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  1. Abstract Aim

    As climate change increases the frequency and severity of droughts in many regions, conservation during drought is becoming a major challenge for ecologists. Droughts are multidimensional climate events whose impacts may be moderated by changes in temperature, water availability or food availability, or some combination of these. Simultaneously, other stressors such as extensive anthropogenic landscape modification may synergize with drought. Useful observational models for guiding conservation decision‐making during drought require multidimensional, dynamic representations to disentangle possible drought impacts, and consequently, they will require large, highly resolved data sets. In this paper, we develop a two‐stage predictive framework for assessing how drought impacts vary with species, habitats and climate pathways.


    Central Valley, California, USA.


    We used a two‐stage counterfactual analysis combining predictive linear mixed models and N‐mixture models to characterize the multidimensional impacts of drought on 66 bird species. We analysed counts from the eBird participatory science data set between 2010 and 2019 and produced species‐ and habitat‐specific estimates of the impact of drought on relative abundance.


    We found that while fewer than a quarter (16/66) of species experienced abundance declines during drought, nearly half of all species (27/66) changed their habitat associations during drought. Among species that shifted their habitat associations, the use of natural habitats declined during drought while use of developed habitat and perennial agricultural habitat increased.

    Main Conclusions

    Our findings suggest that birds take advantage of agricultural and developed land with artificial irrigation and heat‐buffering microhabitat structure, such as in orchards or parks, to buffer drought impacts. A working lands approach that promotes biodiversity and mitigates stressors across a human‐induced water gradient will be critical for conserving birds during drought.

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  2. Item response theory (IRT) models typically rely on a normality assumption for subject-specific latent traits, which is often unrealistic in practice. Semiparametric extensions based on Dirichlet process mixtures (DPMs) offer a more flexible representation of the unknown distribution of the latent trait. However, the use of such models in the IRT literature has been extremely limited, in good part because of the lack of comprehensive studies and accessible software tools. This article provides guidance for practitioners on semiparametric IRT models and their implementation. In particular, we rely on NIMBLE, a flexible software system for hierarchical models that enables the use of DPMs. We highlight efficient sampling strategies for model estimation and compare inferential results under parametric and semiparametric models.

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  3. Abstract

    Correlative species distribution models are widely used to quantify past shifts in ranges or communities, and to predict future outcomes under ongoing global change. Practitioners confront a wide range of potentially plausible models for ecological dynamics, but most specific applications only consider a narrow set. Here, we clarify that certain model structures can embed restrictive assumptions about key sources of forecast uncertainty into an analysis. To evaluate forecast uncertainties and our ability to explain community change, we fit and compared 39 candidate multi‐ or joint species occupancy models to avian incidence data collected at 320 sites across California during the early 20th century and resurveyed a century later. We found massive (>20,000 LOOIC) differences in within‐time information criterion across models. Poorer fitting models omitting multivariate random effects predicted less variation in species richness changes and smaller contemporary communities, with considerable variation in predicted spatial patterns in richness changes across models. The top models suggested avian environmental associations changed across time, contemporary avian occupancy was influenced by previous site‐specific occupancy states, and that both latent site variables and species associations with these variables also varied over time. Collectively, our results recapitulate that simplified model assumptions not only impact predictive fit but may mask important sources of forecast uncertainty and mischaracterize the current state of system understanding when seeking to describe or project community responses to global change. We recommend that researchers seeking to make long‐term forecasts prioritize characterizing forecast uncertainty over seeking to present a single best guess. To do so reliably, we urge practitioners to employ models capable of characterizing the key sources of forecast uncertainty, where predictors, parameters and random effects may vary over time or further interact with previous occurrence states.

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  4. Abstract

    Over 70% of the 62 million hectares of cropland in the Midwestern United States is grown in corn-based rotations. These crop rotations are caught in a century-long simplification trend despite robust evidence demonstrating yield and soil benefits from diversified rotations. Our ability to explore and explain this trend will come in part from observing the biophysical and policy influences on farmers’ crop choices at one key level of management: the field. Yet field-level crop rotation patterns remain largely unstudied at regional scales and will be essential for understanding how national agricultural policy manifests locally and interacts with biophysical phenomena to erode—or bolster—soil and environmental health, agricultural resilience, and farmers’ livelihoods. We developed a novel indicator of crop rotational complexity and applied it to 1.5 million fields across the US Midwest. We used bootstrapped linear mixed models to regress field-level rotational complexity against biophysical (land capability, precipitation) and policy-driven (distance to the nearest biofuel plant and grain elevator) factors. After accounting for spatial autocorrelation, there were statistically clear negative relationships between rotational complexity and biophysical factors (land capability and precipitation during the growing season), indicating decreased rotation in prime growing areas. A positive relationship between rotational complexity and distance to the nearest biofuel plant suggests policy-based, as well as biophysical, constraints on regional rotations. This novel RCI is a promising tool for future fine-scale rotational analysis and demonstrates that the United States’ most fertile soils are the most prone to degradation, with recent policy choices further exacerbating this trend.

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  5. null (Ed.)
    Accurate estimation of forest biomass is important for scientists and policymakers interested in carbon accounting, nutrient cycling, and forest resilience. Estimates often rely on the allometry of trees; however, limited datasets, uncertainty in model form, and unaccounted for sources of variation warrant a re-examination of allometric relationships using modern statistical techniques. We asked the following questions: (1) Is there among-stand variation in allometric relationships? (2) Is there nonlinearity in allometric relationships? (3) Can among-stand variation or nonlinearities in allometric equations be attributed to differences in stand age? (4) What are the implications for biomass estimation? To answer these questions, we synthesized a dataset of small trees from six different studies in the White Mountains of New Hampshire. We compared the performance of generalized additive models (GAMs) and linear models and found that GAMs consistently outperform linear models. The best-fitting model indicates that allometries vary among both stands and species and contain subtle nonlinearities which are themselves variable by species. Using a planned contrasts analysis, we were able to attribute some of the observed among-stand heterogeneity to differences in stand age. However, variability in these results point to additional sources of stand-level heterogeneity, which if identified could improve the accuracy of live-tree biomass estimation. 
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  6. Abstract

    Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open‐source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N‐mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block‐sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one‐size‐fits‐all best strategy, but rather problem‐specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10–12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model‐generic MCMC procedures in open‐source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim.

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  7. Abstract

    Disconnected habitat fragments are poor at supporting population and community persistence; restoration ecologists, therefore, advocate for the establishment of habitat networks across landscapes. Few empirical studies, however, have considered how networks of restored habitat patches affect metacommunity dynamics. Here, using a 10‐year study on restored hedgerows and unrestored field margins within an intensive agricultural landscape, we integrate occupancy modelling with network theory to examine the interaction between local and landscape characteristics, habitat selection and dispersal in shaping pollinator metacommunity dynamics. We show that surrounding hedgerows and remnant habitat patches interact with the local floral diversity, bee diet breadth and bee body size to influence site occupancy, via colonisation and persistence dynamics. Florally diverse sites and generalist, small‐bodied species are most important for maintaining metacommunity connectivity. By providing the first in‐depth assessment of how a network of restored habitat influences long‐term population dynamics, we confirm the conservation benefit of hedgerows for pollinator populations and demonstrate the importance of restoring and maintaining habitat networks within an inhospitable matrix.

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  8. Abstract

    Climate and land‐use changes are thought to be the greatest threats to biodiversity, but few studies have directly measured their simultaneous impacts on species distributions. We used a unique historic resource—early 20th‐century bird surveys conducted by Joseph Grinnell and colleagues—paired with contemporary resurveys a century later to examine changes in bird distributions in California's Central Valley, one of the most intensively modified agricultural zones in the world and a region of heterogeneous climate change. We analyzed species‐ and community‐level occupancy using multispecies occupancy models that explicitly accounted for imperfect detection probability, and developed a novel, simulation‐based method to compare the relative influences of climate and land‐use covariates on site‐level species richness and beta diversity (measured by Jaccard similarity). Surprisingly, we show that mean occupancy, species richness and between‐site similarity have remained remarkably stable over the past century. Stability in community‐level metrics masked substantial changes in species composition; occupancy declines of some species were equally matched by increases in others, predominantly species with generalist or human‐associated habitat preferences. Bird occupancy, richness and diversity within each era were driven most strongly by water availability (precipitation and percent water cover), indicating that both climate and land‐use are important drivers of species distributions. Water availability had much stronger effects than temperature, urbanization and agricultural cover, which are typically thought to drive biodiversity decline.

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