Cheryl S. Brehme

Joint estimation of habitat dynamics and species interactions: disturbance reduces co‐occurrence of non‐native predators with an endangered toad

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the environment as a static variable. 2. We fit detection and non-detection data collected from repeat visits using a dynamic site occupancy model that simultaneously accounts for the temporal dynamics of a focal prey species, its predators and its habitat. Our objective was to determine how disturbance and species interactions affect the co-occurrence probabilities of an endangered toad and recently introduced non-native predators in stream breeding habitats. For this, we determined statistical support for alternative processes that could affect co-occurrence frequency in the system. 3. We collected occurrence data at stream segments in two watersheds where streams were largely ephemeral and one watershed dominated by perennial streams. Co-occurrence probabilities of toads with non-native predators were related to disturbance frequency, with low co-occurrence in the ephemeral watershed and high co-occurrence in the perennial watershed. This occurred because once predators were established at a site, they were rarely lost from the site except in cases when the site dried out. Once dry sites became suitable again, toads colonized them much more rapidly than predators, creating a period of predator-free space. 4. We attribute the dynamics to a storage effect, where toads persisting outside the stream environment during periods of drought rapidly colonized sites when they become suitable again. Our results support that even in highly connected stream networks, temporal disturbance can structure frequencies with which breeding amphibians encounter non-native predators. 5. Dynamic multi-state occupancy models are a powerful tool for rigorously examining hypotheses about inter-species and species-habitat interactions. In contrast to previous methods that infer dynamic processes based on static patterns in occupancy, the approach we took allows the dynamic processes that determine species-species and species-habitat interactions to be directly estimated.

Permeability of Roads to Movement of Scrubland Lizards and Small Mammals

A primary objective of road ecology is to understand and predict how roads affect connectivity of wildlife populations. Road avoidance behavior can fragment populations, whereas lack of road avoidance can result in high mortality due to wildlife-vehicle collisions. Many small animal species focus their activities to particular microhabitats within their larger habitat. We sought to assess how different types of roads affect the movement of small vertebrates and to explore whether responses to roads may be predictable on the basis of animal life history or microhabitat preferences preferences. We tracked the movements of fluorescently marked animals at 24 sites distributed among 3 road types: low-use dirt, low-use secondary paved, and rural 2-lane highway. Most data we collected were on the San Diego pocket mouse (Chaetodipus fallax), cactus mouse (Peromyscus eremicus), western fence lizard (Sceloporus occidentalis), orange-throated whiptail (Aspidoscelis hyperythra), Dulzura kangaroo rat (Dipodomys simulans) (dirt, secondary paved), and deer mouse (Peromyscus maniculatus) (highway only). San Diego pocket mice and cactus mice moved onto dirt roads but not onto a low-use paved road of similar width or onto the highway, indicating they avoid paved road substrate. Both lizard species moved onto the dirt and secondary paved roads but avoided the rural 2-lane rural highway, indicating they may avoid noise, vibration, or visual disturbance from a steady flow of traffic. Kangaroo rats did not avoid the dirt or secondary paved roads. Overall, dirt and secondary roads were more permeable to species that prefer to forage or bask in open areas of their habitat, rather than under the cover of rocks or shrubs. However, all study species avoided the rural 2-lane highway. Our results suggest that microhabitat use preferences and road substrate help predict species responses to low-use roads, but roads with heavy traffic may deter movement of a much wider range of small animal species.

Reptile and Amphibian Responses to Large-Scale Wildfires in Southern California

Abstract In 2003, southern California experienced several large fires that burned thousands of hectares of wildlife habitats and conserved lands. To investigate the effects of these fires on the reptile and amphibian communities, we compared the results from prefire herpetofauna and vegetation sampling to two years of postfire sampling across 38 burned and 17 unburned plots. The sampling plots were spread over four vegetation types and four open space areas within San Diego County. Our capture results indicated that burned chaparral and coastal sage scrub plots lost herpetofaunal species diversity after the fires and displayed a significant shift in overall community structure. Shrub and tree cover at the burned plots, averaged across the second and third postfire years, had decreased by 53% in chaparral and 75% in coastal sage scrub. Additionally, postfire herpetofauna community structure at burned plots was more similar to that found in unburned grasslands. In grassland and woodland/riparian vegetation plots, where shrub and tree cover was not significantly affected by fires, we found no differences in the herpetofaunal species diversity or community composition. At the individual species level, Sceloporus occidentalis was the most abundant reptile in these areas both before and after the fires. We saw increases in the net capture rates for several lizard species, including Aspidoscelis tigris, Phrynosoma coronatum, and Uta stansburiana in burned chaparral plots and Aspidoscelis hyperythra and U. stansburiana in burned coastal sage scrub plots. The toad, Bufo boreas, was detected at significantly fewer burned plots in chaparral after the fires. Additionally, we documented decreases in the number of plots occupied by lizards (Elgaria multicarinata), salamanders (Batrachoseps major), and snakes (Coluber constrictor, Lampropeltis getula, Pituophis catenifer, and Masticophis lateralis) in coastal sage scrub and chaparral after the fires. We discuss the individual species results as they relate to such life-history traits as the susceptibility to initial mortality, the response to the altered postfire habitat, and shifts in the availability of potential prey. We foresee that a continued unnatural fire regime will result in a simplification of the southern California reptile and amphibian communities.

Effects of Large-Scale Wildfires on Ground Foraging Ants (Hymenoptera: Formicidae) in Southern California

ABSTRACT We investigated the effect of broad-scale wildfire on ground foraging ants within southern California. In October and November of 2003, two wildfires burned large portions of the wildlands within San Diego County. Between January 2005 and September 2006, we surveyed 63 plots across four sites to measure the effect of the fires on the ant assemblages present in four vegetation types: 1) coastal sage scrub, 2) chaparral, 3) grassland, and 4) woodland riparian. Thirty-six of the 63 plots were sampled before the fires between March 2001 and June 2003. Mixed model regression analyses, accounting for the burn history of each plot and our pre- and postfire sampling efforts, revealed that fire had a negative effect on ant species diversity. Multivariate analyses showed that ant community structure varied significantly among the four vegetation types, and only the ant assemblage associated with coastal sage scrub exhibited a significant difference between burned and unburned samples. The most notable change detected at the individual species level involved Messor andrei (Mayr), which increased from <1% of prefire coastal sage scrub ant samples to 32.1% in burned plots postfire. We theorize that M. andrei responded to the increase of bare ground and postfire seed production, leading to an increase in the detection rate for this species. Collectively, our results suggest that wildfires can have short-term impacts on the diversity and community structure of ground foraging ants in coastal sage scrub. We discuss these findings in relation to management implications and directions for future research.

Metabarcoding of fecal samples to determine herbivore diets: A case study of the endangered Pacific pocket mouse

Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

An improved camera trap for amphibians, reptiles, small mammals, and large invertebrates

Camera traps are valuable sampling tools commonly used to inventory and monitor wildlife communities but are challenged to reliably sample small animals. We introduce a novel active camera trap system enabling the reliable and efficient use of wildlife cameras for sampling small animals, particularly reptiles, amphibians, small mammals and large invertebrates. It surpasses the detection ability of commonly used passive infrared (PIR) cameras for this application and eliminates problems such as high rates of false triggers and high variability in detection rates among cameras and study locations. Our system, which employs a HALT trigger, is capable of coupling to digital PIR cameras and is designed for detecting small animals traversing small tunnels, narrow trails, small clearings and along walls or drift fencing.

An objective road risk assessment method for multiple species: ranking 166 reptiles and amphibians in California

AbstractContextTransportation and wildlife agencies may consider the need for barrier structures and safe wildlife road-crossings to maintain the long-term viability of wildlife populations. In order to prioritize these efforts, it is important to identify species that are most at risk of extirpation from road-related impacts.PurposeOur goal was to identify reptiles and amphibians in California most susceptible to road mortality and fragmentation. With over 160 species and a lack of species-specific research data, we developed an objective risk assessment method based upon road ecology science.MethodsRisk scoring was based upon a suite of life history and space-use characteristics associated with negative road effects applied in a hierarchical manner from individuals to species. We evaluated risk to both aquatic and terrestrial connectivity and calculated buffer distances to encompass 95% of population-level movements. We ranked species into five relative categories of road-related risk (very-high to very-low) based upon 20% increments of all species scores.ResultsAll chelonids, 72% of snakes, 50% of anurans, 18% of lizards and 17% of salamander species in California were ranked at high or very-high risk from negative road impacts. Results were largely consistent with local and global scientific literature in identifying high risk species and groups. ConclusionsThis comparative risk assessment method provides a science-based framework to identify species most susceptible to negative road impacts. The results can inform regional-scale road mitigation planning and prioritization efforts and threat assessments for special-status species. We believe this approach is applicable to numerous landscapes and taxonomic groups.

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.Amphibians have seen large population declines, but the key drivers are hard to establish. Here, Miller et al. investigate trends of occupancy for 81 species of amphibians across North America and find greater sensitivity to water availability during breeding and winter conditions than mean climate.

Longevity and population age structure of the arroyo southwestern toad (Anaxyrus californicus) with drought implications

Abstract The arroyo southwestern toad is a specialized and federally endangered amphibian endemic to the coastal plains and mountains of central and southern California and northwestern Baja California. It is largely unknown how long these toads live in natural systems, how their population demographics vary across occupied drainages, and how hydrology affects age structure. We used skeletochronology to estimate the ages of adult arroyo toads in seven occupied drainages with varying surface water hydrology in southern California. We processed 179 adult toads with age estimates between 1 and 6 years. Comparisons between skeletochronological ages and known ages of PIT tagged toads showed that skeletochronology likely underestimated toad age by up to 2 years, indicating they may live to 7 or 8 years, but nonetheless major patterns were evident. Arroyo toads showed sexual size dimorphism with adult females reaching a maximum size of 12 mm greater than males. Population age structure varied among the sites. Age structure at sites with seasonally predictable surface water was biased toward younger individuals, which indicated stable recruitment for these populations. Age structures at the ephemeral sites were biased toward older individuals with cohorts roughly corresponding to higher rainfall years. These populations are driven by surface water availability, a stochastic process, and thus more unstable. Based on our estimates of toad ages, climate predictions of extreme and prolonged drought events could mean that the number of consecutive dry years could surpass the maximum life span of toads making them vulnerable to extirpation, especially in ephemeral freshwater systems. Understanding the relationship between population demographics and hydrology is essential for predicting species resilience to projected changes in weather and rainfall patterns. The arroyo toad serves as a model for understanding potential responses to climatic and hydrologic changes in Mediterranean stream systems. We recommend development of adaptive management strategies to address these threats.