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The Arizona Toad (Anaxyrus microscaphus) is restricted to riverine corridors and adjacent uplands in the arid southwestern United States. As with numerous amphibians worldwide, populations are declining and face various known or suspected threats, from disease to habitat modification resulting from climate change. The Arizona Toad has been petitioned to be listed under the U.S. Endangered Species Act and was considered “warranted but precluded” citing the need for additional information – particularly regarding natural history (e.g., connectivity and dispersal ability). The objectives of this study were to characterize population structure and genetic diversity across the species’ range. We used reduced-representation genomic sequencing to genotype 3,601 single nucleotide polymorphisms in 99 Arizona Toads from ten drainages across its range. Multiple analytical methods revealed two distinct genetic groups bisected by the Colorado River; one in the northwestern portion of the range in northwestern Arizona, southwestern Utah, and eastern Nevada and the other in the southeastern portion of the range in central and eastern Arizona and New Mexico. We also found subtle substructure within both groups, particularly in central Arizona where toad populations in lower elevations were less connected than those at higher elevations. The northern and southern parts of the Arizona Toad range are not well connected genetically and could be managed as separate units. Further, these data could be used to identify source populations for assisted migration or translocations to support small or potentially declining populations.

Recent ARMI-led research showed the removal of invasive American bullfrogs from livestock ponds and small lakes in southern Arizona also resulted in the apparent local extirpation of two pathogens associated with the bullfrogs. The American bullfrog is native eastern North America but has become widespread in the West, where it preys on many native species of conservation concern. Other recent ARMI-led research from the area suggested that American Bullfrogs could act as reservoirs for pathogens like amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) and ranaviruses, which are often lethal to native amphibians, but less so to American Bullfrogs.

In the early 2000s, American bullfrogs were eradicated from ponds in the Buenos Aires National Wildlife Refuge near the Arizona-Mexico border to assist with the reintroduction efforts for the federally threatened Chiricahua Leopard Frog. In 2015, the bullfrog reinvaded the refuge and was once again removed. This reinvasion from outside the refuge motivated funding for a multi-year, landscape-scale eradication program. In the fall-winter of 2016 and the winter of 2020-2021, the research team tested the water at bullfrog eradication and control (no eradication efforts occurred) sites for the DNA (environmental DNA or eDNA) of invasive bullfrogs, federally threatened Chiricahua Leopard Frogs, and Bd and ranaviruses.

Results from the eDNA sampling showed American Bullfrogs were eradicated successfully from most sites, and where bullfrogs were eradicated, the pathogens were also no longer detected. Chiricahua Leopard Frogs did not increase in occurrence after eradicating bullfrogs, possibly due to an exceptional drought that could have limited the ability of native amphibians to colonize sites.

To our knowledge, this is one of the few studies to link eradication of an invasive species to co-eradication of emerging pathogens. Our spatially replicated experimental approach provides strong evidence that management of invasive species can simultaneously reduce predation and disease risk for imperiled species.

To view the full article click this link: https://doi.org/10.1111/conl.12970

Interventions of host-pathogen dynamics provide strong tests of relationships, yet they are still rarely applied across multiple populations. After American Bullfrogs (Rana catesbeiana) invaded a wildlife refuge where federally threatened Chiricahua Leopard Frogs (R. chiricahuensis) were reintroduced 12 years prior, managers launched a landscape-scale eradication effort to help ensure continued recovery of the native species. We used a before-after-control-impact (BACI) design and environmental DNA sampling of 19 eradication sites and 18 control sites between fall 2016 and winter 2020–2021 to measure community-level responses to bullfrog eradication, including for 2 pathogens. Dynamic occupancy models revealed successful eradication from 94% of treatment sites. Native amphibians did not respond to bullfrog eradication, but the pathogens amphibian chytrid fungus (Batrachochytrium dendrobatidis) and ranaviruses were co-extirpated with bullfrogs. Our spatially replicated experimental approach provides strong evidence that management of invasive species can simultaneously reduce predation and disease risk for imperiled species.

Invasive species and emerging infectious diseases are two of the greatest
threats to biodiversity. American Bullfrogs (Rana [Lithobates] catesbeiana),
which have been introduced to many parts of the world, are often linked with
declines in native amphibians via predation and the spread of emerging pathogens
such as amphibian chytrid fungus (Batrachochytrium dendrobatidis [Bd])
and ranaviruses. Although many studies have investigated the potential role of
bullfrogs in the decline of native amphibians, analyses that account for shared
habitat affinities and imperfect detection have found limited support for
clear effects. Similarly, the role of bullfrogs in shaping the patch-level distribution
of pathogens is unclear. We used eDNA methods to sample 233 sites in the southwestern USA and Sonora, Mexico (2016–2018) to estimate how
the presence of bullfrogs affects the occurrence of four native amphibians,
Bd, and ranaviruses. Based on two-species, dominant-subordinate occupancy
models fitted in a Bayesian context, federally threatened Chiricahua Leopard
Frogs (Rana chiricahuensis) and Western Tiger Salamanders (Ambystoma
mavortium) were eight times (32% vs. 4%) and two times (36% vs. 18%), respectively,
less likely to occur at sites where bullfrogs occurred. Evidence for the
negative effects of bullfrogs on Lowland Leopard Frogs (Rana yavapaiensis)
and Northern Leopard Frogs (Rana pipiens) was less clear, possibly because of
smaller numbers of sites where these native species still occurred and because
bullfrogs often occur at lower densities in streams, the primary habitat for
Lowland Leopard Frogs. At the community level, Bd was most likely to occur
where bullfrogs co-occurred with native amphibians, which could increase the
risk to native species. Ranaviruses were estimated to occur at 33% of bullfrogonly
sites, 10% of sites where bullfrogs and native amphibians co-occurred,
and only 3% of sites where only native amphibians occurred. Of the 85 sites
where we did not detect any of the five target amphibian species, we also did
not detect Bd or ranaviruses; this suggests other hosts do not drive the distribution
of these pathogens in our study area. Our results provide landscape-scale
evidence that bullfrogs reduce the occurrence of native amphibians and
increase the occurrence of pathogens, information that can clarify risks and
aid the prioritization of conservation actions.

Dr. Cecil Schwalbe passed away on 3 April 2022 from complications after a heart attack and pneumonia. Cecil was one of the early Principal Investigators for ARMI. His lab provided long term data from the desert southwest on summer breeding amphibians, bullfrog eradication, disease, and leopard frog conservation. Cecil’s work at Buenos Aires National Wildlife Refuge laid a foundation for additional ARMI efforts in expanding model development on occupancy, spatially explicit metapopulation theory, Chiricahua leopard frog survival, and habitat connectivity. ARMI post doc Richard Chandler and graduate students Chris Jarchow and Paige Howell led this work, but Cecil was supportive and interested in the research and how it contributed to conservation efforts (e.g., Chandler et al. 2015, Jarchow et al. 2016, Howell et al. 2016, 2018, 2019).

Cecil also contributed to collaborative ARMI efforts (e.g., Muths et al. 2005) and was always present at ARMI meetings to keep things field-oriented and to maintain an appropriate sense of humor. He retired from ARMI and the USGS in 2013, but remained active in the herpetological community. Cecil was an old-school herpetologist and while he would rather be investigating frog populations in the field or showing Gila monsters to school kids, he would thoughtfully listen to the reasoning behind monitoring protocols and models and provide input on field implementation for ARMI projects.

In addition to his PhD in zoology and physiology from the University of Arizona and a master’s degree from Washington State, Cecil held a bachelor’s degree in mechanical engineering from Rice University and was Arizona’s first State Herpetologist. His enthusiasm and dedication to conservation influenced many young scientists including some of us in ARMI. In recognition of his mentoring and influence, Cecil received the Jarchow Conservation Award in 1997 and the Charlie W. Painter Memorial Award in 2021 from SW Partners in Amphibian and Reptile Conservation.

Cecil is survived by his wife Carol, sons Adam and Ethan, two granddaughters, and his sister. The family requests that in lieu of flowers, donations be made in memory of Cecil, to the Cold-Blooded Research Fund in the School of Natural Resources and the Environment at the University of Arizona: https://give.uafoundation.org/cecilschwalbe. In keeping with Cecil’s profession and passion, the annual payout from this endowed fund will support research awards for undergraduate students, graduate students and faculty members who are studying amphibians, reptiles, or fish.

Cecil’s laugh and his off-color sense of humor will be missed by all of us and the herpetofauna that he cared about.

For species with variable phenology, it is often challenging to produce reliable estimates of population dynamics or changes in occupancy. The Arizona Toad (Anaxyrus microscaphus) is a southwestern USA endemic that has been petitioned for legal protection, but status assessments are limited by a lack of information on population trends. Also, timing and consistency of Arizona Toad breeding varies greatly, making it difficult to predict optimal survey times or effort required for detection. To help fill these information gaps, we conducted breeding season call surveys during 2013–2016 and 2019 at 86 historically occupied sites and 59 control sites across the species’ range in New Mexico. We estimated variation in mean dates of arrival and departure from breeding sites, changes in occupancy, and site-level extinction since 1959 with recently developed multi-season staggered-entry models, which relax the within-season closure assumption common to most occupancy models. Optimal timing of surveys in our study areas was approximately March 5 - March 30. Averaged across years, estimated probability of occupancy was https://0.58 (SE = 0.09) for historical sites and https://0.19 (SE = 0.08) for control sites. Occupancy increased from 2013 through 2019. Notably, even though observer error was trivial, annual detection probabilities varied from https://0.23 to https://0.75 and declined during the study; this means naïve occupancy values would have been misleading, indicating apparent declines in toad occupancy. Occupancy was lowest during the first year of the study, possibly due to changes in stream flows and conditions in many waterbodies following extended drought and recent wildfires. Although within-season closure was violated by variable calling phenology, simple multi-season models provided nearly identical estimates as staggered-entry models. Surprisingly, extinction probability was unrelated to the number of years since the first or last record at historically occupied sites. Collectively, our results suggest a lack of large, recent declines in occupancy by Arizona Toads in New Mexico, but we still lack population information from most of the species’ range.

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

Data release and code for Ecological Applications paper: A statistical forecasting approach to metapopulation viability analysis

The Buenos Aires National Wildlife Refuge (BANWR) has developed a new pond designed to replicate ciénega conditions that will provide habitat for the federally threatened Chiricahua leopard frog. Reintroduced to the Refuge after extirpation in the early 2000s, the Chiricahua leopard frog has colonized areas beyond the initial reintroduction sites, now inhabiting several human-made stock tanks on the Refuge. The species’ persistence on the Refuge depends on the ongoing eradication of invasive bullfrogs and the availability of water. In desert habitats such as BANWR, the ciénega (a Spanish word for wetland) is a marsh-like habitat that is critical for numerous desert-dwelling creatures. Ciénegas on BANWR are characterized by a spring or seep that saturates the soil and allows water to pool in small areas (Hendrickson and Minckley, 1985). Ciénega vegetation includes rushes, watercress, and smartweed; they are often bordered by cottonwood and willow trees which the Refuge will plant at the new ciénega once the water has settled into the excavated depression. The new ciénega on BANWR is plumbed, meaning that water levels can be modified and maintained in response to environmental conditions that range from multi-year droughts to heavy monsoon conditions (Bezy et. al. 2007).

ARMI has collected data at BANWR since 2000, gathering information about native species (e.g., Chandler et al. 2015, Jarchow et al. 2016, , Howell et al. 2018, 2020a), invasive species such as American bullfrogs and sunfish (Suhr 2010, Howell et al. 2020b), and disease (Sigafus et al. 2014). Models assessing occupancy and movement of the Chiricahua leopard frog indicate that water availability and permanency are critical components to the its persistence at BANWR. The Refuge has used this information to make decisions about management actions such as building plumbed ponds — a non-trivial action in terms of cost and logistics. The new ciénega will not only support the Chiricahua leopard frog but will provide water for many other species that call BANWR home including the federally endangered masked bobwhite quail, great blue herons, yellow-billed cuckoos, and pronghorn.

Bezy, J., C. F. Hutchinson, and C. J. Bahre. 2007. Buenos Aires National Wildlife Refuge, 373 Arizona. Desert Plants 23:3–44.

Chandler, R., E. Muths, B. H. Sigafus, C.R. Schwalbe, C. Jarchow, and B.R. Hossack. 2015. Realizing the potential of spatially explicit metapopulation theory for predicting extinction risk. Journal of Applied Ecology. DOI: 10.1111/1365-2664.12481.

Howell, P., E. Muths, B.R. Hossack, B.H. Sigafus, and R.B. Chandler. 2018. Increasing connectivity between metapopulation ecology and landscape ecology. Ecology 99: 1119-1128.

Howell, P.E., B.R. Hossack, E. Muths, B. Sigafus, A. Chenevert- Steffler, and R. Chandler. 2020a. A statistical forecasting approach to metapopulation viability analysis. Ecological Applications 30(2), e02038

Howell, P.E. E. Muths, B.H. Sigafus, and B.R. Hossack. 2020b. Survival estimates for the invasive American bullfrog. Amphibia-Reptilia.

Hendrickson, D. A. and W. L. Minckley. 1985. Ciénegas vanishing climax communities of the American southwest. Desert Plants 6 (3): 131-175.

Sigafus, B. H., C.R. Schwalbe, B.R. Hossack, and E. Muths. 2014. Prevalence of the amphibian chytrid fungus at Buenos Aires National Wildlife Refuge, Arizona. Herpetological Review 45: 41-42.

Suhre, D. O. 2010. Dispersal and demography of the American Bullfrog (Rana catesbeiana) in a 455 semi-arid grassland. M.S. Thesis, University of Arizona, USA.

Jarchow, C.J., and Sigafus, B.H., 2019, Surface water data for isolated stock ponds in southern Arizona, USA and northern Sonora, Mexico: U.S. Geological Survey data release, https://doi.org/10.5066/P95ZFPT1.

We used five years of capture mark-recapture data to estimate annual apparent survival of post-metamorphic bullfrogs in a population on the Buenos Aires National Wildlife Refuge in their invaded range in Arizona, U.S.A.

Small waterbodies are numerically dominant in many landscapes and provide several important ecosystem services, but automated measurement of waterbodies smaller than a standard Landsat pixel (https://0.09 ha) remains challenging. To further evaluate sub-Landsat pixel techniques for estimating inundation extent of small waterbodies (basin area: https://0.06 – https://1.79 ha), we used a partial spectral unmixing method with matched filtering applied to September 1985–2018 Landsat 5 and 8 imagery from southern Arizona, USA. We estimated trends in modeled surface water area each September and evaluated the ability of several common drought indices to explain variation in mean water area. Our methods accurately classified waterbodies as dry or inundated (Landsat 5: 91.3%; Landsat 8: 98.9%) and modeled and digitized surface water areas were strongly correlated (R2 = https://0.70 – https://0.92; bias = -https://0.024 – -https://0.015 ha). Estimated surface water area was best explained by the 3-month seasonal standardized precipitation index (SPI03; July?September) and. We found a wide range of estimated relationships between drought indices (e.g., SPI vs. Palmer Drought Severity Index) and estimated water area, even for different durations of the same drought index (e. g., SPI01 vs SPI12). Mean surface area of waterbodies decreased by ~14% from September 1985 to September 2018, which matched declines in annual precipitation in the area and is consistent with broader trends of reduced inundation extent based on larger waterbodies. Estimated of surface water area and trends over time were also consistent when we limited analyses to waterbodies ? https://0.04 ha or those that varied most in size (based on CV). These results emphasize the importance of understanding local systems when relying on drought indices to infer variation in past or future surface water dynamics. Several challenges remain before widespread application of sub-pixel methods is feasible, but our results provide further evidence that partial spectral unmixing with matched filtering provides reliable measures of inundation extent of small waterbodies.

In metapopulations, dispersal and population growth rates are influenced by patch quality, spatial structure, and local population density. Recently developed spatial metapopulation models allow inferences about distance effects on dispersal, but these models typically focus on patch occupancy rather than abundance of animals. Spatial occupancy models are useful for studying colonization-extinction dynamics, but richer insights can be gained from estimating abundance and density-dependent demographic rates. We used presence-absence and count data from an 11-year study of a reintroduced metapopulation of federally-threatened Chiricahua leopard frogs (Lithobates chiricahuensis) to develop an integrated abundance-based metapopulation model to draw inferences about the processes contributing to spatiotemporal variation in density. Pond-specific population growth was influenced by pond hydroperiod and frog density, such that permanent and semi-permanent ponds with low densities of adult frogs experienced the highest annual population growth. Immigration rate declined as the distance among ponds increased. Metapopulation-level abundance increased from 2004 until 2015, when it stabilized around 1323 adult frogs (95% CI, 1166–1539). Further, changes in metapopulation abundance were driven mostly by changes in abundance at a few ponds. These high-density populations, which would not have been identifiable with traditional metapopulation models, are likely especially important for species recovery in the area. Our study extends existing statistical models of metapopulation dynamics by focusing on abundance and making it possible to test hypotheses regarding the influence of pond quality and density on local dynamics and colonization.

Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on
distributions and threats often hinders management. To provide information on the distribution of the Western Tiger
Salamander (Ambystoma mavortium), including the USA-federally endangered Sonoran Tiger Salamander (Ambystoma
mavortium stebbinsi), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample
91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by
introgressive hybridization and potential replacement by another sub-species of theWestern Tiger Salamander, the non-native
Barred Tiger Salamander (A. m. mavortium). Based on occupancy models that accounted for imperfect detection, eDNA
sampling provided a similar detection probability (https://0.82 [95% CI: 0.56-0.94]) as seining (https://0.83 [0.46-0.96]) and much higher
detection than dip-netting (https://0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid
sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora.
These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps
aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be
reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we
detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is
an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

Many natural wetlands around the world have disappeared or been replaced, resulting in the dependence of many wildlife species on small, artificial earthen stock ponds. These ponds provide critical wildlife habitat, such that the accurate detection of water and assessment of inundation extent is required. We applied a full (linear spectral mixture analysis; LSMA) and partial (matched filtering; MF) spectral unmixing algorithm to a 2007 Landsat 5 and a 2014 Landsat 8 satellite image to determine the ability of a time-intensive (i.e., more spectral input; LSMA) vs. a more efficient (less spectral input; MF) spectral unmixing approach to detect and estimate surface water area of stock ponds in southern Arizona, USA and northern Sonora, Mexico. Spearman rank correlations (rs) between modeled and actual inundation areas less than a single Landsat pixel (< 900 m2) were low for both techniques (rs range = https://0.22 to 0.62), but improved for inundation areas > 900 m2 (rs range = https://0.34 to 0.70). Our results demonstrate that the MF approach can model ranked inundation extent of known pond locations with results comparable to or better than LSMA, but further refinement is required for estimating absolute inundation areas and mapping wetlands < 1 Landsat pixel.

Conservation of at-risk species is aided by reliable forecasts of the consequences of environmental change and management actions on population viability. Forecasts from conventional population viability analysis (PVA) are made using a two-step procedure in which parameters are estimated, or elicited from expert opinion, and then plugged into a stochastic population model without accounting for parameter uncertainty. Recently-developed statistical PVAs differ because forecasts are made conditional on models that are fitted to empirical data. The statistical forecasting approach allows for uncertainty about parameters, but it has rarely been applied in metapopulation contexts where spatially-explicit inference is needed about colonization and extinction dynamics and other forms of stochasticity that influence metapopulation viability. We conducted a statistical metapopulation viability analysis (MPVA) using 11 years of data on the federally-threatened Chiricahua leopard frog to forecast responses to landscape heterogeneity, drought, environmental stochasticity, and management. We evaluated several future environmental scenarios and pond restoration options designed to reduce extinction risk. Forecasts over a 50-yr time horizon indicated that metapopulation extinction risk was <8% for all scenarios, but uncertainty was high. Without pond restoration, extinction risk is forecasted to be 5.6% (95% CI: 0?60%) by year 2060. Restoring six ponds by increasing hydroperiod reduced extinction risk to 1.0% (0 ? 11%) in year 2060. We found little evidence that drought influences metapopulation viability when managers have the ability to maintain ponds that hold water throughout the year and are free of invasive species. Our study illustrates the utility of the spatially explicit statistical forecasting approach to MPVA in conservation planning efforts.

Invasive species are a major threat to the persistence of native species, particularly in systems where ephemeral aquatic habitats have been converted to or replaced by permanent water and predators such as fish have been introduced. Within the Altar Valley, Arizona, USA, the invasive American bullfrog (Lithobates [=Rana] catesbeianus) has been successfully eradicated to help recover Chiricahua leopard frogs (Lithobates chiricahuensis). However, other non-native predators including sunfish (Lepomis spp) are present in some permanent water bodies. During four consecutive years (2014-2017) we detected both the federally-threatened Chiricahua leopard frog and sunfish at one permanent water body in the Altar Valley. This suggests that despite the potential negative effect of predatory fish on amphibians, there may be conditions where the Chiricahua leopard frog may be able to co-occur with this non-native predator. A better understanding of rare situations of co-occurrence with non-native predators may contribute to our understanding of why co-occurrence happens in some but not all systems and whether conservation strategies can be developed in situations where complete eradication of non-native predators is infeasible.

We quantified the response of amphibian communities to climatic variability across the United States and Canada using more than 500,000 observations for 81 species across 86 study areas. We estimated the relationships between annual variation in climate variables and local colonization and persistence probabilities across more than 5000 surveyed sites. This allowed us to estimate sensitivity to change in five climate variables. Climate sensitivity differs greatly among eco-regions and depends on local climate, species life-history, and phylogeny. Local species richness was especially sensitive to changes in water availability during breeding and changes in winter temperature. These results allowed us to ask whether changing climate explains strong overall rates of decline in species richness observed in our data set. We found that recent change in the climate variables we measured does not explain why North American amphibian richness is rapidly declining, but does explain why some populations decline faster than others.&#8195;