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Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least 2, and possibly 3 major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically, but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.

First-order dynamic occupancy models (FODOMs) are a class of state-space model in which the true state (occurrence) is observed imperfectly. An important assumption of FODOMs is that site dynamics only depend on the current state and that variations in dynamic processes are adequately captured with covariates or random effects. However, it is often difficult to measure the covariates that generate ecological data, which are often spatio-temporally correlated. Consequently, the non-independent error structure of correlated data causes underestimation of parameter uncertainty and poor ecological inference. Here, we extend the FODOM framework with a second-order Markov process to accommodate site memory when covariates are not available. Our modeling framework can be used to make reliable inference about site occupancy, colonization, extinction, turnover, and detection probabilities. We present a series of simulations to illustrate the data requirements and model performance. We then applied our modeling framework to 13 years of data from an amphibian community in southern Arizona, USA and find that site memory helps describe dynamic processes for most species. Our approach represents a valuable advance in obtaining inference on population dynamics, especially as they relate to metapopulations.

1. Fragmentation within urbanized environments often leads to a loss of native species diversity; however, variation exists in responses among-species and among-populations within species.
2. We aimed to identify patterns in species biogeography in an urbanized landscape to understand anthropogenic effects on vertebrate communities and identify species that are more sensitive or resilient to landscape change.
3. We investigated patterns in species richness and species responses to fragmentation in southern Californian small vertebrate communities using multispecies occupancy models and determined factors associated with overall commonness and sensitivity to patch size for 45 small vertebrate species both among and within remaining non-developed patches.
4. In general, smaller patches had fewer species, with amphibian species richness being particularly sensitive to patch size effects. Mammals were generally more common, occurring both in a greater proportion of patches and a higher proportion of the sites within occupied patches. Alternatively, amphibians were generally restricted to larger patches but were more ubiquitous within smaller patches when occupied. Species range size was positively correlated with how common a species was across and within patches, even when controlling for only patches that fell within a species’ range. We found sensitivity to patch size was greater for more fecund species and depended on where the patch occurred within a species’ range. While all taxa were more likely to occur in patches in the warmer portions of their ranges, amphibians and mammals were more sensitive to fragmentation in these warmer areas as compared to the rest of their ranges. Similarly, amphibians occurred at a smaller proportion of sites within patches in drier portions of their ranges. Mammals occurred at a higher proportion of sites that were also in drier portions of their range while reptiles did not differ in their sensitivity to patch size by range position.
5. We demonstrate that taxonomy, life history, range size, and range position can predict commonness and sensitivity of species across this highly fragmented yet biodiverse landscape. The impacts of fragmentation on species communities within an urban landscape depend on scale, with differences emerging among and within species and populations.

A principal challenge impeding strong inference in analyses of wild populations is the lack of robust and long-term data sets. Recent advancements in analytical tools used in wildlife science may increase our ability to integrate smaller data sets and enhance the statistical power of population estimates. One such advancement, the development of spatial capture-recapture (SCR) methods, explicitly accounts for differences in spatial study designs, making it possible to equate multiple study designs in one analysis. SCR has been shown to be robust to variation in design as long as minimal sampling guidance is adhered to. However, these expectations are based on simulation and have yet to be evaluated in wild populations. Here we conduct a rigorously designed field experiment by manipulating the arrangement of artificial cover objects (ACOs) used to collect data on red-backed salamanders (Plethodon cinereus) to empirically evaluate the effects of design configuration on inference made using SCR. Our results suggest that, using SCR, estimates of space use and detectability are sensitive to study design configuration, namely the spacing and extent of the array, and that caution is warranted when assigning biological interpretation to these parameters. However, estimates of population density remain robust to design except when the configuration of detectors grossly violates existing recommendations.

The Coyote Mountain desert snail (Sonorelix harperi carrizoensis) was described in 1937 from 30 dry shells collected the previous year. We reviewed the literature and museum records and found two additional shell collections for this subspecies from the type locality one from 1958, and one from an adjacent mountain range in 1938. There is no evidence previously of any live snails being collected from the Coyote Mountains, Imperial County, California. All shell collections of S. harperi carrizoensis have the same locality data as the type series, which is Painted Gorge, Coyote Mountains except for one recorded collection of shells from the Vallecito Mountains from 1938. Using geological maps and other data sources, a potential mesic habitat was identified in the Coyote Mountains. During recent field work for salamanders at this location we detected two live specimens of S. harperi carrizoensis approximately 2 km north of its type location. This new data confirms this subspecies is still extant and has occurred at least at two sites historically in these mountains. Despite the presence of mesic habitats (i.e., mosses, liverworts and ferns) at the type locality, we found no evidence of S. harperi carrizoensis or salamanders.

Abstract: The National Park Service (NPS) manages hundreds of parks in the United States, and many contain important aquatic ecosystems and/or threatened and endangered aquatic species vulnerable to hydro-climatic change. More effective management of park resources under future hydro-climatic uncertainty requires information on both baseline conditions and the range of projected future conditions. A monthly water balance model was used to assess baseline (1981–1999) conditions and a range of projected future hydro-climatic conditions in 374 NPS parks. General circulation model outputs representing 214 future climate simulations were used to drive the model. Projected future changes in air temperature (T), precipitation (p), and runoff (R) are expressed as departures from historical baselines. Climate simulations indicate increasing T by 2030 for all parks with 50th percentile simulations projecting increases of https://1.67 °C or more in 50% of parks. Departures in 2030 p indicate a mix of mostly increases and some decreases, with 50th percentile simulations projecting increases in p in more than 70% of parks. Departures in R for 2030 are mostly decreases, with the 50th percentile simulations projecting decreases in R in more than 50% of parks in all seasons except winter. Hence, in many NPS parks, R is projected to decrease even when p is projected to increase because of increasing T in all parks. Projected changes in future hydro-climatic conditions can also be assessed for individual parks, and Rocky Mountain National Park and Congaree National Park are used as examples.

Batrachochytrium salamandrovorans (Bsal) is a fungal pathogen that can cause the emerging infectious disease Bsal chytridiomycosis in some amphibians, and is currently causing dramatic declines in European urodeles. To date, Bsal has not been detected in North America but has the potential to cause severe declines in naïve hosts if introduced. Therefore, it is critical that wildlife managers are prepared with effective management actions to combat the fungus. Research has been initiated to identify strategies; however, managers need guidance to prepare for an outbreak until results are available. Here, we conducted a workshop with participants of a Bsal symposium to describe the expected effect of eleven management actions that could be implemented for Bsal in three salamander communities in the northwestern, northeastern, and southeastern United States. Participants expected variation in the proposed management actions to decrease pathogen transmission and increase host survival, but also expected that the selection of a management action may depend on the specific membership of the amphibian community. Collectively, this assessment will help refine research and modeling priorities in an effort to mitigate the risk of Bsal to native U.S. amphibians.

Emerging infectious diseases can result in species declines and hamper recovery efforts for at-risk populations. Generalizing considerations for reducing the risk of pathogen introduction and mitigating the effects of disease remains challenging and inhibits our ability to provide guidance for species recovery planning. Given the growing rates of emerging pathogens globally, we identify key principles and mechanisms for maintaining sustainable populations in the face of emerging diseases (including minimizing the risk of pathogen introductions and their future effects on hosts). Our synthesis serves as a reference for minimizing the risk of future disease outbreaks, mitigating the deleterious effects of future disease outbreaks on species extinction risk, and a review of the theoretical and/or empirical examples supporting these considerations.

The state of an ecosystem is governed by dynamic biotic and abiotic processes, which can only be partially observed. Costs associated with measuring each component limit the feasibility of comprehensive assessments of target ecosystems. Instead, indicator species are recommended as a surrogate index. While this is an attractive concept, indicator species have rarely proven to be an effective tool for monitoring ecosystems and informing management decisions. One deficiency in the existing theoretical development of indicator species may be overcome with the incorporation of latent (i.e., unobservable) states. Advancements in quantitative ecological models allow for latent-state models to be tested empirically, facilitating the robust evaluation and practical use of indicator species for ecosystem science and management. Here, we extend the existing conceptual models of indicator species to include a direct relationship between an indicator species, ecosystem change drivers, and latent processes and variables. Our approach includes explicit consideration of important estimation uncertainty and narrows the range of values a latent variable may take by relating it to measurable attribute(s) of an indicator species. We demonstrate the utility of this approach by relating a commonly cited indicator species, the red-backed salamander (Plethodon cinereus), to a typical latent process of interest – ecosystem health.

Introduced species often disrupt established food webs, but some native predators can come to rely on introduced prey. Understanding the net effects of the non-natives on imperiled predators is crucial for planning conservation measures. The invasive American bullfrog (Lithobates catesbeianus) can be prey, predator, and competitor for the critically endangered San Francisco garter snake (Thamnophis sirtalis tetrataenia). We examined the seasonal prey use of a San Francisco garter snake population that co-occurs with American bullfrogs to examine intraguild predation between these species. Juvenile and adult snakes mainly consumed native anurans instead of American bullfrogs, and this diet pattern peaked in spring, a critical foraging period for the snakes. In spring, large adult American bullfrogs also foraged heavily on native anurans and displayed a high degree of diet overlap with San Francisco garter snakes. Invasive American bullfrogs are detrimental to San Francisco garter snakes mainly through seasonal competition rather than reciprocal predation. Removal of invasive species provided further evidence that eliminating American bullfrogs can benefit San Francisco garter snakes by reducing predation pressure on their shared amphibian prey. Better understanding the interactions of invasive species with native species of conservation concern informs management practices and improves conservation outcomes.

The disproportionate effects of warming for high-latitude, freshwater ecosystems has been well documented, but in some areas, changes have been further impacted by human-subsidized increases of waterfowl. To gain insight into how predicted changes in temperature and nutrient inputs might affect ecosystem function, we conducted a mesocosm experiment in the Canadian Subarctic with three levels of simulated goose enrichment and warming to measure changes in size and survival of larval wood frogs and boreal chorus frogs and primary productivity (phytoplankton and periphyton biomass). Our results highlight that the consequences of these rapid changes are non-linear and even non-intuitive, with species-specific consumer and ecosystem responses that depend on the magnitude of temperature and nutrient changes as well as community composition.

The U.S. Fish and Wildlife Service listed Anaxyrus canorus, the Yosemite toad, as federally threatened in 2014 based upon reported population declines and vulnerability to global-change factors. A. canorus lives only in California’s central Sierra Nevada at medium to sub-alpine elevations. Lands throughout its range are protected from development, but climate and other global-change factors potentially can limit populations. A. canorus reproduces in ultra-shallow wetlands that typically hydrate seasonally via melting of the winter snowpack. Lesser snowpacks in drier years can render wetland water volumes and hydroperiods insufficient to allow for successful breeding and reproduction. Additionally, breeding and embryogenesis occur very soon after wetlands thaw when overnight temperatures can be below freezing. Diseases, such as chytridiomycosis, which recently decimated regional populations of ranid species, also might cause declines of A. canorus populations. However, reported studies focused on whether climate interacts with any pathogens to affect fitness in A. canorus have been scarce. We investigated effects of these factors on A. canorus near Tioga Pass from 1996 to 2001. We found breeding subpopulations were distributed widely but inconsistently among potentially suitable wetlands and frequently consisted of small numbers of adults. We occasionally observed small but not alarming numbers of dead adults at breeding sites. In contrast, embryo mortality often was notably high, with the majority of embryos dead in some egg masses while mortality among coincidental Pseudacris regilla (Pacific treefrog) embryos in deeper water was lower. After sampling and experimentation, we concluded that freezing killed A. canorus embryos, especially near the tops of egg masses, which enabled Saprolegnia diclina (a water mold [Oomycota]) to infect and then spread through egg masses and kill more embryos, often in conjunction with predatory flatworms (Turbellaria spp.). We also concluded exposure to ultraviolet-B radiation did not play a role. Based upon our assessments of daily minimum temperatures recorded around snow-off during years before and after our field study, the freezing potential we observed at field sites during embryogenesis might have been commonplace beyond the years of our field study. However, interactions among snow quantity, the timing of snow-off, and coincidental air temperatures that determine such freezing potential make projections of future conditions highly uncertain, despite overall warming trends. Our results describe important effects from ongoing threats to the fitness and abundance of A. canorus via reduced reproduction success and demonstrate how climate conditions can exacerbate effects from pathogens to threaten the persistence of amphibian populations.

Biodiversity loss is a major threat to the integrity of ecosystems and is projected to
worsen, yet the path to successful conservation remains elusive. Decision support
frameworks (DSFs) are increasingly applied by resource managers to navigate the
complexity, uncertainty, and differing socio-ecological objectives inherent to
conservation problems. Most published conservation research that uses DSFs focuses
on analytical stages (e.g., identifying an optimal decision), making it difficult to assess
and learn from previous examples in a conservation practice context. Here, we (1)
evaluate the relationship between the application of decision science and the resulting
conservation outcomes, and (2) identify and address existing barriers to the application
of DSFs to conservation practice. To do this, we develop a framework for evaluating
conservation initiatives using decision science that emphasizes setting attainable
goals, building momentum, and obtaining partner buy-in. We apply this framework to a
systematic review of amphibian conservation decision support projects, including a
follow-up survey of the pertinent conservation practitioners, stakeholders, and
scientists. We found that all projects identified optimal solutions to reach stated
objectives, but positive conservation outcomes were limited when implementation
challenges arose. Further, we identified multiple barriers (e.g., dynamic and
hierarchical leadership, scale complexity, limited resource availability) that can inhibit
the progression from decision identification to action implementation (i.e., ‘decision-implementation gap’), and to successful conservation outcomes. Based on these results, we provide potential actionable steps and avenues for future development of DSFs to facilitate the transition from decision to action and the realization of conservation successes.

Dispersal is a central process in ecology and evolution. It strongly influences the dynamics of spatially structured populations and affects evolutionary processes by shaping patterns of gene flow. For these reasons, dispersal has received considerable attention from ecologists, evolutionary biologists, and conservationists. However, although it has been studied extensively in taxa such as birds and mammals, much less is known about dispersal in vertebrates with complex life cycles such as pond-breeding amphibians. Over the past two decades researchers have taken an ever-increasing interest in amphibian dispersal and initiated both fundamental and applied studies, using a broad range of experimental and observational approaches. This body of research reveals complex dispersal patterns, causations and syndromes, with dramatic consequences for the demography, genetic, and the conservation of amphibian populations. In this review, our goals are to (1) redefine and clarify the concept of amphibian dispersal, (2) review current knowledge about the effects of individual (i.e., condition-dependent dispersal) and environmental (i.e., context-dependent dispersal) factors during the three stages of dispersal (i.e., emigration, immigration, transience), (3) identify the demographic and genetic consequences of dispersal in spatially structured amphibian populations, and (4) propose new research avenues to extend our understanding of amphibian dispersal.

Populations of pond-breeding amphibians often have boom and bust patterns in recruitment, with large numbers of individuals metamorphosing in some years and few or none in other years. Environmental processes, such as pond freezing and drying, and biological factors (e.g., disease and predator community) can influence survival of early life stages and the probability of complete reproductive failure for amphibian populations. We used multi-state occupancy models to estimate probability of breeding and successful metamorphosis (the complements of reproductive failure), and explored environmental and biological factors influencing these processes.We applied both static and dynamic multistate occupancy modeling techniques to ten years (2001-2010) of boreal toad (Anaxyrus boreas boreas) data from 116 sites, and tested relationships between these probabilities and the presence of a pathogen (Batrachochytrium dendrobatidis), elevation, hydrology, relative snowpack in a given year, and the presence of trout (Onchorhyncus spp., Salvelinus fontinalis, and Salmo trutta). The probability of breeding at a site was influenced by elevation, with higher-elevation sites more likely to support breeding. The probability of metamorphosis, given breeding, was influenced by an interaction between hydrology and relative annual snowpack. The probability of metamorphosis was higher at ephemeral sites in years of relatively high snowpack, while at permanent sites, years of low snowpack lead to higher probabilities of metamorphosis. Across all sites, the probability of metamorphosis was high (0.75) for years with median snowpack levels at sites with recent breeding attempts, but lower (0.25) at newly colonized sites. Our results suggest that boreal toads are well-adapted to their current habitat, with both ephemeral and permanent sites likely to support breeding in years of median snowpack. However shifts in precipitation patterns or temperatures may have negative impacts on this species.

ABSTRACT: We conducted a national-scale assessment of mercury (Hg) bioaccumulation in aquatic ecosystems using dragonfly
larvae as biosentinels by developing a citizen-science network to facilitate biological sampling. Implementing a carefully designed
sampling methodology for citizen scientists, we developed an effective framework for a landscape-level inquiry that might otherwise
be resource limited. We assessed the variation in dragonfly Hg concentrations across >450 sites spanning 100 United States National
Park Service units and examined intrinsic and extrinsic factors associated with the variation in Hg concentrations. Mercury
concentrations ranged between 10.4 and 1411 ng/g of dry weight across sites and varied among habitat types. Dragonfly total Hg
(THg) concentrations were up to 1.8-fold higher in lotic habitats than in lentic habitats and 37% higher in waterbodies, with
abundant wetlands along their margins than those without wetlands. Mercury concentrations in dragonflies differed among families
but were correlated (R2 > 0.80) with each other, enabling adjustment to a consistent family to facilitate spatial comparisons among
sampling units. Dragonfly THg concentrations were positively correlated with THg in both fish and amphibians from the same
locations, indicating that dragonfly larvae are effective indicators of Hg bioavailability in aquatic food webs. Collectively, this
continental-scale study demonstrates the utility of dragonfly larvae for estimating the potential mercury risk to fish and wildlife in
aquatic ecosystems and provides a framework for engaging citizen science as a component of landscape Hg monitoring programs.

Background. The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major.
Methods. We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California.
Results. The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic contact between many of these mtDNA lineages and some biogeographic features that are concordant with lineage boundaries. Batrachoseps nigriventris also has multiple deeply differentiated clades within the region. Comparative analyses highlight the smaller spatial scales over which mitochondrial divergence accumulates in Batrachoseps relative to most other salamander species in southern California. The extralimital populations of Batrachoseps from the San Joaquin Valley are assigned to B. major based on their mitochondrial haplotypes and are shown to result from at least two independent introductions from different source populations. We also suggest that B. major on Catalina Island, where it is considered native, may be the result of an introduction. Some of the same traits that facilitate the build-up of deep phylogeographic structure in Batrachoseps likely also contribute to its propensity for introductions, and we anticipate that additional introduced populations will be discovered.

Relatively few North American anurans overwinter in water and information is sparse on their movement from overwintering habitat to breeding sites. Oregon spotted frogs (Rana pretiosa) breed explosively in early spring and often overwinter submerged at sites that are distanced from breeding habitats. In montane parts of their range, wintering and breeding habitats can remain frozen for months. We investigated timing, duration, and potential cues for R. pretiosa migrations from a wintering lake near the Cascade Mountains in central Oregon, U.S.A. First and median migrant males moved slightly earlier than females. Onset of migration was as early as February 12 (males) and as late as April 4 (females) in years of mild and extended winters, respectively. Frogs were active at water temperatures below those associated with early breeding activities in one lowland R. pretiosa population. Higher proportions of frogs migrated before ice-out in years of prolonged winter conditions. Migrations were temporally compressed in years of later movement. This migration ‘rush’, along with the ability to move at cold temperatures and to vary timing of migrations likely helps montane R. pretiosa deal with colder and more variable spring conditions than lowland populations.

Occupancy methods propelled the quantitative study of species distributions forward by separating the observation process, or the imperfect detectability of species, from the ecological processes of interest governing species distributions. Occupancy studies come at a cost, however: the collection of additional data to account for nondetections at sites where the species is present. The most common occupancy designs (repeated measures designs) require repeat visits to sites or the use of multiple observers or detection methods. Time-to-detection methods have been identified as a potentially efficient alternative, requiring only one visit to each site by a single observer. A comparison of time-to-detection methods to repeated measures designs for visual encounter surveys would allow researchers to evaluate whether time-to-detection methods might be appropriate for their study system and can inform optimal survey design. We collected time-to-detection data during two different repeated measures design occupancy surveys for four amphibians and compared the performance of time-to-detection methods to the other designs using the location (potential bias) and precision of posterior distributions for occurrence parameters. We further used results of time-to-detection surveys to optimize survey design. Time-to-detection methods performed best for species that are widespread and have high detection probabilities and rates, but performed less well for cryptic species with lower probability of occurrence or whose detection was strongly affected by survey conditions. In all cases single surveys were most efficient in terms of person-hours expended, but under some conditions the survey duration required to achieve high detection probabilities would be prohibitively long for a single survey. Regardless of occupancy survey design, time-to-detection methods provide important information that can be used to optimize surveys, allowing researchers and resource managers to efficiently achieve monitoring and conservation goals. Collecting time-to-detection data while conducting repeated measures occupancy surveys requires only small modifications to field methods but could have large benefits in terms of time spent surveying in the long-term.