Individual heterogeneity influences the effects of translocation on urban dispersal of an invasive reptile

Background Invasive reptiles pose a serious threat to global biodiversity, but early detection of individuals in an incipient population is often hindered by their cryptic nature, sporadic movements, and variation among individuals. Little is known about the mechanisms that affect the movement of these species, which limits our understanding of their dispersal. Our aim was to determine whether translocation or small-scale landscape features affect movement patterns of brown treesnakes (Boiga irregularis), a destructive invasive predator on the island of Guam. Methods We conducted a field experiment to compare the movements of resident (control) snakes to those of snakes translocated from forests and urban areas into new urban habitats. We developed a Bayesian hierarchical model to analyze snake movement mechanisms and account for attributes unique to invasive reptiles by incorporating multiple behavioral states and individual heterogeneity in movement parameters. Results We did not observe strong differences in mechanistic movement parameters (turning angle or step length) among experimental treatment groups. We found some evidence that translocated snakes from both forests and urban areas made longer movements than resident snakes, but variation among individuals within treatment groups weakened this effect. Snakes translocated from forests moved more frequently from pavement than those translocated from urban areas. Snakes translocated from urban areas moved less frequently from buildings than resident snakes. Resident snakes had high individual heterogeneity in movement probability. Conclusions Our approach to modeling movement improved our understanding of invasive reptile dispersal by allowing us to examine the mechanisms that influence their movement. We also demonstrated the importance of accounting for individual heterogeneity in population-level analyses, especially when management goals involve eradication of an invasive species.

Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability

ABSTRACT There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour–normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution analyses are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of potentially cancer-related genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.

A space–time Bayesian hierarchical modeling framework for projection of seasonal maximum streamflow

Timely projections of seasonal streamflow extremes can be useful for the early implementation of annual flood risk adaptation strategies. However, predicting seasonal extremes is challenging, particularly under nonstationary conditions and if extremes are correlated in space. The goal of this study is to implement a space–time model for the projection of seasonal streamflow extremes that considers the nonstationarity (interannual variability) and spatiotemporal dependence of high flows. We develop a space–time model to project seasonal streamflow extremes for several lead times up to 2 months, using a Bayesian hierarchical modeling (BHM) framework. This model is based on the assumption that streamflow extremes (3 d maxima) at a set of gauge locations are realizations of a Gaussian elliptical copula and generalized extreme value (GEV) margins with nonstationary parameters. These parameters are modeled as a linear function of suitable covariates describing the previous season selected using the deviance information criterion (DIC). Finally, the copula is used to generate streamflow ensembles, which capture spatiotemporal variability and uncertainty. We apply this modeling framework to predict 3 d maximum streamflow in spring (May–June) at seven gauges in the Upper Colorado River basin (UCRB) with 0- to 2-month lead time. In this basin, almost all extremes that cause severe flooding occur in spring as a result of snowmelt and precipitation. Therefore, we use regional mean snow water equivalent and temperature from the preceding winter season as well as indices of large-scale climate teleconnections – El Niño–Southern Oscillation, Atlantic Multidecadal Oscillation, and Pacific Decadal Oscillation – as potential covariates for 3 d spring maximum streamflow. Our model evaluation, which is based on the comparison of different model versions and the energy skill score, indicates that the model can capture the space–time variability in extreme streamflow well and that model skill increases with decreasing lead time. We also find that the use of climate variables slightly enhances skill relative to using only snow information. Median projections and their uncertainties are consistent with observations, thanks to the representation of spatial dependencies through covariates in the margins and a Gaussian copula. This spatiotemporal modeling framework helps in the planning of seasonal adaptation and preparedness measures as predictions of extreme spring streamflows become available 2 months before actual flood occurrence.

Bayesian Hierarchical Models can Infer Interpretable Predictions of Leaf Area Index From Heterogeneous Datasets

Environmental scientists often face the challenge of predicting a complex phenomenon from a heterogeneous collection of datasets that exhibit systematic differences. Accounting for these differences usually requires including additional parameters in the predictive models, which increases the probability of overfitting, particularly on small datasets. We investigate how Bayesian hierarchical models can help mitigate this problem by allowing the practitioner to incorporate information about the structure of the dataset explicitly. To this end, we look at a typical application in remote sensing: the estimation of leaf area index of white winter wheat, an important indicator for agronomical modeling, using measurements of reflectance spectra collected at different locations and growth stages. Since the insights gained from such a model could be used to inform policy or business decisions, the interpretability of the model is a primary concern. We, therefore, focus on models that capture the association between leaf area index and the spectral reflectance at various wavelengths by spline-based kernel functions, which can be visually inspected and analyzed. We compare models with three different levels of hierarchy: a non-hierarchical baseline model, a model with hierarchical bias parameter, and a model in which bias and kernel parameters are hierarchically structured. We analyze them using Markov Chain Monte Carlo sampling diagnostics and an intervention-based measure of feature importance. The improved robustness and interpretability of this approach show that Bayesian hierarchical models are a versatile tool for the prediction of leaf area index, particularly in scenarios where the available data sources are heterogeneous.

Does Origin Matter? Ethnic Group Position and Attitudes Toward Immigrants: The Case of Russia

This article analyzes the relationship between the relative position of an ethnic group, as measured by its majority/minority status at a subnational level, and attitudes of its members toward immigrants of different origins. Based on the Russian case, it addresses the question whether the effects of in-group majority status within a region on attitudes toward the general category of immigrants hold regardless of out-group origin and, if not, what may drive this variation. Using data from the Russia Longitudinal Monitoring Survey of the Higher School of Economics and Bayesian hierarchical structural equation modeling, the study demonstrates that the relative position of an ethnic in-group is of varying importance as a predictor of attitudes toward migrant groups of European versus non-European origin in Russia. A group’s majority status within a region proved to play a role in predicting attitudes toward migrants originating from the “south” (encompassing North and South Caucasus; Central Asia; and China, Vietnam, and Korea) but not toward migrants coming from the “west” (Ukraine and Moldova). We draw on arguments related to the source and the level of threat induced by the out-groups, ethnic hierarchies, and group cues to explain this pattern of results.

Flight plan for the future: floatplane pilots and researchers team up to predict invasive species dispersal in Alaska

Aircraft can transport aquatic invasive species (AIS) from urban sources to remote waterbodies, yet little is known about this long-distance pathway. In North America and especially Alaska, aircraft with landing gear for water called floatplanes are used for recreation access to remote, often road-less wilderness destinations. Human-mediated dispersal of AIS is particularly concerning for the conservation of pristine wildlands, yet resource managers are often challenged by limited monitoring and response capacity given the vast areas they manage. We collected pathway data through a survey with floatplane pilots and used a Bayesian hierarchical model to inform early detection in a data-limited situation. The study was motivated by Alaska’s first known AIS, Elodea spp. (Elodea) and its floatplane-related dispersal. For 682 identified floatplane destinations, a Bayesian hierarchical model predicts the chance of flights originating from AIS source locations in freshwater and estimates the expected number of flights from these sources. Model predictions show the potential for broad spread across remote regions currently not known to have Elodea and informed monitoring and early detection efforts. Our result underlines the small window of opportunity for Arctic conservation strategies targeting an AIS free Arctic. We recommend management that focuses on long-distance connectivity, keeping urban sources free of AIS. We discuss applicability of the approach for other data-limited situations supporting data-informed AIS management responses.

A novel 14-gene signature for overall survival in lung adenocarcinoma based on the Bayesian hierarchical Cox proportional hazards model

There have been few investigations of cancer prognosis models based on Bayesian hierarchical models. In this study, we used a novel Bayesian method to screen mRNAs and estimate the effects of mRNAs on the prognosis of patients with lung adenocarcinoma. Based on the identified mRNAs, we can build a prognostic model combining mRNAs and clinical features, allowing us to explore new molecules with the potential to predict the prognosis of lung adenocarcinoma. The mRNA data (n = 594) and clinical data (n = 470) for lung adenocarcinoma were obtained from the TCGA database. Gene set enrichment analysis (GSEA), univariate Cox proportional hazards regression, and the Bayesian hierarchical Cox proportional hazards model were used to explore the mRNAs related to the prognosis of lung adenocarcinoma. Multivariate Cox proportional hazard regression was used to identify independent markers. The prediction performance of the prognostic model was evaluated not only by the internal cross-validation but also by the external validation based on the GEO dataset (n = 437). With the Bayesian hierarchical Cox proportional hazards model, a 14-gene signature that included CPS1, CTPS2, DARS2, IGFBP3, MCM5, MCM7, NME4, NT5E, PLK1, POLR3G, PTTG1, SERPINB5, TXNRD1, and TYMS was established to predict overall survival in lung adenocarcinoma. Multivariate analysis demonstrated that the 14-gene signature (HR 3.960, 95% CI 2.710–5.786), T classification (T1, reference; T3, HR 1.925, 95% CI 1.104–3.355) and N classification (N0, reference; N1, HR 2.212, 95% CI 1.520–3.220; N2, HR 2.260, 95% CI 1.499–3.409) were independent predictors. The C-index of the model was 0.733 and 0.735, respectively, after performing cross-validation and external validation, a nomogram was provided for better prediction in clinical application. Bayesian hierarchical Cox proportional hazards models can be used to integrate high-dimensional omics information into a prediction model for lung adenocarcinoma to improve the prognostic prediction and discover potential targets. This approach may be a powerful predictive tool for clinicians treating malignant tumours.

WOMBAT v1.0: a fully Bayesian global flux-inversion framework

WOMBAT (the WOllongong Methodology for Bayesian Assimilation of Trace-gases) is a fully Bayesian hierarchical statistical framework for flux inversion of trace gases from flask, in situ, and remotely sensed data. WOMBAT extends the conventional Bayesian synthesis framework through the consideration of a correlated error term, the capacity for online bias correction, and the provision of uncertainty quantification on all unknowns that appear in the Bayesian statistical model. We show, in an observing system simulation experiment (OSSE), that these extensions are crucial when the data are indeed biased and have errors that are spatio-temporally correlated. Using the GEOS-Chem atmospheric transport model, we show that WOMBAT is able to obtain posterior means and variances on non-fossil-fuel CO2 fluxes from Orbiting Carbon Observatory-2 (OCO-2) data that are comparable to those from the Model Intercomparison Project (MIP) reported in Crowell et al. (2019). We also find that WOMBAT's predictions of out-of-sample retrievals obtained from the Total Column Carbon Observing Network (TCCON) are, for the most part, more accurate than those made by the MIP participants.