Forest management, forest vegetation, and climate influence nesting ecology of a focal bird species in the western USA

Akaike, 1974, A new look at the statistical model identification, IEEE Trans. Autom. Control, 19, 716, 10.1109/TAC.1974.1100705 Allen, 2002, Ecological restoration of southwestern ponderosa pine ecosystems: a broad perspective, Ecol. Appl., 12, 1418, 10.1890/1051-0761(2002)012[1418:EROSPP]2.0.CO;2 Barton, K. 2020. MuMIn: Multi-Model Inference. Battaglia, 2018, Changes in forest structure since 1860 in ponderosa pine dominated forests in the Colorado and Wyoming Front Range, USA, For. Ecol. Manage., 422, 147, 10.1016/j.foreco.2018.04.010 Brooks, M., E., K. Kristensen, K. Benthem J. ,van, A. Magnusson, C. Berg W., A. Nielsen, H. Skaug J., M. Mächler, and B. Bolker M. 2017. glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling. R J. 9:378. Chazarreta, 2011, Division of labour in parental care in the Magellanic Woodpecker Campephilus magellanicus, J. Ornithol., 152, 231, 10.1007/s10336-010-0570-4 Ciuzio, 2013, Opportunities and challenges to implementing bird conservation on private lands: Bird Conservation on Private Land, Wildl. Soc. Bull., 37, 267, 10.1002/wsb.266 Conn, 2018, A guide to Bayesian model checking for ecologists, Ecol. Monogr., 88, 526, 10.1002/ecm.1314 Conway, 2000, Evolution of passerine incubation behavior: influence of food, temperature, and nest predation, Evolution, 54, 670 McKay Curtis, S. 2018. mcmcplots: Create Plots from MCMC Output. Cushman, 2008, Parsimony in landscape metrics: Strength, universality, and consistency, Ecol. Ind., 8, 691, 10.1016/j.ecolind.2007.12.002 Cyphers, 2019, Policy design to support cross-boundary land management: the example of the Joint Chiefs Landscape Restoration Partnership, Land Use Policy, 80, 362, 10.1016/j.landusepol.2018.09.021 Davis, 2019, Microclimatic buffering in forests of the future: the role of local water balance, Ecography, 42, 1, 10.1111/ecog.03836 Davis, K. T., M. D. Robles, K. B. Kemp, P. E. Higuera, T. Chapman, K. L. Metlen, J. L. Peeler, K. C. Rodman, T. Woolley, R. N. Addington, B. J. Buma, C. A. Cansler, M. J. Case, B. M. Collins, J. D. Coop, S. Z. Dobrowski, N. S. Gill, C. Haffey, L. B. Harris, B. J. Harvey, R. D. Haugo, M. D. Hurteau, D. Kulakowski, C. E. Littlefield, L. A. McCauley, N. Povak, K. L. Shive, E. Smith, J. T. Stevens, C. S. Stevens-Rumann, A. H. Taylor, A. J. Tepley, D. J. N. Young, R. A. Andrus, M. A. Battaglia, J. K. Berkey, S. U. Busby, A. R. Carlson, M. E. Chambers, E. K. Dodson, D. C. Donato, W. M. Downing, P. J. Fornwalt, J. S. Halofsky, A. Hoffman, A. Holz, J. M. Iniguez, M. A. Krawchuk, M. R. Kreider, A. J. Larson, G. W. Meigs, J. P. Roccaforte, M. T. Rother, H. Safford, M. Schaedel, J. S. Sibold, M. P. Singleton, M. G. Turner, A. K. Urza, K. D. Clark-Wolf, L. Yocom, J. B. Fontaine, and J. L. Campbell. 2023. Reduced fire severity offers near-term buffer to climate-driven declines in conifer resilience across the western United States. Proceedings of the National Academy of Sciences 120:e2208120120. Dixon, 1995 Dorazio, 2016, Bayesian data analysis in population ecology: motivations, methods, and benefits, Popul. Ecol., 58, 31, 10.1007/s10144-015-0503-4 Drapeau, 2016, Natural disturbance regimes as templates for the response of bird species assemblages to contemporary forest management, Divers. Distrib., 22, 385, 10.1111/ddi.12407 Dudley, 2003 DuRant, 2013, Ecological, evolutionary, and conservation implications of incubation temperature-dependent phenotypes in birds: Incubation temperature and avian offspring phenotype, Biol. Rev., 88, 499, 10.1111/brv.12015 Edworthy, 2011, Woodpeckers increase in abundance but maintain fecundity in response to an outbreak of mountain pine bark beetles, For. Ecol. Manage., 261, 203, 10.1016/j.foreco.2010.10.006 ESRI, 2019 Fox, 2009, Effect displays in R for multinomial and proportional-odds logit models: extensions to the effects package, J. Stat. Softw., 32, 10.18637/jss.v032.i01 Garrett, 1996 Gelman, 2006, Prior distributions for variance parameters in hierarchical models, Bayesian Anal., 1, 515, 10.1214/06-BA117A Gelman, A., J. B. Carlin, H. S. Stern, D. B. Dunson, A. Vehtari, and D. B. Rubin. 2020. Bayesian Data Analysis. Gelman, 1992, Inference from iterative simulation using multiple sequences, Stat. Sci., 7, 10.1214/ss/1177011136 Grolemund, 2011, Dates and times made easy with lubridate, J. Stat. Softw., 40, 1, 10.18637/jss.v040.i03 Guo, 2020, Temporal shifts in iso/anisohydry revealed from daily observations of plant water potential in a dominant desert shrub, New Phytol., 225, 713, 10.1111/nph.16196 Hagmann, 2021, Evidence for widespread changes in the structure, composition, and fire regimes of western North American forests, Ecol. Appl., 31, 10.1002/eap.2431 Harrison, 2011, Carry-over effects as drivers of fitness differences in animals: Carry-over effects in animal populations, J. Anim. Ecol., 80, 4, 10.1111/j.1365-2656.2010.01740.x Hartig, F. 2020. DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models. Hayward, 2016 Heinze, 2018, Variable selection - A review and recommendations for the practicing statistician, Biom. J., 60, 431, 10.1002/bimj.201700067 Herrera, 1982, Seasonal variation in the quality of fruits and diffuse coevolution between plants and avian dispersers, Ecology, 63, 773, 10.2307/1936798 Hessburg, 2005, Dry forests and wildland fires of the inland Northwest USA: contrasting the landscape ecology of the pre-settlement and modern eras, For. Ecol. Manage., 211, 117, 10.1016/j.foreco.2005.02.016 Hessburg, 2021, Wildfire and climate change adaptation of western North American forests: a case for intentional management, Ecol. Appl., 31, e02432, 10.1002/eap.2432 Hollenbeck, 2011, Habitat suitability and nest survival of white-headed woodpeckers in unburned forests of Oregon, J. Wildl. Manag., 75, 1061, 10.1002/jwmg.146 Jones, 2018, Declining old-forest species as a legacy of large trees lost, Divers. Distrib., 24, 341, 10.1111/ddi.12682 Jones, 2021, Forest restoration limits megafires and supports species conservation under climate change, Front. Ecol. Environ. Kehoe, 2017 Kellner, K. 2021. jagsUI: A Wrapper Around “rjags” to Streamline “JAGS” Analyses. Knudson, C. 2022. glmm: Genarlized Linear Mixed Models via Monte Carlo Likelihood Approximation. Kooistra, 2022, Characterizing the context and demand for the Us Forest Service’s collaborative forest landscape restoration program in 2020, J. For., 120, 64 Kozma, 2009, Nest-site attributes and reproductive success of white-headed and hairy woodpeckers along the east-slope Cascades of Washington state, 52 Kozma, 2017, Factors associated with nest survival of Black-throated Sparrows, desert-breeding nest-site generalists, J. Field Ornithol., 88, 274, 10.1111/jofo.12209 Krannitz, P. G., and T. E. Duralia. 2023. cone and seed production in pinus ponderosa: a review. Kuhn, M. 2022. caret: Classification and Regression Training. Latif, 2015, Evaluating habitat suitability models for nesting white-headed woodpeckers in unburned forest: Model Evaluation for White-Headed Woodpeckers, J. Wildl. Manag., 79, 263, 10.1002/jwmg.842 Latif, 2020, Development and evaluation of habitat suitability models for nesting white-headed woodpecker (Dryobates albolarvatus) in burned forest, PLoS One, 15, e0233043, 10.1371/journal.pone.0233043 Latif, 2020, Dry conifer forest restoration benefits Colorado Front Range avian communities, Ecol. Appl., 30, 10.1002/eap.2142 Latif, 2021, Prescribed fire limits wildfire severity without altering ecological importance for birds, Fire Ecology, 17, 37, 10.1186/s42408-021-00123-2 Latif, 2022, Simulated treatment effects on bird communities inform landscape-scale dry conifer forest management, Ecol. Appl., 32, 10.1002/eap.2555 Lenth, R. 2022. emmeans: Estimated Marginal Means, aka Least-Squares Means. Lin Pedersen, T. 2020. patchwork: The Composer of Plots. Lorenz, 2016, Foraging plasticity by a keystone excavator, the white-headed woodpecker, in managed forests: Are there consequences for productivity?, For. Ecol. Manage., 363, 110, 10.1016/j.foreco.2015.12.021 Lozano, 1996, Age, arrival date and reproductive success of male american redstarts Setophaga ruticilla, J. Avian Biol., 27, 164, 10.2307/3677146 Lundquist, 2013, Lower forest density enhances snow retention in regions with warmer winters: A global framework developed from plot-scale observations and modeling, Water Resour. Res., 49, 6356, 10.1002/wrcr.20504 Luneau, 2010, A wireless video camera for viewing tree cavities: Wireless Video Camera for Viewing Cavities, J. Field Ornithol., 81, 176, 10.1111/j.1557-9263.2010.00275.x McGarigal, K., B. J. Marks, S. Cushman, and E. Ene. 2012. FRAGSTATS v4: spatial pattern analysis program for quantifying landscape structure. Page PNW-GTR-351. U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Portland, OR. Mellen-McLean, 2015 Menz, 2013, Hurdles and opportunities for landscape-scale restoration, Science, 339, 526, 10.1126/science.1228334 Miller-ter Kuile, A., Ogle, K., Cavanaugh, C., Dudley, J., Markus, A., Saab, V., Wright, M., Sanderlin, J., 2023. Data for: Forest management, forest vegetation, and climate influence nesting ecology of a focal bird species in the western USA. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2023-0053. Milligan, 2022, Evaluating the cumulative effects of livestock grazing on wildlife with an integrated population model, Front. Ecol. Evol., 10, 10.3389/fevo.2022.818050 Muller, K. 2020. here: A simpler way to find your files. R. Öberg, 2015, Rainfall during parental care reduces reproductive and survival components of fitness in a passerine bird, Ecol. Evol., 5, 345, 10.1002/ece3.1345 Ogle, 2020, Ensuring identifiability in hierarchical mixed effects Bayesian models, Ecol. Appl., 30, 10.1002/eap.2159 Ogle, 2013, Feedback and modularization in a bayesian meta–analysis of tree traits affecting forest dynamics, Bayesian Analysis, 8, 10.1214/13-BA806 Ogle, 2015, Quantifying ecological memory in plant and ecosystem processes, Ecol. Lett., 18, 221, 10.1111/ele.12399 Ott, 2023, Fuel treatment effectiveness at the landscape scale: a systematic review of simulation studies comparing treatment scenarios in North America, Fire Ecol., 19, 10, 10.1186/s42408-022-00163-2 Pasinelli, 2001, Breeding performance of the middle spotted woodpecker Dendrocopos medius in relation to weather and territory quality, Ardea, 89, 353 Patrick, 2009, Physiological responses of two contrasting desert plant species to precipitation variability are differentially regulated by soil moisture and nitrogen dynamics, Glob. Chang. Biol., 15, 1214, 10.1111/j.1365-2486.2008.01750.x Pavlacky, 2022, Landscape-scale conservation mitigates the biodiversity loss of grassland birds, Ecol. Appl., 32, 10.1002/eap.2548 Peltier, 2022, Contemporary tree growth shows altered climate memory, Ecol. Lett., 25, 2663, 10.1111/ele.14130 Phalan, B. T., J. M. Northrup, Z. Yang, R. L. Deal, J. S. Rousseau, T. A. Spies, and M. G. Betts. 2019. Impacts of the Northwest Forest Plan on forest composition and bird populations. Proceedings of the National Academy of Sciences 116:3322–3327. Plummer, 2006, CODA: convergence diagnosis and output analysis for MCMC, R News, 6, 7 Plummer, M. 2003. JAGS: A Program for Analysis of Bayesian Graphical Models Using Gibbs Sampling. Prather, 2008, Real versus perceived conflicts between restoration of ponderosa pine forests and conservation of the Mexican spotted owl, Forest Policy Econ., 10, 140, 10.1016/j.forpol.2007.07.003 Prichard, 2021, Adapting western North American forests to climate change and wildfires: 10 common questions, Ecol. Appl., e02433, 10.1002/eap.2433 Purcell, 2021, White-headed woodpecker nesting habitat at multiple spatial scales: are habitat preferences adaptive?, For. Ecol. Manage., 499, 10.1016/j.foreco.2021.119606 R Core Team, 2020 Raftery, A., Lewis, S.. 1995. Implementing MCMC. Page Markov Chain Monte Carlo in practice. Raftery, 1992, One long run with diagnostics: Implementation strategies for Markov Chain Monte Carlo, Stat. Sci., 7, 493, 10.1214/ss/1177011143 Raphael, 1984, Use of snags by cavity-nesting birds in the Sierra Nevada, Wildl. Monogr., 86, 3 Rich, 2004, 1 Riecke, 2019, Integrated population models: model assumptions and inference, Methods Ecol. Evol., 10, 1072, 10.1111/2041-210X.13195 Rossmanith, 2007, Reproductive success and nestling diet in the Lesser Spotted Woodpecker (Picoides minor): the early bird gets the caterpillar, J. Ornithol., 148, 323, 10.1007/s10336-007-0134-4 Saab, 2004, Factors influencing occupancy of nest cavities in recently burned forests, Condor, 106, 20, 10.1093/condor/106.1.20 Saunders, S. P., M. T. Farr, A. D. Wright, C. A. Bahlai, J. W. Ribeiro, S. Rossman, A. L. Sussman, T. W. Arnold, and E. F. Zipkin. 2019. Disentangling data discrepancies with integrated population models. Ecology:e02714. Savage, 2013, Double whammy: high-severity fire and drought in ponderosa pine forests of the Southwest, Can. J. For. Res., 43, 570, 10.1139/cjfr-2012-0404 Schaub, 2011, Integrated population models: a novel analysis framework for deeper insights into population dynamics, J. Ornithol., 11 Schloerke, B., D. Cook, J. Larmarange, F. Briatte, M. Marbach, E. Thoen, A. Elberg, and J. Crowley. 2021. GGally: Extensions to “ggplot2.”. Schultz, 2012, The collaborative forest landscape restoration program: a history and overview of the first projects, J. For., 110, 381 Shew, 2019, Finer-scale habitat predicts nest survival in grassland birds more than management and landscape: A multi-scale perspective, J. Appl. Ecol., 56, 929, 10.1111/1365-2664.13317 Stephens, S. L., M. A. Battaglia, D. J. Churchill, B. M. Collins, M. Coppoletta, C. M. Hoffman, J. M. Lydersen, M. P. North, R. A. Parsons, S. M. Ritter, and J. T. Stevens. 2020. Forest Restoration and Fuels Reduction: Convergent or Divergent? BioScience:biaa134. Stillman, 2019, Age-dependent habitat relationships of a burned forest specialist emphasise the role of pyrodiversity in fire management, J. Appl. Ecol., 56, 880, 10.1111/1365-2664.13328 Taylor, 2022, Severity patterns of the 2021 Dixie Fire exemplify the need to increase low-severity fire treatments in California’s forests, Environ. Res. Lett., 17, 10.1088/1748-9326/ac7735 Tempel, 2015, Evaluating short- and long-term impacts of fuels treatments and simulated wildfire on an old-forest species, Ecosphere, 6, art261, 10.1890/ES15-00234.1 Thomsen, 2010, Habitat cascades: the conceptual context and global relevance of facilitation cascades via habitat formation and modification, Integr. Comp. Biol., 50, 158, 10.1093/icb/icq042 Tingley, 2023, Multi-trophic occupancy modeling connects temporal dynamics of woodpeckers and beetle sign following fire, PLoS One, 18, e0281687, 10.1371/journal.pone.0281687 USDA, 2022 van Mantgem, 2018, Pre-fire drought and competition mediate post-fire conifer mortality in western U.S. National Parks, Ecol. Appl., 28, 1730, 10.1002/eap.1778 Vergara, 2009, Responses of Chilean forest birds to anthropogenic habitat fragmentation across spatial scales, Landsc. Ecol., 24, 25, 10.1007/s10980-008-9275-y Visser, 1993, Development of temperature regulation in shorebirds, Physiol. Zool., 66, 771, 10.1086/physzool.66.5.30163823 Wang, 2016, Locally Downscaled and spatially customizable climate data for historical and future periods for North America, PLoS One, 11, e0156720, 10.1371/journal.pone.0156720 Weathers, 2000, Thermoregulation in Antarctic fulmarine petrels, J. Comp. Physiol., 170, 561, 10.1007/s003600000134 Wickham, H., Bryan, J.. 2022. readxl: Read Excel Files. Wickham, 2019, Welcome to the Tidyverse, J. Open Source Software, 4, 1686, 10.21105/joss.01686 Wickham, H. 2007. Reshaping Data with the reshape Package 21:1–20. Wiebe, 2001, Microclimate of tree cavity nests: is it important for reproductive success in northern flickers?, Auk, 118, 412, 10.1093/auk/118.2.412 Wiebe, 2010, Influence of spring temperatures and individual traits on reproductive timing and success in a migratory woodpecker, Auk, 127, 917, 10.1525/auk.2010.10025 Wightman, 2010, White-headed woodpecker nesting ecology after wildfire, J. Wildl. Manag., 74, 1098, 10.2193/2009-174 Wiktander, 2001, Annual and seasonal reproductive trends in the Lesser Spotted Woodpecker Dendrocopos minor, Ibis, 143, 72, 10.1111/j.1474-919X.2001.tb04171.x Wisdom, M. J., R. S. Holthausen, B. C. Wales, C. D. Hargis, V. A. Saab, D. C. Lee, W. J. Hann, T. D. Rich, M. M. Rowland, W. J. Murphy, and M. R. Eames. 2000. Source habitats for terrestrial vertebrates of focus in the interior Columbia Basin: broad-scale trends and management implications. General technical report, U.S. Forest Service, Pacific Northwest Research Station. Zipkin, 2018, Synthesizing multiple data types for biological conservation using integrated population models, Biol. Conserv., 217, 240, 10.1016/j.biocon.2017.10.017