palaeoverse: A community‐driven R package to support palaeobiological analysis

1. The open-source programming language ‘R' has become a standard tool in the palaeobiologist's toolkit. Its popularity within the palaeobiological community continues to grow, with published articles increasingly citing the usage of R and R packages. However, there are currently a lack of agreed standards for data preparation and available frameworks to support the implementation of such standards. Consequently, data preparation workflows are often unclear and not reproducible, even when code is provided. Moreover, due to a lack of code accessibility and documentation, palaeobiologists are often forced to ‘reinvent the wheel’ to find solutions to issues already solved by other members of the community. 2. Here, we introduce palaeoverse, a community-driven R package to aid data preparation and exploration for quantitative palaeobiological research. The package is freely available and has three core principles: (1) streamline data preparation and analyses; (2) enhance code readability; and (3) improve reproducibility of results. To develop these aims, we assessed the analytical needs of the broader palaeobiological community using an online survey, in addition to incorporating our own experiences. 3. In this work, we first report the findings of the survey, which shaped the development of the package. Subsequently, we describe and demonstrate the functionality available in palaeoverse and provide usage examples. Finally, we discuss the resources we have made available for the community and our future plans for the broader Palaeoverse project. 4. palaeoverse is a community-driven R package for palaeobiology, developed with the intention of bringing palaeobiologists together to establish agreed standards for high-quality quantitative research. The package provides a user-friendly platform for preparing data for analysis with well-documented open-source code to enhance transparency. The functionality available in palaeoverse improves code reproducibility and accessibility, which is beneficial for both the review process and future research

Palaeoenvironmental constraints on the diversity of eutherian terrestrial mammals through the Cenozoic of South America, and the emergence of\ud the modern-day latitudinal biodiversity gradient on the continent

South America has a unique geobiological history that is at heightened risk from the current climate emergency. Its fossil record provides empirical evidence of long-term interactions between biodiversity and climate, but our understanding of South America’s faunal evolution is still in its infancy. Applying subsampling and Bayesian approaches to a comprehensive dataset of South American terrestrial eutherian mammal fossil occurrences, I demonstrate increases in diversity throughout the Paleogene, resulting from several intervals of high speciation rate. The remainder of the Cenozoic is characterized by greater variability, including a diversity peak in the late Miocene and pulses of heightened extinction rate in the Plio-Pleistocene. These results suggest that the present-day latitudinal biodiversity gradient first appeared in South America in the Plio-Pleistocene, at a similar time as proposed for North American mammals. This appears to have been driven by a decline in mean annual temperatures at higher latitudes in South America, in tandem with an increase in precipitation at lower latitudes that might have been accentuated by Andean uplift in the Pleistocene. Although the Great American Biotic Interchange played a role, Andean uplift appears to have been the primary underlying mechanism driving eutherian diversity patterns in the Cenozoic, radically reshaping the continent’s climate and habitats

Humans and climate as possible drivers of the morphology and function of the mandible of Suncus etruscus in Corsica

International audienceHuman-induced environmental changes have increased rapidly during the Holocene and have reached alarming levels today. Consequently, it is crucial to better understand the impact of humans and climate on the faunas and floras through time. Understanding the direct and underlying effect of past human activity not only contributes to improving our knowledge of human history but also provides insights for the future. We here investigate the effect of the human-induced environmental changes that took place during the modern era (14–19th century AD) on the mandible of a small mammal, Suncus etruscus, in Corsica. We detected rapid morphological changes in mandible shape over the relatively short period of time included in our study, suggesting a strong human impact on the island. The morphological changes observed had functional consequences as they are related to changes in the mechanical potential of the principal masticatory muscle, the temporalis that, in turn, reflects shifts in the animal's diet over time. These results highlight the effect that the 600-year human agricultural activity shifts had on the island and its fauna. The integration of the body and the ramus of the mandible appears to be related to the mechanical potential of the temporalis muscle but does not constitute an indicator of human-induced environmental change. Whether these morphological changes are the result of natural selection (genetic processes) or of phenotypic plasticity (epigenetic processes) remains to be elucidated

palaeoverse: A community‐driven R package to support palaeobiological analysis

Abstract The open‐source programming language ‘R' has become a standard tool in the palaeobiologist's toolkit. Its popularity within the palaeobiological community continues to grow, with published articles increasingly citing the usage of R and R packages. However, there are currently a lack of agreed standards for data preparation and available frameworks to support the implementation of such standards. Consequently, data preparation workflows are often unclear and not reproducible, even when code is provided. Moreover, due to a lack of code accessibility and documentation, palaeobiologists are often forced to ‘reinvent the wheel’ to find solutions to issues already solved by other members of the community. Here, we introduce palaeoverse, a community‐driven R package to aid data preparation and exploration for quantitative palaeobiological research. The package is freely available and has three core principles: (1) streamline data preparation and analyses; (2) enhance code readability; and (3) improve reproducibility of results. To develop these aims, we assessed the analytical needs of the broader palaeobiological community using an online survey, in addition to incorporating our own experiences. In this work, we first report the findings of the survey, which shaped the development of the package. Subsequently, we describe and demonstrate the functionality available in palaeoverse and provide usage examples. Finally, we discuss the resources we have made available for the community and our future plans for the broader Palaeoverse project. palaeoverse is a community‐driven R package for palaeobiology, developed with the intention of bringing palaeobiologists together to establish agreed standards for high‐quality quantitative research. The package provides a user‐friendly platform for preparing data for analysis with well‐documented open‐source code to enhance transparency. The functionality available in palaeoverse improves code reproducibility and accessibility, which is beneficial for both the review process and future research