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1. Host density is hypothesized to be a major driver of variability in the responses and outcomes of wildlife populations following pathogen invasion. While the effects of host density on pathogen transmission have been extensively studied, these studies are dominated by theoretical analyses and small-scale experiments. This focus leads to an incomplete picture regarding how host density drives observed variability in disease outcomes in the field. 2. Here, we leveraged a dataset of hundreds of replicate amphibian populations that varied by orders of magnitude in host density. We used these data to test the effects of host density on three outcomes following the arrival of the amphibian-killing fungal pathogen Batrachochytrium dendrobatidis (Bd): the probability that Bd successfully invaded a host population and led to a pathogen outbreak, the magnitude of the host population-level decline following an outbreak and within-host infection dynamics that drive population-level outcomes in amphibian-pathogen systems. 3. Based on previous small-scale transmission experiments, we expected that populations with higher densities would be more likely to experience Bd outbreaks and would suffer larger proportional declines following outbreaks. To test these predictions, we developed and fitted a Hidden Markov Model that accounted for imperfectly observed disease outbreak states in the amphibian populations we surveyed. 4. Contrary to our predictions, we found minimal effects of host density on the probability of successful Bd invasion, the magnitude of population decline following Bd invasion and the dynamics of within-host infection intensity. Environmental conditions, such as summer temperature, winter severity and the presence of pathogen reservoirs, were more predictive of variability in disease outcomes. 5. Our results highlight the limitations of extrapolating findings from small-scale transmission experiments to observed disease trajectories in the field and provide strong evidence that variability in host density does not necessarily drive variability in host population responses following pathogen arrival. In an applied context, we show that feedbacks between host density and disease will not necessarily affect the success of reintroduction efforts in amphibian-Bd systems of conservation concern.

Vast alteration of the biosphere by humans is causing a sixth mass extinction. Adaptation to modified environments often is the only means for species to persist, but the extent to which such “evolutionary rescue” can prevent or reverse biodiversity loss is largely unknown. Us- ing results from genomic analyses, a 15-year reintroduction effort, and population modeling, we provide a compelling example of evolution reversing the declines of an imperiled amphibian and allowing the reestablishment of extirpated populations. The once-common mountain yellow-legged (MYL) frog is threatened with extinction by the human-facilitated emergence of a lethal fungal pathogen (Batrachochytrium dendrobatidis; “Bd”). Although most MYL frog populations are extirpated following disease outbreaks, some persist and eventually begin to recover. Using an exome capture approach, we show that MYL frogs have undergone substantial evolutionary change following disease outbreaks. Moreover, in naturally recovering populations observed changes in immune function loci are associated with increased resis- tance/tolerance to Bd infection. Large-scale reintroduction of frogs from rescued populations resulted in the establishment of reproducing populations despite ongoing disease. In addition, results from viability modeling suggest that established populations have a low prob- ability of extinction over 50 years. Collectively, these results provide a rare example of how evolutionary rescue and the reintroduction of resistant/tolerant individuals can allow the landscape-scale recovery of disease-impacted species. This example has potentially broad implications for the many taxa worldwide that are threatened with extinction by anthropogenic stressors.

1. Invasive alien species are among the most important threats to biodiversity. Plans for their eradication have been implemented worldwide but estimating residual population size and eradication probability to assess removal success is complicated by the imperfect detection of residual individuals. 2. Most methods to assess residual abundance and eradication probability rely on the often unrealistic assumption that a population is closed to mortality and recruitment processes during the implementation of removal actions. We extended existing removal models and developed a novel analytical approach to estimate residual population size and derive eradication probability in open populations, while accounting for multiple removal methods. 3. We apply this approach to 20 eradication projects in Europe and the United States that used mechanical methods to return high mountain lakes to their original fishless condition. 4. The new removal model incorporates i) a mechanistic description of the ecological process underlying survival and recruitment probabilities during the eradication period, and ii) the use of multiple, concomitant removal methods (i.e., electrofishing, gillnetting, fyke-netting) at multiple sites simultaneously. 5. We used a subset of “control” lakes where eradication success was confirmed by more than 5 years of post-removal surveys to validate the model. For these lakes, eradication success, evaluated by whether the 95% Bayesian credible interval for estimated residual population size encompassed values of less than 2 individuals, was confirmed in 13 out of 15 lake-by-species case studies. In addition, the model correctly assigned an eradication probabilities equal to 0 for the eradications that are still in progress. 6. Synthesis and applications. Our study provides insights into the dynamics of fish populations subject to eradication in high mountain lakes of different countries. In addition, the analytical approach proposed accounts for demographic processes and multiple removal methods in multiple sites and seasons. It can represent an informative tool to estimate residual population size and eradication probability of alien species to optimize eradication efforts and efficacy of conservation actions. The extension to open populations makes the approach useful to evaluate long-term eradication plans.

Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.

Significance Batrachochytrium dendrobatidis [Bd] is one of the most devastating wildlife pathogens ever documented. Most surveys for Bd report only the presence/absence of the pathogen. However, Bd has distinct genetic lineages that vary in geographic extent and virulence, thus reporting Bd presence alone is not particularly informative. Our study uses a custom method for genotyping degraded Bd DNA samples, such as those nondestructively collected from live animal or museum specimen skin swabs, and presents the discovery of a divergent lineage of Bd—BdASIA3. This study advances our understanding of the evolutionary origins of Bd, highlights areas of the world where Bd lineages are coming into contact, and opens the door to affordable, rapid genetic monitoring of this pathogen., Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history—and predict the future impacts—of this devastating pathogen.

The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.

The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies against this pathogen. We conducted field antifungal treatment experiments in populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of the treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the two months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than one year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the three-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment of new individuals into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, bathing frogs in a J. lividum solution after Bd load reduction with itraconazole increased concentrations of this bacterium on frogs, but concentrations declined to baseline levels within one month and did not have a protective effect against Bd infection. Collectively, these results suggest that Bd mitigation efforts focused on frog populations that have recently declined due to Bd emergence are ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd and resulting high susceptibility. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.

Capture–recapture studies are widely used in ecology to estimate population sizes and demographic rates. In some capture–recapture studies, individuals may be visually encountered but not identified. For example, if individual identification is only possible upon capture and individuals escape capture, visual encounters can result in failed captures where individual identities are unknown. In such cases, the data consist of capture histories with known individual identities, and counts of failed captures for individuals with unknown identities. These failed captures are ignored in traditional capture–recapture analyses that require known individual identities. Here, we show that if animals can be encountered at most once per sampling occasion, failed captures provide lower bounds on population size that can increase the precision of abundance estimates. Analytical results and simulations indicate that visual encounter data improve abundance estimates when capture probabilities are low, and when there are few repeat surveys. We present a hierarchical Bayesian approach for integrating failed captures and auxiliary encounter data in statistical capture–recapture models. This approach can be integrated with existing capture–recapture models and may prove particularly useful for hard to capture species in data‐limited settings.

The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.

Moving animals on a landscape through translocations and reintroductions is an important management tool used in the recovery of endangered species, particularly for the maintenance of population genetic diversity and structure. Management of imperiled amphibian species rely heavily on translocations and reintroductions, especially for species that have been brought to the brink of extinction by habitat loss, introduced species, and disease. One striking example of amphibian declines and associated management efforts is in California's Sequoia and Kings Canyon National Parks with the mountain yellow-legged frog species complex (Rana sierrae/muscosa). Mountain yellow-legged frogs have been extirpated from more than 93% of their historic range, and limited knowledge of their population genetics has made long-term conservation planning difficult. To address this, we used 598 archived skin swabs from both extant and extirpated populations across 48 lake basins to generate a robust Illumina-based nuclear amplicon data set. We found that samples grouped into three main genetic clusters, concordant with watershed boundaries. We also found evidence for historical gene flow across watershed boundaries with a north-to-south axis of migration. Finally, our results indicate that genetic diversity is not significantly different between populations with different disease histories. Our study offers specific management recommendations for imperiled mountain yellow-legged frogs and, more broadly, provides a population genetic framework for leveraging minimally invasive samples for the conservation of threatened species.

Emerging infectious diseases are a pressing threat to global biological diversity. Increased incidence and severity of novel pathogens underscores the need for methodological advances to understand pathogen emergence and spread. Here, we use genetic epidemiology to test, and challenge, key hypotheses about a devastating zoonotic disease impacting amphibians globally. Using an amplicon-based sequencing method and non-invasive samples we retrospectively explore the history of the fungal pathogen Batrachochytrium dendrobatidis ( Bd ) in two emblematic amphibian systems: the Sierra Nevada of California and Central Panama. The hypothesis in both regions is the hypervirulent Global Panzootic Lineage of Bd ( Bd GPL) was recently introduced and spread rapidly in a wave-like pattern. Our data challenge this hypothesis by demonstrating similar epizootic signatures can have radically different underlying evolutionary histories. In Central Panama, our genetic data confirm a recent and rapid pathogen spread. However, Bd GPL in the Sierra Nevada has remarkable spatial structuring, high genetic diversity and a relatively older history inferred from time-dated phylogenies. Thus, this deadly pathogen lineage may have a longer history in some regions than assumed, providing insights into its origin and spread. Overall, our results highlight the importance of integrating observed wildlife die-offs with genetic data to more accurately reconstruct pathogen outbreaks.

The mountain yellow-legged species complex (Rana sierrae and Rana muscosa) has declined precipitously in distribution and abundance during the last century. The two primary threats are chytrid epidemic-associated population collapses and predation from the introduction of non-native trout. Widespread declines have occurred throughout the ranges of these species, including populations of R. sierrae in Yosemite National Park. A clear picture of genetic structure of remaining Yosemite R. sierrae populations is critical to short-term management and conservation. We conducted a population genetics study that included samples from 23 geographic sites distributed throughout the range of R. sierrae in Yosemite NP. We used minimally-invasive swab samples to collect genetic data from mitochondrial and nuclear DNA via sequencing (43 transcriptome-derived markers) and analyzed the distribution of genetic variation in a geographic context. Our mtDNA analysis partially confirmed previous results suggesting that two haplotype groups occur in Yosemite: one haplotype group contained high bootstrap support for monophyly while the other did not. However, increased geographic sampling demonstrated that the two haplotypes are not completely geographically partitioned into the two main drainages (Merced drainage and Tuolumne drainage) as previously postulated. Our nuclear DNA analysis revealed a general pattern of genetic isolation by distance, where genetic differentiation was correlated with geographic distance between sites. In addition, our analyses suggested that three clusters of genetically cohesive sites occur in the study area. Understanding population genetic patterns of variability will inform management strategies such as translocations, reintroductions, and monitoring for this endangered frog. Lastly, our next generation sequencing enabled approach allowed us to obtain multi-locus data from minimally-invasive swab samples. Thus researchers can now leverage extensive archives of swab samples (initially collected for pathogen testing) to study host genetics in previously surveyed amphibian populations.

Lakes are connected to surrounding terrestrial habitats by reciprocal flows of energy and nutrients. We synthesize data from California’s mountain lake catchments to investigate how these reciprocal subsidies change along an elevational gradient and with the introduction of a top aquatic predator. At lower elevations, well-developed terrestrial vegetation provides relatively large inputs of organic material to lakes, whereas at higher elevations, the paucity of terrestrial vegetation provides minimal organic input but allows for higher inputs of inorganic nitrogen. There are also pronounced elevational patterns in amphibians and aquatic insects, which represent important vectors for resource flows from lakes back to land. The introduction of trout can reduce this lake-to-land resource transfer, as trout consume amphibians and aquatic insects. We propose a conceptual model in which within-lake processes influence terrestrial consumers at higher elevations, while terrestrial inputs govern within-lake processes at lower elevations. This model contributes to a more general understanding of the connections between aquatic and terrestrial habitats in complex landscapes.

The global emergence of Batrachochytrium dendrobatidis (Bd) has caused the extinction of hundreds of amphibian species worldwide. It has become increasingly important to be able to precisely predict time to Bd arrival in a population. The data analyzed herein present a unique challenge in terms of modeling because there is a strong spatial component to Bd arrival time and the traditional proportional hazards assumption is grossly violated. To address these concerns, we develop a novel marginal Bayesian nonparametric survival model for spatially correlated right-censored data. This class of models assumes that the logarithm of survival times marginally follow a mixture of normal densities with a linear-dependent Dirichlet process prior as the random mixing measure, and their joint distribution is induced by a Gaussian copula model with a spatial correlation structure. To invert high-dimensional spatial correlation matrices, we adopt a full-scale approximation that can capture both large- and small-scale spatial dependence. An efficient Markov chain Monte Carlo algorithm with delayed rejection is proposed for posterior computation, and an R package spBayesSurv is provided to fit the model. This approach is first evaluated through simulations, then applied to threatened frog populations in Sequoia-Kings Canyon National Park.

In California, River Otters (Lontra canadensis) are most commonly associated with food-rich lowland aquatic habitats where they forage primarily on fish and crustaceans. Their distribution in high-elevation montane regions of the state, areas in which fish and crayfish were absent historically, is largely unknown. We compiled occurrence records of River Otters in California from elevations >1100 m, and evaluated them using evidentiary standards. Based on 126 records, we report the widespread presence of River Otters in the Klamath, southern Cascades, and Sierra Nevada mountain ranges, including at elevations exceeding 3000 m. Sixty-three percent of the records met our definition as “verified”, and the remaining 37% were considered “unverified”. The distribution of observations through time and habitats in which observations were made were similar between verified and unverified records. River Otter records spanned the period from 1900 to 2010, with 50% occurring between 1991 and 2010. Ninety-three percent of the water bodies with records of River Otters contained nonnative prey (fish and crayfish). Those lacking nonnative prey all supported native prey, including amphibians and reptiles. Based on records that contained River Otter foraging observations, nonnative fishes and crayfish were represented in 89% of the total accounts, and native frogs and invertebrates were represented in 22%. It remains unclear whether River Otters occurred in California's high-elevation water bodies prior to the introduction of fish and crayfish, and additional research is needed to understand the possible influence of nonnative prey in allowing River Otters to expand their distribution in these habitats.

Amphibians are one of the most threatened animal groups, with 32% of species at risk for extinction. Given this imperiled status, is the disappearance of a large fraction of the Earth’s amphibians inevitable, or are some declining species more resilient than is generally assumed? We address this question in a species that is emblematic of many declining amphibians, the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Based on >7,000 frog surveys conducted across Yosemite National Park over a 20-y period, we show that, after decades of decline and despite ongoing exposure to multiple stressors, including introduced fish, the recently emerged disease chytridiomycosis, and pesticides, R. sierrae abundance increased sevenfold during the study and at a rate of 11% per year. These increases occurred in hundreds of populations throughout Yosemite, providing a rare example of amphibian recovery at an ecologically relevant spatial scale. Results from a laboratory experiment indicate that these increases may be in part because of reduced frog susceptibility to chytridiomycosis. The disappearance of nonnative fish from numerous water bodies after cessation of stocking also contributed to the recovery. The large-scale increases in R. sierrae abundance that we document suggest that, when habitats are relatively intact and stressors are reduced in their importance by active management or species’ adaptive responses, declines of some amphibians may be partially reversible, at least at a regional scale. Other studies conducted over similarly large temporal and spatial scales are critically needed to provide insight and generality about the reversibility of amphibian declines at a global scale.

While disease-induced extinction is generally considered rare, a number of recently emerging infectious diseases with load-dependent pathology have led to extinction in wildlife populations. Transmission is a critical factor affecting disease-induced extinction, but the relative importance of transmission compared to load-dependent host resistance and tolerance is currently unknown. Using a combination of models and experiments on an amphibian species suffering extirpations from the fungal pathogen Batrachochytrium dendrobatidis (Bd), we show that while transmission from an environmental Bd reservoir increased the ability of Bd to invade an amphibian population and the extinction risk of that population, Bd-induced extinction dynamics were far more sensitive to host resistance and tolerance than to Bd transmission. We demonstrate that this is a general result for load-dependent pathogens, where non-linear resistance and tolerance functions can interact such that small changes in these functions lead to drastic changes in extinction dynamics.

Dramatic changes in environmental conditions or community composition may impose severe selective pressures on resident populations. These changes in the selective regime can lead to demographic bottlenecks or local extinction. The consequence of demographic contraction is often a reduction of standing genetic variation. Since the level of adaptive genetic variation in populations plays an important role in persistence and adaptive response, understanding genetic resilience and the time course for re-establishment of genetic diversity following demographic perturbations is a critical component of assessing the consequences of changing environments. The introduction of nonnative fish into historically fishless lakes is a particularly dramatic environmental change frequently contributing to demographic bottlenecks and local extinction of native populations. We examine the quantitative- and molecular-genetic recovery of two alpine populations of the zooplankton Daphnia melanica from the Sierra Nevada, California, USA. These populations were extirpated by introduced salmonids and subsequently re-established following the experimental removal of nonnative fish. We obtained data for nuclear and mitochondrial markers and conducted a common-garden experiment to assess the levels of molecular- and quantitative-genetic variation following experimental fish removal. Reestablished D. melanica populations attained levels of nuclear genetic diversity only slightly lower than surrounding fishless populations in the first year following fish removal and substantial mitochondrial and quantitative-genetic diversity within 8 years. This high level of genetic resilience was likely facilitated by multiple sources of genetic variation, including immigration from neighboring populations and hatching from a local reservoir of diapausing eggs. Our results highlight the genetic resilience of taxa with reservoirs of genetic variation in seed or egg banks.

The introduction of fishes into naturally fishless mountain lakes often results in the extirpation of large-bodied zooplankton species. The ability to predict whether or not particular species will recover following fish removal is critically important for the design and implementation of lake restoration efforts but is currently not possible because of a lack of information on what factors affect recovery. The objective of this study was to identify the factors influencing recovery probability in two large-bodied zooplankton species following fish removal. We predicted that (1) Daphnia melanica would have a higher probability of recovery than Hesperodiaptomus shoshone due to differences in reproductive mode (D. melanica is parthenogenetic, H. shoshone is obligately sexual), (2) recovery probability would be a decreasing function of fish residence time due to the negative relationship between fish residence time and size of the egg bank, and (3) recovery probability would be an increasing function of lake depth as a consequence of a positive relationship between lake depth and egg bank size. To test these predictions, we sampled contemporary zooplankton populations and collected paleolimnological data from 44 naturally fishless lakes that were stocked with trout for varying lengths of time before reverting to a fishless condition. D. melanica had a significantly higher probability of recovery than did H. shoshone (0.82 vs. 0.54, respectively). The probability of recovery for H. shoshone was also significantly influenced by lake depth, fish residence time, and elevation, but only elevation influenced the probability of recovery in D. melanica. These results are consistent with between-species differences in reproductive mode combined with the much greater longevity of diapausing eggs in D. melanica than in H. shoshone. Our data also suggest that H. shoshone will often fail to recover in lakes with fish residence times exceeding 50 years.

Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geography, local frog extirpation by a single fungal genotype, and evidence of human-assisted fungus migration. In support of endemism, at a local scale, we find some diverse, recombining populations. Therefore neither epidemic spread nor endemism alone explains this particular amphibian decline. Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen.

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

The mountain yellow-legged frog (Rana muscosa) was once a common inhabitant of the Sierra Nevada (California, USA), but has declined precipitously during the past century due in part to the introduction of nonnative fish into naturally fishless habitats. The objectives of the current study were to describe (1) the effect of fish removal from three lakes (located in two watersheds) on the small, remnant R. muscosa populations inhabiting those lakes, and (2) the initial development of metapopulation structure in each watershed as R. muscosa from expanding populations in fish-removal lakes dispersed to adjacent habitats. At all three fish-removal lakes, R. muscosa population densities increased significantly following the removal of predatory fish. The magnitude of these increases was significantly greater than that observed over the same time period in R. muscosa populations inhabiting control lakes that remained in their natural fishless condition. Following these population increases, R. muscosa dispersed to adjacent suitable (but unoccupied) sites, moving between 200 and 900 m along streams or across dry land. Together, these results suggest that large-scale removal of introduced fish could result in at least partial reversal of the decline of R. muscosa. Continued monitoring of R. muscosa at the fish-removal sites will be necessary to determine whether the positive effects of fish eradication are sustained over the long-term, especially in light of the increasingly important role played by an emerging infectious disease (chytridiomycosis, caused by Batrachochytrium dendrobatidis) in influencing R. muscosa populations.

Statistical models often use observational data to predict phenomena; however, interpreting model terms to understand their influence can be problematic. This issue poses a challenge in species conservation where setting priorities requires estimating influences of potential stressors using observational data. We present a novel approach for inferring influence of a rare stressor on a rare species by blending predictive models with nonparametric permutation tests. We illustrate the approach with two case studies involving rare amphibians in Yosemite National Park, USA. The endangered frog, Rana sierrae, is known to be negatively impacted by non-native fish, while the threatened toad, Anaxyrus canorus, is potentially affected by packstock. Both stressors and amphibians are rare, occurring in ~10% of potential habitat patches. We first predict amphibian occupancy with a statistical model that includes all predictors but the stressor to stratify potential habitat by predicted suitability. A stratified permutation test then evaluates the association between stressor and amphibian, all else equal. Our approach confirms the known negative relationship between fish and R. sierrae, but finds no evidence of a negative relationship between current packstock use and A. canorus breeding. Our statistical approach has potential broad application for deriving understanding (not just prediction) from observational data.

Chytridiomycosis is an emerging infectious disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis, and its role in causing population declines and species extinctions worldwide has created an urgent need for methods to detect it. Several reports indicate that in anurans chytridiomycosis can cause the depigmentation of tadpole mouthparts, but the accuracy of using depigmentation to determine disease status remains uncertain. Our objective was to determine for the Mountain Yellow-legged Frog (Rana muscosa) whether visual inspections of the extent of tadpole mouthpart depigmentation could be used to accurately categorize individual tadpoles or R. muscosa populations as B. dendrobatidis-positive or negative. This was accomplished by assessing the degree of mouthpart depigmentation in tadpoles of known disease status (based on PCR assays). The depigmentation of R. muscosa tadpole mouthparts was associated with the presence of B. dendrobatidis, and this association was particularly strong for upper jaw sheaths. Using a rule that classifies tadpoles with upper jaw sheaths that are 100% pigmented as uninfected and those with jaw sheaths that are

Chytridiomycosis is an emerging infectious disease that has recently been reported in amphibian populations throughout the world. It has been associated with many cases of population declines and extinctions. In some areas of the Sierra Nevada of Cali- fornia the disease appears to be the causal factor in the rapid extinction of local populations of the mountain yellow-legged frog, Rana muscosa, within a few years of the first detection of the disease. In other areas, however, R. muscosa populations appear to persist for many years, despite high levels of infection in tadpoles. Here we present simple models of the dynamics of the disease within an individual lake and ask whether our current understanding of the disease is consistent with the field survey observations of: (a) extinction due to the disease over a wide range of host population sizes, and (b) persistence of frog populations with the disease at some sites. Despite our laboratory observation of chytridiomycosis being invariably lethal to postmetamorphic frogs, the observed long-term persistence of infected frog populations can only be explained if at least some infected adult frogs survive and reproduce.

In a multilake experiment, we found little effect of nutrient excretion by zooplanktivorous fish, but a large effect of herbivorous zooplankton, on phytoplankton biomass and phosphorus (P) limitation. Whole-lake removal of fish from small alpine lakes resulted in little change in phytoplankton biomass or the intensity of P limitation during 1‐6 postremoval years, over which herbivorous zooplankton did not change. In contrast, significant decreases in phytoplankton biomass and the intensity of phytoplankton P limitation were observed after Daphnia became reestablished. Fish removal also caused large increases in the biomass of benthic macroinvertebrates, but the timing of these increases suggested that P recycling by the benthos did not confound our attempt to measure the effects of P recycling by fish. Estimates of the amount of P recycled by fish and zooplankton and estimates of P demand by the phytoplankton also supported the conclusion that fish recycling was not a major source of P to the phytoplankton in these lakes. Relative to Daphnia grazing, fish recycling of P appears to be relatively unimportant as a driver of trophic cascades in these alpine lakes.

Ultraviolet-B radiation (UV-B, 280–320-nm wavelengths) doses were estimated for 1024 wetlands in six national parks: Acadia (Acadia), Glacier (Glacier), Great Smoky Mountains (Smoky), Olympic (Olympic), Rocky Mountain (Rocky), and Sequoia/ Kings Canyon (Sequoia). Estimates were made using ground-based UV-B data (Brewer spectrophotometers), solar radiation models, GIS tools, field characterization of vegetative features, and quantification of DOC concentration and spectral absorbance. UV-B dose estimates were made for the summer solstice, at a depth of 1 cm in each wetland. The mean dose across all wetlands and parks was 19.3 W-h m )2 (range of 3.4–32.1 W-h m )2 ). The mean dose was lowest in Acadia (13.7 W-h m )2 ) and highest in Rocky (24.4 W-h m )2 ). Doses were significantly different among all parks. These wetland doses correspond to UV-B flux of 125.0 lW cm )2 (range 21.4–194.7 l Wc m )2 ) based on a day length, averaged among all parks, of 15.5 h. Dissolved organic carbon (DOC), a key determinant of water-column UV-B flux, ranged from 0.6 (analytical detection limit) to 36.7 mg C L )1 over all wetlands and parks, and reduced potential maximal UV-B doses at 1-cm depth by 1%–87 %. DOC concentration, as well as its effect on dose, was lowest in Sequoia and highest in Acadia (DOC was equivalent in Acadia, Glacier, and Rocky). Landscape reduction of potential maximal UV-B doses ranged from zero to 77% and was lowest in Sequoia. These regional differences in UV-B wetland dose illustrate the importance of considering all aspects of exposure in evaluating the potential impact of UV-B on aquatic organisms.

The amount, chemical composition, and source of dissolved organic carbon (DOC), together with in situ ultraviolet (UV-B) attenuation, were measured at 1–2 week intervals throughout the summers of 1999, 2000, and 2001 at four sites in Rocky Mountain National Park (Colorado). Eight additional sites, four in Sequoia and Kings Canyon National Park/John Muir Wilderness (California) and four in Glacier National Park (Montana), were sampled during the summer of 2000. Attenuation of UV-B was significantly related to DOC concentrations over the three years in Rocky Mountain (R2 = 0.39, F = 25.71, P < 0.0001) and across all parks in 2000 (R2 = 0.44, F = 38.25, P < 0.0001). The relatively low R2 values, however, reflect significant temporal and spatial variability in the specific attenuation per unit DOC. Fluorescence analysis of the fulvic acid DOC fraction (roughly 600–2,000 Daltons) indicated that the source of DOC significantly affected the attenuation of UV-B. Sites in Sequoia–Kings Canyon were characterized by DOC derived primarily from algal sources and showed much deeper UV-B penetration, whereas sites in Glacier and Rocky Mountain contained a mix of algal and terrestrial DOC-dominated sites, with more terrestrially dominated sites characterized by greater UV-B attenuation per unit DOC. In general, site characteristics that promoted the accumulation of terrestrially derived DOC showed greater attenuation of UV-B per unit DOC; however, catchment vegetation and soil characteristics, precipitation, and local hydrology interacted to make it difficult to predict potential exposure from DOC concentrations.

An increase in ultraviolet-B (UV-B) radiation has been posited to be a potential factor in the decline of some amphibian population. This hypothesis has received support from laboratory and field experiments showing that current levels of UV-B can cause embryo mortality in some species, but little research has addressed whether UV-B is influencing the distribution of amphibian populations. We compared patterns of amphibian presence to sitespecific estimates of UV-B dose at 683 ponds and lakes in Glacier, Olympic, and Sequoia‐Kings Canyon National Parks. All three parks are located in western North America, a region with a concentration of documented amphibian declines. Sitespecific daily UV-B dose was estimated using modeled and field-collected data to incorporate the effects of elevation, landscape, and water-column dissolved organic carbon. Of the eight species we examined (Ambystoma gracile, Ambystoma macrodactylum, Bufo boreas, Pseudacris regilla, Rana cascadae, Rana leuteiventris, Rana muscosa, Taricha granulosa), two species (T. granulosa and A. macrodactylum) had quadratic relationships with UV-B that could have resulted from negative UV-B effects. Both species were most likely to occur at moderate UV-B levels. Ambystoma macrodactylum showed this pattern only in Glacier National Park. Occurrence of A. macrodactylum increased as UV-B increased in Olympic National Park despite UV-B levels similar to those recorded in Glacier. We also found marginal support for a negative association with UV-B for P. regilla in one of the two parks where it occurred. We did not find evidence of a negative UV-B effect for any other species. Much more work is still needed to determine whether UV-B, either alone or in concert with other factors, is causing widespread population losses in amphibians.

The ratio of the number of taxa observed at a site to that expected to occur in the absence of anthropogenic impacts (O/E) is an ecologically meaningful measure of the degree of faunal alteration. We used O/E ratios to describe the response by amphibian, reptile, benthic macroinvertebrate, and zooplankton taxa in originally fishless lakes in Yosemite National Park to the introduction and subsequent disappearance of nonnative fish. To quantify resistance (the degree to which a system is altered when the environment changes) and resilience (the degree to which a system returns to its previous configuration once the perturbation is removed), we compared O/E ratios between lakes that were never stocked, were previously stocked and still contained fish, or were previously stocked but had reverted to a fishless condition. On average, stocked-fish-present sites had 16% fewer taxa than never-stocked sites (O/E = 0.84 vs. 1.00, respectively). This statistically significant difference in O/E ratios indicates that n...

Nonnative fishes have been introduced into naturally fishless mountain lakes worldwide, often with negative consequences for native fauna. In this study, I used data collected during a census of native herpetofauna, nonnative trout, and habitat characteristics at all lentic water bodies in Yosemite National Park (n=2655) to quantify the effect of trout introductions and habitat on the distribution of four amphibian species and two reptile species. Impacts of trout on amphibians and reptiles were characterized using generalized additive models that included as predictor variables fish presence/absence, amphibian presence/absence (only in models for the two reptile species), elevation, water depth, littoral zone and shoreline substrate composition, relative survey date, and location. All species showed significant associations with habitat characteristics, and elevation and water depth appeared particularly important in influencing distributions. In addition, distributions of the mountain yellow-legged frog (Rana muscosa) and Pacific treefrog (Hyla regilla) were strongly negatively associated with the presence of nonnative trout while those of the Yosemite toad (Bufo canorus) and Sierra newt (Taricha torosa sierrae) were unrelated to trout presence. The distribution of the mountain garter snake (Thamnophis elegans elegans) was strongly negatively associated with the presence of nonnative trout and positively associated with the presence of native amphibians. Regression results for the Sierra garter snake (Thamnophis couchi couchi) were similar except that the direct effect of nonnative trout was considerably weaker. Together, these results indicate that trout introductions have resulted in considerable alteration of Yosemite's herpetofauna. Long-term studies will be necessary to determine whether removal of nonnative trout populations, where possible, would allow these impacts to be partially reversed.

Trout are often stocked into alpine lakes based on the generally untested assumption that resident populations would go extinct without stocking. The objectives of our study were to estimate the proportion of currently or formerly stocked alpine lakes in the Sierra Nevada, California, containing naturally reproducing trout populations (Oncorhynchus mykiss, Oncorhynchus mykiss aguabonita, Oncorhynchus clarki henshawi), identify characteristics of lakes associated with successful reproduction, and quantify the effects of stocking termination on trout density and individual growth rates in reproducing populations. We surveyed trout populations in 95 lakes in the John Muir Wilderness before and after a 4- to 8-year stocking halt and in 84 lakes in Sequoia–Kings Canyon National Park after a ≥20-year stocking hiatus. Based on recruitment during the no-stocking period, 70% and 68% of study lakes in the John Muir Wilderness and Sequoia-Kings Canyon National Park, respectively, contained reproducing populations. Results indicated that lakes with >2.1 m2 of spawning habitat and at elevations

The Allee effect, operating via mate limitation, theoretically reduces the probability of recovery from local extinction of dioecious zooplankton relative to species that can reproduce asexually. We removed fish from four alpine lakes in the Sierra Nevada in which both Hesperodiaptomus shoshone(a calanoid copepod) and Daphnia middendorffianawere historically present but had become locally extinct after fish stocking. After complete fish removal, D. middendorffianareturned to all four lakes, whereas H. shoshone failed to return in any of the lakes, despite diapausing eggs observed in the sediments of two lakes and a few individuals in the water column of one lake during the first summer after fish removal. We estimated the potential magnitude of the Allee effect, as it may have affected the recovery of H. shoshone, by comparing estimates of minimum founding population size of H. shoshone with estimates of actual founding population sizes of D. middendorffiana.It took 4 yr for D. middendorffianato recover to detectable levels in one of the four lakes, which we suggest was the result of a very small founding population. The latter was three to four orders of magnitude smaller than the minimum founding population size we calculated for H. shoshone, indicating the potential for a large effect of mate limitation on the copepod’s ability to recover. H. shoshone might never return to these lakes without human intervention because of the combined effects of mate limitation and low rates of overland dispersal.

Human-caused fragmentation of habitats is threatening an increasing number of animal and plant species, making an understanding of the factors influencing patch occupancy ever more important. The overall goal of the current study was to develop probabilistic models of patch occupancy for the mountain yellow-legged frog (Rana mus- cosa). This once-common species has declined dramatically, at least in part as a result of habitat fragmentation resulting from the introduction of predatory fish. We first describe a model of frog patch occupancy developed using semiparametric logistic regression that is based on habitat characteristics, fish presence/absence, and a spatial location term (the latter to account for spatial autocorrelation in the data). This model had several limitations in- cluding being constrained in its use to only the study area. We therefore developed a more general model that incorporated spatial autocorrelation through the use of an autocovariate term that describes the degree of isolation from neighboring frog populations (autologistic model). After accounting for spatial autocorrelation in patch occupancy, both models in- dicated that the probability of frog presence was strongly influenced by lake depth, elevation, fish presence/absence, substrate characteristics, and the degree of lake isolation. Based on cross-validation procedures, both models provided good fits to the data, but the autologistic model was more useful in predicting patch occupancy by frogs. We conclude by describing a possible application of this model in assessing the likelihood of persistence by frog

Infectious diseases have serious impacts on human and wildlife populations, but the effects of a disease can vary, even among individuals or populations of the same host species. Identifying the reasons for this variation is key to understanding disease dynamics and mitigating infectious disease impacts, but disentangling cause and correlation during natural outbreaks is extremely challenging. This study aims to understand associations between symbiotic bacterial communities and an infectious disease, and examines multiple host populations before or after pathogen invasion to infer likely causal links. The results show that symbiotic bacteria are linked to fundamentally different outcomes of pathogen infection: host–pathogen coexistence (endemic infection) or host population extirpation (epidemic infection). Diversity and composition of skin-associated bacteria differed between populations of the frog, Rana sierrae , that coexist with or were extirpated by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Data from multiple populations sampled before or after pathogen invasion were used to infer cause and effect in the relationship between the fungal pathogen and symbiotic bacteria. Among host populations, variation in the composition of the skin microbiome was most strongly predicted by pathogen infection severity, even in analyses where the outcome of infection did not vary. This result suggests that pathogen infection shapes variation in the skin microbiome across host populations that coexist with or are driven to extirpation by the pathogen. By contrast, microbiome richness was largely unaffected by pathogen infection intensity, but was strongly predicted by geographical region of the host population, indicating the importance of environmental or host genetic factors in shaping microbiome richness. Thus, while both richness and composition of the microbiome differed between endemic and epidemic host populations, the underlying causes are most likely different: pathogen infection appears to shape microbiome composition, while microbiome richness was less sensitive to pathogen-induced disturbance. Because higher richness was correlated with host persistence in the presence of Bd, and richness appeared relatively stable to Bd infection, microbiome richness may contribute to disease resistance, although the latter remains to be directly tested.

We used analyses based on surveys of > 1700 water bodies in a 100,000-ha area in the John Muir Wilderness (JMW) and Kings Canyon National Park (KCNP) to determine the influence of nonnative trout on the distribution and abundance of Hyla regilla in the High Sierra Nevada. At the landscape scale (JMW compared to KCNP), a negative relationship between trout and frogs in lakes was evident. In the JMW study area where trout are more abundant, only 7.2% of all water bodies contained H. regilla versus 26.6% in the KCNP study area. Also, the percentage of the total water body surface area containing H. regilla was 19.4 times higher in the KCNP study area than in the JMW study area. Hyla regilla were most abundant in portions of KCNP where the probability of finding lakes with trout is lowest and least abundant in the northern part of the JMW where the probability of finding lakes with trout is highest. At the water body scale, after accounting for the effects of all significant habitat and isolation var...

Because they have the potential to provide the best remaining standards of relatively unmodified landscapes, protected areas in North America (such as wilderness areas and national parks) have tremendous ecological and scientific value (Cole and Landres 1996). Although the montane ecosystems of western North America are particularly well represented in this complex of protected lands, aquatic habitats within these protected areas are often subject to management practices that are inconsistent with the goal of maintaining natural processes. The most prevalent of these practices is the introduction of salmonid fishes (such as trout) into historically fishless ecosystems to create recreational fisheries. These montane landscapes are the result of repeated glaciation during the Pleistocene epoch. The recession of glaciers 10,000 years ago created thousands of lakes, most of which were separated from downstream fish populations by impassible barriers on rivers and streams. These extensive fishless habitats were subsequently colonized by a diversity of aquatic species, many of which required fishless habitats for their persistence. Starting in the mid1800s, Euro-American settlers began introducing salmonid fishes into these lakes and streams. By the mid-1900s, these fish-stocking efforts had been largely subsumed by the various agencies responsible for the management of fish and wildlife. Trout stocking was halted in most national parks in western North America during the 1970s and 1980s (Knapp 1996; Parker and others 2001), but the practice continues in other protected areas, such as wilderness areas in the western United States managed by the US Forest Service (Landres and others 2001). These stocking programs have dramatically transformed the formerly fishless aquatic ecosystems within protected areas of western North America. For example, of the estimated 16,000 naturally fishless mountain lakes in the western US, the majority of which are located within national parks and wilderness areas, 60% of all lakes and 95% of larger, deeper lakes now contain nonnative trout (Oncorhynchus spp., Salmo spp., Salvelinus spp.) (Bahls 1992). Many of these introduced fish populations persisted even after the termination of stocking (Donald 1987; Boiano 1999). In the western US, trout are still stocked into more than 7000 mountain lakes on a regular basis, usually with the use of aircraft (Bahls 1992). The purpose of this ongoing stocking is generally not to introduce trout into the remaining fishless lakes, but instead to supplement nonnative trout populations maintained by natural reproduction or to maintain nonnative trout popuReceived 28 March 2000;: accepted 12 April 2000. *Corresponding author; e-mail: knapp@lifesci.ucsb.edu

The introduction of salmonid fishes into naturally fishless lakes represents one of the most prevalent environmental modifications of aquatic ecosystems in western North America. Introduced fish may alter lake nutrient cycles and primary production, but the magnitude and variation of these effects have not been fully explored. We used bioenergetics modeling to estimate the contributions of stocked trout to phosphorus (P) cycles across a wide range of fish densities in lakes of the Sierra Nevada, California. We also assessed the larger effects of fish-induced changes in phosphorus cycling on primary production using paleolimnological analyses from lakes in the southern Canadian Rockies. Our analyses showed that total P recycling by fish was independent of fish density but positively related to fish biomass in the Sierra Nevada. In lakes with fish populations maintained by continued stocking, fish recycled P at over twice the rate of those in lakes where introduced fish populations are maintained by natural reproduction and stocking has been discontinued. We estimate that P regeneration by introduced fishes is approximately equivalent to atmospheric P deposition to these lakes. Paleolimnological analyses indicated that algal production increased substantially following trout introductions to Rocky Mountain lakes and was maintained for the duration of fish presence. The results of our modeling and paleolimnological analyses indicate that introduced trout fundamentally alter nutrient cycles and stimulate primary production by accessing benthic P sources that are not normally available to pelagic communities in oligotrophic mountain lakes. These effects pose a difficult challenge for managers charged with balancing the demand for recreational fisheries with the need to maintain natural ecosystem processes.

Copepods (Class Crustacea, Order Copepoda) are rarely included in paleoecological studies of lakes because they lack long-lasting exoskeletal remains. We describe the remains of eggs (egg shells) from Hesperodiaptomus copepods that are well preserved and abundant in alpine lake sediments. We demonstrate that the egg shells are the remains of Hesperodiaptomus eggs based on (i) the similar size and morphology of egg shells collected from sediments and those produced from the hatching of eggs obtained from laboratory-maintained Hesperodiaptomus, and (ii) the finding that diapausing eggs collected from lake sediments and hatched in the laboratory produced copepod nauplii that were morphologically indistinguishable from those hatched from eggs produced by laboratory-maintained Hesperodiaptomus. Egg shells were approximately two orders of magnitude more abundant in sediment cores than were viable diapausing eggs, making egg shells superior to viable diapausing eggs for quantifying the historical presence and abundance of Hesperodiaptomus. These results have important implications for alpine lake restoration as egg shells can be used to identify lakes in which Hesperodiaptomus was eliminated by fish introductions but has failed to return after fish eradication, lakes in which the pre-disturbance conditions are likely to be restored only by reintroductions of this important taxon.

One of the most puzzling aspects of the worldwide decline of amphibians is their disappearance from within protected areas. Because these areas are ostensib ly undisturbed, habitat alterations are generally perceived as unlikely causes. The introduction of non-native fishes into protected areas,however, is a common practice throughout the world and may exert an important influence on amphibian distributions. We quantified the role of introduced fishes (several species of trout) in the decline of the mountain yello w-legged-frog (Rana muscosa) in California's Sier ra Nevada through surveys of >1700 sites in two adjacent and historically fishless protected areas that dif fered primarily in the distribution of introduced fish. Negat ive effects of fishes on the distri bution of frogs we re evident at three spatial scales. At the l a n d s c ape scale, c o m p a risons between The two protected areas indicated that fish distri bution was stro n g ly n egat ive ly corre l at e d with the distribution of frogs. At the watershed scale, the percentage of total water-body surface area occupied by fishes was a highly significant predictor of the percenta ge of total water-body surface area occupied by fr ogs. At the scale (if individual water bodies, frogs were three times more likely to be found and six times more abundant in fishless than in fish-containing water bodies, after habitat effects were accounted for. The strong effect of introduced fishes on mountain yello w-legged frogs appears to result from the unique life history of this amphibian whic h frequently restricts larvae to deeper water bodies, the same habitats into which fishes have most frequently been introduced. Because fish populations in at least some Sierra Ne vada lakes can be remo ved with minimal effort, our results suggest that the decline of the mountain yellow-legged frog might be relatively easy to reverse.

It is widely believed that stream salmonids select spawning sites based on water depth, water velocity, and substrate size. Attempts to predict spawning locations using these habitat features have met with little success, however. In this study, we used nonparametric logistic regression to determine what habitat features were associated with the locations chosen by spawning California golden trout (Oncorhynchus mykiss aguabonita). From this nonparametric model, we developed a parametric model that incorporated the habitat features most strongly associated with spawning sites and used this model to calculate the probability of use by spawning golden trout for specific stream locations. The overall nonparametric model was highly significant and explained 62% of the variation in spawning location. Four of the eight habitat variables, substrate size, water depth, water velocity, and stream width, had highly significant effects and alone explained 59% of the variation in spawning location. The results of a cross-validation procedure indicated that the parametric model generally provided a good fit to the data. These results indicate that location-specific probabilities of use were predictable based on easily measured habitat characteristics and that nonparametric regression, an approach still rarely used in ecological studies, may have considerable utility in the development of fish-habitat models. Given the escalating pace at which fish habitats are being altered, such models are increasingly important in predicting the effects of these alterations on populations.

Nearly all mountain lakes in the western United States were historically fishless, but most now contain introduced trout populations. As a result of the impacts of these introductions on ecosystem structure and func tion, there is increasing interest in restoring some lakes to a fishless condition. To date, however, the only effective method of fish eradication is the application of rotenone, a pesticide that is also toxic to nontar get native species. The objective of this study was to assess the effectiveness of intensi ve gill netting in eradicating the trout population from a small subalpine lake in the Sierra Ne vada, California. We remo ved the resident trout population and a second trout population acci dentally stocked into the study lake within 18 and 15 gill net sets, respectively. Adult trout were highly vulnerable to gill nets, but younger fish were not readily captured until they reached approximately 110 mm. To determine the utility of gill netting as a fish eradication technique in other Sierra Nevada lakes, we used morphometry data from 330 Sier ra Nevada lakes to determine what proportion had characteristics similar to the study lake (i.e., small, isolated lakes with little s p awning hab i t at). We estimated that gill netting would be a viable eradication method in 15-20% of the high mountain lakes in the Sierra Nevada. We conclude that although gill netting is likely to be more expensi ve and time consuming than rotenone application, it is a viable alternati ve under some conditions and should

Impacts of livestock grazing on California golden trout Oncorhynchus mvkiss aguabonita and their habitat were studied inside and outside of livestock exclosures in the Golden Trout Wilderness, California. In two consecutive years, the majority of stream physical characteristics showed large differences between grazed and ungrazed areas, and the directions of these differences were consistent with the recovery of exclosed streams and riparian areas from impacts caused by livestock grazing. Ungrazed areas consistently had greater canopy shading, stream depths, and bank-full heights and smaller stream widths than grazed areas. California golden trout were very abundant in the study sites; their densities and biomasses were among the highest ever recorded for stream-dwelling trout in the western United States. California golden trout density and biomass per unit area were significantly higher in ungrazed than in grazed areas in three of four comparisons. Differences between grazed and ungrazed areas ...

Stream substrates are frequently sampled with several different devices, and it is often assumed that the resulting samples have comparable compositions. We compared substrate samples taken with an excavated corer (15-cm-diameter plastic pipe) with those taken with a freeze corer from redds of California golden trout Oncorhynchus mykiss aguabonita in a stream dominated by small substrates (geometric mean diameter of redd substrates, approximately 6 mm). The proportions of individual particle size-fractions and the percent of fine sediment in the upper portion of excavated cores were similar to those in freeze cores. Geometric mean particle diameters of excavated-core and freeze-core samples were influenced by differences in the proportional weight of particles larger than 12.5 mm; as a result, geometric mean diameters were most similar when these larger size-fractions were omitted. Samplers did not differ in their probability of encountering egg pockets. A power analysis of the substrate size-fra...