amount of contact. We observed predominantly short-lived interactions in a free-ranging tortoise population and thus, expect transmission patterns in this population to vary considerably with the frequency and duration of high infection levels. Mean field models may misrepresent natural transmission patterns in this and other populations depending on the distribution of high-risk contact and shedding events. Rapid outbreaks in generally solitary species may result from changes to their naturally low-risk contact patterns or due to increases in the frequency of severe infections or super-shedding events - population characteristics that should be further investigated to develop effective management strategies.

Many of the threats to the persistence of populations of sensitive species have physiological or pathological mechanisms, and those mechanisms are best understood through the inherently integrative discipline of physiological ecology. The desert tortoise was listed under the Endangered Species Act largely due to a newly recognized upper respiratory disease thought to cause mortality in individuals and severe declines in populations. Numerous hypotheses about the threats to the persistence of desert tortoise populations involve acquisition of nutrients, and its connection to stress and disease. The nutritional wisdom hypothesis posits that animals should forage not for particular food items, but instead, for particular nutrients such as calcium and phosphorus used in building bones. The optimal foraging hypothesis suggests that, in circumstances of resource abundance, tortoises should forage as dietary specialists as a means of maximizing intake of resources. The optimal digestion hypothesis suggests that tortoises should process ingesta in ways that regulate assimilation rate. Finally, the cost-of-switching hypothesis suggests that herbivores, like the desert tortoise, should avoid switching food types to avoid negatively affecting the microbe community responsible for fermenting plants into energy and nutrients. Combining hypotheses into a resource acquisition theory leads to novel predictions that are generally supported by data presented here. Testing hypotheses, and synthesizing test results into a theory, provides a robust scientific alternative to the popular use of untested hypotheses and unanalyzed data to assert the needs of species. The scientific approach should focus on hypotheses concerning anthropogenic modifications of the environment that impact physiological processes ultimately important to population phenomena. We show how measurements of such impacts as nutrient starvation, can cause physiological stress, and that the endocrine mechanisms involved with stress can result in disease. Finally, our new syntheses evince a new hypothesis. Free molecules of the stress hormone corticosterone can inhibit immunity, and the abundance of "free corticosterone" in the blood (thought to be the active form of the hormone) is regulated when the corticosterone molecules combine with binding globulins. The sex hormone, testosterone, combines with the same binding globulin. High levels of testosterone, naturally occurring in the breeding season, may be further enhanced in populations at high densities, and the resulting excess testosterone may compete with binding globulins, thereby releasing corticosterone and reducing immunity to disease. This sequence could result in physiological and pathological phenomena leading to population cycles with a period that would be essentially impossible to observe in desert tortoise. Such cycles could obscure population fluctuations of anthropogenic origin.