USGS Science⌕ Search

Geology topics

Patrick M. Kleeman

Publications and source records attributed to Patrick M. Kleeman.

At least 19 recordsLinked to original sources
USGS2026

Conducting feasibility assessments of potential conservation reintroductions: A case study with the imperiled foothill yellow-legged frog, Rana boylii

Conservation translocations are an increasingly common and often necessary component of recovering species that have become extirpated from portions of their range. Understanding and ameliorating potential threats that reduce the likelihood of successful population establishment at recipient sites is a key component of successful translocation planning. We examined multiple potential threats, including pathogens, contaminants, and invasive species, as well as habitat suitability and food resources, to assess the feasibility of reintroducing threatened, stream-obligate foothill yellow-legged frogs, Rana boylii , to Pinnacles National Park. Foothill yellow-legged frogs were extirpated from this protected area more than half a century ago. Although invasive species, disease, contaminants, food resources, and water temperatures are unlikely to inhibit foothill yellow-legged frog population establishment, potential recipient streams at Pinnacles National Park had shorter hydroperiods and much higher canopy cover than reference streams with extant foothill yellow-legged frog populations. Although the exact cause of extirpation of foothill yellow-legged frogs from Pinnacles National Park is unknown, translocations of foothill yellow-legged frogs to the park are more likely to succeed if riparian canopy cover is reduced and stream hydroperiods increased to better match those at nearby populations. Thoroughly understanding the threats to and characteristics of potential recipient sites could improve the likelihood of success of translocation outcomes in natural areas.

California↗
USGS2025

Long-term monitoring of island night lizards on San Nicolas Island

We describe the results of long-term population monitoring of the island night lizard Xantusia riversiana on San Nicolas Island, California, following the species' removal from the U.S. Endangered Species list in 2014. Monitoring activities were carried out from October 2014 through November 2023, but we also incorporate data from earlier work dating back to 1993. Because of habitat loss on the western part of the island, the island night lizard is almost entirely confined to the island's eastern half. The species' distribution remains largely the same since studies in the 1990s, though small increases in distribution were noted at the island's west end. Numbers at most long-term monitoring sites appeared to show a slight decrease associated with a multi-year drought, with numbers returning to previous levels by the end of the monitoring period. Models fit to counts of newly recruited lizards suggested a positive association between winter precipitation and abundance; however, we found a simpler model including constant abundance throughout the study to be more parsimonious. Two monitoring sites showed marked decreases in numbers, with one site declining to zero following infestation of the area by non-native Argentine ants Linepithema humile . The island's vegetation and natural communities continue to gradually recover from a century of overgrazing by sheep and the widespread introduction of aggressive non-native plants. Habitat restoration efforts by U.S. Navy natural resources staff on the island may lead to increasing population numbers and genetic connectivity, but persistent threats remain for the island night lizard on San Nicolas Island.

California↗
USGS2025

Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations

Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus ( Batrachochytrium dendrobatidis ; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of amphibians globally. Laboratory evidence shows ubiquitous contaminants like methylmercury (MeHg) can reduce vigor and survival of amphibians, but population-level effects remain unclear. We used non-lethal sampling to assess how Bd and MeHg affected survival of juvenile and adult amphibians in 20 populations across the USA. Survival of several species declined with increasing Bd loads, including some species previously considered resistant to Bd (e.g., eastern newt [ Notophthalmus viridescens ]). Although our sampling for MeHg was less intensive than for Bd, we found MeHg can both directly reduce survival and synergistically magnify the effects of Bd infection. For a population of foothill yellow-legged frogs ( Rana boylii ), the estimated reduction in survival from MeHg exceeded that from Bd. Although effects varied widely among populations and species, our results help clarify the potential for synergistic effects of disease and contaminants and emphasize the complexity of identifying and quantifying the population-level effects of interactions among stressors.

Scientific Reports↗
USGS2025

Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence

Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in and near the 2021 Dixie Fire footprint using double-observer visual encounter surveys that incorporated time-to-detection methods, and used structural causal modeling to improve post-fire inference while lacking pre-fire data. We found that foothill yellow-legged frog probability of occurrence was 4.93 (95% equal-tailed interval = 0.52 – 160) times higher outside the footprint of the Dixie Fire than within it, though probability of occurrence was generally low within our sampling frame (ψ unburned = 0.21 [0.08 – 0.49]; ψ burned = 0.05 [0.002 – 0.28]). Measured environmental characteristics, however, were similar within and outside the fire footprint, and observed occupancy patterns might reflect the recent historical distribution of the frogs. Our study emphasizes the importance of site-specific pre-disturbance data when attempting to evaluate the causal effects of disturbances on wildlife. Although it remains to be seen how this species will fare in an increasingly frequent and intense fire regime, foothill yellow-legged frogs may tolerate some level of fire disturbance.

California↗
USGS2025

Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature

Batrachochytrium dendrobatidis (Bd) is a globally distributed fungal pathogen of amphibians that has contributed to one of the largest disease-related biodiversity losses in wildlife. Bd is regularly viewed through the lens of a global wildlife epizootic because the spread of highly virulent genetic lineages has resulted in well-documented declines and extinctions of multiple amphibian species. However, the current state of Bd occurrence, host range, host impacts, and ecological drivers remains poorly understood outside of the most negatively affected amphibian species and regions. Our objective was to describe the macroecology of Bd occurrence and infection intensity on caudates (salamanders) across the United States and to compare these patterns with better-studied anurans (frogs and toads). We collected swabs from 11,183 amphibians at 609 sites from 54 species across the United States from 2015 to 2017. We analyzed the prevalence and intensity of Bd infection jointly using a Bayesian hurdle model with covariates of site-level temperature and precipitation, as well as individual characteristics and species identification. Bd was distributed widely across sites and species sampled across the spatial extent of the conterminous United States. We found that Bd prevalence and intensity were most strongly influenced by temperature in the month preceding sampling and by differences among taxon groups. We estimated that temperature had a strong and nonlinear influence on both Bd prevalence and intensity with peak infection at intermediate temperatures and lower infection at low and high temperatures. We found Caudate hosts tended to have higher prevalence than Anuran hosts and Anuran hosts tended to have higher intensity at optimal temperatures for Bd infection. Our findings suggest that Bd has an amphibian-wide host range, temperature gradients exert a strong influence on Bd, and enzootic transmission likely encompasses a much larger spatial and species distribution than previously recognized across North America.

conterminous United States↗
USGS2025

Climatological effects on survival, recruitment, and possible extirpation of a Sierra Nevada anuran

The drivers of population dynamics are a primary interest of ecologists, and predicting the consequences of climate variability on wildlife populations benefits from an understanding of how weather causes variation in the vital rates of populations. Given recent and projected extremes in annual precipitation in the Sierra Nevada of California, USA, including two severe droughts, we sought to examine the role of snowpack and summer water availability on the population dynamics and potential extirpation of a meadow population of the U.S. Endangered Sierra Nevada yellow-legged frog ( Rana sierrae ) using a long-term capture-mark-recapture dataset. We found that snowpack and summer water availability affected both survival and recruitment probabilities. Although these variables only explained approximately 17 % of the annual variation in adult survival, they explained 81 % of the variation in recruitment into the adult population. Following two severe, extended droughts and a nearby wildfire, the population consisted of 20 or fewer individuals with >95 % certainty, and 10 or fewer individuals with 64 % certainty. If realized, increased precipitation volatility and extended droughts likely present an additional threat to some meadow populations of this endangered frog.

California↗
USGS2025

Occurrence and surface availability of Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in northern California

Estimating the distributions of cryptic species is essential for conservation, yet our understanding is hampered by animal behavior and imperfect detection. We developed and implemented a multiscale occupancy survey protocol to estimate the probability of occurrence, probability of being active on the surface, and detection probability of two range-restricted terrestrial salamanders, Scott Bar Salamanders ( Plethodon asupak ) and Siskiyou Mountains Salamanders ( P. stormi ), in interior northern California, USA. We established survey sites near locations of historical occurrence of these salamanders and surveyed each site on one to six visits in late fall 2023 and spring 2024. We compared models with different environmental variables for predicting salamander occurrence and surface activity. Much model selection uncertainty in the effects of covariates existed, but the model with most support indicated that Plethodon salamanders in interior northern California were more likely to occur at sites near recent historical occurrences that had longer growing seasons after controlling for elevation and aspect. Plethodon stormi or P. asupak surface activity was higher at night than during the day and was highest when substrates were cool and moist. Our survey protocol was successful for quantifying the effects of site and visit characteristics on P. stormi or P. asupak occurrence and availability; minor modifications will likely improve its utility for providing unbiased inference about salamander occurrence and surface activity.

California↗
USGS2024

Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point Reyes National Seashore, California, USA.

Non-native plants can affect communities through direct competition, and by providing refuge to seed predators, creating apparent competition with native plants. Ammophila arenaria (European beachgrass) has been introduced to coastal dune habitats throughout the western United States where it forms dense monocultures, stabilizes dunes, and alters abiotic and biotic conditions. The dominance of European beachgrass has been linked to declines of Lupinus tidestromii (Tidestrom’s lupine), an herb endemic to coastal dune communities in central and northern California. Peromyscus sonoriensis (western deer mice), a native seed predator, use beachgrass as refuge from predators. Tidestrom’s lupine plants near European beachgrass stands experience greater predation pressure from deer mice. At Point Reyes National Seashore, California, USA (PRNS), mechanical removal, manual pulling, and herbicide treatment have been used to reduce the density of European beachgrass near Tidestrom’s lupine populations. We trapped deer mice at five sites in PRNS that experienced different management regimes and used spatially-explicit capture-recapture models to estimate deer mouse density as a function of site and habitat treatment. We found that deer mouse density was lowest in areas where European beachgrass was mechanically removed and in herbicide-treated foredunes, and highest in areas highly invaded by European beachgrass and Carpobrotus spp. (iceplant). The density of deer mice increased from 2021 to 2022 at every site except one that underwent extensive mechanical removal of European beachgrass from 2010-2011. This study shows enduring effects of European beachgrass removal on the density of a native seed predator and highlights the importance of habitat management for conservation of Tidestrom’s lupine.

California↗
USGS2024

From eDNA to decisions using a multi-method approach to restoration planning in streams

Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted comprehensive environmental DNA (eDNA) and visual encounter surveys to determine the distribution of native and non-native aquatic species in two high-priority watersheds to address key uncertainties—such as the distribution of threats and the status of existing populations—inherent in restoration planning. We then used these occurrence data to develop a menu of potential conservation actions and a decision framework to benefit an endangered vertebrate (foothill yellow-legged frog, Rana boylii ) in dynamic stream systems. Our framework combines the strengths of multiple methods, allowing managers and conservation scientists to incorporate conservation science and site-specific knowledge into the planning process to increase the likelihood of achieving conservation goals.

Scientific Reports↗
USGS2024

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog ( Rana boylii ) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897–2005) and field samples (2005–2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

California↗
USGS2024

Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California

Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles ( Actinemys marmorata ) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distribution of northwestern pond turtles and introduced American bullfrogs ( Lithobates catesbeianus ), we surveyed streams on private timberlands of the interior foothills of northern California using visual encounter surveys and collecting samples of environmental DNA. We found that northwestern pond turtle occurrence was negatively related to elevation in our sampling frame. Detection probabilities with environmental DNA were approximately twice those of visual encounter surveys, but both methods were effective for detecting turtles in streams. American bullfrogs were detected in a single sample at each of 2 sites (one by environmental DNA, one by visual encounter surveys). Management for northwestern pond turtles in forest streams within our sample area will likely have the largest effect at lower elevation sites where turtles are most likely to occur.

California↗
USGS2023

Broad-scale assessment of methylmercury in adult amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017–2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R 2 ≥ 0.67), whereas total Hg in sediment was not (R 2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Environmental Science and Technology↗
USGS2023

Sierra Nevada amphibians demonstrate stable occupancy despite precipitation volatility in the early 21st Century

Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change. We examined the relationship between adult occupancy dynamics of three high elevation anurans and site and annual variation in measures of winter severity, summer wetness, and cumulative drought. We further evaluated how these weather conditions affected the probability that each species would reproduce, conditional on their occurrence at a site. We found that although different aspects of weather affected the occupancy dynamics of each species differently, adult occupancy probabilities were generally stable throughout our 15-year study period. The probability of reproduction, although slightly more variable than adult occupancy, was similarly stable throughout the study. Although occurrence of the three species was resilient to recent extremes in precipitation, more detailed demographic study would inform the extent to which amphibian populations will remain resilient to increasing severity, duration, and frequency of drought and flood cycles.

California↗
USGS2023

Keeping the heat on: Weighted surveillance for Chytrid fungus (Batrachochytirum dendrobatidis) in Dixie Valley toads (Anaxyrus [= Bufo] williamsi)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecurity measures to prevent the spread of pathogens, surveillance programs may enable early detection of pathogens, when management actions to limit the effects of pathogens on naïve hosts might be most beneficial. We analyzed surveillance data for the endangered and narrowly endemic Dixie Valley toad ( Anaxyrus [= Bufo ] williamsi ) from two time periods (2011–2014 and 2019–2021) to estimate the minimum detectable prevalence of the amphibian fungal pathogen Batrachochytrium dendrobatidis ( Bd ). We assessed if detection efficiency could be improved by using samples from both Dixie Valley toads and co-occurring introduced American bullfrogs ( Lithobates catesbeianus ) and literature-derived surveillance weights. We further evaluated a weighted surveillance design to increase the efficiency of surveillance efforts for Bd within the toad’s small (<6 km 2 ) range. We found that monitoring adult and larval American bullfrogs would probably detect Bd more efficiently than monitoring Dixie Valley toads alone. Given that no Bd was detected, minimum detectable prevalence of Bd was <3% in 2011–2014, and <5% (Dixie Valley toads only) and <10% (American bullfrogs only) in 2019–2021. Optimal management for Bd depends on the mechanisms underlying its apparent absence from the range of Dixie Valley toads, but a balanced surveillance scheme that includes sampling American bullfrogs to increase the likelihood of detecting Bd , and adult Dixie Valley toads to ensure broad spatial coverage where American bullfrogs do not occur, would probably result in efficient surveillance, which might permit timely management of Bd if it is detected.

Journal of Wildlife Diseases↗
USGS2022

Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad

Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. Aims: We sought to model the occupancy dynamics of the Dixie Valley toad ( Anaxyrus williamsi ), a recently described species endemic to a small desert spring wetland complex in Nevada, USA. Methods: We divided the species’ range into 20 m × 20 m cells and surveyed for Dixie Valley toads at 60 cells during six primary periods from 2018 to 2021, following an occupancy study design. We analysed our survey data by using a multi-state dynamic occupancy model to estimate the probability of adult occurrence, colonisation, site survival, and larval occurrence and the relationship of each to environmental covariates. Key results: The detection probabilities of adult and larval toads were affected by survey length and time of day. Adult Dixie Valley toads were widely distributed, with detections in 75% of surveyed cells at some point during the 3-year study, whereas larvae were observed only in 20% of cells during the study. Dixie Valley toad larvae were more likely to occur in cells far from spring heads with a high coverage of surface water, low emergent vegetation cover, and water temperatures between 20°C and 28°C. Adult toads were more likely to occur in cells with a greater coverage of surface water and water depth >10 cm. Cells with more emergent vegetation cover and surface water were more likely to be colonised by adult toads. Conclusions: Our results showed that Dixie Valley toads are highly dependent on surface water in both spring and autumn. Adults and larvae require different environmental conditions, with larvae occurring farther from spring heads and in fewer cells. Implications: Disturbances to the hydrology of the desert spring wetlands in Dixie Valley could threaten the persistence of this narrowly distributed toad.

Wildlife Research↗
USGS2022

Multi-scale patterns in occurrence of an ephemeral pool-breeding amphibian

Species distributions are governed by processes occurring at multiple spatial scales. For species with complex life cycles, the needs of all life stages must be met within the dispersal limitations of the species. Multi-scale processes can be particularly important for these species, where small-scale patterns in specific habitat components can affect the distribution of one life stage, whereas large-scale patterns in land cover might better explain the distribution of other life stages. Using a conditional multi-scale model, we evaluated which aspects of the landscape and local environment are most strongly related to occupancy patterns of western spadefoots ( Spea hammondii ). In northern and central California, the proportion of grassland land cover within 2 km of a site was positively related to the occurrence of the northern clade of the western spadefoot. At the pond scale, we found that western spadefoots were more likely to breed in pools with lower pH. Our results indicate that protecting remaining grasslands for adult spadefoots and ensuring multiple pools with diverse characteristics and hydroperiods so at least some pools result in successful breeding will likely be necessary to conserve western spadefoots, especially with a changing climate. Considering the processes that affect species distributions at multiple life stages and spatial scales is an essential component of effective conservation.

California↗
USGS2022

Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

Science↗