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Structural enrichment in commercial tree plantations is a potential tool to increase snag numbers but relatively little information is available about how species, size, and spatial distribution of created snags are associated with longevity of these structures. We created 1197 snags in 31 harvest units from 1997 to 1999 in the Cascade and Coast Ranges, Oregon, USA, by topping live trees with harvesting equipment. We used an experimental design to distribute created snags at three densities and as either single or clumped created snags. We fit Weibull and log-logistic Accelerated Failure Time models and found that the median failure time was insensitive to the choice of distribution. We found a small positive effect of diameter at breast height (DBH) and a slight negative effect of increasing distance between created snags on survival. Assuming Weibull and log-logistic distributions at mean observed values of DBH and distance between snags, median survival times for Douglas-fir (Pseudotsuga menziesii) were 21.0 (95% confidence interval: 19.3, 22.8) years and 21.2 (19.7, 22.8) years, respectively. For western hemlock (Tsuga heterophylla), median survival times were 13.0 (11.9, 14.2) years and 12.5 (11.4, 13.7) years, respectively. Although the two failure distributions had similar median failure times, the log-logistic implies a higher survival probability over time for snags that remained standing at the end of the study period. Created snags can be a useful supplement for harvest units rotated at ∼45 years and Douglas-fir will be available for longer as standing structures. For example, under the log-logistic model, a predicted 5% of Douglas-fir snags are retained to rotation age, so that 40 snags per hectare would be required at harvest to maintain 2 snags per hectare through stand rotation. Snags created from western hemlock will provide an early rotation pulse but are unlikely to last longer than 20 years. Our results suggest that longevity can be increased by maximizing the snag size within the safety constraints of harvesting equipment. Scattering of snags may have a slightly negative effect on snag survival but this outcome should be weighed against potential ecological benefits of variation in snag distributions.

In 2012 the Oregon Board of Forestry (Board) determined that current forestry rules were insufficient at preventing the degradation of cold water in salmonid-bearing streams. Consequently, the Oregon Department of Forestry required a means for evaluating and comparing the effectiveness of newly-proposed harvest scenarios. We derived a field-data based method for simulating riparian harvest and modeling the resulting effects on stream temperature that could be used for evaluating different harvest scenarios. We simulated prescribed harvests by using previously-collected riparian stand data. To create a predictive model, we modified and joined two earlier stream temperature and shade models from Groom et al. (2011b) into a Bayesian hierarchical model. The predictive model produced parameter estimates and temperature change metrics that aligned with the previous findings. The model predicted that harvest according to a full implementation of the State forest harvest plan would on average result in a 0.19 °C increase, while the model predicted that a similarly-scaled harvest to current private forest regulation specifications would lead to an average increase of 1.45 °C. Further simulations suggested that employing a no-cut slope-distance riparian zone of 27.4 m would result in average warming below 0.3 °C of unharvested conditions. The Board considered these results along with other information and directed the Oregon Department of Forestry to develop harvest rule revisions. Those revisions became effective as of July 2017.

Summary 1.Tree plantations occur globally and are often promoted as a strategy to supply wood products for an expanding human population while reducing pressure on natural forests. Herbicides can accelerate growth of crop trees by suppressing competing vegetation, but little information is available about potential trade-offs with early seral biodiversity resulting from more intensive management. 2.Using data collected over five years immediately following stand-replacing disturbance (clear-felling), we used a large-scale experiment to test how environmental filtering influences dynamics of avian community assembly. We evaluated avian responses to three levels of plant cover reduction (Light, Moderate, and Intensive herbicide applications) in relation to a control without herbicide. Under the environmental filtering hypothesis, we expected reduced avian species richness and higher turnover as broadleaf plant cover decreases with increasing management intensity. We predicted that the most intensive treatments would exert strong negative effects on leaf-gleaning insectivores, including several species of conservation concern due to long-term population declines. 3.Richness of leaf-gleaning bird species was reduced by 23-52% over the five years on Moderate (standard practice) vs. control treatments, but effects were substantially smaller for the non-leaf-gleaner guild in years 1-4 (8-25%) and disappeared by year 5 (0%). Both leaf-gleaner and non-leaf-gleaner functional groups continued to colonize Moderate and Intensive treatments at higher probabilities than the control in Year 5 (range: 0.17-0.29), likely due to rapid vegetation recovery after herbicide applications ceased. Planted conifers were >35% taller and >70% larger in diameter in the two most intensive treatments, leading to substantially more wood volume produced per unit area than on stands without herbicide applications. 4.Synthesis and applications. Under current management regimes, stand-level trade-offs between conservation of avian diversity and production of wood commodities may be less severe than previously recognized. However, in landscapes where biodiversity conservation rather than wood production is the primary goal, managers can adjust the trade-off by making relatively small reductions in herbicide use that should have positive impacts on richness of leaf-gleaning insectivorous birds. This article is protected by copyright. All rights reserved.

As human demand for ecosystem products increases, managers of landscapes used for commodity production require information about effects of management regimes on biological diversity. Landscape attributes, however, may moderate ecological responses to local-scale conservation and management actions. As a result, uniform application of local management prescriptions may yield variable biodiversity responses. We examined how interactions between local habitat structure and landscape forest cover were associated with avian community composition in the Ouachita Mountains, Arkansas, USA, 1995–1998. We used Bayesian hierarchical models to estimate occupancy for 63 breeding bird species, while accounting for variable detection with data collected from 1941 temporally replicated point count stations. Specifically, we estimated how interactions of four local habitat covariates (canopy cover of mature coniferous and hardwood trees, number of snags, and shrub cover) with percentage of mature hardwood forest at the landscape scale were associated with species occupancy and richness. Average predictive comparisons indicated that snag count and shrub cover had the strongest associations with species richness. Estimated associations for each of the four local forest cover variables was similar across all levels of landscape forest cover, suggesting weak or negligible interactions between these local measures and the landscape covariate. We found little support for our main prediction that local/landscape habitat interactions would be strongest at low levels of landscape forest cover (1–20%). Consequently, we suggest that forest managers consider prescriptions that result in a broad spatial distribution of heterogeneous habitat structural conditions (e.g., variation in understory cover and composition), irrespective of landscape context, to maintain a diverse avian breeding assemblage on landscapes in this region.

Components of biodiversity in intensively managed forest stands may be reduced in comparison to naturally regenerated stands. Use of herbicides to suppress herbaceous and woody plant species that compete with planted seedlings has been implicated in negative impacts. We designed a large-scale experimental study to test the influence of intensive forest management on the abundance of early seral bird species in the Oregon Coast Range, US. Experimental applications consisted of ‘Intensive’ (i.e., heavy use of herbicides), ‘Moderate’ and ‘Light’ treatments, as well as controls with no herbicide application. In relation to the control, abundance of six out of thirteen bird species was significantly reduced in at least one of the three treatments. Leaf-gleaning insectivorous birds were more negatively affected by heavier herbicide treatments in general than bird species with other foraging behavior. Long-term bird population trends, derived from the Breeding Bird Survey, were correlated with the effect of intensive treatment; species more negatively associated with intensive treatments at the stand scale, were more likely to be in decline across the Pacific Northwest, US. Our results also indicate that reducing intensity of herbicide applications has positive effects on early seral bird abundance during the first 2 years of stand growth – particularly those species exhibiting negative population trends. To balance biodiversity conservation and timber production, research examining the tradeoffs between reduced application of herbicide and tree growth is required.

Conservation and management programs use populations of sentinel taxa, such as stream-associated amphibians, as indicator species due to their perceived sensitivity to environmental change. Estimating population size with traditional tools such as mark–recapture estimators may be impractical for forest-dwelling stream-associated amphibians, many of which are cryptic and have low detection probabilities. In addition, sampling techniques can alter habitat conditions, particularly with repeat sampling, and compromise inferences about management impacts. We used simulated and empirical data and N-mixture models to estimate detection probabilities and abundances for two amphibian genera, giant Dicamptodon and torrent Rhyacotriton salamanders, sampled with a less-invasive approach than other methods. We surveyed forested headwater streams located in western Washington, USA, for salamanders 7 July–27 August 2008. We assessed model sensitivity to changes in animal abundance (5 and 15) and detection probability (0.05–0.5), as well as study design alternatives including number of sample plots (50–150) and number of sampling visits (2–4). We also evaluated the effects of stream temperature and stream order on detection probability using data collected from forested streams in Washington, USA. Precision of detection probability estimates improved as the number of plots and sampling occasions increased. Variability of estimated population sizes decreased with higher detection probability, although species abundance had little effect on precision of detection probability estimates. Detection probability estimated from empirical data ranged from 0.07 to 0.65 for giant salamanders and 0.06–0.67 for torrent salamanders. Giant salamander detection probability was positively associated with stream temperature regardless of stream order, and was higher in second- and third-order streams than first-order streams. Detection probability for torrent salamanders varied with stream temperature, order, and the interaction of those covariates, with detection increasing with temperature for second- and third-order streams but showing a flat or decreasing trend for first-order streams. N-mixture models, paired with careful consideration of study design alternatives, can produce robust estimates of abundance and obviate the traditional reliance on indices of relative abundance for many rare and sensitive taxa. Use of a less invasive technique for sampling stream-associated amphibians resulted in sufficient animal captures for suitable model performance. Our simulation results can inform study design and direct efficient allocation of field effort.

Evaluating spatial and temporal variation in abundance due to anthropogenic and environmental disturbances is a central aspect of wildlife ecology and management. We conducted an experiment to evaluate the effects of salvage logging on the abundance of 22 avian species and 6 foraging guilds in lodgepole pine (Pinus contorta) forests affected by beetle outbreaks, south-central Oregon, USA, 1996–1998. Treatments consisted of the removal of lodgepole pine snags only; live trees and ponderosa pine snags were not harvested. Our hierarchical model requires replicated count data from multiple sample units across several time periods, during which the population is closed, to estimate abundance as a function of logging treatment and management district while accounting for imperfect and variable detection probability. We fit the model to point counts from 12 control and 12 treatment plots with 3 surveys during each breeding season, 1996–1998. We found evidence for a large, but imprecise, effect of salvage logging in all 3 years for only 1 species, the gray flycatcher (Empidonax wrightii). The abundance of the remaining species either did not change or displayed weak positive responses to the treatment. Although 3 foraging guilds increased in total abundance, 2 guilds did not change and the response of 1 guild changed direction in different years. Our results suggest that, unlike most postfire salvage logging prescriptions, selective harvesting after beetle outbreaks may meet multiple management objectives, including the maintenance of avian population sizes comparable to those found in unharvested stands. Future research should consider different sampling programs for those species with large home ranges (e.g., woodpeckers) that may not be sampled adequately using commonly employed programs (e.g., point count stations). © 2012 The Wildlife Society.

Dibenzo(a,l)pyrene (DBP) is among the most potent carcinogenic polycyclic aromatic hydrocarbons. Previously, we showed that DBP administration to pregnant mice resulted in high mortality of offspring from an aggressive T-cell lymphoma. All mice that survive to 10 months of age exhibit lung tumors with high multiplicity. Recombinant cytochrome P450 (cyp) 1b1 from mice and the homologue 1B1 in humans exhibit high activity toward the metabolic activation of DBP. Targeted disruption of the cyp1b1 gene protects against most DBP-dependent cancers. Mice heterozygous for the disrupted cyp1b1 allele were used to examine the effect of cyp1b1 gene dosage on DBP transplacental carcinogenesis. Dams were treated with 1 or 15 mg/kg of DBP or 50 mg/kg of benzo(a)pyrene. Cyp1b1-null offspring did not develop lymphoma, whereas wild-type and heterozygous siblings, born to dams given the high dose of DBP, exhibited significant mortalities between 10 and 30 weeks of age. At 10 months, all groups had lung adenomas or carcinomas [9.5%, 40.3%, 25.6%, and 100% incidences for controls, benzo(a)pyrene, 1 and 15 mg/kg DBP, respectively]. Cyp1b1 status did not alter benzo(a)pyrene-dependent carcinogenesis. At 1 mg/kg DBP, cyp1b1 status altered the incidence of lung tumors (19.0, 27.8, and 28.6% for nulls, heterozygous, and wild-type, respectively). At 15 mg/kg, tumor multiplicities in cyp1b1 wild-type (9.3) and heterozygous (9.5) offspring were nearly twice that of cyp1b1-null siblings (5.0). These data confirm that cyp1b1 bioactivation of DBP occurs in fetal target tissues, following transplacental exposure, with the thymus and lung as primary and secondary targets, respectively.

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).

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.

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.

Our laboratory recently developed a mouse model of transplacental induction of lymphoma, lung and liver cancer by the polycyclic aromatic hydrocarbon, dibenzo[a,l]pyrene (DBP). Pregnant B6129SF1 females, bred to 129S1/SvIm males, were treated on day 17 of gestation with an oral dose of 15 mg/kg DBP. Beginning on day 0 of gestation, dams were given (ad lib) buffered water, 0.5% green tea, 0.5% decaffeinated green tea, caffeine or epigallocatechin-3-gallate (EGCG) (both at equivalent concentrations found in tea). The concentration of the teas (and corresponding caffeine and EGCG) was increased to 1.0% upon entering the second trimester, 1.5% at onset of the third trimester and continued at 1.5% until pups were weaned at 21 days of age. Offspring were raised with normal drinking water and AIN93G diet. Beginning at 2 months of age, offspring experienced significant mortalities due to an aggressive T-cell lymphoma as seen in our previous studies. Ingestion of caffeinated, but not decaffeinated, green tea provided modest but significant protection (P = 0.03) against mortality. Caffeine provided a more robust (P = 0.006) protection, but EGCG was without effect. Offspring also developed DBP-dependent lung adenomas. All treatments significantly reduced lung tumor multiplicity relative to controls (P < 0.02). EGCG was most effective at decreasing tumor burden (P = 0.005) by on average over 40% compared with controls. Induction of Cytochrome P450 (Cyp)1b1 in maternal liver may reduce bioavailability of DBP to the fetus as a mechanism of chemoprevention. This is the first demonstration that maternal ingestion of green tea, during pregnancy and nursing, provides protection against transplacental carcinogenesis.

Clinical outcomes that are difficult to measure directly are often graded with ordinal scales in the veterinary dermatology literature to approximate objective evaluation. Ordered categorical scales require statistical presentation and analysis methods consistent with the structure of the data. The objective of this study was to determine the frequency of inappropriate presentation and analysis methods of ordered categorical data in the recent veterinary dermatology literature. A total of 62 articles published between 1 January 2003 and 30 June 2006 in 16 journals reported categorical scales and were included in the study. The presentation and analysis methods of ordered categorical data were classified as appropriate or inappropriate based on published recommendations. Forty articles (64.5%) utilized a median of four ordinal scales (range 1-13). Inappropriate presentation methods of ordered categorical data were identified in 23 of 40 articles (57.5%). These included reporting inappropriate summary statistics (n = 17) and summation of ad hoc numerical rating scales (n = 15). Inappropriate analytical methods were used in nine of 40 articles (22.5%). These included inappropriate use of t-tests (n = 3) and analysis of variance (anova, n = 6). The frequency of inappropriate presentation and analysis methods of ordered categorical data in the veterinary dermatology literature is similar to that reported for several fields in the human medical literature. In order to reduce the likelihood of making unwarranted implications or conclusions regarding ordinal data, authors should follow established guidelines for methods of presentation and analysis of ordered categorical scales.

The polycyclic aromatic hydrocarbons (PAHs) benzo[a]pyrene (B[a]P) and dibenzo[a,l]pyrene (DB[a,l]P) are well-studied environmental carcinogens, however, their potency within a complex mixture is uncertain. We investigated the influence of urban dust particulate matter (UDPM) on the bioactivation and tumor initiation of B[a]P and DB[a,l]P in an initiation-promotion tumorigenesis model. SENCAR mice were treated topically with UDPM or in combination with B[a]P or DB[a,l]P, followed by weekly application of the promoter 12-O-tetradecanoylphorbol-13 acetate. UDPM exhibited weak tumor-initiating activity but significantly delayed the onset of B[a]P-induced tumor initiation by two-fold. When cotreated with UDPM, DB[a,l]P-treated animals displayed no significant difference in tumor-initiating activity, compared with DB[a,l]P alone. Tumor initiation correlated with PAH-DNA adducts, as detected by (33)P-postlabeling and reversed-phase high-performance liquid chromatography. Induction of cytochrome P450 (CYP)1A1 and 1B1 proteins was also detected following UDPM treatment or cotreatment with B[a]P or DB[a,l]P, indicating PAH bioactivation. Further genotoxicity analyses by the comet assay revealed that cotreatment of UDPM plus B[a]P or DB[a,l]P resulted in increased DNA strand breaks, compared with PAH treatment alone. The metabolizing activities of CYP1A1 and CYP1B1, as measured by the 7-ethoxyresorufin O-deethylation (EROD) assay, revealed that UDPM noncompetitively inhibited CYP1A1 and CYP1B1 EROD activity in a dose-dependent manner. Overall, these data suggest that components within complex mixtures can alter PAH-induced carcinogenesis by inhibiting CYP bioactivation and influence other genotoxic effects, such as oxidative DNA damage. These data further suggest that in addition to the levels of potent PAH, the effects of other mixture components must be considered when predicting human cancer risk.

Ethanol is a well-established developmental toxicant; however, the molecular and cellular mechanism(s) of toxicity remains unclear. It has been suggested that ethanol metabolism leads to oxidative stress resulting in an increase in cell death. Alcohol developmental toxicity has not been well studied in zebrafish; however, zebrafish represent an excellent vertebrate model for investigating and understanding normal and aberrant development. To evaluate ethanol metabolism dependent toxicity, chemical inhibitors of the ethanol metabolizing enzymes were utilized. Embryos co-exposed to ethanol and a combination of ethanol metabolism inhibitors led to a significant increase in the occurrence of pericardial edema. Further, in the presence of the inhibitor mixture there was an increase in developmental malformations at lower ethanol concentrations. Cell death has been implicated as a potential explanation for ethanol-dependent toxicity. Using cell death assays, ethanol significantly increased embryonic cell death. To determine if oxidative stress underlies cardiovascular dysfunction, embryos were co-exposed to ethanol and several antioxidants. The antioxidants, glutathione and lipoic acid, partially attenuated the incidence of pericardial edema. The effectiveness of the antioxidants to protect the embryos from ethanol-induced cell death was also evaluated. The antioxidants provided no protection against cell death. Thus, ethanol-mediated pericardial edema and cell death appear to be mechanistically distinct.