Identifying engaging bird species and traits with community science observations.

Identifying rates at which birders engage with different species can inform the impact and efficacy of conservation outreach and the scientific use of community-collected biodiversity data. Species that are thought to be "charismatic" are often prioritized in conservation, and previous researchers have used sociological experiments and digital records to estimate charisma indirectly. In this study, we take advantage of community science efforts as another record of human engagement with animals that can reveal observer biases directly, which are in part driven by observer preference. We apply a multistage analysis to ask whether opportunistic birders contributing to iNaturalist engage more with larger, more colorful, and rarer birds relative to a baseline approximated from eBird contributors. We find that body mass, color contrast, and range size all predict overrepresentation in the opportunistic dataset. We also find evidence that, across 472 modeled species, 52 species are significantly overreported and 158 are significantly underreported, indicating a wide variety of species-specific effects. Understanding which birds are highly engaging can aid conservationists in creating impactful outreach materials and engaging new naturalists. The quantified differences between two prominent community science efforts may also be of use for researchers leveraging the data from one or both of them to answer scientific questions of interest.

Multiple prenatal exposures and acute-care clinical encounters for asthma among children born to mothers living near a Superfund site.

Prenatal exposures are associated with childhood asthma, and risk may increase with simultaneous exposures. Pregnant women living in lower-income communities tend to have elevated exposures to a range of potential asthma risk factors, which may interact in complex ways. We examined the association between prenatal exposures and the risk of childhood acute-care clinical encounters for asthma (hospitalizations, emergency department visits, observational stays) using conditional logistic regression with a multivariable smoothing term to model the interaction between continuous variables, adjusted for maternal characteristics and stratified by sex. All births near the New Bedford Harbor (NBH) Superfund site (2000-2006) in New Bedford, Massachusetts, were followed through 2011 using the Massachusetts Pregnancy to Early Life Longitudinal (PELL) Data System to identify children aged 5-11 years with acute-care clinical asthma encounters (265 cases among 7787 children with follow-up). Hazard ratios (HRs) were higher for children living closer to the NBH site with higher umbilical cord blood lead levels than in children living further away from the NBH site with lower lead levels (P <.001). HRs were higher for girls (HR = 4.17; 95% CI, 3.60-4.82) than for boys (HR = 1.72; 95% CI, 1.46-2.02). Our results suggest that prenatal lead exposure in combination with residential proximity to the NBH Superfund site is associated with childhood asthma acute-care clinical encounters. This article is part of a Special Collection on Environmental Epidemiology.

Non-linear relationships in clinical research.

True linear relationships are rare in clinical data. Despite this, linearity is often assumed during analyses, leading to potentially biased estimates and inaccurate conclusions. In this introductory paper, we aim to first describe - in a non-mathematical manner - how to identify non-linear relationships. Various methods are then discussed that can be applied to deal with non-linearity, including transformations, polynomials, splines, and Generalized Additive Models (GAMs), along with their strengths and weaknesses. Finally, we illustrate the use of these methods with a practical example from nephrology, providing guidance on how to report the results from non-linear relationships.

Community-science reveals delayed fall migration of waterfowl and spatiotemporal effects of a changing climate.

Climate change has well-documented, yet variable, influences on the annual movements of migratory birds. The effects of climate change on fall migration remains understudied compared with spring but appears to be less consistent among species, regions and years. Changes in the pattern and timing of waterfowl migration in particular may result in cascading effects on ecosystem function, and socio-economic and cultural outcomes. We investigated changes in the migration of 15 waterfowl species along a major flyway corridor of continental importance in northeastern North America using 43 years of community-science data. We built spatially- and temporally explicit hierarchical generative additive models for each species and demonstrated that climate, specifically the interaction between minimum temperature and precipitation, significantly influences migration phenology for most species. Certain species' migratory movements responded to specific temperature thresholds (climate migrants) and others reacted more to the interaction of temperature and precipitation (extreme event migrants). There are already significant changes in the fall migration phenology of common waterfowl species with high ecological and economic importance, which may simply increase in the context of a changing climate. If not addressed, climate change could induce mismatches in management, regulations and population surveys which would negatively impact the hunting industry. Our findings highlight the importance of considering species-specific spatiotemporal scales of effect on climate on migration and our methods can be widely adapted to quantify and forecast climate-driven changes in wildlife migration.

Les changements climatiques ont des influences bien documentées, mais variables, sur les mouvements annuels des oiseaux migrateurs. Les effets des changements climatiques sur les migrations automnales demeurent peu étudiés par rapport aux migrations printanières, mais il semble qu'ils soient moins constants d'une espèce, d'une région et d'une année à l'autre. Les changements dans le patron et le calendrier de la migration de la sauvagine en particulier peuvent avoir des effets en chaîne sur la fonction des écosystèmes et des impacts socio­économiques et culturels. Nous avons étudié les changements dans la migration de 15 espèces de sauvagine le long d'un corridor de migration d'importance continentale dans le nord­est de l'Amérique du Nord, en utilisant 43 ans de données scientifiques communautaires. Nous avons construit des modèles additifs généralisés hiérarchiques spatialement et temporellement explicites pour chaque espèce et avons démontré que le climat, en particulier l'interaction entre la température minimale et les précipitations, influence de manière significative la phénologie de la migration pour la plupart des espèces. Les mouvements migratoires de certaines espèces répondent à des seuils de température spécifiques (migrateurs climatiques) et d'autres réagissent davantage à l'interaction entre la température et les précipitations (migrateurs d'événements extrêmes). La phénologie des migrations automnales d'espèces de sauvagine commune qui ont une grande importance écologique et économique connaît déjà des changements importants, qui pourraient simplement s'accentuer dans le cadre des changements climatiques. S'ils ne sont pas pris en compte, les changements climatiques pourraient induire des décalages dans la gestion, les réglementations et les enquêtes de population, ce qui aurait un impact négatif sur l'industrie de la chasse. Nos résultats soulignent l'importance de prendre en compte les échelles spatio­temporelles spécifiques sur la migration et nos méthodes peuvent être largement adaptées pour quantifier et prévoir les changements induits par le climat dans la migration de la faune.

Using fractal dimension analysis to assess the effects of normal aging and sex on subregional cortex alterations across the lifespan from a Chinese dataset.

Fractal dimension (FD) is used to quantify brain structural complexity and is more sensitive to morphological variability than other cortical measures. However, the effects of normal aging and sex on FD are not fully understood. In this study, age- and sex-related differences in FD were investigated in a sample of 448 adults age of 19-80 years from a Chinese dataset. The FD was estimated with the surface-based morphometry (SBM) approach, sex differences were analyzed on a vertex level, and correlations between FD and age were examined. Generalized additive models (GAMs) were used to characterize the trajectories of age-related changes in 68 regions based on the Desikan-Killiany atlas. The SBM results showed sex differences in the entire sample and 3 subgroups defined by age. GAM results demonstrated that the FD values of 51 regions were significantly correlated with age. The trajectories of changes can be classified into 4 main patterns. Our results indicate that sex differences in FD are evident across developmental stages. Age-related trajectories in FD are not homogeneous across the cerebral cortex. Our results extend previous findings and provide a foundation for future investigation of the underlying mechanism.

Trace metals pollution and trophic position of three sea urchin species in the Gulf of California.

Sea urchin species are ecologically important in the Gulf of California and are becoming popular as a local fishery due to their commercial value. The most abundant species are Echinometra vanbrunti, Eucidaris thouarsii, and Tripneustes depressus. The objective of this study was to evaluate cadmium, lead, copper, zinc, and iron concentrations, as well as stable isotope values in these sea urchin species in the Santa Rosalia mining area (STR), in three sites: Punta Gorda, Punta el Aterrizaje, and Punta Salina. The highest Fe concentration (100.2 mg kg-1) was found in E. vanbrunti, while the highest concentrations of Pb (15.1 mg kg-1), Cu (14.5 mg kg-1), and Zn (347.7 mg kg-1) were recorded in E. thouarsii, and the highest Cd concentration (10.8 mg kg-1) was found in T. depressus. The main health risk of trace metal pollution in STR may be caused by Cd and Pb. δ15N and δ13C values were higher in E. thouarsii and T. depressus, respectively; E. thouarsii has the highest trophic position. Specimen size was not related to metal concentrations, but a positive relationship was observed between specimen size and isotopic values in T. depressus. The three species showed different bioaccumulation patterns for the metals analyzed. Additionally, collection sites and seasons play an important role in the variability of metal concentration.

Multilevel Semiparametric Latent Variable Modeling in R with "galamm".

We present the R package galamm, whose goal is to provide common ground between structural equation modeling and mixed effect models. It supports estimation of models with an arbitrary number of crossed or nested random effects, smoothing splines, mixed response types, factor structures, heteroscedastic residuals, and data missing at random. Implementation using sparse matrix methods and automatic differentiation ensures computational efficiency. We here briefly present the implemented methodology, give an overview of the package and an example demonstrating its use.

Boosting multivariate structured additive distributional regression models.

We develop a model-based boosting approach for multivariate distributional regression within the framework of generalized additive models for location, scale, and shape. Our approach enables the simultaneous modeling of all distribution parameters of an arbitrary parametric distribution of a multivariate response conditional on explanatory variables, while being applicable to potentially high-dimensional data. Moreover, the boosting algorithm incorporates data-driven variable selection, taking various different types of effects into account. As a special merit of our approach, it allows for modeling the association between multiple continuous or discrete outcomes through the relevant covariates. After a detailed simulation study investigating estimation and prediction performance, we demonstrate the full flexibility of our approach in three diverse biomedical applications. The first is based on high-dimensional genomic cohort data from the UK Biobank, considering a bivariate binary response (chronic ischemic heart disease and high cholesterol). Here, we are able to identify genetic variants that are informative for the association between cholesterol and heart disease. The second application considers the demand for health care in Australia with the number of consultations and the number of prescribed medications as a bivariate count response. The third application analyses two dimensions of childhood undernutrition in Nigeria as a bivariate response and we find that the correlation between the two undernutrition scores is considerably different depending on the child's age and the region the child lives in.

Sediment core records and impact factors of polycyclic aromatic hydrocarbons in Chinese lakes.

Lake sediment is a natural sink for polycyclic aromatic hydrocarbons (PAHs). PAH sedimentation characteristics and their impact factors of Chinese lakes have mainly been qualitative assessed. However, quantitative impacts of PAH sedimentation from different factors have not been well analyzed. To fill this gap, we screened PAH sedimentation records from the literature, for 51 lakes in China and other regions of the world, to identify historical concentration variation and the impact factors of PAHs in different regions, in lake sediment. The results show that PAH concentrations in the sediment core in the selected Chinese lakes (478 ± 812 ng/g dry weight (dw)) were significantly lower than those in North America (5518 ± 6572 ng/g dw) and Europe (3817 ± 4033 ng/g dw). From 1900 to 2015, most of the lakes in China showed an increasing trend of PAH sedimentation concentrations, with the lakes in Southeastern China showed a decreasing trend of PAH concentration in the period of 2001-2015, which was later than the peak times shown in Western countries (1941-1970). The 2-3-ring PAHs were the main components in the sediment core of Chinese lakes, but the proportion to the total PAHs decreased from 72% in 1900-1940 to 55% in 2001-2015. Generalized additive modeling (GAM) was adopted to simulate the associations between PAH sedimentation records and the impact factors. There are large regional variations of economic and industrial development in China. The impact factors of PAH accumulation in the lake sediments differ in different regions. However, population and the consumption of coal, pesticides, and fertilizer were identified to be the most important impact factors influencing PAH sedimentation. The Chinese government needs to strengthen control measures on pollutant discharge to reduce the anthropogenic impact of PAH sedimentation in lakes.

Predictors of Prolonged Euthyroidism After Radioactive Iodine Treatment for Graves' Disease: A Pilot Study.

OBJECTIVE: Patients with Graves' disease who remain hyperthyroid under the treatment of antithyroid drugs (ATD) or cannot tolerate ATD usually receive radioactive iodine (RAI) to control disease activity. This pilot study aimed to identify predictors of prolonged euthyroidism > 12 months after receiving RAI. METHODS: Demographic, clinical, and laboratory data from 117 patients receiving RAI were retrospectively collected, including age, gender, body surface area, smoking status, free thyroxine, thyrotropin, thyrotropin binding inhibiting immunoglobulin, microsomal antibody, thyroglobulin antibody, medication history, and thyroid volume. Only 85 patients without missing values were included in statistical analysis. The calculated RAI dose was the estimated thyroid volume × 0.4. The difference and ratio between the actual and calculated RAI doses were examined. A stepwise logistic regression analysis was conducted to identify important predictors of prolonged euthyroidism > 12 months. The cut-off values for discretizing continuous covariates were estimated by fitting generalized additive models. RESULTS: Among the 85 patients on RAI, 18 (21.2%) achieved prolonged euthyroidism > 12 months, 38 (44.7%) remained hyperthyroid with decreased ATD doses, but 29 (34.1%) suffered permanent hypothyroidism and needed long-term levothyroxine. Logistic regression analysis revealed that patients with age > 66 years, 33 < age ≤ 66 years, quitting smoking vs nonsmoking or current smoking, 600 < micorsomal antibody ≤ 1729 IU/mL, 47% < thyrotropin binding inhibiting immunoglobulin ≤ 81%, 7 < thyroglobulin antibody ≤ 162 IU/mL, 0.63 < ratio between actual and calculated RAI doses ≤ 1.96, or taking hydroxychloroquine would have a higher chance of reaching prolonged euthyroidism > 12 months after receiving RAI. Its area under the Receiver Operating Characteristic (ROC) curve was 0.932. CONCLUSION: Patients with Graves' disease who received an actual RAI dose close to the calculated RAI dose achieved prolonged euthyroidism > 12 months if they also took hydroxychloroquine during RAI treatment.

A note of feature screening via a rank-based coefficient of correlation.

Feature screening is a useful and popular tool to detect informative predictors for ultrahigh-dimensional data before developing statistical analysis or constructing statistical models. While a large body of feature screening procedures has been developed, most methods are restricted to examine either continuous or discrete responses. Moreover, even though many model-free feature screening methods have been proposed, additional assumptions are imposed in those methods to ensure their theoretical results. To address those difficulties and provide simple implementation, in this paper we extend the rank-based coefficient of correlation to develop a feature screening procedure. We show that this new screening criterion is able to deal with continuous and binary responses. Theoretically, the sure screening property is established to justify the proposed method. Simulation studies demonstrate that the predictors with nonlinear and oscillatory trajectories are successfully retained regardless of the distribution of the response. Finally, the proposed method is implemented to analyze two microarray datasets.

Short-term variations and correlations in water quality after dam removal in the Chishui river basin.

Dam damming has an adverse effect on river connectivity, leading to downstream nutrient transport and ecosystem fragmentation. Dam demolition has already been used as an effective measurement to promote the ecological restoration of rivers. Few studies have analyzed the short-term variations of water quality following dam removal. This study investigated the response of multi-element and multi-form water quality parameters, such as water temperature (TEM), dissolved oxygen (DO), pH, biochemical oxygen demand (BOD5), chemical oxygen demand (COD), ammonia nitrogen (NH3-N), total nitrogen (TN) and total phosphorus (TP), to the demolition of 4 dams in Chishui River Basin in short term. The study employed Spearman correlation analysis and Generalized Additive Models to identify the critical variables and examine the inter-relationship between these water quality parameters. Our results show that COD, BOD5, and TP increased after two weeks of dam removal, while NH3-N and TN decreased. Dams with larger volumes and higher heights led to more obvious deterioration for DO, COD, and BOD5. We also found that denitrification and resuspension dominantly affect the water quality indicators following dam removal. Denitrification is responsible for downstream TN increase, and resuspension and related sediment transport contribute to downstream TP increase. Our study provides an opportunity to explore the transformation and migration of N and P in reservoirs following dam removal in the short term and presents a scientific basis and new thought for the short-term protection and management following the clean-up and rectification of multiple small hydropower plants.

Association of the components of ambient fine particulate matter (PM2.5) and chronic kidney disease prevalence in China.

Previous research has implicated PM2.5 as a potential environmental risk factor for CKD, but little is known about the associations between its components and CKD. We conducted a nationwide cross-sectional study using the updated air pollution data in the nationwide population (N = 2,938,653). Using generalized additive models, we assessed the association between long-term exposure to PM2.5 and its components (i.e., black carbon [BC], organic matter [OM], nitrate [NO3-], ammonium [NH4+], sulfate [SO42-]), and CKD prevalence. The air pollution data was estimated using high-resolution and high-quality spatiotemporal datasets of ground-level air pollutants in China. Besides, we adopted a novel quantile-based g-computation approach to assess the effect of a mixture of PM2.5 constituents on CKD prevalence. The average concentration of PM2.5 was 78.67 ± 22.5 µg/m3, which far exceeded WHO AQG. In the fully adjusted generalized additive model, at a 10 km × 10 km spatial resolution, the ORs per IQR increase in previous 1-year average PM2.5 exposures was 1.380 (95%CI: 1.345-1.415), for NH4+ was 1.094 (95%CI: 1.062-1.126), for BC was 1.604 (95%CI: 1.563-1.646), for NO3- was 1.094 (95%CI: 1.060-1.130), for SO42- was 1.239 (95%CI: 1.208-1.272), and for the OM was 1.387 (95%CI: 1.354-1.421), respectively. Subgroup analysis showed females, younger, and healthier were more vulnerable to this effect. In the further exploration of the joint effect of PM2.5 compositions (OR 1.234 [95%CI 1.222-1.246]) per quartile increase in all 5 PM2.5 components, we found that PM2.5SO42- contributed the most. These findings provide important evidence for the positive relationship between long-term exposure to PM2.5 and its chemical constituents and CKD prevalence in a Chinese health check-up population, and identified PM2.5SO42- has the highest contribution to this relationship. This study provides clinical and public health guidance for reducing specific air particle exposure for those at risk of CKD.

A general semiparametric Bayesian discrete-time recurrent events model.

Event time variables are often recorded in a discrete fashion, especially in the case of patient-reported outcomes. This work is motivated by a study of illicit drug users, in which time to drug use cessation has been recorded as a number of whole months. Existing approaches for handling such discrete data include treating the survival times as continuous (with adjustments for inevitable tied outcomes), or using discrete models that omit important features like random effects. We provide a general Bayesian discrete-time proportional hazards model, incorporating a number of features popular in continuous-time models such as competing risks and frailties. Our model also provides flexible baseline hazards for time effects, as well as generalized additive models style semiparametric incorporation of other time-varying covariates. Our specific modeling choices enable efficient Markov chain Monte Carlo inference algorithms, which we provide to the user in the form of a freely available R package called $\texttt{brea}$. We demonstrate that our model performs better on our motivating substance abuse application than existing approaches. We also present a reproducible application of the $\texttt{brea}$ software to a freely available data set from a clinical trial of anesthesia administration methods.

Stepping up to the thermogradient plate: a data framework for predicting seed germination under climate change.

BACKGROUND AND AIMS: Seed germination is strongly influenced by environmental temperatures. With global temperatures predicted to rise, the timing of germination for thousands of plant species could change, leading to potential decreases in fitness and ecosystem-wide impacts. The thermogradient plate (TGP) is a powerful but underutilized research tool that tests germination under a broad range of constant and alternating temperatures, giving researchers the ability to predict germination characteristics using current and future climates. Previously, limitations surrounding experimental design and data analysis methods have discouraged its use in seed biology research. METHODS: Here, we have developed a freely available R script that uses TGP data to analyse seed germination responses to temperature. We illustrate this analysis framework using three example species: Wollemia nobilis, Callitris baileyi and Alectryon subdentatus. The script generates >40 germination indices including germination rates and final germination across each cell of the TGP. These indices are then used to populate generalized additive models and predict germination under current and future monthly maximum and minimum temperatures anywhere on the globe. KEY RESULTS: In our study species, modelled data were highly correlated with observed data, allowing confident predictions of monthly germination patterns for current and future climates. Wollemia nobilis germinated across a broad range of temperatures and was relatively unaffected by predicted future temperatures. In contrast, C. baileyi and A. subdentatus showed strong seasonal temperature responses, and the timing for peak germination was predicted to shift seasonally under future temperatures. CONCLUSIONS: Our experimental workflow is a leap forward in the analysis of TGP experiments, increasing its many potential benefits, thereby improving research predictions and providing substantial information to inform management and conservation of plant species globally.

Generalized additive models to analyze nonlinear trends in biomedical longitudinal data using R: Beyond repeated measures ANOVA and linear mixed models.

In biomedical research, the outcome of longitudinal studies has been traditionally analyzed using the repeated measures analysis of variance (rm-ANOVA) or more recently, linear mixed models (LMEMs). Although LMEMs are less restrictive than rm-ANOVA as they can work with unbalanced data and non-constant correlation between observations, both methodologies assume a linear trend in the measured response. It is common in biomedical research that the true trend response is nonlinear and in these cases the linearity assumption of rm-ANOVA and LMEMs can lead to biased estimates and unreliable inference. In contrast, GAMs relax the linearity assumption of rm-ANOVA and LMEMs and allow the data to determine the fit of the model while also permitting incomplete observations and different correlation structures. Therefore, GAMs present an excellent choice to analyze longitudinal data with non-linear trends in the context of biomedical research. This paper summarizes the limitations of rm-ANOVA and LMEMs and uses simulated data to visually show how both methods produce biased estimates when used on data with non-linear trends. We present the basic theory of GAMs and using reported trends of oxygen saturation in tumors, we simulate example longitudinal data (2 treatment groups, 10 subjects per group, 5 repeated measures for each group) to demonstrate their implementation in R. We also show that GAMs are able to produce estimates with non-linear trends even when incomplete observations exist (with 40% of the simulated observations missing). To make this work reproducible, the code and data used in this paper are available at: https://github.com/aimundo/GAMs-biomedical-research.

Spike-and-slab least absolute shrinkage and selection operator generalized additive models and scalable algorithms for high-dimensional data analysis.

There are proposals that extend the classical generalized additive models (GAMs) to accommodate high-dimensional data ( p ≫ n $$ p\gg n $$ ) using group sparse regularization. However, the sparse regularization may induce excess shrinkage when estimating smooth functions, damaging predictive performance. Moreover, most of these GAMs consider an "all-in-all-out" approach for functional selection, rendering them difficult to answer if nonlinear effects are necessary. While some Bayesian models can address these shortcomings, using Markov chain Monte Carlo algorithms for model fitting creates a new challenge, scalability. Hence, we propose Bayesian hierarchical generalized additive models as a solution: we consider the smoothing penalty for proper shrinkage of curve interpolation via reparameterization. A novel two-part spike-and-slab LASSO prior for smooth functions is developed to address the sparsity of signals while providing extra flexibility to select the linear or nonlinear components of smooth functions. A scalable and deterministic algorithm, EM-Coordinate Descent, is implemented in an open-source R package BHAM. Simulation studies and metabolomics data analyses demonstrate improved predictive and computational performance against state-of-the-art models. Functional selection performance suggests trade-offs exist regarding the effect hierarchy assumption.

Multiple imputation procedures for estimating causal effects with multiple treatments with application to the comparison of healthcare providers.

Choosing between multiple healthcare providers requires us to simultaneously compare the expected outcomes under each provider. This comparison is complex because the composition of patients treated by each provider may differ. Similar issues arise when simultaneously comparing the adverse effects of interventions using non-randomized data. To simultaneously estimate the effects of multiple providers/interventions we propose procedures that explicitly impute the set of potential outcomes for each subject. The procedures are based on different specifications of the generalized additive models (GAM) and the Bayesian additive regression trees (BART). We compare the performance of the proposed procedures to previously proposed matching and weighting procedures using an extensive simulation study for continuous outcomes. Our simulations show that when the distributions of the covariates across treatment groups have adequate overlap, the multiple imputation procedures based on separate BART or GAM models in each treatment group are generally superior to weighting based methods and have similar and sometimes better performance than matching on the logit of the generalized propensity score. Another advantage of these multiple imputation procedures is the ability to provide point and interval estimates to a wide range of causal effect estimands. We apply the proposed procedures to comparing multiple nursing homes in Massachusetts for readmission outcomes. The proposed approach can be applied to other causal effects applications with multiple treatments.

A newly invasive species may promote dissimilarity of pest populations between organic and conventional farming systems.

Insect taxa vary in their phenology across space creating dissimilar patterns of species abundance over time. The role of human disturbances and invasive species in these patterns of temporal dissimilarity (phenological differences) across space, however, remain largely unexplored. To dissect these patterns, we evaluated four common pests and one newly invasive species (Contarinia nasturtii; Swede midge) at 220 time points across 2 years on organic and conventional farms. We first summarized across time and evaluated differences in pest abundance between farm management (organic and conventional). We then used generalized additive models to describe temporal patterns of abundance, disentangling phenological differences across management systems. Last, we conducted a temporal beta diversity analysis to identify which species and management practices contribute most to dissimilarity. We found that aggregating pest abundance across time and species masked differences in pest phenology across management systems and concealed variation in pest abundance that was strongly driven by an invasive species, respectively. Overall, our results suggest that organic and conventional farms may be only superficially similar in pest abundance. Rather, by accounting for time, we demonstrate a more nuanced understanding of pest communities moving beyond abundance that may be particularly important for management of newly invasive species.

Spatio-temporal changes in chimpanzee density and abundance in the Greater Mahale Ecosystem, Tanzania.

Species conservation and management require reliable information about animal distribution and population size. Better management actions within a species' range can be achieved by identifying the location and timing of population changes. In the Greater Mahale Ecosystem (GME), western Tanzania, deforestation due to the expansion of human settlements and agriculture, annual burning, and logging are known threats to wildlife. For one of the most charismatic species, the endangered eastern chimpanzee (Pan troglodytes schweinfurthii), approximately 75% of the individuals are distributed outside national park boundaries, requiring monitoring and protection efforts over a vast landscape of various protection statuses. These efforts are especially challenging when we lack data on trends in density and population size. To predict spatio-temporal chimpanzee density and abundance across the GME, we used density surface modeling, fitting a generalized additive model to a 10-year time-series data set of nest counts based on line-transect surveys. The chimpanzee population declined at an annual rate of 2.41%, including declines of 1.72% in riparian forests (from this point forward, forests), 2.05% in miombo woodlands (from this point forward, woodlands) and 3.45% in nonforests. These population declines were accompanied by ecosystem-wide declines in vegetation types of 1.36% and 0.32% per year for forests and woodlands, respectively; we estimated an annual increase of 1.35% for nonforests. Our model predicted the highest chimpanzee density in forests (0.86 chimpanzees/km2 , 95% confidence intervals (CIs) 0.60-1.23; as of 2020), followed by woodlands (0.19, 95% CI 0.12-0.30) and nonforests (0.18, 95% CI 0.10-1.33). Although forests represent only 6% of the landscape, they support nearly one-quarter of the chimpanzee population (769 chimpanzees, 95% CI 536-1103). Woodlands dominate the landscape (71%) and therefore support more than a half of the chimpanzee population (2294; 95% CI 1420-3707). The remaining quarter of the landscape is represented by nonforests and supports another quarter of the chimpanzee population (750; 95% CI 408-1381). Given the pressures on the remaining suitable habitat in Tanzania, and the need of chimpanzees to access both forest and woodland vegetation to survive, we urge future management actions to increase resources and expand the efforts to protect critical forest and woodland habitat and promote strategies and policies that more effectively prevent irreversible losses. We suggest that regular monitoring programs implement a systematic random design to effectively inform and allocate conservation actions and facilitate interannual comparisons for trend monitoring, measuring conservation success, and guiding adaptive management.