Steven D. Duke

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.

A Logistic Regression Model for Predicting the Upstream Extent of Fish Occurrence Based on Geographical Information Systems Data

Abstract Regulations governing human activities in streams and riparian zones frequently differ depending on whether or not a stream reach supports fish. Fish presence or absence is usually determined by sampling or by assuming the presence of fish if the stream exhibits certain physical characteristics. Field surveys of fish occurrence in streams are time consuming and expensive. Inference of fish presence from simple thresholds of physical attributes, such as gradient or channel width alone, is inaccurate. We attempted to improve the accuracy and efficiency of this determination by developing a geographical information systems (GIS)-based predictive model. A 10-m digital elevation model incorporated field data on fish distribution from 517 streams in western Washington State and GIS-derived representations of the physical characteristics of stream networks. A model predicting the upstream extent of fish occurrence was derived using logistic regression models coupled with a heuristic “stopping rule.” Can...

Field survival and early height growth of Douglas-fir rooted cuttings: relationship to stem diameter and root system quality

Abstract In 1990, three studies involving 11 half-sib families of Douglas-fir rooted cuttings were established at three sites in western Washington State (USA): two with low regeneration difficulty (RD) and one with high RD. Grading and cull studies were installed on each site and a root number study on one site. The grading study compared the performance of nine classes of rooted cuttings based on stem diameter and root system quality. The cull study evaluated five different types of putative culls. The root number study determined the correlation between the number of initial roots and field performance. In the grading study survival and height growth reflected stem diameter and relative root quality on all three sites. Mean survival by treatment was in the range 92–100%, 82–97% and 66–87% across the three sites. First year height growth varied from approximately 10 cm to 20 cm and was greatest on the low RD sites. Second year height growth was from three to four times greater than first year height growth on the low RD sites and two to three times greater on the high RD site. Plants with larger diameter had higher survival and better growth than those with smaller diameter. Within each diameter class, plants with good or fair root systems outperformed those with poor root systems. Performance of seedlings and transplants was nearly identical to that of rooted cuttings with corresponding diameter and root system quality. In the cull study only trees with stem diameter

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.

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.

Winter Longitudinal Thermal Regime in Four Mountain Streams

Abstract We measured winter thermal characteristics longitudinally in four third-order streams, two each in the Idaho Batholith and Blue Mountain ecoregions. From November to April we measured temperature along 3.7 km to 11.9 km of stream at six to eight sites. Streams were snow covered for most of the winter. There was a seasonal pattern of stream-wide cooling in November and warming in April at all streams. In the mid-winter months (December, January, and February), the sites in the Blue Mountain streams had mean monthly maxima ranging from 0.2 to 3.0 °C and minima -0.1 to 1.5 °C stream-wide, whereas both Idaho Batholith streams were near 0.0 °C throughout their length and had monthly ranges of 0.2 °C or less. Winter temperature differences between streams of the two ecoregions create substantial differences in cumulative degree-days which could be a factor in the structure of instream biotic communities.

Drift distance of macroinvertebrates throughout summer in headwater tributaries of the Calapooia River

Drifting invertebrates from small headwater streams are a food subsidy for fishes and other downstream consumers in larger streams. This subsidy can become especially important for stream fishes during summer due to high metabolic demand caused by elevated water temperatures. The source length in small streams contributing these drifting invertebrates to fish bearing habitat has not been established. We conducted an experiment to determine if summer drift delivered by headwater streams to larger channels is influenced by contributions originating more than 100 m upstream. We conducted this experiment on tributaries of the Calapooia River, Oregon, USA. We blocked drift with 250 μm mesh nets in three streams 100 m upstream of our sample nets continuously for 48 d. We also sampled five streams without blocking nets. Four 24 h samples of drift were collected prior to the placement of blocking nets and every two weeks afterwards at each stream. Overall mean abundance and mean biomass of drift did not differ between blocked and unblocked streams for any sampling period. There was a temporal trend at all sites of declining invertebrate abundance and biomass. We found no treatment effect for any of the most common insect orders or for the 16 genera that comprised at least 1% of the total organisms captured. The majority of invertebrate drift is of local origin in headwater streams during summer baseflow.