Evaluating multi-level models to test occupancy state responses of Plethodontid salamanders

Andrew J. Kroll; Tiffany S. Garcia; Jay E. Jones; Katie M. Dugger; Blake Murden; Josh Johnson; Summer Peerman; Ben Brintz; Michael Rochelle

doi:10.1371/journal.pone.0142903

USGS · 70173741

Evaluating multi-level models to test occupancy state responses of Plethodontid salamanders

Andrew J. Kroll·Tiffany S. Garcia·Jay E. Jones·Katie M. Dugger·Blake Murden·Josh Johnson·Summer Peerman·Ben Brintz·Michael Rochelle

View original source ↗Export metadata ↓

Abstract

Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI) experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24); Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29) . Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of study questions and objectives prior to sampling data and fitting models.

Explore related subjects

PLoS ONE Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Andrew J. Kroll, Tiffany S. Garcia, Jay E. Jones, Katie M. Dugger, Blake Murden, Josh Johnson, Summer Peerman, Ben Brintz, Michael Rochelle. 2015-11-30. Evaluating multi-level models to test occupancy state responses of Plethodontid salamanders. https://doi.org/10.1371/journal.pone.0142903

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

USGS2026

Analyses of eye lens stable isotopes across ontogeny of trophically diverse freshwater salmonids

Ontogenetic niche shifts in fishes are nearly universal but remain poorly understood in many species despite being fundamentally important for the persistence, management, and conservation of fish populations, including those of vulnerable salmonids. Eye lens stable isotope analysis has proven useful in studying ontogeny in some marine species but has rarely been applied in freshwater fishes. We conducted among the first applications of eye lens stable isotope analysis in two salmonids, Arctic Charr ( Salvelinus alpinus ) and Brook Trout ( Salvelinus fontinalis ), in four North American lakes at the southern extent of the range of Arctic Charr (Maine, USA). Our goal was to determine if ontogenetic patterns varied between individuals and populations in ways that relate to differential vulnerability. Like studies in marine systems, we found patterns in lens isotopic values that agree with expected ontogenetic patterns to reach known adult trophic niches. Within lakes and individuals examined in this study, Arctic Charr appeared more dependent on pelagic resources than co-occurring Brook Trout through life. Using Bayesian hierarchical linear regressions, we found evidence that ontogenetic shifts in trophic position (measured by δ 15 N) of Arctic Charr may vary among lakes. Arctic Charr in some populations increased in trophic position through life (population lifetime δ 15 N posterior mean slope estimate = 1.01) while others showed no substantial changes (population lifetime δ 15 N posterior mean slope = 0.05), which may relate to differences in habitat and fish assemblage among our study lakes. Our study suggests that individual life stages and populations of salmonids are likely to respond to climate variability (e.g., basal resource shifts) differentially, which could warrant population and life-stage-specific management.

Maine↗

USGS2026

Modeling chronic wasting disease transmission risk in mule deer related to habitat characteristics

Chronic wasting disease (CWD) is a prion disease of cervids that spreads to uninfected individuals through direct transmission (contact with infected individuals), vertical transmission (from mother to offspring), or indirect transmission (exposure to contaminated environments). The risk of indirect transmission is unevenly distributed on the landscape, and risk levels are expected to be controlled by patterns of habitat use by infected and uninfected individuals as well as environmental properties that alter the length of time prions remain infectious and available for uptake. Despite evidence from controlled or laboratory studies identifying environmental properties likely to affect patterns of CWD prion locations on the landscape, it remains difficult to connect mechanisms to realized increased or decreased risk of disease transmission, and few studies have attempted to detect patterns of different CWD risk in different environments. Using data from GPS-collared mule deer in Wyoming that were CWD-tested annually, we constructed models predicting annual probability of disease transmission contingent on environmental properties extracted from GPS use points. We compared models that emphasized different pathways of disease transmission by including or excluding sets of covariates that described deer density, habitat selection, and covariates expected to affect prion persistence in the environment. Results indicated that key habitat characteristics often selected by mule deer, such as proximity to secondary roads, were also associated with higher risk of testing positive for CWD, which supports the hypothesis that disease risk was correlated to patterns of habitat use by deer. We also found increased risk associated with spatial properties that were not selected-for by deer, such as areas where topography collects moisture, suggesting that prion retention mechanisms also play a role in risk. Incorporating these spatially-varying risk factors into our understanding of CWD transmission and outbreak progression can support managers in designing data collection and disease management strategies.

Wyoming↗

USGS2026

Estimating GPS-based social aggregation metrics using collar data

Understanding social aggregation patterns in ungulate herds is essential for gaining behavioral insights, optimizing resource use, reducing human-wildlife conflict, and managing disease risk. As chronic wasting disease is the preeminent disease-related threat to cervid populations in North America, knowledge of contact between individuals and spatiotemporal patterns of aggregation provides opportunity to understand and potentially reduce disease risk while supporting sustainable population sizes. Herd density metrics, derived from global positioning system (GPS) data, can be used to inform management decisions. To effectively compare aggregation behavior within and between herds, aggregation metrics must be accurate. However, the consistency of metrics across different GPS collar sample sizes remains unclear and robust studies of big game require understanding how these factors may vary in different contexts. We examined the minimum sample size necessary for reliable calculations of three aggregation metrics: pairwise inter-animal distances, daily proximity rates, and kernel density estimate (KDE) areas. We used GPS collar data from the Jackson and West Green River elk herds ( Cervus canadensis ) in western Wyoming, USA, that differ in herd size and group structure (single versus multiple sub-groups), representing common practical contexts. Elk locations were acquired for the Jackson herd between 2016 and 2019 and from 2005 to 2010 for the West Green River herd. Herd-specific characteristics substantially influence the sample size necessary for accurate density measurements. As predicted, larger herds with many groups require more GPS collars than small herds with fewer groups. The sample size needed to accurately estimate aggregation varies by metric, with KDE areas, useful for indexing environmentally transmitted disease risk, generally requiring fewer samples, especially in high-density contexts. The required sample size also varies with seasonal changes in density. During periods of highest density, similar sample sizes are required to estimate inter-animal distances and proximity rates regardless of herd characteristics. Our results have implications for costs associated with studying big game herds, indicating fewer collars may be sufficient in some cases. These insights can aid researchers and managers in determining the appropriate number of GPS collars required for effective herd monitoring and informing relevant aggregation metrics for their management goals.

Wyoming↗