Geology topics

Robert N. Fisher

Publications and source records attributed to Robert N. Fisher.

At least 19 recordsLinked to original sources

USGS2026

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

Journal of Heredity↗

USGS2026

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

BioRxiv↗

USGS2025

Speciation genomics in the tiger whiptail lizards ( Aspidoscelis tigris complex)

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards ( Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

northern Mexico, southwestern United States↗

USGS2025

Wake Atoll vessel movement biosecurity program efficacy

Executive Summary The purpose of this Wake Atoll Vessel Movement Biosecurity Program Efficacy document is to provide the United States Air Force (USAF) with an unbiased review of the current (2015; hereafter referred to as the 2015 Biosecurity Plan) biosecurity plan for the military base Wake Island Airfield (WIA) on Wake Atoll (hereafter Wake). Periodic reviews are an integral step for evaluating plan efficacy and updating plans with new information for improving plan effectiveness. The U.S. Geological Survey (USGS) acted as an external expert to provide the first unbiased assessment of the program and observe how it was being implemented. The USAF 2015 Wake Island Biosecurity Management Plan goes beyond sea vessel and container biosecurity; however, those aspects were not included in this evaluation. We used several methods for a quality assurance evaluation of the 2015 sea vessel and shipping container biosecurity program specified in the Biosecurity Plan. Our evaluation included real-time observations in Hawai`i and at Wake. We surveyed cargo staging areas and empty shipping containers before supply shipment and the containers, barge, and marina at Wake after shipment. We used various detection tools and techniques (for example, visual encounter surveys, glue boards, chew cards, camera traps, and so on). We carried out an insect mortality experiment trial using one of the required shipping container biosecurity tools (dichlorvos impregnated pest strips). We also included a table-top review of documentation (largely the 2015 Biosecurity Plan) with respect to our observations to provide an assessment of how well the Biosecurity Plan protocols were carried out and how well they serve their intended purpose. We observed biosecurity concerns in each focal area and stage of cargo handling (before and after barge movement) across all surveys of containers, flat racks, break bulk, warehouses, and dock areas. Using visual inspections, we recorded biosecurity concerns for every empty container we inspected before it was to be stuffed with cargo. Most containers had structural integrity issues (such as holes and damaged floorboards) and sanitation concerns, including live animals and plant matter or seeds. About one third of the containers had mold and a few had wet floorboards or standing water. We detected live animals on the break bulk, and flat racks were in poor condition. Next, we inspected cargo staging areas and noted extensive permeability of the building where cargo was staged for the 2018 resupply shipment and the building that had typically been used. We included the adjacent dock area used for staging break bulk, shipping containers and mooring the barge. We detected more than 5,000 individuals of 105 species. We also detected seeds in each location and scattered vegetation in the dock area, including growing in from the area outside separated by a chain link fence. During surveys at Wake, we observed that 100 percent of the shipping containers, including all containers sent with required biosecurity tools, had live animals. The barge had only one unsecured snap trap for intercepting rodents aboard, we saw areas with fairly deep layers of dirt (or soil; we did not examine it to determine its properties), and there was plant matter with seed heads on the barge gangway that could easily be transported onto the barge. There was also only one snap trap station that was improperly placed on the dock. We also observed piled wood and vegetation nearby that could provide refuge to potential stowaway animals escaping. Combined, surveys of the containers, staging areas, barges, and receiving area in Hawai`i and at Wake resulted in detection of more than 9,000 individuals of 131 animal species; nearly 4,000 individuals of 62 species were detected in surveys of containers once they had arrived at Wake. None of the species identified are known to be native to Wake. Our preliminary risk analysis of all species detected included eight species that we scored as high risk of potentially negative effects to biodiversity, infrastructure, or human health should they arrive at Wake and become established. Six of these species were only recorded using tools not clearly required by the Biosecurity Plan or being used to implement the plan. We observed that the required biosecurity tools intended to intercept animals in the cargo staging area did not target the suite nor number of species present. Our analysis also indicated the required biosecurity tools intended to intercept animals in shipping containers were inadequate to handle the volume of organisms that were in the containers. The insect mortality trial experiment showed the pest strips were highly effective for only one of the three species tested, leaving uncertainty about how effective they are across the suite of potential species stowing away in cargo and containers. Base Operating Support (BOS) did not carry out all Biosecurity Plan actions, but we also noted the document uses terminology such as “recommendation” as opposed to “requirement” which may lead contractors to consider those actions as optional. However, USAF provided evidence of BOS training and follow up; this included detailed identification of specific requirements for some of the biosecurity actions that we did not observe being carried out. The 2015 Biosecurity Plan contains critical and useful components that seem to be well carried out. However, we also saw discrepancies, weaknesses, or both across methods and protocols currently used for Wake Atoll biosecurity. We observed shortcomings at each stage of our survey as well as in the plan as written, and we suggest general modifications to the Biosecurity Plan for consideration to potentially strengthen biosecurity overall. Prevention is the most efficient and cost-effective biosecurity measure. Based on our findings, we see possible solutions to improve existing preventative biosecurity efforts and reduce potential incursion at Wake. These potential solutions include creating and implementing the following: Minimum cargo staging area sanitation and permeability standards, Minimum shipping container integrity and sanitation standards, Stand-alone inspection protocols, Inspection checklists, Monitoring protocols, Accountability reporting, Horizon scanning for prioritizing and targeting species of highest concern, Expansion of educational materials and outreach, Schedules for biosecurity plan reviews and updates Management of invasive species enhances capability to protect human health and the environment as well as to advance mission accomplishment. Biosecurity plans are an integral component for addressing invasive species. Periodic evaluation of the efficacy of these plans is useful for identifying elements that are working well and for illuminating those that can be improved. Evaluations encourage consideration of new tools and adaptation of processes to achieve better outcomes and accommodate potential future threats more efficiently and more cost effectively.

Open-File Report↗

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

Biodiversity surveys of Wake Atoll—Featuring field guides for plants, arthropods, and herpetofauna

Introduction The U.S. Air Force (USAF) issued funds to the U.S. Geological Survey (USGS) to update the biosecurity plan, create a current (2019) flora and fauna species identification index, and do container evaluations for the presence of potential invasives. The current (2019) biosecurity protocols used for prevention were evaluated, and new biodiversity surveys were completed for terrestrial vegetation and arthropods and included the first formal reptile surveys. Results from field efforts add to existing knowledge and may identify new species arrivals to Wake. One goal of this project was to update and compile established species information for the atoll and create species identification guides for the three taxonomic groups surveyed. We made these flora and fauna species identification guides by compiling results of the recent (2019) and historical surveys. The guides can be used as resident desktop references, as a baseline for assessing future natural resource surveys, and to assist with guiding management actions. We refer herein to biosecurity and integrated pest management plan materials, which we created simultaneously to inform current (2019) biosecurity and to identify some of the top invasive species at Wake. This study was done in cooperation with the USAF, and surveys were performed for the 611th Civil Engineer Squadron Natural Resources Program, ACES PROJECT #YGFZ170002 under agreement number F2MUAA7116GW02 between the USAF and the USGS Western Ecological Research Center.

Open-File Report↗

USGS2025

Terrestrial mammal diversity at Hansen Dam (Los Angeles, California, USA): Flood control area acts as habitat in a human-dominated landscape

Urban expansion is a prominent threat to biodiversity, particularly for terrestrial mammals, which are significantly impacted by disruptions in habitat connectivity and loss. It can also lead to increased human‑wildlife conflicts that contribute to species decline. Urban public works projects, such as flood control areas, may coincidentally preserve significant habitat, but their potential for conservation remains understudied. Hansen Dam, located in the city of Los Angeles, California, USA, is one of these flood control areas, hosting some of the last remaining riparian habitat in the greater Los Angeles area. We deployed motion‑triggered camera traps at 36 stratified random locations and completed small mammal trapping at 20 sites at Hansen Dam. We detected a total of 15 species, not including domesticated animals, but there is potential that additional species inhabit the area. All species detected were common and expected but demonstrate that the Hansen Dam flood control basin has a terrestrial mammal community similar to that reported for other urban habitats. These results suggest incidental habitat conservation could play a significant role in future conservation planning efforts.

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

Widespread dispersal of a human commensal across the Pacific: Reconstructing the human-mediated invasion history of the house gecko (Hemidactylus frenatus)

The spread of human commensal species is intricately tied to human movements and historical events. Through waves of human migrations, colonization, trade routes, commercial activities, and war, humans have redistributed species from their native ranges to widely scattered areas across the Pacific. Deciphering the invasion history of recent human-mediated introductions is challenging due to similar genetic signatures arising from these factors, which complicates the identification of specific pathways or sources. The extensive timeline of human events in the Pacific further compounds this challenge, potentially leading to numerous introductions from various regions over an extended period. The house gecko ( Hemidactylus frenatus ), a human commensal native to Southeast Asia, is now widespread in the Pacific region. While its current range is often attributed to activities during and following World War II (WWII), its invasion history necessitates a finer-scale dissection given the dynamic and extensive history of human-mediated introductions in the Pacific. We combine population genetics, phylogenetics, and approximate Bayesian computation to infer the invasion history of the house gecko from its native to its introduced range in the Pacific. Patterns of differentiation across native and introduced populations align with the extent of each region’s wartime involvement and the invasion history reconstruction supports the predicted chronology of introductions given a war-induced spread. This marks the first comprehensive genetic assessment of the house gecko’s invasion history in the Pacific and provides evidence in support of an initial spread across the Pacific consistent with WWII activities.

Biological Invasions↗

USGS2025

Understanding and predicting infection dynamics for an endangered amphibian using long-term surveys of wild and translocated frogs

Amphibians are a prominent component of Earth's sixth mass extinction and the fungal pathogen Batrachochytrium dendrobatidis (Bd) is a primary driver of declines. Although Bd dynamics are well studied, the environmental drivers, exacerbating risk factors, and value of conservation interventions like translocations remain challenging to predict. Here, we present results from two decades of Bd monitoring for mountain yellow-legged frogs ( Rana muscosa) in the southern California Transverse and Peninsular mountain ranges. We describe Bd prevalence and infection intensity across sites; model how variables associated with climate, habitat, and populations relate to prevalence; and integrate Bd data from wild and translocated frogs to test whether a machine learning system can predict infection prevalence at new sites. Our findings indicate substantial spatiotemporal variation in Bd dynamics. Bd was present at all sites but prevalence and infection intensities were often low. Environmental features including temperature, precipitation, vegetation, and shortwave radiation explained significant variation in Bd prevalence, but their predictive value varied across mountain ranges. Although clear environmental predictors across populations remain elusive, we provide evidence for the importance of warmer and wetter springs and winters, with implications of increased risk under climate change predictions. We also found evidence for higher Bd prevalence among translocated than wild frogs. Although our machine learning model predicted a Bd prevalence threshold with relatively high accuracy, understanding the factors driving within- and between-population Bd dynamics is complex. Taken together, our findings provide new insights into the complicated role of Bd in amphibian declines and suggest revised management approaches.

California↗

USGS2024

Intrinsic and environmental drivers of pairwise cohesion in wild Canis social groups

Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group-level processes such as subgroup formation and fission–fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals. We tracked 574 individuals from six species within the genus Canis in 15 countries on four continents with GPS telemetry to estimate the time that pairs of individuals within social groups spent in close proximity and test hypotheses regarding drivers of cohesion. Pairs of social canids ( Canis spp.) varied widely in the proportion of time they spent together (5%–100%) during seasonal monitoring periods relative to both intrinsic characteristics and environmental conditions. The majority of our data came from three species of wolves (gray wolves, eastern wolves, and red wolves) and coyotes. For these species, cohesion within social groups was greatest between breeding pairs and varied seasonally as the nature of cooperative activities changed relative to annual life history patterns. Across species, wolves were more cohesive than coyotes. For wolves, pairs were less cohesive in larger groups, and when suitable, small prey was present reflecting the constraints of food resources and intragroup competition on social associations. Pair cohesion in wolves declined with increased anthropogenic modification of the landscape and greater climatic variability, underscoring challenges for conserving social top predators in a changing world. We show that pairwise cohesion in social groups varies strongly both within and across Canis species, as individuals respond to changing ecological context defined by resources, competition, and anthropogenic disturbance. Our work highlights that cohesion is a highly plastic component of animal sociality that holds significant promise for elucidating ecological and evolutionary mechanisms underlying cooperative behavior.

Ecology↗

USGS2024

Amphibian richness, rarity, threats, and conservation prospects across the U.S. National Park System

We assessed amphibian diversity, rarity, and threats across the National Park System (U.S.A.), which covers 3.5% of the country and 12% of federal lands. At least 230 of 354 (65%) amphibian species documented in the country occur on National Park Service lands. Of species in parks, 17% are at-risk globally and 20% are uncategorized, reflecting still-widespread data deficiencies. National parks in the Northwest and Northeast had the steepest species‒area relationships. Non-native crayfishes and amphibians occur within 50 km of 60% and 25% of parks, respectively, illustrating the broad threat of non-native predators. Projected mid-century (2040–2069) changes in climatic water deficit, based on 25 climate futures, produced an expected 34% increase in dryness across all national parks in the conterminous U.S.A. Our analyses highlight the extent and regional differences in current and future threats and reveal gaps in species protection, but also reveal opportunities for targeted expansion and active management.

npj Biodiversity↗

USGS2024

Quantification of threats to bats at localized spatial scales for conservation and management

In a rapidly changing world, where species conservation needs vary by local habitat, concentrated conservation efforts at small spatial scales can be critical. Bats provide an array of value to the ecosystems they inhabit; many bat species are also of conservation concern. San Diego County, California, contains 22 of the 41 bat species that occur in the United States, 16 of which are on conservation watchlists. Thus, management of bat communities in San Diego County is a pressing need. Because bats exploit vast areas of the landscape and historical sampling strategies have shifted over time, a standardized way of prioritizing areas of the landscape for management would provide an integral asset to bat conservation. We leveraged long-term bat community survey data from sampling areas across San Diego County to prioritize areas with the most management need. We calculated two types of scores: species scores and threat scores. Species scores incorporated richness and conservation status, and threat scores included landscape level threats that bats could encounter. We found that urbanization, the presence of artificial lights, and areas sampled on unconserved land were all significantly associated with decreases in species richness. Further, using species and threat scores, each sampling area was placed into one of four conservation categories, in order from greatest to least conservation need, ranging from highest priority (high species score, high threat score) to lowest (low species score, low threat score). Additionally, we focused on sampling areas in which Townsend’s big-eared bat ( Corynorhinus townsendii ) and/or pallid bat ( Antrozous pallidus ) occurred. These two species are of exceptional conservation concern in San Diego County and across the western United States. We identified urbanization, the presence of artificial lights, and areas sampled on unconserved land as threats that were all significantly associated with the absence of Townsend’s big-eared bat, but not pallid bat. The strategy, methodology, and solutions proposed in our study should assist bat conservation and management efforts wherever bats occur, and can be extended to other species that require conservation attention.

California↗

USGS2024

Effects of temporal hydrologic shifts on the population biology of an endangered freshwater fish in a dryland river ecosystem

Species occupying dryland river ecosystems often experience “boom-and-bust” demographic cycles that coincide with shifts in habitat availability. Knowing whether declines are within natural thresholds versus those caused by acute human disturbance is critical for managing protected species. We investigated temporal shifts in abundance and habitat use of an endangered population of the threespine stickleback Gasterosteus aculeatus in southern California, where a Mediterranean climate leads to ephemeral habitat in one of the regions' least hydrologically modified rivers, the Santa Clara River. We conducted population surveys over a period of below-average rainfall in the upper watershed in Soledad Canyon, with predefined reaches surveyed multiple times per year to capture different hydrologic conditions. Abundances were stable across years but varied significantly depending on location, with some reaches remaining dry and others drying seasonally to varying degrees. Occupancy models showed that the presence of stable perennial reaches, drying regime, and other site-specific factors were important predictors of habitat use, and that certain reaches may be key to ensuring source-sink dynamics as flow dissipates over the dry season. Low occupancy in two sections was driven by different predominant mechanisms, one by diel cycles of evapotranspiration and the other by cattails ( Typha spp.), with both having greater effects during the hotter, drier parts of the year. As dryland river ecosystems are vulnerable to the effects of anthropogenic-induced climate change, this study demonstrates how temporal monitoring can delimit dry-state benchmarks for improving management interventions (i.e., translocation and habitat restoration) for protected species under conditions that are predicted to worsen in the coming years.

California↗

USGS2024

Conservation genetics of the endangered California Freshwater Shrimp (Syncaris pacifica): Watershed and stream networks define gene pool boundaries

Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica . Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, F ST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, F ST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (N e = 62.4–147.1). Genetic diversity was variable across sites and watersheds ( H e = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity.

California↗

USGS2024

Long-term occupancy monitoring reveals value of moderate disturbance for an open-habitat specialist, the Stephens' kangaroo rat (Dipodomys stephensi)

For species of conservation concern, long-term monitoring is vital to properly characterize changes in population distribution and abundance over time. In addition, long-term monitoring guides management decisions by informing and evaluating the efficacy of management actions. A long-term monitoring initiative for the federally threatened Stephens' Kangaroo rat ( Dipodomys stephensi, SKR) was established in 2005, across 628 hectares within Marine Corps Base Camp Pendleton (MCBCP), San Diego, California, USA. From 2005 to 2018, we tracked trends in area occupied by SKR, trends in relative SKR densities within occupied habitat, and modeled probabilities of SKR occupancy, colonization, extinction, with habitat, climate, and disturbance covariates. Area occupied by SKR increased almost 2-fold from 2005 to 2018 on MCBCP, while density in occupied habitat increased almost 3-fold. Increased area occupied was correlated with increases in estimated density among years, indicating SKR population growth occurs by expansion into suitable habitat patches, as well as increases in numbers within occupied habitat. SKR occupancy was positively associated with gentle slopes (<10%) and moderate open ground (40–80%) and forb cover (>40%). They were more likely to colonize previously unoccupied habitat when there were moderate levels of open ground (40–80%) and low shrub cover (<20%), while more likely to go locally extinct in areas with high slopes (>10%), less open ground (<20%), and increased non-native grass cover (>40%). Additionally, probabilities of SKR occupancy and colonization were higher in areas with moderate levels of disturbance, which was positively associated with open ground and forb cover. We conclude that long-term occupancy and density monitoring is effective in informing status and trends of spatially dynamic species and that moderate habitat-based disturbance is compatible with the management of SKR.

California↗

USGS2024

A dataset of amphibian species in U.S. National Parks

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park units have a list of amphibian species observed within their borders compiled from various sources and available publicly through the NPSpecies platform. However, many of the observations in NPSpecies remain unverified and the lists are often outdated. We updated the amphibian dataset for each park unit by collating old and new park-level records and had them verified by regional experts. The new dataset contains occurrence records for 292 of the 424 NPS units and includes updated taxonomy, international and state conservation rankings, hyperlinks to a supporting reference for each record, specific notes, and related fields which can be used to better understand and manage amphibian biodiversity within a single park or group of parks.

Scientific Data↗

USGS2024

Variation in dietary ecology of two invasive American Bullfrog (Lithobates catesbeianus) populations in Southern California

Invasive American Bullfrogs (Lithobates catesbeianus) are a threat to native species in riparian ecosystems worldwide. They are indiscriminate predators consuming both vertebrate and invertebrate prey, negatively affecting biodiversity. Documenting the diet and feeding ecology of invasive L. catesbeianus can help management agencies identify affected species and facilitate eradication efforts. We present a dietary analysis of two invasive L. catesbeianus populations over multiple breeding seasons (2016–2020), elucidating ontogenetic changes in diet and dietary differences between sexes and habitats. This is the first study to analyze dietary variation from contemporary populations of invasive L. catesbeianus occupying different watersheds in Southern California, an area where their invasion presents acute conservation challenges. Our analysis of 667 gut contents shows that adult females had more prey in their guts than adult males, even though male and female body size was not significantly different. Adults were more likely than juveniles to consume vertebrate prey, and juveniles were more likely than adults to have empty stomachs. We also found that invasive Red Swamp Crayfish (Procambarus clarkii), made up a substantial portion of the diet of adult L. catesbeianus at the site where they were present. These results provide an important ecological context for designing mitigation actions that ameliorate the impacts of invasive L. catesbeianus.

California↗