Appendix D. Partial-correlation analysis.

Partial-correlation analysis

Appendix F. Models of development and contagion for the entire land bird community and species groups.

Models of development and contagion for the entire land bird community and species groups

Appendix E. Core variable groups for all land bird species and species groups.

Core variable groups for all land bird species and species groups

Appendix C. Six groups of explanatory variables used in analyses of landbird community structure in the Lake Tahow basin, 2003–2004.

Six groups of explanatory variables used in analyses of landbird community structure in the Lake Tahow basin, 2003–2004

Appendix B. List of species detected and membership in three groups based on general ecological characteristics.

List of species detected and membership in three groups based on general ecological characteristics

Appendix A. Sufficiency of a single year of sampling per site.

Sufficiency of a single year of sampling per site

Conservation of Avian Diversity in the Sierra Nevada: Moving beyond a Single-Species Management Focus

<div><p>Background</p><p>As a result of past practices, many of the dry coniferous forests of the western United States contain dense, even-aged stands with uncharacteristically high levels of litter and downed woody debris. These changes to the forest have received considerable attention as they elevate concerns regarding the outcome of wildland fire. However, attempts to reduce biomass through fuel reduction (i.e., thinning of trees) are often opposed by public interest groups whose objectives include maintaining habitat for species of concern such as the spotted owl, <i>Strix occidentalis</i>, the northern goshawk, <i>Accipiter gentilis,</i> and the Pacific fisher, <i>Martes pennanti</i>. Whether protection of these upper-trophic level species confers adequate conservation of avian forest diversity is unknown.</p><p>Methodology and Principal Findings</p><p>We use a multi-species occurrence model to estimate the habitat associations of 47 avian species detected at 742 sampling locations within an 880-km² area in the Sierra Nevada. Our approach, which accounts for variations in detectability of species, estimates occurrence probabilities of all species in a community by linking species occurrence models into one hierarchical community model, thus improving inferences on all species, especially those that are rare or observed infrequently. We address how the avian community is influenced by covariates related to canopy cover, tree size and shrub cover while accounting for the impacts of abiotic variables known to affect species distributions.</p><p>Conclusions and Significance</p><p>Environmental parameters estimated through our approach emphasize the importance of within and between stand-level heterogeneity in meeting biodiversity objectives and suggests that many avian species would increase under more open canopy habitat conditions than those favored by umbrella species of high conservation concern. Our results suggest that a more integrated approach that emphasizes maintaining a diversity of habitats across environmental gradients and minimizing urbanization may have a greater benefit to ecosystem functioning then a single-species management focus.</p></div

Location of the study area in California/Nevada, USA with 172 primary sample points indicated.

<p>Sampling points were distributed across forested areas (green) using systematic random sampling. Cluster sampling was conducted within 200 m of each primary sample point. Each of these 742 sites was sampled multiple times within a year for a total 2021 data points over the four-year study.</p

Mean parameter estimates and posterior intervals for the effect of A) percent canopy cover, B) standard deviation in canopy cover, C) mean DBH, D) standard deviation in DBH, E) percent shrub cover for each of the 47 species included in our analysis.

<p>Values indicate the change in occurrence predicted as a function of the change in one standard deviation of change in each response variable. For purposes of illustration, species were classified as very common (occupancy probability ≥85%, N = 6), common (≥50% and <85%, N = 8), uncommon (≥25% and <50%, N = 13), rare (≥10% and <25%, N = 8) and very rare (<10%, N = 11) based on their mean probability of occurrence for average environmental and habitat conditions in the Tahoe Basin (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063088#pone.0063088.s001" target="_blank">Appendix S1</a>). Panels F-J show comparisons of the covariate estimates across these groups.</p

Number of species in which the species-specific parameter estimate was positive or negative.

<p>Values in parenthesis indicate the subset of species in which the posterior intervals do not overlap zero<b>.</b></p