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Abstract We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers. 

Research has shown differences in pro-social and pro-environmental attitudes after exposure to different physical environments. It is unclear whether these perspective shifts are associated with changes in conscious thoughts and feelings about other people and the environment. In Study 1, we used a within-subject experiment to measure social and environmental thought content throughout 1-h environmental explorations of a nature conservatory and an indoor mall. At three survey time points, participants (N = 86, undergraduates and community members) reported whom they were thinking about and how connected they felt to the physical and social environment. Using Bayesian multi-level models, we found that while visiting the conservatory, participants were less likely to think about themselves, felt closer to people nearby and around the world, and felt higher connectedness to their social and physical environment. In Study 2, we used a correlational design to investigate the association between perceived naturalness of city parks and feelings of connection to nearby others and the physical environment while visiting. Participants (N = 303, Chicago residents) reported feeling higher levels of connection to nearby people and the physical environment when they were visiting city parks rated as more natural. These studies further our understanding of the ways in which natural environments influence conscious thoughts and feelings about the social and physical environment. 

Abstract MotivationJBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization. ResultsWe have developed a package that provides a Python interface to JBrowse 2’s suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google’s Colab notebooks, providing reproducible interactive views. Availability and implementationJBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter. 

Abstract MotivationGenome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development. ResultsWe have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents. Availability and implementationJBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https://github.com/GMOD/JBrowseR/. 

A key component of economic decisions is the integration of information about reward outcomes and probabilities in selecting between competing options. In many species, risky choice is influenced by the magnitude of available outcomes, probability of success and the possibility of extreme outcomes. Chimpanzees are generally regarded to be risk-seeking. In this study, we examined two aspects of chimpanzees' risk preferences: first, whether setting the value of the non-preferred outcome of a risky option to zero changes chimpanzees’ risk preferences, and second, whether individual risk preferences are stable across two different measures. Across two experiments, we found chimpanzees (Pan troglodytes,n= 23) as a group to be risk-neutral to risk-avoidant with highly stable individual risk preferences. We discuss how the possibility of going empty-handed might reduce chimpanzees' risk-seeking relative to previous studies. This malleability in risk preferences as a function of experimental parameters and individual differences raises interesting questions about whether it is appropriate or helpful to categorize a species as a whole as risk-seeking or risk-avoidant. This article is part of the theme issue ‘Existence and prevalence of economic behaviours among non-human primates’. 

The geological record encodes the relationship between climate and atmospheric carbon dioxide (CO₂) over long and short timescales, as well as potential drivers of evolutionary transitions. However, reconstructing CO₂beyond direct measurements requires the use of paleoproxies and herein lies the challenge, as proxies differ in their assumptions, degree of understanding, and even reconstructed values. In this study, we critically evaluated, categorized, and integrated available proxies to create a high-fidelity and transparently constructed atmospheric CO₂record spanning the past 66 million years. This newly constructed record provides clearer evidence for higher Earth system sensitivity in the past and for the role of CO₂thresholds in biological and cryosphere evolution.