Short-term responses of small mammal diversity to varying stand-scale patterns of retention tree patches.

Retention forestry is a common practice for biodiversity conservation in forests managed for wood production. Retention forestry often leaves unharvested patches of trees that vary in size and spatial pattern but experiments evaluating the effects of different retention patch configurations at a constant level of retention are lacking for many regions and taxonomic groups. We implemented an experimental study in clearcut conifer stands with retention across the U.S. Pacific Northwest region. The study consisted of five stand-level (11-55 ha) experimental treatments each replicated 10 times within a randomized complete block design, resulting in 50 treated stands. Retained tree density was comparable across treatments but size, number, and location (upland or riparian) of patches within stands varied among the five treatments. Within experimental treatments, we measured small mammal (<1kg) species and functional trait (i.e., body size, diet, activity stratum) richness in retention patches, surrounding harvested portions of stands, and nearby unharvested stands. We evaluated species and functional trait richness by treatment using generalized linear mixed-effects models and species-specific responses to retention placement using a community occupancy model. We obtained repeat captures of 21 species of small mammals but found limited evidence of a treatment effect on species richness, and no differences in functional trait richness. Species richness was highest where all retained trees were aggregated into one patch placed adjacent to a forested riparian buffer (mean = 6.6 species, 95% CI = 5.7-7.5), and lowest in the treatment containing one retention patch in the upland portion of a harvested stand (mean = 4.7 species, 95% CI = 3.8-5.6). Furthermore, estimates of species richness within retention patches of harvested stands (i.e., not considering species in harvested areas) did not differ among treatments, indicating that the slightly elevated species richness in riparian-associated retention results from 1-2 species in these patches that do not occur in adjacent harvested portions of each treated stand. Patch occupancy of several species was higher in riparian patches than harvested portions of the treated stands, and fewer species had higher occupancy in upland patches compared to harvested portions of treated stands. Our results indicated that at retention densities currently required in Oregon and Washington, the location of retention patches had a small influence on stand-scale measures of small mammal diversity, but local increases in species richness may be obtained by retaining trees adjacent to riparian buffers.

Reconciling biodiversity with timber production and revenue via an intensive forest management experiment.

Understanding how land-management intensification shapes the relationships between biodiversity, yield, and economic benefit is critical for managing natural resources. Yet, manipulative experiments that test how herbicides affect these relationships are scarce, particularly in forest ecosystems where considerable time lags exist between harvest revenue and initial investments. We assessed these relationships by combining 7 yr of biodiversity surveys (>800 taxa) and forecasts of timber yield and economic return from a replicated, large-scale experiment that manipulated herbicide application intensity in operational timber plantations. Herbicides reduced species richness across trophic groups (-18%), but responses by higher-level trophic groups were more variable (0-38% reduction) than plant responses (-40%). Financial discounting, a conventional economic method to standardize past and future cash flows, strongly modified biodiversity-revenue relationships caused by management intensity. Despite a projected 28% timber yield gain with herbicides, biodiversity-revenue trade-offs were muted when opportunity costs were high (i.e., economic discount rates ≥7%). Although herbicides can drive biodiversity-yield trade-offs, under certain conditions, financial discounting provides opportunities to reconcile biodiversity conservation with revenue.

Conservation and production responses vary by disturbance intensity in a long-term forest management experiment.

Reductions in management intensity are often proposed to support a broader range of beneficial ecosystem responses than traditional management approaches. However, few studies evaluate ecosystem responses across approaches. Also, managers lack information about how species traits mediate responses across management approaches, a potentially substantial source of spatial and temporal variation in population and community responses that if ignored may hinder effectiveness of management programs. We used data collected over eight years from a manipulative experiment to test how four forest management strategies influenced avian community composition and wood production. After harvesting, we evaluated responses to three levels of plant cover suppression (Light, Moderate, and Intensive herbicide applications) in relation to a control without herbicide. We predicted the Moderate and Intensive treatments would exert strong negative effects on leaf-gleaning insectivores, including species of conservation concern due to long-term population declines. However, given high forest productivity, we expected temporal duration of effects to be short. Richness of leaf-gleaning bird species was reduced by 20-50% during the first four years post-harvest (when herbicide treatments were on-going), but the effect size declined over the next four years once treatments were completed (13-20% reduction). Effect sizes were substantially smaller for the non-leaf-gleaner group during years 1-4 (19-27%) and disappeared during years 5-8 (2-3%). However, in our final year of observation, we did find an average of five fewer non-leaf-gleaner species on Light vs. Control units. In the last two years of observation, turnover probabilities for the leaf-gleaner species remained higher on all treatments compared to the Control (0.11-0.21), indicating that new species continued to colonize treatments. Planted conifers were 40-44% taller and 74-81% larger in diameter in the Moderate and Intensive treatments compared to the Control, leading to substantial gains in wood biomass. Current practices provided more balance between two ecosystem responses, avian diversity and wood production, compared to less intensive alternatives. When short-term negative effects occur, the spatial distribution of harvesting and regeneration regionally indicates that habitat is often available locally to support leaf-gleaning and non-leaf-gleaning bird populations while releasing other portions of the region for high priority conservation objectives including late-successional forest reserves.

Do birds help trees grow? An experimental study of the effects of land-use intensification on avian trophic cascades.

By regulating populations of herbivores, predators can indirectly influence plant production. However, the factors influencing the strength of this type of trophic cascade are still unclear. We hypothesized that changes to plant community structure would affect the number of avian predators, thereby mediating cascade strength. Using a 4-yr, blocked, split-plot experiment, we independently manipulated both predators (birds) and plants in an early seral managed forest system in western Oregon, USA, and measured abundance across three trophic levels. We applied herbicides, as a surrogate for land-use intensification, to recently clear-cut stands to establish an experimental gradient in plant abundance and species richness, and excluded birds using 28, 225 m2 exclosures. In total, we counted and identified 94,738 arthropods of 141 families in paired control and bird exclosure plots. On average, insectivorous birds reduced arthropod abundance by 16% and plant damage by 14%, and some well-known pests (e.g., Adelges cooleyi) of crop trees (mostly Pseudotsuga menziesii) in our system were reduced by as much as 30%. However, this effect did not translate into a trophic cascade that increased crop-tree growth in the presence of birds. We experimentally reduced plant abundance and diversity by 67% and 55%, respectively, in the most intensive herbicide treatment in relation to untreated controls, but reduced vegetative resources did not change the strength of the direct effect of birds on arthropods or the indirect effect of birds on plants.

Describing vegetation characteristics used by two rare forest-dwelling species: Will established reserves provide for coastal marten in Oregon?

Forest management guidelines for rare or declining species in the Pacific Northwest, USA, include both late successional reserves and specific vegetation management criteria. However, whether current management practices for well-studied species such as northern spotted owls (Strix occidentallis caurina) can aid in conserving a lesser known subspecies-Humboldt martens (Martes caurina humboldtensis)-is unclear. To address the lack of information for martens in coastal Oregon, USA, we quantified vegetation characteristics at locations used by Humboldt martens and spotted owls in two regions (central and southern coast) and at two spatial scales (the site level summarizing extensive vegetation surveys and regionally using remotely sensed vegetation and estimated habitat models). We estimated amount of predicted habitat for both species in established reserves. If predicted overlap in established reserves was low, then we reported vegetation characteristics to inform potential locations for reserves or management opportunities. In the Central Coast, very little overlap existed in vegetation characteristics between Humboldt martens and spotted owls at either the site or regional level. Humboldt martens occurred in young forests composed of small diameter trees with few snags or downed logs. Humboldt martens were also found in areas with very dense vegetation when overstory canopy and shrub cover percentages were combined. In the South Coast, Humboldt martens occurred in forests with smaller diameter trees than spotted owl sites on average. Coastal Humboldt martens may use stands of predicted high quality spotted owl habitat in the Pacific Northwest. Nonetheless, our observations suggest that coastal Humboldt martens exist in areas that include a much higher diversity of conifer size classes as long as extensive dense shrub cover, predominantly in the form of high salal and evergreen huckleberry, are available. We suggest that managers consider how structural characteristics (e.g., downed logs, shrub cover, patch size), are associated with long-term species persistence rather than relying on reserves based on broad cover types. Describing vegetation may partially describe suitability, but available prey or predation risk ultimately influence likelihood of individual Humboldt marten use. Guidelines for diversifying vegetation management, and retaining or restoring appropriate habitat conditions at both the stand level and regionally, may increase management flexibility and identify forest conditions that support both spotted owls and Humboldt martens.

Multistate Models Reveal Long-Term Trends of Northern Spotted Owls in the Absence of a Novel Competitor.

Quantifying spatial and temporal variability in population trends is a critical aspect of successful management of imperiled species. We evaluated territory occupancy dynamics of northern spotted owls (Strix occidentalis caurina), California, USA, 1990-2014. The study area possessed two unique aspects. First, timber management has occurred for over 100 years, resulting in dramatically different forest successional and structural conditions compared to other areas. Second, the barred owl (Strix varia), an exotic congener known to exert significant negative effects on spotted owls, has not colonized the study area. We used a Bayesian dynamic multistate model to evaluate if territory occupancy of reproductive spotted owls has declined as in other study areas. The state-space approach for dynamic multistate modeling imputes the number of territories for each nesting state and allows for the estimation of longer-term trends in occupied or reproductive territories from longitudinal studies. The multistate approach accounts for different detection probabilities by nesting state (to account for either inherent differences in detection or for the use of different survey methods for different occupancy states) and reduces bias in state assignment. Estimated linear trends in the number of reproductive territories suggested an average loss of approximately one half territory per year (-0.55, 90% CRI: -0.76, -0.33), in one management block and a loss of 0.15 per year (-0.15, 90% CRI: -0.24, -0.07), in another management block during the 25 year observation period. Estimated trends in the third management block were also negative, but substantial uncertainty existed in the estimate (-0.09, 90% CRI: -0.35, 0.17). Our results indicate that the number of territories occupied by northern spotted owl pairs remained relatively constant over a 25 year period (-0.07, 90% CRI: -0.20, 0.05; -0.01, 90% CRI: -0.19, 0.16; -0.16, 90% CRI: -0.40, 0.06). However, we cannot exclude small-to-moderate declines or increases in paired territory numbers due to uncertainty in our estimates. Collectively, we conclude spotted owl pair populations on this landscape managed for commercial timber production appear to be more stable and do not show sharp year-over-year declines seen in both managed and unmanaged landscapes with substantial barred owl colonization and persistence. Continued monitoring of reproductive territories can determine whether recent declines continue or whether trends reverse as they have on four previous occasions. Experimental investigations to evaluate changes to spotted owl occupancy dynamics when barred owl populations are reduced or removed entirely can confirm the generality of this conclusion.

Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders.

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.

Breeding Bird Community Continues to Colonize Riparian Buffers Ten Years after Harvest.

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 (~13 m) forested buffers on each side of the stream, and sites with wider (~30 m) 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).

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.

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.