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Autonomous sensors provide opportunities to observe organisms across spatial and temporal scales that humans cannot directly observe. By processing large data streams from autonomous sensors with deep learning methods, researchers can make novel and important natural history discoveries. In this study, we combine automated acoustic monitoring with deep learning models to observe breeding-associated activity in the endangered Sierra Nevada yellow-legged frog (Rana sierrae), a behavior that current surveys do not measure. By deploying inexpensive hydrophones and developing a deep learning model to recognize breeding-associated vocalizations, we discover three undocumented R. sierrae vocalization types and find an unexpected temporal pattern of nocturnal breeding-associated vocal activity. This study exemplifies how the combination of autonomous sensor data and deep learning can shed new light on species' natural history, especially during times or in locations where human observation is limited or impossible. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract Successful reintroductions of endangered species rely on comprehensive knowledge of habitat requirements across spatial and temporal scales. To inform designs of reintroduction programs, we studied habitat selection of the federally endangered Sierra Nevada yellow‐legged frog (Rana sierrae) in streams in its northern range. We quantified multi‐scale habitat use across diverse streams, habitat types within streams, and seasonal flows. In one intermittent stream, we compared habitat selection between wild and captive‐reared frogs that were released as a population augmentation. We analyzed habitat selection of seasonal habitat unit types (e.g., pool, riffle, cascades) and dimensions, and microhabitat hydrology and cover. R. sierrae appeared able to meet its ecological requirements in a variety of habitats. Study streams ranged from third‐order perennial streams to first‐order intermittent headwater creeks. Perennial streams retained a variety of habitats across flows whereas intermittent streams dried to just a few pools. Frogs used all seasonal habitat types but selected deeper pools most often relative to available habitats in intermittent streams and selected riffles or showed no preference in perennial streams. Frogs avoided fast deep‐water microhabitats, but, otherwise, preferred flowing water or deeper water without flow. Our results suggest that diverse streams can be considered candidates for reintroductions. Within intermittent streams, deeper perennial pools may provide more stable release sites, whereas non‐pool habitats may be safer in perennial streams with fish. Importantly, captive‐reared frogs selected similar habitats as wild frogs, suggesting that captivity does not alter habitat selection behaviors post‐release and that reintroduction designs for this species can be based on wild frog preferences. By improving our understanding of how habitat use varies among different types of streams and differs seasonally in response to changing habitat conditions, our results inform the design of effective reintroduction programs for frogs in streams.

Successful reintroductions of endangered species rely on comprehensive knowledge of habitat requirements across spatial and temporal scales. To inform designs of reintroduction programs, we studied habitat selection of the federally endangered Sierra Nevada yellow‐legged frog (Rana sierrae) in streams in its northern range. We quantified multi‐scale habitat use across diverse streams, habitat types within streams, and seasonal flows. In one intermittent stream, we compared habitat selection between wild and captive‐reared frogs that were released as a population augmentation. We analyzed habitat selection of seasonal habitat unit types (e.g., pool, riffle, cascades) and dimensions, and microhabitat hydrology and cover. R. sierrae appeared able to meet its ecological requirements in a variety of habitats. Study streams ranged from third‐order perennial streams to first‐order intermittent headwater creeks. Perennial streams retained a variety of habitats across flows whereas intermittent streams dried to just a few pools. Frogs used all seasonal habitat types but selected deeper pools most often relative to available habitats in intermittent streams and selected riffles or showed no preference in perennial streams. Frogs avoided fast deep‐water microhabitats, but, otherwise, preferred flowing water or deeper water without flow. Our results suggest that diverse streams can be considered candidates for reintroductions. Within intermittent streams, deeper perennial pools may provide more stable release sites, whereas non‐pool habitats may be safer in perennial streams with fish. Importantly, captive‐reared frogs selected similar habitats as wild frogs, suggesting that captivity does not alter habitat selection behaviors post‐release and that reintroduction designs for this species can be based on wild frog preferences. By improving our understanding of how habitat use varies among different types of streams and differs seasonally in response to changing habitat conditions, our results inform the design of effective reintroduction programs for frogs in streams. [ABSTRACT FROM AUTHOR]

Abstract The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow‐legged frog (Rana sierrae) and the foothill yellow‐legged frog (Rana boylii). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2–9.19X) in our protocol, from a probability of 0.51–0.85 per technical replicate. Lake sample volumes were limited by filter clogging, and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3–2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow‐legged frog eDNA captured in streams ceased between 100 and 200 m, indicating that sampling at close intervals is important.

Genetic tools that identify species from trace DNA samples could supplement traditional survey methods to clarify distributional limits of rare species. For species with legal habitat protection, elevational limits of distributions are used to determine where management actions may affect endangered species. The endangered Sierra Nevada yellow‐legged frog (Rana sierrae) generally is found down to 1,370 m, but in the Plumas National Forest, California, USA, there are a number of historical records below this elevation, resulting in protections extending to 1,067 m. This species is phenotypically similar to the foothill yellow‐legged frog (R. boylii), with which it occasionally hybridizes. We used a combination of genetic methods to investigate the fine‐scale distribution of the Sierra Nevada yellow‐legged frog in the Plumas National Forest. We collected and analyzed environmental DNA (eDNA) samples from all accessible lower elevation sites with records of Sierra Nevada yellow‐legged frog (n = 17) and swabbed 220 individuals for genetic identification from 2016–2018 to clarify the distribution of this endangered species. We created a climatic suitability model using the validated Sierra Nevada yellow‐legged frog records and current (1970–2000) climate models to assess additional highly suitable localities for Sierra Nevada yellow‐legged frog presence using eDNA capture. We did not confirm detection of Sierra Nevada yellow‐legged frog eDNA at any historical sites and identified all swabbed individuals from below 1,370 m (n = 144) as foothill yellow‐legged frogs. We located a new Sierra Nevada yellow‐legged frog site (at 1,919 m) during surveys guided by the climatic suitability model. It does not appear after extensive eDNA and genetic sampling that the Sierra Nevada yellow‐legged frog occurs below 1,370 m in this portion of their range at present. Our results show that eDNA sampling can be used as an effective management tool to evaluate historical locations and previously unknown suitable localities for current presence of a species of interest. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society. : We evaluated historical locations below the listed elevational range and identied and sampled highly suitable locations for Sierra Nevada yellow‐legged frogs using a combination of environmental DNA (eDNA) sampling, species distribution modeling, and genetic identification. We did not detect Sierra Nevada yellow‐legged frogs at historical locations below its listed elevational threshold and found a new occupied location from a climatic suitability model we developed using the records corrected using our eDNA sampling results. [ABSTRACT FROM AUTHOR]

The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow‐legged frog (Rana sierrae) and the foothill yellow‐legged frog (Rana boylii). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2–9.19X) in our protocol, from a probability of 0.51–0.85 per technical replicate. Lake sample volumes were limited by filter clogging, and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3–2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow‐legged frog eDNA captured in streams ceased between 100 and 200 m, indicating that sampling at close intervals is important. [ABSTRACT FROM AUTHOR]

Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species‐specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients. [ABSTRACT FROM AUTHOR]

The Sierra Nevada yellow-legged frog (Rana sierrae) was once an abundant and widely distributed amphibian in California's alpine ranges. Rana sierrae is adapted to high-elevation, fishless habitats. Its adaptions are reflected in a unique life cycle that involves a flexible, extended juvenile phase due to the short growing season typical of its alpine habitat. However, today this species is critically endangered, and most populations have been extirpated from their native range. Here, we present an 18-yr-long demographic study of a R. sierrae population in 15 lakes at Dusy Basin in Kings Canyon National Park. We focused on the period leading up to the arrival of the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), and the subsequent local extinction of R. sierrae. We used N-mixture abundance modeling, which accounts for detection probabilities, to quantify factors affecting frog abundance at different life stages. The abundance of subadult and adult frogs was negatively associated with the presence of introduced trout (Oncorhynchus mykiss and O. aquabonita). Frog abundance in all life stages was positively associated with lake surface area. The propensity of lakes drying correlated negatively with abundance of eggs, subadults, and adults in the following year. Moreover, drought years, characterized by longer summers and less winter snowpack, led to higher rates of lakes drying. Finally, our results suggest that the frequency of such droughts in the region has increased since 1937. Increased frequency or severity of droughts is expected to decrease the value of shallow lakes for Sierra Nevada yellow-legged frogs because these habitats are prone to drying.We discuss our results in terms of future restoration strategies, including reintroduction and probiotic treatment, in this changed and changing ecosystem. [ABSTRACT FROM AUTHOR]

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern. [ABSTRACT FROM AUTHOR]

Symbiotic microbial communities play key roles in the health and development of their multicellular hosts. Understanding why microbial communities vary among different host species or individuals is an important step toward understanding the diversity and function of the microbiome. The amphibian skin microbiome may affect resistance to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Still, the factors that determine the diversity and composition of the amphibian skin microbiome, and therefore may ultimately contribute to disease resistance, are not well understood. We conducted a two-phase experiment to first test how host and environment shape the amphibian skin microbiome, and then test if the microbiome affects or is affected by Bd infection. Most lab experiments testing assembly of the amphibian skin microbiome so far have compared sterile to non-sterile environments or heavily augmented to non-augmented frogs. A goal of this study was to evaluate, in an experimental setting, realistic potential drivers of microbiome assembly that would be relevant to patterns observed in nature. We tested effects of frog genetic background (2 source populations) and 6 natural lake water sources in shaping the microbiome of the frog Rana sierrae. Water in which frogs were housed affected the microbiome in a manner that partially mimicked patterns observed in natural populations. In particular, frogs housed in water from disease-resistant populations had greater bacterial richness than frogs housed in water from populations that died out due to Bd. However, in the experiment this difference in microbiomes did not lead to differences in host mortality or rates of pathogen load increase. Frog source population also affected the microbiome and, although none of the frogs in this study showed true resistance to infection, host source population had a small effect on the rate of pathogen load increase. This difference in infection trajectories could be due to the observed differences in the microbiome, but could also be due to other traits that differ between frogs from the two populations. In addition to examining effects of the microbiome on Bd, we tested the effect of Bd infection severity on the microbiome. Specifically, we studied a time series of the microbiome over the course of infection to test if the effects of Bd on the microbiome are dependent on Bd infection severity. Although limited to a small subset of frogs, time series analysis suggested that relative abundances of several bacterial phylotypes changed as Bd loads increased through time, indicating that Bd-induced disturbance of the R. sierrae microbiome is not a binary effect but instead is dependent on infection severity. We conclude that both host and aquatic environment help shape the R. sierrae skin microbiome, with links to small changes in disease resistance in some cases, but in this study the effect of Bd on the microbiome was greater than the effect of the microbiome on Bd. Assessment of the microbiome differences between more distantly related populations than those studied here is needed to fully understand the role of the microbiome in resistance to Bd.

Symbiotic microbial communities play key roles in the health and development of their multicellular hosts. Understanding why microbial communities vary among different host species or individuals is an important step toward understanding the diversity and function of the microbiome. The amphibian skin microbiome may affect resistance to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Still, the factors that determine the diversity and composition of the amphibian skin microbiome, and therefore may ultimately contribute to disease resistance, are not well understood. We conducted a two-phase experiment to first test how host and environment shape the amphibian skin microbiome, and then test if the microbiome affects or is affected by Bd infection. Most lab experiments testing assembly of the amphibian skin microbiome so far have compared sterile to non-sterile environments or heavily augmented to non-augmented frogs. A goal of this study was to evaluate, in an experimental setting, realistic potential drivers of microbiome assembly that would be relevant to patterns observed in nature. We tested effects of frog genetic background (2 source populations) and 6 natural lake water sources in shaping the microbiome of the frog Rana sierrae. Water in which frogs were housed affected the microbiome in a manner that partially mimicked patterns observed in natural populations. In particular, frogs housed in water from diseaseresistant populations had greater bacterial richness than frogs housed in water from populations that died out due to Bd. However, in the experiment this difference in microbiomes did not lead to differences in host mortality or rates of pathogen load increase. Frog source population also affected the microbiome and, although none of the frogs in this study showed true resistance to infection, host source population had a small effect on the rate of pathogen load increase. This difference in infection trajectories could be due to the observed differences in the microbiome, but could also be due to other traits that differ between frogs from the two populations. In addition to examining effects of the microbiome on Bd, we tested the effect of Bd infection severity on the microbiome. Specifically, we studied a time series of the microbiome over the course of infection to test if the effects of Bd on the microbiome are dependent on Bd infection severity. Although limited to a small subset of frogs, time series analysis suggested that relative abundances of several bacterial phylotypes changed as Bd loads increased through time, indicating that Bd-induced disturbance of the R. sierrae microbiome is not a binary effect but instead is dependent on infection severity. We conclude that both host and aquatic environment help shape the R. sierrae skin microbiome, with links to small changes in disease resistance in some cases, but in this study the effect of Bd on the microbiome was greater than the effect of the microbiome on Bd. Assessment of the microbiome differences between more distantly related populations than those studied here is needed to fully understand the role of the microbiome in resistance to Bd. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract Species extinctions have the potential to dramatically reshape ecological communities. In the Sierra Nevada mountains of California, the emergence of a lethal amphibian pathogen (Batrachochytrium dendrobatidis) drives mountain yellow‐legged frog (Rana muscosa and Rana sierrae) populations to local extinction. Prior to population declines, these frogs and their tadpoles were abundant, high‐level predators and grazers with high trophic connectance. To quantify how these low diversity aquatic macroinvertebrate communities respond to nonrandom single‐species local extinctions, we quantified aquatic macroinvertebrate communities using two approaches: a natural experiment (“Resurveys”) and a large‐scale synoptic observational study (“Snapshot” surveys). In the Resurveys, we compared benthic macroinvertebrate communities in 22 Sierra Nevada alpine lakes that we categorized as either having extant frog populations, experiencing ongoing disease‐driven frog declines, or having previously experienced local disease‐driven frog extirpation. In the Resurveys, taxonomic richness was about one taxa (17%) higher in lakes where frogs were declining or extinct, compared to lakes where frogs were extant. However, multivariate analyses revealed no strong dissimilarities among Resurvey communities, and there were no differences in the abundances of individual taxa between lakes in the frogs extant, declining, or extinct categories. In the Snapshot surveys, we reanalyzed previously collected data from a large‐scale survey of 157 lakes with and without frogs. In the Snapshot survey, invertebrate taxonomic richness was less than one taxa (9%) lower in lakes without frogs, and multivariate analyses again indicated only small differences between lakes with and without frogs. Overall, disease‐driven mountain yellow‐legged frog extinctions had small effects on lake benthic macroinvertebrate communities, with no large changes in invertebrate abundance, richness or evenness, no clear secondary extinctions or invasions, and few taxa showing distinct responses to frog extinctions. Our study highlights how even for conspicuous, highly connected, omnivorous taxa that are experiencing large, rapid, and widespread declines and extinctions, the ecological effects of extinctions will sometimes be small and subtle.

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 yellowlegged 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 tomultiple 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. [ABSTRACT FROM AUTHOR]

Species extinctions have the potential to dramatically reshape ecological communities. In the Sierra Nevada mountains of California, the emergence of a lethal amphibian pathogen ( Batrachochytrium dendrobatidis) drives mountain yellow-legged frog ( Rana muscosa and Rana sierrae) populations to local extinction. Prior to population declines, these frogs and their tadpoles were abundant, high-level predators and grazers with high trophic connectance. To quantify how these low diversity aquatic macroinvertebrate communities respond to nonrandom single-species local extinctions, we quantified aquatic macroinvertebrate communities using two approaches: a natural experiment ('Resurveys') and a large-scale synoptic observational study ('Snapshot' surveys). In the Resurveys, we compared benthic macroinvertebrate communities in 22 Sierra Nevada alpine lakes that we categorized as either having extant frog populations, experiencing ongoing disease-driven frog declines, or having previously experienced local disease-driven frog extirpation. In the Resurveys, taxonomic richness was about one taxa (17%) higher in lakes where frogs were declining or extinct, compared to lakes where frogs were extant. However, multivariate analyses revealed no strong dissimilarities among Resurvey communities, and there were no differences in the abundances of individual taxa between lakes in the frogs extant, declining, or extinct categories. In the Snapshot surveys, we reanalyzed previously collected data from a large-scale survey of 157 lakes with and without frogs. In the Snapshot survey, invertebrate taxonomic richness was less than one taxa (9%) lower in lakes without frogs, and multivariate analyses again indicated only small differences between lakes with and without frogs. Overall, disease-driven mountain yellow-legged frog extinctions had small effects on lake benthic macroinvertebrate communities, with no large changes in invertebrate abundance, richness or evenness, no clear secondary extinctions or invasions, and few taxa showing distinct responses to frog extinctions. Our study highlights how even for conspicuous, highly connected, omnivorous taxa that are experiencing large, rapid, and widespread declines and extinctions, the ecological effects of extinctions will sometimes be small and subtle. [ABSTRACT FROM AUTHOR]

Land-management agencies need quantitative, statistically rigorous monitoring data, often at large spatial and temporal scales, to support resource-management decisions. Monitoring designs typically must accommodate multiple ecological, logistical, political, and economic objectives and constraints. We present a long-term bioregional monitoring program to assess the status and change in populations of the federally listed candidate frog species, Yosemite toad (Anaxyrus [Bufo] canorus) and mountain yellowlegged frog (.Rana muscosa/sierrae complex), on USDA Forest Service lands in the Sierra Nevada, California. The program takes advantage of advances in survey design and analysis to: 1) collect data at a metapopulation scale (i.e., small basins), 2) provide occupancy data on ≥2 species with overlapping ranges with the same field-monitoring protocols, 3) provide occupancy estimates applicable to the entire range of each species in the study region, 4) incorporate information from historical occupancy records, and 5) link the survey design to an existing survey design. We estimated occupancy assuming imperfect detection by extending existing procedures for maximum likelihood estimation to incorporate the unequal probability of selection used in the survey design. From 2002 to 2009, we estimate that the Yosemite toad used 0.25 ± 0.01 (SE), 0.86 ± 0.04, and 0.86 ± 0.03 of basins over its range, with historical presence, and with presence since 1990, respectively, and the mountain yellow-legged frog used 0.04 ± 0.01, 0.43 ± 0.04, and 0.47 ± 0.04 of basins over its range, with historical presence, and with presence since 1990, respectively. Survey date and snow pack affected detection of the Yosemite toad but not of the mountain yellow-legged frog. Monitoring costs were reduced by using a complex survey design with panels that required generalizing existing methods for estimating occupancy under imperfect detection. [ABSTRACT FROM AUTHOR]

Based on 2431 captures of 757 individual frogs over a 9-yr period, we found that the population of R. sierrae in one meadow-stream complex in Yosemite National Park ranged from an estimated 45 to 115 adult frogs. Rana sierrae at our relatively low elevation site (2200 m) grew at a fast rate (K=0.73-0.78), had high overwintering survival rates (44.6-95%), lived a long time (up to 16 yr), and tended to be fairly sedentary during the summer (100% minimum convex polygon annual home ranges of 139 m2) but had low year-to-year site fidelity. Even though the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) has been present in the population for at least 13 yr, there was no clear downward trend as might be expected from reports of R. sierrae population declines associated with Bd or from reports of widespread population decline of R. sierrae throughout its range. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The emergence of the infectious disease chytridiomycosis is a major factor responsible for amphibian extinctions in pristine habitats. However, some populations coexist with Batrachochytrium dendrobatidis (Bd), the agent of chytridiomycosis, and others go extinct when Bd arrives. Variation of pathogen severity among populations may be explained by differences of antimicrobial skin peptides and anti-Bd skin bacteria. Previous work showed that a population of the frog Rana sierrae had a high proportion of individuals with at least one species of cultured anti-Bd skin bacteria and was coexisting with Bd for more than 6years. A population of the closely related sister species Rana muscosa had a significantly lower proportion of individuals with anti-Bd bacteria, and the following year, it went extinct due to Bd. We extended previous work to include another sampling of the R. sierrae population coexisting with Bd and found that, although the anti-Bd bacterial community somewhat differed, both populations had a high proportion of individuals with antifungal bacteria. We also included a population of R. muscosa that was naïve of Bd and predicted to go extinct once Bd emerged since that was the fate of neighboring populations. However, the naïve R. muscosa population had a high proportion of antifungal bacteria, which suggested that the population might survive if Bd emerged. Two years later, the population was surviving with Bd endemic. Variation in the proportion of individuals with anti-Bd skin bacteria appears to explain why some populations persist when Bd emerges in a population. [Copyright &y& Elsevier]