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1.  Breeding Bird Community Continues to Colonize Riparian Buffers Ten Years after Harvest 
PLoS ONE  2015;10(12):e0143241.
Riparian ecosystems integrate aquatic and terrestrial communities and often contain unique assemblages of flora and fauna. Retention of forested buffers along riparian habitats is a commonly employed practice to reduce potential negative effects of land use on aquatic systems. However, very few studies have examined long-term population and community responses to buffers, leading to considerable uncertainty about effectiveness of this practice for achieving conservation and management outcomes. We examined short- (1–2 years) and long-term (~10 years) avian community responses (occupancy and abundance) to riparian buffer prescriptions to clearcut logging silvicultural practices in the Pacific Northwest USA. We used a Before-After-Control-Impact experimental approach and temporally replicated point counts analyzed within a Bayesian framework. Our experimental design consisted of forested control sites with no harvest, sites with relatively narrow (~13m) forested buffers on each side of the stream, and sites with wider (~30m) and more variable width unharvested buffer. Buffer treatments exhibited a 31–44% increase in mean species richness in the post-harvest years, a pattern most evident 10 years post-harvest. Post-harvest, species turnover was much higher on both treatments (63–74%) relative to the controls (29%). We did not find evidence of local extinction for any species but found strong evidence (no overlap in 95% credible intervals) for an increase in site occupancy on both Narrow (short-term: 7%; long-term 29%) and Wide buffers (short-term: 21%; long-term 93%) relative to controls after harvest. We did not find a treatment effect on total avian abundance. When assessing relationships between buffer width and site level abundance of four riparian specialists, we did not find strong evidence of reduced abundance in Narrow or Wide buffers. Silviculture regulations in this region dictate average buffer widths on small and large permanent streams that range from ~22–25 m. Guidelines for this region are within the range of buffers included in our study, in which we observed no evidence for avian species loss or for a decline in species abundance (including riparian associated species).
PMCID: PMC4670142  PMID: 26637120
2.  Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders 
PLoS ONE  2015;10(11):e0142903.
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.
PMCID: PMC4664280  PMID: 26619010
3.  Effects of Management Intervention on Post-Disturbance Community Composition: An Experimental Analysis Using Bayesian Hierarchical Models 
PLoS ONE  2013;8(3):e59900.
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.
PMCID: PMC3606292  PMID: 23533659
4.  Avian Species Richness in Relation to Intensive Forest Management Practices in Early Seral Tree Plantations 
PLoS ONE  2012;7(8):e43290.
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.
PMCID: PMC3419709  PMID: 22905249

Results 1-4 (4)