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Papers & Reports Western pond turtles in the Mojave Desert? A review of their past, present, and possible future
Authors: J Lovich; G . Jefferson; Robert Reynolds; P Scott; H B Shaffer; Shellie Puffer; Sarah Greely; Kristy Cummings; Robert N Fisher; Katherin Meyer-Wilkins; Doug Gomez; Morgan Ford; Christopher D. Otahal
Date: 2021-05-25 | Outlet: Vertebrate Zoology 71:317-334.
The western pond turtle (WPT) was formerly considered a single species (Actinemys or Emys marmorata[I/}) that ranged from southern British Columbia, Canada to Baja California, México. More recently it was divided into a northern and a southern species. WPTs are found primarily in streams that drain into the Pacific Ocean, although scattered populations exist in endorheic drainages of the Great Basin and Mojave deserts. Populations in the Mojave Desert were long thought to be restricted to the Mojave River, but recently another population was documented in Piute Ponds, a terminal wetland complex associated with Amargosa Creek on Edwards Air Force Base. WPT fossils in the Mojave Desert are known from the Miocene to the Pleistocene. Recently, Pleistocene fossils have been found as far into the desert as Salt Springs, just south of Death Valley. The oldest fossil records suggest that WPTs were present in wetlands and drainages of the geological feature known as the Mojave block prior to the uplift of the Sierra Nevada Range about 8 Ma and prior to the ~ 3 Ma uplift of the Transverse Ranges. Archaeological records document use of turtles by Native Americans for food and cultural purposes 1,000 or more years ago at the Cronese Lakes on the lower Mojave River and Oro Grande on the upper river. The first modern publication documenting their presence in the Mojave River was 1861. Museum specimens were collected as early as 1937. These fossil and early literature records support the indigenous status of WPTs to the Mojave River. However, mtDNA-based genetic evidence shows that Mojave River turtles share an identical haplotype with turtles on the California coast. Limited nuclear data show some minor differences. Overdraft of the Mojave River for municipal and agricultural uses, urban development, and saltcedar expansion are threats to the continued survival of WPTs in the Mojave River.
Papers & Reports Resilience of native amphibian communities following catastrophic drought: evidence from a decade of regional-scale monitoring
Authors: W Moss; T McDevitt-Galles; Erin Muths; Steven Bobzien; J Purificato; P TJ Johnson
1. The increasing frequency and severity of drought has the potential to exacerbate existing global amphibian declines. However, interactions between drought and coincident stressors, coupled with high interannual variability in amphibian abundances, can mask the extent and underlying mechanisms of drought-induced declines. The application of dynamic occupancy modeling to longitudinal monitoring data estimates the effect of specific variables on population change, providing key insights into potential management strategies for drought resilience.
2. We synthesized a decade (2009 – 2019) of amphibian survey data from multiple monitoring programs across the California Bay Area and used occupancy modeling to estimate the influence of drought, invasive species, and land use on species’ persistence and colonization probabilities. The geographic and temporal scale of our dataset, consisting of 2574 surveys of seven species in 473 ponds, allowed us to quantify regional trends for an entire community of pond-breeding amphibians.
3. An extreme drought from 2012 – 2015 resulted in losses of breeding sites, with 51% of ponds drying in 2014 compared to <10% in non-drought years. Pond drying reduced persistence rates, and nearly every species exhibited reduced occupancy during the drought, with some species (American bullfrogs and California newts) declining by > 25%. Drought reduced occupancy via additional mechanisms beyond habitat loss; for example, lower spring precipitation (an important cue for breeding) was associated with reduced colonization.
4. During drought, native species’ persistence was higher in permanent relative to temporary ponds, even though these sites were also more likely to contain invasive fish and bullfrogs, which generally reduced native amphibian occupancy. Many of these permanent ponds dried during the worst year of drought, leading to extirpations of invasive species that appeared long-lasting. In contrast, native species rebounded quickly with returning rains and showed evidence of full recovery.
5. Synthesis and applications: Despite experiencing one of most severe droughts in a millennium, native species displayed high resilience. Due to longer recovery times by non-native relative to native species, drought presents a valuable management opportunity to remove invaders from key refugia, and we highlight the value of maintaining hydroperiod diversity to promote the persistence of multiple species.
2. We synthesized a decade (2009 – 2019) of amphibian survey data from multiple monitoring programs across the California Bay Area and used occupancy modeling to estimate the influence of drought, invasive species, and land use on species’ persistence and colonization probabilities. The geographic and temporal scale of our dataset, consisting of 2574 surveys of seven species in 473 ponds, allowed us to quantify regional trends for an entire community of pond-breeding amphibians.
3. An extreme drought from 2012 – 2015 resulted in losses of breeding sites, with 51% of ponds drying in 2014 compared to <10% in non-drought years. Pond drying reduced persistence rates, and nearly every species exhibited reduced occupancy during the drought, with some species (American bullfrogs and California newts) declining by > 25%. Drought reduced occupancy via additional mechanisms beyond habitat loss; for example, lower spring precipitation (an important cue for breeding) was associated with reduced colonization.
4. During drought, native species’ persistence was higher in permanent relative to temporary ponds, even though these sites were also more likely to contain invasive fish and bullfrogs, which generally reduced native amphibian occupancy. Many of these permanent ponds dried during the worst year of drought, leading to extirpations of invasive species that appeared long-lasting. In contrast, native species rebounded quickly with returning rains and showed evidence of full recovery.
5. Synthesis and applications: Despite experiencing one of most severe droughts in a millennium, native species displayed high resilience. Due to longer recovery times by non-native relative to native species, drought presents a valuable management opportunity to remove invaders from key refugia, and we highlight the value of maintaining hydroperiod diversity to promote the persistence of multiple species.
Papers & Reports Staggered-entry analysis of breeding and occupancy dynamics of Arizona Toads from historically occupied habitats of New Mexico, USA
Authors: M J Forzley; Mason J Ryan; I M Latella; J T Giermakowski; Erin Muths; Brent H Sigafus; Blake R Hossack
Date: 2021 | Outlet: Ichthyology & Herpetology
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.
Papers & Reports Thermal conditions predict intraspecific variation in senescence rate in frogs and toads
Authors: Hugo Cayuela; Rebecca M McCaffery; Thierry Frétey; Benedikt R Schmidt; Kurt Grossenbacher; Omar Lenzi; Blake R Hossack; Brad A Lambert; Johan Elmberg; J Merilä; J Gippet; David S Pilliod; Erin Muths
Date: 2021-11 | Outlet: PNAS
Variation in temperature is known to influence mortality patterns in ectotherms. Even though a few experimental studies on model organisms have reported a positive relationship between temperature and actuarial senescence (i.e., the increase in mortality risk with age), how variation in climate influences senescence rate across the range of a species is still poorly understood in free-ranging animals. We filled this knowledge gap by investigating the relationships linking senescence rate, adult lifespan, and climatic conditions using long-term, capture-recapture data from multiple amphibian populations. We considered two pairs of related anuran species from the Ranidae (Rana luteiventris, Rana temporaria) and Bufonidae (Anaxyrus boreas, Bufo bufo) families, which diverged more than 100 mya and are broadly distributed in North America and Europe. Senescence rates were positively associated with mean annual temperature in all species. In addition, lifespan was negatively correlated with mean annual temperature in all species except A. boreas. In both R. luteiventris and A. boreas, mean annual precipitation and human environmental footprint both had negligible effects on senescence rates or lifespans. Overall, our findings demonstrate the critical influence of thermal conditions on mortality patterns across anuran species from temperate regions. In the current context of further global temperature increase predicted by IPCC scenarios, a widespread acceleration of aging in amphibians is expected to occur in the decades to come, which might threaten even more seriously the viability of populations and exacerbate global decline.
Papers & Reports Sex-related differences in aging rate are associated with sex chromosome system in amphibians
Authors: Hugo Cayuela; J Lemaître; Jean-Paul Lena; Victor Ronget; Iñigo Martinez-Solano; Erin Muths; David S Pilliod; Jean-Francois Lemaitre
Date: 2021-12 | Outlet: Evolution
Sex-related differences in mortality are widespread in the living world. Although sexual selection and environmental conditions might drive sex-specific variation in lifespan, recent findings suggest that sex chromosome systems are also involved. However, the influence of sex chromosome systems on aging rate (i.e., the rate of increase of mortality with age), a mortality metric that only partially correlates with lifespan, has not been investigated so far, due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (with heterogametic females) sex-determination systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly switched over the past 200 million years we examine whether sex heterogamety can predict sex-differences in aging rates. We show that variation in aging rate only accounts for a moderate proportion of the variation in lifespan, similarly to what has been reported in mammals. Moreover, our results demonstrate that the system of genetic sex-determination has a critical impact on aging rate in clades that include closely related taxa with XY vs. ZW systems. In both systems the heterogametic sex experiences a higher aging rate compared to the homogametic sex. This new finding suggests that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex.
Papers & Reports Demography of the Oregon spotted frog along a hydrologically modified river
Authors: Jennifer C Rowe; Adam Duarte; Christopher A Pearl; Brome McCreary; P K Haggerty; John W Jones; Michael J Adams
Date: 2021-06-21 | Outlet: Ecosphere
Altered flow regimes can contribute to dissociation between life history strategies and environmental conditions, leading to reduced persistence reported for many wildlife populations inhabiting regulated rivers. The Oregon spotted frog (Rana pretiosa) is a threatened species occurring in floodplains, ponds, and wetlands in the Pacific Northwest with a core range in Oregon, USA. All life stages of R. pretiosa are reliant on aquatic habitats, and inundation patterns across the phenological timeline can have implications for population success. We conducted capture-mark-recapture (CMR) sampling of adult and subadult R. pretiosa at three sites along the Deschutes River downstream from two dams that regulate flows. We related the seasonal extent of inundated habitat at each site to monthly survival probabilities using a robust design CMR model. We also developed matrix projection models to simulate population dynamics into the future under current river flows. Monthly survival was strongly associated with the extent and variability of inundated habitat, suggesting some within-season fluctuations at higher water levels could be beneficial. Seasonal survival was lowest in the winter for all three sites, owing to limited water availability and the greater number of months within this season relative to other seasons. Population growth for the two river-connected sites was most strongly linked to adult survival, whereas population growth at the river-disconnected site was most strongly tied to survival in juvenile stages. This research identifies population effects of seasonally limited water and highlights conservation potential of enhancing survival of particularly influential life stages.
Papers & Reports Enhanced between-site biosecurity to minimize herpetofaunal disease-causing pathogen transmission
Authors: Deanna H Olson; K H Haman; M J Gray; Reid N Harris; T Thompson; M Iredale; M Christman; J Williams; Michael J Adams; Jennifer R Ballard
Date: 2021 | Outlet: Herpetological Review
We describe biotic and abiotic factors that interact with field work to contribute to gradients in human-mediated herpetofaunal pathogen transmission (i.e., translocation) risk between sites. Using biotic and abiotic criteria, we identify site conditions that correspond to high risk for pathogen import [to a site] or high risk for pathogen export [from a site] for implementation of enhanced between-site biosecurity procedures to forestall human-mediated pathogen transmission. Our field-site criteria are based on seven contexts of the pathogen (occurrence, habitat), host(s) (occurrence, habitat, species richness), and geography (distance/topography, geopolitical land use) (Table 1). We do not provide an explicit decision tree because site contexts can be complex, and single contexts may be weighted heavily in some biosecurity decisions, warranting case-by-case decisions. A more conceptual decision tree (Fig. 1) about pathogen export or import can be more flexibly applied as site context vary. Our aim is to provide a rapid process to develop a qualitative narrative to support decisions for between-site herpetological disease biosecurity.
Papers & Reports New Parish Records for Louisiana Amphibians and Reptiles
Authors: Brad M Glorioso
Date: 2021-06-01 | Outlet: Herpetological Review
Dundee and Rossman (1989) published distribution maps of Louisiana herpetofaunal species in The Amphibians and Reptiles of Louisiana over 30 years ago. Since then many records have been published, mostly in Herpetological Review, documenting additions to these original maps. Though many are single species additions, several compilations of new Louisiana records have been published (Boundy 1994, 1998; 2004; Rosenzweig et al. 2007; Boundy and Gregory 2012; Battaglia et al. 2015). Here I report a total of 22 records that help to fill distributional gaps primarily in southern Louisiana. Most records are a result of targeted surveys during work projects or opportunistic encounters by the author. Those records where the author is not listed as an observer were submitted by others to the author via email. All records are photo vouchers deposited in the Florida Museum of Natural History (FMNH) Herpetology collection. Charles D. Battaglia of the Louisiana Department of Wildlife and Fisheries (LDWF) and Coleman Sheehy of the FMNH verified species identification. All records represent new parish records unless otherwise stated as determined by a list compiled by now-retired LDWF state herpetologist Jeff Boundy and through queries at https://VertNet.org. I thank Raymond P. Kidder for his assistance with querying https://VertNet.org. This is contribution number XXX of the U.S. Geological Survey Amphibian Research and Monitoring Initiative (ARMI).
Papers & Reports Abundance of Gulf Coast Waterdogs (Necturus beyeri) along Bayou Lacombe, Saint Tammany Parish, Louisiana
Authors: Brad M Glorioso; Hardin J Waddle; L J Muse; S T Godfrey
Date: 2021-06-11 | Outlet: Journal of Herpetology
Few ecological studies have been conducted on Gulf Coast Waterdogs (Necturus beyeri), and published studies have focused on relatively small stream sections of 125 m to https://1.75 km. In 2015, we sampled Gulf Coast Waterdogs at 25 locations along a 13.4-km stretch of Bayou Lacombe (Saint Tammany Parish, Louisiana, USA) to better understand factors that may influence the distribution of Gulf Coast Waterdogs within streams. We checked 250 unbaited traps once per week for three weeks and captured 170 Gulf Coast Waterdogs at 18 of the 25 sites. We used hierarchical models of abundance to estimate abundance at each site as a function of site covariates including pH, turbidity, and distance from headwaters. The abundance of Gulf Coast Waterdogs within Bayou Lacombe was highest toward the center of the segment of stream we sampled, but we found no evidence that pH or turbidity affected abundance within our study area. Site level abundance estimates of Gulf Coast Waterdogs ranged from 0 to 82, and we estimated that there were 767 (95% Bayesian credible interval [CRI]: 266–983) Gulf Coast Waterdogs summed across all 25 sampling sites. We derived an estimate of 6,321 (95% CRI: 2,139–15,922) Gulf Coast Waterdogs for the entire 13.4 km section of Bayou Lacombe, which includes our 25 sites and the adjoining stream reaches between our sites. Our results suggest that Gulf Coast Waterdogs may be uncommon or absent in the headwaters, possibly because of shallow water and swift currents with little preferred habitats, and prefer the middle stream reaches with adequate depth and an abundance of preferred microhabitats.
Papers & Reports Enigmatic Near-Extinction in a Boreal Toad Metapopulation in Northwestern Montana
Authors: Rebecca M McCaffery; Robin E Russell; Blake R Hossack
Outlet: Journal of Wildlife Management
North America’s protected lands harbor significant biodiversity and provide habitats where species threatened by a variety of stressors in other environments can thrive. Yet disease, climate change, and other threats are not limited by land management boundaries and can interact with conditions within protected landscapes to affect sensitive populations. We examined the population dynamics of a boreal toad (Anaxyrus boreas) metapopulation at a wildlife refuge in northwestern Montana over a 16-year period (2003-2018). We used robust design capture-recapture models to estimate male population size, recruitment, and apparent survival over time and in relation to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. We estimated female population size in years with sufficient captures. Finally, we examined trends in male and female toad body size and condition. We found no evidence of an effect of disease or time on male toad survival but detected a strong negative trend in recruitment of new males to the population. Estimates of male and female abundance decreased dramatically over time. Body size of males and females was inversely related to estimated population size, consistent with reduced recruitment to replace adults, but body condition of adult males was only weakly associated with abundance. Together, these results describe the demography of a near-extinction event, and point to dramatic decreases in the recruitment of new individuals to the breeding population as the cause of this decline. We surmise that processes related to the restoration of historical hydrology within the refuge adversely affected amphibian breeding habitat, and that these changes interacted with disease, life history, and other factors to restrict the recruitment of new individuals to the breeding population over time. Our results point to challenges in understanding and predicting drivers of population change and highlight that current metrics for assessing population status can have limited predictive ability.
Papers & Reports Why disease ecology needs life-history theory: a host perspective
Authors: Andrés Valenzuela-Sánchez; M Wilbur; Stefano Canessa; Leonardo Bacigalupe; Erin Muths; Benedikt R Schmidt; A C Cunningham; A Ozgul; P TJ Johnson; Hugo Cayuela
Date: 2020-12 | Outlet: Ecology Letters
When facing an emerging infectious disease of conservation concern, we often have little
information on the nature of the host-parasite interaction to inform management decisions.
However, it is becoming increasingly clear that the life-history strategies of host species
can be predictive of individual- and population-level responses to infectious disease, even
without detailed knowledge on the specifics of the host-parasite interaction. Here, we argue
that a deeper integration of life-history theory into disease ecology is timely and necessary
to improve our capacity to understand, predict, and mitigate the impact of endemic and
emerging infectious diseases in wild populations. Using wild vertebrates as an example, we
show that host life-history characteristics influence host responses to parasitism at different
levels of organization, from individuals to communities. We also highlight knowledge gaps
and future directions for the study of life-history and host responses to parasitism. We
conclude by illustrating how this theoretical insight can inform the monitoring and control
of infectious diseases in wildlife.
information on the nature of the host-parasite interaction to inform management decisions.
However, it is becoming increasingly clear that the life-history strategies of host species
can be predictive of individual- and population-level responses to infectious disease, even
without detailed knowledge on the specifics of the host-parasite interaction. Here, we argue
that a deeper integration of life-history theory into disease ecology is timely and necessary
to improve our capacity to understand, predict, and mitigate the impact of endemic and
emerging infectious diseases in wild populations. Using wild vertebrates as an example, we
show that host life-history characteristics influence host responses to parasitism at different
levels of organization, from individuals to communities. We also highlight knowledge gaps
and future directions for the study of life-history and host responses to parasitism. We
conclude by illustrating how this theoretical insight can inform the monitoring and control
of infectious diseases in wildlife.
Papers & Reports Monitoring wetland water quality related to livestock grazing in amphibian habitats
Authors: Kelly L Smalling
Date: 2021-01-13 | Outlet: Environmental Monitoring and Assessment 193, 58
Land use alteration such as livestock grazing can affect water quality in habitats of at-risk wildlife species. Data from managed wetlands are needed to understand levels of exposure for aquatic life stages and monitor grazing-related changes afield. We quantified spatial and temporal variation in water quality in wetlands occupied by threatened Oregon spotted frog (Rana pretiosa) at Klamath Marsh National Wildlife Refuge in Oregon, US. We used analyses for censored data to evaluate the importance of habitat type and grazing history in predicting concentrations of nutrients, turbidity, fecal indicator bacteria (FIB; total coliforms, E. coli, and enterococci), and estrogenicity, an indicator of estrogenic activity. Nutrients (orthophosphate and ammonia) and enterococci varied over time and space, while E. coli, total coliforms, turbidity, and estrogenicity were more strongly associated with local livestock grazing metrics. Turbidity was correlated with several grazing-related constituents and may be particularly useful for monitoring water quality in landscapes with livestock use. Concentrations of orthophosphate and estrogenicity were elevated at several sites relative to published health benchmarks, and their potential effects on R. pretiosa warrant further investigation. Our data provided an initial assessment of potential exposure of amphibians to grazing related constituents in western US wetlands.
Papers & Reports Density dependence and adult survival drive dynamics in two high elevation amphibian populations
Authors: Amanda M Kissel; S Tenan; Erin Muths
Date: 2020-12-12 | Outlet: Diversity 2020, 12, 478; doi:10.3390/d12120478
Amphibian conservation has progressed from the identification of declines to mitigation, but efforts are hampered by the lack of nuanced information about the effects of environmental characteristics and stressors on mechanistic processes of population regulation. Challenges include a paucity of long-term data and scant information about the relative roles of extrinsic (e.g., weather) and intrinsic (e.g., density dependence) factors. We used a Bayesian formulation of an open population capture-recapture model and >30 years of data to examine intrinsic and extrinsic factors regulating two adult boreal chorus frogs (Pseudacris maculata) populations. We modelled population growth rate and apparent survival directly, assessed their temporal variability, and derived estimates of recruitment. Populations were relatively stable (geometric mean population growth rate >1), and regulated by negative density dependence (i.e., higher population sizes reduced population growth rate). In the smaller population, density dependence also acted on adult survival. In the larger population, higher population growth was associated with warmer autumns. Survival estimates ranged from https://0.30-0.87, per-capita recruitment was <1 in most years, and mean seniority probability was >https://0.50, suggesting adult survival is more important to population growth than recruitment. Our analysis indicates density dependence is a primary driver of population dynamics for P. maculata adults.
Papers & Reports Water Temperature and Availability Shape the Spatial Ecology of a Hot Springs Endemic Toad (Anaxyrus williamsi)
Authors: Brian J Halstead; Patrick M Kleeman; Jonathan P Rose; Kristen J Fouts
Date: 2021-02-26 | Outlet: Herpetologica
Desert amphibians are limited to exploiting ephemeral resources and aestivating or to inhabiting scarce refuges of permanent water, such as springs. Understanding how amphibians use these resources is essential for their conservation. Dixie Valley Toads (Anaxyrus williamsi) are precinctive to a small system of cold and hot springs in the Dixie Valley, Nevada, USA. The toads have been petitioned for listing under the US Endangered Species Act, and information about how they use terrestrial and aquatic resources will help managers to conserve the toads and identify threats like geothermal energy development that might affect these toads. We used radiotelemetry to study the seasonal home ranges, movements, and habitat associations of Dixie Valley Toads in autumn 2018 and spring 2019. We found that toads were very closely associated with water in both seasons, with most observations occurring in water, especially for males in spring and all toads in the autumn. Even when found in terrestrial habitat, toads were a median distance of 4.2 m (95% credible interval = 3.3–5.3) from water; 95% of the time in spring and autumn, toads were within 14 m of water. Dixie Valley Toad habitat selection indicated a similar pattern, with selection in both spring and autumn for locations closer to water and for warmer water and substrates than at nearby available locations. In autumn, toads also avoided bare ground and terrestrial graminoids. Dixie Valley Toads selected brumation sites in, over (within dense vegetation), or near water, often near springs where water depths and temperatures are likely stable through the winter. The reliance of Dixie Valley Toads on water in spring, autumn, and during brumation suggests that alteration to historical flows and water temperatures are likely to affect the toads. Changes to the hydrothermal environment when toads are brumating could be particularly detrimental, potentially killing inactive toads.
Papers & Reports Estimating the survival of unobservable life stages for a declining frog with a complex life-history.
Authors: Jonathan P Rose; Sarah J Kupferberg; Clara A Wheeler; Patrick M Kleeman; Brian J Halstead
Date: 2021-02-15 | Outlet: Ecosphere 12(2):e03381
Demographic models enhance understanding of drivers of population growth and inform conservation efforts to prevent population declines and extinction. For species with complex life histories, however, parameterizing demographic models is challenging because some life stages can be dif?cult to study directly. Integrated population models (IPMs) empower researchers to estimate vital rates for organisms that have cryptic or widely dispersing early life stages by integrating multiple demographic data sources. For a stream-inhabiting frog(Rana boylii) that is declining through much of its range in Oregon and California, USA, we collected egg-mass counts and capture–mark–recapture data on adults from two populations in California to ?t IPMs that estimate adult abundance and the survival rate of both marked and unobserved life stages. Estimates of adult abundance based on long-term monitoring of egg-mass counts showed that study populations ?uctuated greatly inter-annually but were stable at longer timescales (i.e., decades). Adult female survival during 5–6 yr of capture–mark–recapture study periods was nearly equal in each population. Survival rate of R. boylii eggs to the subadult stage is low on average (0.002) but highly variable among years depending on post-oviposition stream ?ow. Population viability analysis showed that survival of adult and subadult life stages has the greatest proportional effect on population growth; the survival of egg and tadpole life stages, however, is more malleable by management interventions. For example, simulations showed head-starting of tadpoles, salvaging stranded egg masses, and limiting aseasonal pulsed ?ows could dramatically reduce the threat of extirpation. This study demonstrates the value of integrating multiple demographic data sources to construct models of population dynamics in species with complex life histories.
Papers & Reports Conservation genomics of the threatened western spadefoot, Spea hammondii, in urbanized southern California
Authors: K M Neal; Robert N Fisher; M J Mitrovich; H B Shaffer
Date: 2020-11-27 | Outlet: Journal of Heredity 2020:613-627
Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least 2, and possibly 3 major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically, but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.
Papers & Reports Accommodating the role of site memory in dynamic species distribution models using detection/non-detection data
Authors: Graziella V DiRenzo; A David; Blake R Hossack; Brent H Sigafus; P E Howell; Evan HC Grant; Erin Muths
Outlet: Ecology xx:xxx-xxx
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.
Papers & Reports The influence of species life history and distribution characteristics on species responses to habitat fragmentation in an urban landscape
Authors: Staci M Amburgey; David AW Miller; Carlton J Rochester; Katy S Delaney; Seth PD Riley; Cheryl S Brehme; Stacie A Hathaway; Robert N Fisher
Date: 2021-01-20 | Outlet: Journal of Animal Ecology
1. Fragmentation within urbanized environments often leads to a loss of native species diversity; however, variation exists in responses among-species and among-populations within species.
2. We aimed to identify patterns in species biogeography in an urbanized landscape to understand anthropogenic effects on vertebrate communities and identify species that are more sensitive or resilient to landscape change.
3. We investigated patterns in species richness and species responses to fragmentation in southern Californian small vertebrate communities using multispecies occupancy models and determined factors associated with overall commonness and sensitivity to patch size for 45 small vertebrate species both among and within remaining non-developed patches.
4. In general, smaller patches had fewer species, with amphibian species richness being particularly sensitive to patch size effects. Mammals were generally more common, occurring both in a greater proportion of patches and a higher proportion of the sites within occupied patches. Alternatively, amphibians were generally restricted to larger patches but were more ubiquitous within smaller patches when occupied. Species range size was positively correlated with how common a species was across and within patches, even when controlling for only patches that fell within a species’ range. We found sensitivity to patch size was greater for more fecund species and depended on where the patch occurred within a species’ range. While all taxa were more likely to occur in patches in the warmer portions of their ranges, amphibians and mammals were more sensitive to fragmentation in these warmer areas as compared to the rest of their ranges. Similarly, amphibians occurred at a smaller proportion of sites within patches in drier portions of their ranges. Mammals occurred at a higher proportion of sites that were also in drier portions of their range while reptiles did not differ in their sensitivity to patch size by range position.
5. We demonstrate that taxonomy, life history, range size, and range position can predict commonness and sensitivity of species across this highly fragmented yet biodiverse landscape. The impacts of fragmentation on species communities within an urban landscape depend on scale, with differences emerging among and within species and populations.
2. We aimed to identify patterns in species biogeography in an urbanized landscape to understand anthropogenic effects on vertebrate communities and identify species that are more sensitive or resilient to landscape change.
3. We investigated patterns in species richness and species responses to fragmentation in southern Californian small vertebrate communities using multispecies occupancy models and determined factors associated with overall commonness and sensitivity to patch size for 45 small vertebrate species both among and within remaining non-developed patches.
4. In general, smaller patches had fewer species, with amphibian species richness being particularly sensitive to patch size effects. Mammals were generally more common, occurring both in a greater proportion of patches and a higher proportion of the sites within occupied patches. Alternatively, amphibians were generally restricted to larger patches but were more ubiquitous within smaller patches when occupied. Species range size was positively correlated with how common a species was across and within patches, even when controlling for only patches that fell within a species’ range. We found sensitivity to patch size was greater for more fecund species and depended on where the patch occurred within a species’ range. While all taxa were more likely to occur in patches in the warmer portions of their ranges, amphibians and mammals were more sensitive to fragmentation in these warmer areas as compared to the rest of their ranges. Similarly, amphibians occurred at a smaller proportion of sites within patches in drier portions of their ranges. Mammals occurred at a higher proportion of sites that were also in drier portions of their range while reptiles did not differ in their sensitivity to patch size by range position.
5. We demonstrate that taxonomy, life history, range size, and range position can predict commonness and sensitivity of species across this highly fragmented yet biodiverse landscape. The impacts of fragmentation on species communities within an urban landscape depend on scale, with differences emerging among and within species and populations.
Papers & Reports Experimental evaluation of spatial capture-recapture study design
Authors: Jill Fleming; Evan HC Grant; S C Sterrett; C Sutherland
Date: 2021-07-18 | Outlet: Ecological Applications
A principal challenge impeding strong inference in analyses of wild populations is the lack of robust and long-term data sets. Recent advancements in analytical tools used in wildlife science may increase our ability to integrate smaller data sets and enhance the statistical power of population estimates. One such advancement, the development of spatial capture-recapture (SCR) methods, explicitly accounts for differences in spatial study designs, making it possible to equate multiple study designs in one analysis. SCR has been shown to be robust to variation in design as long as minimal sampling guidance is adhered to. However, these expectations are based on simulation and have yet to be evaluated in wild populations. Here we conduct a rigorously designed field experiment by manipulating the arrangement of artificial cover objects (ACOs) used to collect data on red-backed salamanders (Plethodon cinereus) to empirically evaluate the effects of design configuration on inference made using SCR. Our results suggest that, using SCR, estimates of space use and detectability are sensitive to study design configuration, namely the spacing and extent of the array, and that caution is warranted when assigning biological interpretation to these parameters. However, estimates of population density remain robust to design except when the configuration of detectors grossly violates existing recommendations.
Papers & Reports The Coyote Mountains’ Desert Snail (Sonorelix harperi carrizoensis), a Lazarus Species with the First Documentation of Live Individuals
Authors: Robert N Fisher; S R Fisher
Date: 2020-08 | Outlet: Bulletin Southern California Academy of Sciences 119:49-54.
The Coyote Mountain desert snail (Sonorelix harperi carrizoensis) was described in 1937 from 30 dry shells collected the previous year. We reviewed the literature and museum records and found two additional shell collections for this subspecies from the type locality one from 1958, and one from an adjacent mountain range in 1938. There is no evidence previously of any live snails being collected from the Coyote Mountains, Imperial County, California. All shell collections of S. harperi carrizoensis have the same locality data as the type series, which is Painted Gorge, Coyote Mountains except for one recorded collection of shells from the Vallecito Mountains from 1938. Using geological maps and other data sources, a potential mesic habitat was identified in the Coyote Mountains. During recent field work for salamanders at this location we detected two live specimens of S. harperi carrizoensis approximately 2 km north of its type location. This new data confirms this subspecies is still extant and has occurred at least at two sites historically in these mountains. Despite the presence of mesic habitats (i.e., mosses, liverworts and ferns) at the type locality, we found no evidence of S. harperi carrizoensis or salamanders.