Andrew J. Kroll

Modeling Habitat Occupancy of Orange-Crowned Warblers in Managed Forests of Oregon and Washington, USA

Abstract As part of a habitat management planning process for commercially managed forests, we developed and evaluated habitat occupancy models for the orange-crowned warbler (Vermivora celata), a conservation priority species in Oregon and Washington, USA. We used repeated surveys to classify a random sample of managed conifer stands at the McKenzie, PeEll, and Tolt study sites in western Oregon and Washington as either occupied or unoccupied during 1994–1995. We modeled occupancy and detection probabilities as a function of stand-level habitat characteristics subject to manipulation by management activities. The best-fitting model indicated that orange-crowned warblers were 2 times (95% CI: 0.99–5.1) and 3.8 times (95% CI: 1.5–6.1) as likely to occupy a stand for every 5% increase in evergreen shrub cover and 5-m decrease in canopy lift (ht to lowest live branch), respectively. Management actions that maintain evergreen shrub cover >10% and permit development of low canopy lifts (4–10 m) should promote habitat occupancy by the orange-crowned warbler in commercial forests in western Oregon and Washington.

Site Occupancy Dynamics of Northern Spotted Owls in the Eastern Cascades, Washington, USA, 1990–2003

Abstract Northern spotted owls (Strix occidentalis caurina) have received intense research and management interest since their listing as a threatened species by the United States Fish and Wildlife Service in 1990. Several spotted owl (Strix occidentalis) response variables have been examined in various investigations, but recent advances in statistical modeling permit evaluations of temporal and spatial variability in site occupancy, local-extinction, and colonization probabilities while incorporating imperfect detection probabilities. Following recent work by other researchers on site occupancy dynamics of spotted owls in Oregon, USA, we evaluated temporal variability of detection, occupancy, local-extinction, and colonization probabilities for spotted owls, as well as potential influences of barred owl (Strix varia) presence on these parameters. We used spotted owl survey data collected from 1990 to 2003 on a study area in the eastern Cascades Mountains, Washington, USA, to compare competing occupancy models from Program PRESENCE using Akaikes Information Criterion. Detection probabilities for individual spotted owls ranged from 0.54 to 0.80 if barred owls were not detected during the survey season and from 0.19 to 0.71 if barred owls were detected during the survey season. Pair detection probabilities ranged from 0.27 to 0.67 if barred owls were not detected during an individual survey and from 0.09 to 0.36 if barred owls were detected during an individual survey. During the study, site occupancy probabilities for spotted owl pairs declined by approximately 50%. For all spotted owls, both singles and pairs, site occupancy probabilities declined moderately during the study. Barred owl presence was negatively associated with spotted owl detection probabilities, and it had a positive association with local-extinction probabilities for all spotted owls, both singles and pairs. Given that our study area has supported higher densities of barred owls for longer periods than other study areas, our results may provide insight into how barred owls have influenced spotted owl site occupancy dynamics in adjacent British Columbia, Canada, or will influence spotted owl site occupancy dynamics in Oregon and California, USA, in the future.

Integrating Professional Skills in Wildlife Student Education

Abstract Recent articles have called for enhanced quantitative proficiency in wildlife students, arguing that such training will increase scientific rigor and produce wildlife researchers and managers who are better able to remedy current problems and to address future challenges in wildlife management. The idea that better, or more rigorous, science is the panacea for controversial natural resource problems is a cavalier and common presumption in many applied professions and one to which wildlife science and management is not immune. However, science and management are distinct processes and although scientific rigor is important, dialogue between the 2 processes is more critical for successful interaction. Integrated training that exposes students to nontraditional coursework and develops essential professional skills, such as planning, consensus-building, and communication, can help produce graduates to bridge the science–management gap and promote the conservation of natural resources. Changes in the structure and coursework of university wildlife departments can help to develop more effective wildlife professionals.

Avian species richness in relation to intensive forest management practices in early seral tree plantations.

Background Managers of landscapes dedicated to forest commodity production require information about how practices influence biological diversity. Individual species and communities may be threatened if management practices truncate or simplify forest age classes that are essential for reproduction and survival. For instance, the degradation and loss of complex diverse forest in young age classes have been associated with declines in forest-associated Neotropical migrant bird populations in the Pacific Northwest, USA. These declines may be exacerbated by intensive forest management practices that reduce hardwood and broadleaf shrub cover in order to promote growth of economically valuable tree species in plantations. Methodology and Principal Findings We used a Bayesian hierarchical model to evaluate relationships between avian species richness and vegetation variables that reflect stand management intensity (primarily via herbicide application) on 212 tree plantations in the Coast Range, Oregon, USA. Specifically, we estimated the influence of broadleaf hardwood vegetation cover, which is reduced through herbicide applications, on bird species richness and individual species occupancy. Our model accounted for imperfect detection. We used average predictive comparisons to quantify the degree of association between vegetation variables and species richness. Both conifer and hardwood cover were positively associated with total species richness, suggesting that these components of forest stand composition may be important predictors of alpha diversity. Estimates of species richness were 35–80% lower when imperfect detection was ignored (depending on covariate values), a result that has critical implications for previous efforts that have examined relationships between forest composition and species richness. Conclusion and Significance Our results revealed that individual and community responses were positively associated with both conifer and hardwood cover. In our system, patterns of bird community assembly appear to be associated with stand management strategies that retain or increase hardwood vegetation while simultaneously regenerating the conifer cover in commercial tree plantations.

NEST SURVIVAL Of WESTERN BLUEBIRDS USINg TREE CAVITIES IN MANAgED PONDEROSA PINE fORESTS Of CENTRAL WAShINgTON

Abstract. We examined the association of temporal and spatial factors with nest survival of Western Bluebirds (Sialia mexicana) nesting in tree cavities in ponderosa pine (Pinus ponderosa) forests along the east slope of the Cascade Mountains, Washington. All study areas were managed for timber production through planned harvests or postfire salvage logging. Bluebirds laid a mean clutch of 5.3 ± 0.1 (SE) eggs (n = 131), and successful nests fledged an average of 4.5 ± 0.2 young (n = 85). Using a model-selection framework, we found that nest survival was a function of clutch size and treatment and that there was a quadratic effect of nest age. Daily survival rates decreased after the onset of incubation, then increased through the nestling period, and were higher for clutches with ≥5 eggs and in stands that were burned and salvaged. Survivorship over the entire period for clutches (n = 131 nests) with ≤4, 5, and ≥6 eggs was 0.39 (95% CI: 0.11, 0.65), 0.61 (95% CI: 0.34, 0.80), and 0.71 (95% CI: 0.46, 0.85), respectively. Vegetation variables associated with nest sites did not significantly affect nest survival. Predation accounted for the most nest failures (34% of nests). We suggest that parental defense of nests accounts for the quadratic effect of nest age, with adult bluebirds defending nests more aggressively as nestlings approach fledging, and that bluebirds laying larger clutches are older, more experienced birds, resulting in greater nest survival.

Estimating thresholds in occupancy when species detection is imperfect

Identification of thresholds (state changes over a narrow range of values) is of basic and applied ecological interest. However, current methods of estimating thresholds in occupancy ignore variation in the observation process and may lead to erroneous conclusions about ecological relationships or to the development of inappropriate conservation targets. We present a model to estimate a threshold in occupancy while accounting for imperfect species detection. The threshold relationship is described by a break-point (threshold) and the change in slope (threshold effect). Imperfect species detection is incorporated by jointly modeling species occurrence and species detection. We used WinBUGS to evaluate the model through simulation and to fit the model to avian occurrence data for three species from 212 sites with two replicate surveys in 2007-2008. To determine if accounting for imperfect detection changed the inference about thresholds in avian occupancy in relation to habitat structure, we compared our model to results from a commonly used threshold model (segmented logistic regression). We fit this model in both frequentist and Bayesian modes of inference. Results of the simulation study showed that 95% posterior intervals contained the true value of the parameter in approximately 95% of the simulations. As expected, the simulations indicated more precise threshold and parameter estimates as sample size increased. In the empirical study, we found evidence for threshold relationships for four species by covariate combinations when ignoring species detection. However, when we included variation from the observation process, threshold relationships were not supported in three of those four cases (95% posterior intervals included 0). In general, confidence intervals for the threshold effect were larger when we accounted for species nondetection than when we ignored nondetection. This model can be extended to investigate abundance thresholds as a function of ecological and anthropogenic factors, as well as multispecies hierarchical models.

Effects of Management Intervention on Post-Disturbance Community Composition: An Experimental Analysis Using Bayesian Hierarchical Models

As human demand for ecosystem products increases, management intervention may become more frequent after environmental disturbances. Evaluations of ecological responses to cumulative effects of management interventions and natural disturbances provide critical decision-support tools for managers who strive to balance environmental conservation and economic development. We conducted an experiment to evaluate the effects of salvage logging on avian community composition in lodgepole pine (Pinus contorta) forests affected by beetle outbreaks in Oregon, USA, 1996–1998. Treatments consisted of the removal of lodgepole pine snags only, and live trees were not harvested. We used a Bayesian hierarchical model to quantify occupancy dynamics for 27 breeding species, while accounting for variation in the detection process. We examined how magnitude and precision of treatment effects varied when incorporating prior information from a separate intervention study that occurred in a similar ecological system. Regardless of which prior we evaluated, we found no evidence that the harvest treatment had a negative impact on species richness, with an estimated average of 0.2–2.2 more species in harvested stands than unharvested stands. Estimated average similarity between control and treatment stands ranged from 0.82–0.87 (1 indicating complete similarity between a pair of stands) and suggested that treatment stands did not contain novel assemblies of species responding to the harvesting prescription. Estimated treatment effects were positive for twenty-four (90%) of the species, although the credible intervals contained 0 in all cases. These results suggest that, unlike most post-fire salvage logging prescriptions, selective harvesting after beetle outbreaks may meet multiple management objectives, including the maintenance of avian community richness comparable to what is found in unharvested stands. Our results provide managers with prescription alternatives to respond to severe beetle outbreaks that continue to occur across extensive portions of the dry forests of western North America.

Age and clutch size variation in Dusky Flycatcher nest survival

Examination of spatial and temporal factors that influence nest survival can provide insight into habitat selection, reproductive decisions (e.g., clutch size), population dynamics, and conservation requirements for species. We used nest survival data for the Dusky Flycatcher Empidonax oberholseri to examine several factors that may influence nesting success. Our prediction was that the number of nest initiations would be positively associated with period nest survival. We used a model selection framework and found that nesting success was a function of clutch size and a cubic effect of age. Clutches with one, two, three, and four eggs had period survival rates of 0, 0.05, 0.33, and 0.49, respectively. Daily survival rates decreased from the onset of egg-laying and increased during the later stages of incubation before remaining relatively constant through the later portions of the nestling stage. Model-selection criterion provided support for a date effect on daily survival (i.e., daily nest survival declined across the nesting season) although the 95% confidence interval for the estimate included zero. We found that the majority of nest initiations occurred early in the nest season and declined across the season as period nest survival declined. Our prediction concerning nest survival was partially supported. In addition, we found substantial positive associations between clutch size and nest survival. While low daily survival rates for clutches with one or two eggs suggested that individuals may have reduced reproductive effort in response to nest predation risk, we did not find strong evidence that individuals reduced their clutch sizes in subsequent nest attempts. Alternative predictions, including the preferential settlement of higher quality individuals (e.g., those with the ability to lay full clutches to replace depredated nests) into high-quality habitat and differences in behavior patterns (e.g., number of visits to provision nestlings), may provide more consistent explanations for these patterns.

Evaluating Habitat Quality for the Dusky Flycatcher

Abstract We studied the dusky flycatcher (Empidonax oberholseri) at 8 sites in central Idaho, USA, in 2002 and 2003 to examine relationships among vegetation cover, density of breeding conspecifics, and indicators of habitat quality. Number of breeding territories and number of fledglings per hectare were positively associated, suggesting that the dusky flycatcher experienced increased reproductive success where it bred at the highest densities. However, the relationships between nesting success, annual reproductive success, number of fledglings per hectare, and amount of understory cover showed substantial annual variation. Nesting success did not differ significantly across sites or between years. Both reproductive success, expressed as young produced per hectare (range: 0.34–3.09 in 2002 and 0.79–3.82 in 2003) and young produced per nesting attempt (range: 0.71–2.78 in 2002 and 1.11–3.10 in 2003), differed across study sites in each year. Mean clutch size did not differ significantly among sites or years. Mean egg weight showed significant variation across some sites within years and was associated negatively with the 3 measures of reproductive success in 2002, although small sample sizes prevented reliable inference about the appropriateness of this measure as an indicator of habitat quality. Mean clutch size and mean egg weight were not associated with vegetation cover variables. Thus, dusky flycatcher reproductive success showed inconsistencies with individual vegetation measurements at the site scale. Forest managers who use vegetation treatments to increase amounts of understory shrub cover (e.g., by removing portions of the overstory conifer canopy) should increase densities of this species and, in turn, increase number of fledglings produced, but these responses appear to be better measured at the territory or nest scales than at the stand or site scales.

Factors Associated with Amphibian Detection and Occupancy in Southern Michigan Forests

Abstract Large-scale amphibian conservation often relies on remotely sensed data to describe spatial patterns in occupancy. Commonly used data include ownership, forest type, soil class, and proximity of wetlands. We evaluated the influence of these variables on terrestrial amphibian occupancy in southern Michigan. We trapped amphibians using drift-fence arrays in 82 forest patches and estimated detection probabilities for all captured species. Ten species were captured, but only three were detected at levels suitable for occupancy modeling. We concluded that drift-fence arrays alone were not sufficient for adequately detecting the majority of terrestrial amphibians. The best detection models for American Toad (Anaxyrus americanus), Wood Frog (Lithobates sylvaticus), and Spring Peeper (Pseudacris crucifer) consistently included a positive relationship with temperature and precipitation. Detection-adjusted occupancy models for the three anurans indicated relatively high occupancy (>0.43). Ownership, forest type, and soil class did not occur in higher ranking occupancy models. Rather, the higher ranking models often included the distance to National Wetlands Inventory (NWI) wetland and sample year factors. However, these effects were highly variable and of no use in consistently predicting terrestrial amphibian occupancy. Our results substantiate the importance of incorporating detection probabilities into studies of amphibian habitat relationships and suggest that coarse descriptors of environmental conditions may not adequately portray factors important to terrestrial amphibian occupancy.