Geology ReportsSearch

Geology topics

Brian J. Halstead

Publications and source records attributed to Brian J. Halstead.

At least 55 records · Page 3Linked to original sources

Rural turtles: Estimating the occupancy of Northwestern Pond Turtles and non-native red-eared sliders in agricultural habitats in California's Sacramento Valley and Sacramento-San Joaquin River Delta

The Northwestern Pond Turtle ( Actinemys marmorata ; WPT) was once widespread throughout the Sacramento Valley and the Sacramento-San Joaquin River Delta. Much of its historical range has been converted into agricultural land, reducing and altering aquatic habitat and surrounding uplands. Red-eared Sliders ( Trachemys scripta elegans ; RES) have been introduced throughout much of the existing WPT range, particularly near urban centers, potentially competing with WPT for resources. Previous surveys for turtles in central California have primarily focused on rivers, lakes, and protected wetlands. Little is known about where WPT and RES occur in the vast expanses of agricultural land across the Sacramento Valley and Sacramento-San Joaquin River Delta. Using aquatic hoop nets, we surveyed 142 locations (102 irrigation canal sites, 39 wetlands, 1 tidally influenced slough) across 8 counties during the summers of 2018 and 2019. Both species were detected in agricultural habitats. Using occupancy modeling, we estimated that WPT occur at 44 (95% CRI = 38–53) of our trapping sites and RES occur at 51 (41–66) sampled sites. Co-occurrence of these 2 species was rare; the species were found together at only 6 sites. RES were primarily found in restored wetlands near major roads and the Sacramento metropolitan area, whereas WPT were more commonly found farther from urban areas in wider canals. Our work provides a picture of how WPT and RES occupy this modified agroecosystem that can inform future conservation efforts.

California

Are canned sardines or dry cat food more effective as bait for capturing Northwestern Pond Turtles (Actinemys marmorata) and Red-eared Sliders (Trachemys scripta elegans)?

During an occupancy study of Northwestern Pond Turtles ( Actinemys marmorata ) and Red-eared Sliders ( Trachemys scripta elegans ) in California’s Sacramento Valley in 2018, we tested the relative effectiveness of 2 bait types: sardines packed in soybean oil and Meow Mix ® Original Choice dry cat food. We sampled 116 sites with 2 traps each: one baited with sardines and one baited with dry cat food. Sardines were 1.7 (95% confidence interval, 1.2–2.6) times more effective than dry cat food at capturing turtles in our study, and 63% of all captured turtles were caught in traps baited with sardines. Despite the slightly lower capture rate in traps baited with dry cat food, the significantly lower cost of cat food (about one-tenth the cost of sardines) makes it an appealing alternative bait if cost-effectiveness is a primary concern.

California

Increased growth rates of stream salamanders following forest harvesting

Timber harvesting can influence headwater streams by altering stream productivity, with cascading effects on the food web and predators within, including stream salamanders. Although studies have examined shifts in salamander occupancy or abundance following timber harvest, few examine sublethal effects such as changes in growth and demography. To examine the effect of upland harvesting on growth of the stream-associated Ouachita dusky salamander ( Desmognathus brimleyorum ), we used capture–mark–recapture over three years at three headwater streams embedded in intensely managed pine forests in west-central Arkansas. The pine stands surrounding two of the streams were harvested, with retention of a 14- and 21-m-wide forested stream buffer on each side of the stream, whereas the third stream was an unharvested control. At the two treatment sites, measurements of newly metamorphosed salamanders were on average 4.0 and 5.7 mm larger post-harvest compared with pre-harvest. We next assessed the influence of timber harvest on growth of post-metamorphic salamanders with a hierarchical von Bertalanffy growth model that included an effect of harvest on growth rate. Using measurements from 839 individual D . brimleyorum recaptured between 1 and 6 times (total captures, n = 1229), we found growth rates to be 40% higher post-harvest. Our study is among the first to examine responses of individual stream salamanders to timber harvesting, and we discuss mechanisms that may be responsible for observed shifts in growth. Our results suggest timber harvest that includes retention of a riparian buffer (i.e., streamside management zone) may have short-term positive effects on juvenile stream salamander growth, potentially offsetting negative sublethal effects associated with harvest.

Arkansas

Conservation implications of spatiotemporal variation in the terrestrial ecology of Western spadefoots

Conservation of species reliant on ephemeral resources can be especially challenging in the face of a changing climate. Western spadefoots ( Spea hammondii ) are small burrowing anurans that breed in ephemeral pools, but adults spend the majority of their lives underground in adjacent terrestrial habitat. Western spadefoots are of conservation concern throughout their range because of habitat loss, but little is known about the activity patterns and ecology of their terrestrial life stage. We conducted a radio-telemetry study of adult western spadefoots at 2 sites in southern California, USA, from December 2018 to November 2019 to characterize their survival, behavior, and movements from breeding through aestivation to refine conservation and management for the species. Western spadefoot survival varied seasonally, with risk of mortality higher in the active season than during aestivation. The probability of movement between successive observations was higher during the winter and spring and when atmospheric moisture was high and soil water content at 10-cm depth was low. The amount of rain between observations had the strongest effect on the probability of movement between observations; for every 20 mm of rainfall between observations, western spadefoots were 2.4 times more likely to move. When movements occurred, movement rates were highest when both relative humidity and soil water content at 10-cm depth were high. The conditions under which western spadefoots were likely active on the surface, likely to have moved, and moved at the highest rates are conditions that reduce the risk of desiccation of surface-active spadefoots. Western spadefoot home range areas varied between study sites and were mostly <1 ha, although 1 individual's home range area was >6 ha. Western spadefoots rapidly dispersed from the breeding pools, and asymptotic distances from the breeding pool were generally reached by June. The asymptotic distance from the breeding pool varied between sites, with the 95th percentile of the posterior predictive distribution reaching 486 m at 1 site and 187 m at the other. Western spadefoots did not select most habitat components disproportionately to their availability, but at Crystal Cove State Park, they avoided most evaluated vegetation types (graminoids, forbs, and shrubs). Spatial variation was evident in most evaluated western spadefoot behaviors; context-dependent behavior suggests that site-specific management is likely necessary for western spadefoots. Furthermore, comparison with an earlier study of western spadefoots at Crystal Cove State Park indicated substantial temporal variation in western spadefoot behavior. Therefore, basing management decisions on short-term studies might fail to meet conservation objectives. Better understanding the influences of spatial context and climatic variation on western spadefoot behavior will improve conservation efforts for this species.

California

A tale of two valleys: Endangered species policy and the fate of the giant gartersnake

By the mid-20th Century, giant gartersnakes (Thamnophis gigas) had lost more than 90% of their Central Valley marsh habitat and were extirpated from more than two-thirds of their range. This massive habitat loss led to their inclusion in the inaugural list of rare species under the California Endangered Species Act (CESA). Listing under the CESA provided giant gartersnakes legal protection and mechanisms for recovery, and subsequent listing under the U.S. Endangered Species Act (U.S. ESA) further fortified these protections. But how effective has listing under these endangered species acts (ESAs) been at achieving their goal of giant gartersnake recovery? Herein, we review relevant aspects of giant gartersnake ecology, illustrate how listing has benefitted giant gartersnakes and what challenges have been faced in slowing declines and recovering populations, and chart a course towardprovide options for improved conservation, management, and recovery of giant gartersnakes. Although listing as threatened under both state and federal ESAs has not yet achieved recovery of giant gartersnakes, the increased knowledge gained and mechanisms for protecting giant gartersnake habitat on private and public lands developed over the past 50 years has improved conservation of this endemic California snake.

California

Estimating the survival of unobservable life stages for a declining frog with a complex life-history

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 difficult 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 fit 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 fluctuated 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 flow. 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 flows 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.

California

Time-to-detection occupancy methods: Performance and utility for improving efficiency of surveys

Occupancy methods propelled the quantitative study of species distributions forward by separating the observation process, or the imperfect detectability of species, from the ecological processes of interest governing species distributions. Occupancy studies come at a cost, however: the collection of additional data to account for nondetections at sites where the species is present. The most common occupancy designs (repeated measures designs) require repeat visits to sites or the use of multiple observers or detection methods. Time‐to‐detection methods have been identified as a potentially efficient alternative, requiring only one visit to each site by a single observer. A comparison of time‐to‐detection methods to repeated measures designs for visual encounter surveys would allow researchers to evaluate whether time‐to‐detection methods might be appropriate for their study system and can inform optimal survey design. We collected time‐to‐detection data during two different repeated measures design occupancy surveys for four amphibians and compared the performance of time‐to‐detection methods to the other designs using the location (potential bias) and precision of posterior distributions for occurrence parameters. We further used results of time‐to‐detection surveys to optimize survey design. Time‐to‐detection methods performed best for species that are widespread and have high detection probabilities and rates, but performed less well for cryptic species with lower probability of occurrence or whose detection was strongly affected by survey conditions. In all cases single surveys were most efficient in terms of person‐hours expended, but under some conditions the survey duration required to achieve high detection probabilities would be prohibitively long for a single survey. Regardless of occupancy survey design, time‐to‐detection methods provide important information that can be used to optimize surveys, allowing researchers and resource managers to efficiently achieve monitoring and conservation goals. Collecting time‐to‐detection data while conducting repeated measures occupancy surveys requires only small modifications to field methods but could have large benefits in terms of time spent surveying in the long‐term.

California

When introduced prey violates trophic hierarchy: Conservation of an endangered predator

Introduced species often disrupt established food webs, but some native predators can come to rely on introduced prey. Understanding the net effects of the non-natives on imperiled predators is crucial for planning conservation measures. The invasive American bullfrog ( Lithobates catesbeianus ) can be prey, predator, and competitor for the critically endangered San Francisco garter snake ( Thamnophis sirtalis tetrataenia ). We examined the seasonal prey use of a San Francisco garter snake population that co-occurs with American bullfrogs to examine intraguild predation between these species. Juvenile and adult snakes mainly consumed native anurans instead of American bullfrogs, and this diet pattern peaked in spring, a critical foraging period for the snakes. In spring, large adult American bullfrogs also foraged heavily on native anurans and displayed a high degree of diet overlap with San Francisco garter snakes. Invasive American bullfrogs are detrimental to San Francisco garter snakes mainly through seasonal competition rather than reciprocal predation. Removal of invasive species provided further evidence that eliminating American bullfrogs can benefit San Francisco garter snakes by reducing predation pressure on their shared amphibian prey. Better understanding the interactions of invasive species with native species of conservation concern informs management practices and improves conservation outcomes.

Biological Conservation

Metal accumulation varies with life history, size, and development of larval amphibians

Amphibian larvae are commonly used as indicators of aquatic ecosystem health because they are susceptible to contaminants. However, there is limited information on how species characteristics and trophic position influence contaminant loads in larval amphibians. Importantly, there remains a need to understand whether grazers (frogs and toads [anurans]) and predators (salamanders) provide comparable information on contaminant accumulation or if they are each indicative of unique environmental processes and risks. To better understand the role of trophic position in contaminant accumulation, we analyzed composite tissues for 10 metals from larvae of multiple co-occurring anuran and salamander species from 20 wetlands across the United States. We examined how metal concentrations varied with body size (anurans and salamanders) and developmental stage (anurans) and how the digestive tract (gut) influenced observed metal concentrations. Across all wetlands, metal concentrations were greater in anurans than salamanders for all metals tested except mercury (Hg), selenium (Se), and zinc (Zn). Concentrations of individual metals in anurans decreased with increasing weight and developmental stage. In salamanders, metal concentrations were less correlated with weight, indicating diet played a role in contaminant accumulation. Based on batches of similarly sized whole-body larvae compared to larvae with their digestive tracts removed, our results indicated that tissue type strongly affected perceived concentrations, especially for anurans (gut represented an estimated 46–97% of all metals except Se and Zn). This suggests the reliability of results based on whole-body sampling could be biased by metal, larval size, and development. Overall, our data shows that metal concentrations differs between anurans and salamanders, which suggests that metal accumulation is unique to feeding behavior and potentially trophic position. To truly characterize exposure risk in wetlands, species of different life histories, sizes and developmental stages should be included in biomonitoring efforts.

Environmental Pollution

Water temperature and availability shape the spatial ecology of a hot springs endemic toad

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.

Herpetologica

Distribution of giant gartersnakes (Thamnophis gigas) in the Sacramento–San Joaquin Delta, California, 2018–2019

Summary We examined the occurrence of giant gartersnakes in the Sacramento–San Joaquin Delta, California, in 2018 and 2019. We made eight captures of seven giant gartersnakes (three females, four males) in 2018, and six captures of six giant gartersnakes (four females, two males) in 2019. Detection probabilities were exceedingly low despite using methods that achieve much higher detection probabilities in the rice-growing regions of the Sacramento Valley, California. Our results indicated negative effects of salinity and prey abundance and positive effects of percent emergent vegetation on giant gartersnake occurrence in the Delta, but credible intervals of effect sizes broadly overlapped zero. Estimates of giant gartersnake probability of occurrence were characterized by substantial uncertainty. Additional study with a larger sample of randomly selected but accessible sites would help to further resolve the distribution of giant gartersnakes in the Delta and clarify how the physical and biotic environment in the Delta affects where giant gartersnakes exist. Methodological development to increase detection probabilities in the Delta also would improve inference about giant gartersnake occupancy in the region.

California

Batrachochytrium salamandrivorans (Bsal) not detected in an intensive survey of wild North American amphibians

The salamander chytrid fungus (Batrachochytrium salamandrivorans [Bsal]) is causing massive mortality of salamanders in Europe. The potential for spread via international trade into North America and the high diversity of salamanders has catalyzed concern about Bsal in the U.S. Surveillance programs for invading pathogens must initially meet challenges that include low rates of occurrence on the landscape, low prevalence at a site, and imperfect detection of the diagnostic tests. We implemented a large-scale survey to determine if Bsal was present in North America designed to target taxa and localities where Bsal was determined highest risk to be present based on species susceptibility and geography. Our analysis included a Bayesian model to estimate the probability of occurrence of Bsal given our prior knowledge of the occurrence and prevalence of the pathogen. We failed to detect Bsal in any of 11,189 samples from 594 sites in 223 counties within 35 U.S. states and one site in Mexico. Our modeling indicates that Bsal is highly unlikely to occur within wild amphibians in the U.S. and suggests that the best proactive response is to continue mitigation efforts against the introduction and establishment of the disease and to develop plans to reduce impacts should Bsal establish.

Continental United States

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake

Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species’ ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake ( Thamnophis sirtalis tetrataenia ), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T . s . tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T . s . tetrataenia populations could promote persistence of this endangered snake.

California

Intrinsic prey preference and selection of the giant gartersnake: A threatened predator in a nonnative prey-dominated community

The introduction of exotic species into an environment can introduce great change in the trophic dynamics of native species. This is of even greater concern if the native species is of conservation concern. The giant gartersnake, Thamnophis gigas , an endemic predator of the Central Valley of California and a species of conservation concern at the state and federal levels, has declined as a result of conversion of its once vast wetland habitat to agriculture. Another anthropogenic factor contributing to this snake's changing ecology is the introduction of nonnative prey into the species' habitats. These introductions have resulted in a prey community that is almost completely composed of exotic species and have potential for considerable effects. In order to assess prey preference and selection we performed three sets of behavioral trials on naïve neonates. We examined 1) neonate prey preference in response to olfactory cues of prepared prey extracts, 2) neonate consumption of different live prey items presented simultaneously; and 3) terrestrial feeding behavior and/or latency to successful attack. Results from the olfactory study suggest that native Sierran treefrogs, Pseudacris sierra, are preferred by neonates. Results from consumption trials suggest that neonates are more likely to select frog species than fish species. This is the first study that we are aware of that examines prey selection of this threatened species and serves to inform its conservation and management.

Journal of Fish and Wildlife Management

Integrating multiple data sources and multi-scale land-cover data to model the distribution of a declining amphibian

Determining the spatial scale at which landscape features influence population persistence is an important task for conservation planning. One challenge is that sampling biases confound factors that influence species occurrence and survey effort. Recent developments in Point Process Models (PPMs) enable researchers to disentangle the sampling process from ecological drivers of species' distributions. Land-cover change is a driver of decline for the western spadefoot (Spea hammondii), which has been extirpated from much of its range in California. Assessing this species' status requires information on the current distribution of suitable habitat within its historical range, but little is known about the effect of the landscape surrounding breeding ponds on spadefoot occurrence. Critically, surveys for western spadefoots often occur along roads, potentially biasing data used to fit species distribution models. We created PPMs integrating historical presence/non-detection and presence-only data for western spadefoots and land-cover data at multiple spatial scales to model the distribution of this species while removing the influence of sampling bias. There was spatial sampling bias in presence-only data; records were more likely to be reported near roads and urban centers and PPMs that removed sampling bias outperformed models that ignored sampling bias. The occurrence of western spadefoots was positively related to the proportion of grassland within a 2000 m buffer. The remaining habitat for western spadefoots is largely found in the foothills surrounding California's Central Valley. Our study illustrates how PPMs can improve projections of habitat suitability and our understanding of the drivers of species' distributions.

California

Conservation reliance of a threatened snake on rice agriculture

Conservation-reliant species require perpetual management by humans to persist. But do species that persist largely in human-dominated landscapes actually require conditions maintained by humans? Because most extant populations of giant gartersnakes (Thamnophis gigas) inhabit the highly modified rice agricultural regions of the Sacramento Valley, we sought to evaluate whether giant gartersnakes are indeed a conservation-reliant species dependent on maintenance of rice agriculture and its infrastructure for their continued existence. Specifically, we examined the extent to which giant gartersnakes use rice fields themselves, and whether survival of adult giant gartersnakes was influenced by the amount of rice grown near their home ranges and daily movements. We found that although giant gartersnakes only use rice fields minimally and then only between mid-June and early September, their survival was lower when less rice agriculture was available near the areas they inhabited. Survival was particularly low in early spring, when giant gartersnakes emerge from brumation but rice fields are not yet flooded. The incongruity between the phenology of rice growing and giant gartersnake foraging requirements suggests that although giant gartersnakes are reliant on the rice agroecosystem, rice agriculture is likely suboptimal habitat for giant gartersnakes. Giant gartersnakes’ reliance on the rice agroecosystem challenges the notion of preservation-based conservation, but provides opportunities for win-win scenarios benefitting both rice farmers and giant gartersnakes. Our study highlights that in addition to land use, the timing of land management might be crucial for conservation-reliant species.

Global Ecology and Conservation

Virome of bat guano from nine northern California roosts

Bats are hosts to a large variety of viruses, including many capable of cross species transmissions to other mammals or humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Near or complete genomes of a novel parvovirus, astrovirus, nodavirus, CRESS-DNA viruses and densoviruses and more partial genomes of a novel alphacoronavirus, and bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found likely reflecting their wide distribution among different bats. Unexpectedly a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR possibly originating from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent indicating that numerous viruses still remain to be characterized even from such a heavily investigated order as Chiroptera.

California

Giant Gartersnakes (Thamnophis gigas) exploit abundant non-native prey while maintaining their appetite for native anurans

The introductions of nonnative species can cause great change in the trophic dynamics of native species. Giant Gartersnakes, endemic predators in the Central Valley of California, are listed as threatened because of the conversion of their once vast wetland habitat to agriculture. Further contributing to this snake's changing ecology is the introduction of many nonnative prey species, resulting in a diet that is almost completely composed of nonnative species. In order to determine whether these snakes actively select their prey or simply consume what is abundant, we examined prey selection by adult Giant Gartersnakes in the context of what prey was available to each individual. Giant Gartersnakes selected a native anuran over nonnative anuran and fish species despite these nonnatives dominating the available species composition. These results contribute to understanding the mechanisms underlying Giant Gartersnake diets in the contemporary landscape and can lead to improved management of prey communities for Giant Gartersnakes and other native predators.

Herpetologica