Abstract Phanerozoic marine biodiversity dynamics have been shaped by continuous environmental change and biotic interactions. Although ecosystem engineers – animals whose behaviours modify resource availability – have established impacts on modern community ecology and diversity, their impacts on ancient ecosystems over geologic time have remained quantitatively underexplored. Here, we investigate how biodiversity was impacted by reef-building or bioturbating ecosystem engineers at each stage of the Phanerozoic, including their ability to maintain biodiversity over mass extinctions, and identify extrinsic conditions that modulate their impacts. We analyse fossil communities with and without ecosystem engineers to calculate effect sizes, thereby quantifying the effects of the presence of ecosystem engineers on Shannon’s Diversity ( H ) at each stage in the Phanerozoic. We show that ecosystem engineers are significantly associated with increased biodiversity during the majority of the Phanerozoic. We also show that, over the last ~250 million years, the effectiveness of modern-type reef-builders is more sensitive to climate-driven stress than for modern-style bioturbators. Finally, our results reveal that climate may modulate ecosystem engineer impacts, with both bioturbators and reef-builders exhibiting the strongest effect sizes within an optimal moderate temperature range. These results underscore ecosystem engineers’ crucial role in contributing to fluctuating biodiversity dynamics over the Phanerozoic.

1. Data- and code-archiving are important components of open science, as both make research more transparent, reproducible, accountable, and credible, allowing future researchers to identify errors and build on previous work. Despite progress in implementing data- and code-archiving policies in journals publishing ecology and evolution research, issues remain. To be more useful to future researchers, archived data and code must not only be archived, but also meet good practice standards. 2. We collected data from 1,861 papers published between 2017 and 2024 in the seven British Ecological Society (BES) journals, during a hackathon event. We systematically checked associated data and/or code, metadata, help files and annotations to assess archiving practices. We determined if and where data and code files were archived, whether they could be located, downloaded, and opened, and whether they had associated READMEs, digital object identifiers (DOI) and licenses. We also recorded the file extensions used to save data/code files, and which programming languages code was written in. 3. 93% of the 1,861 papers we examined used data and ~90% used code. While 97% of the 1,735 papers that used data also archived it, only 35% of the 1,670 papers that used code also archived code. Over 85% of archived data and code could be located, downloaded, and opened. Reusability, however, was more limited; around a third of papers did not have a README or similar to explain their data/code files, and the quality of READMEs varied substantially. 4. We recommend that researchers archive their code, and that archived code be explicitly mentioned in the Data (or Code) Availability statement. We also encourage researchers to provide more accessible and informative READMEs for data and code. To help achieve these recommendations, we advocate that journals employ Data/Code editors to review data and code quality, research institutions deliver more training in open science practices, and funding bodies set clear expectations on open data and code practices.

Large datasets of fossil occurrences, often downloaded from online community-maintained databases, are a vital resource for understanding broad-scale evolutionary patterns, such as how biodiversity has changed through time and space. Such datasets, however, are not infallible and must be ‘cleaned’ of inaccurate, incomplete, or duplicate data prior to analysis. Researchers must decide upon the extent, feasibility, and value of data cleaning steps to perform, but while guides are available for working with neontological occurrences, there is currently no clear procedure for palaeobiological data despite its unique attributes. Here, we outline ten rules that aim to aid the process of cleaning fossil occurrence data for downstream analysis. These rules cover the major steps involved in processing data prior to analysis, including project setup, data exploration and cleaning, and finalizing and reporting work. We provide accompanying examples and a vignette covering the entire data cleaning process to demonstrate the application of each rule. We believe that these rules will serve as a useful guideline to support data cleaning and foster new standards for the palaeobiological community.

Aims: Today, we are experiencing rapid biodiversity loss due to climate change and human impacts. Such biodiversity loss is not only harmful to the environment but can also alter the composition of communities and the interactions of their members. The late Pleistocene experienced a drastic loss of large-bodied mammals which resulted in significant changes in community structure due to changes in body size, diet, and species associations. However, the effect of climate change on species interactions and community structure across the Pleistocene-Holocene transition remains poorly understood. Location: Edwards Plateau, Texas. Time Period: Late Pleistocene-Holocene. Major Taxa Studied: Terrestrial Mammals. Methods: Using a robust data set on mammal species composition, stable isotopes, and body size, we constructed ecological networks for 16 time intervals across the last 22,000 years on the Edwards Plateau, Texas. We compared the structure and shifts in the food web over time using modularity and an index of node overlap and segregation. Results: We found that node overlap and connectance increased while modularity decreased over time. Spearman-Rank correlation analyses indicate that changes in all network metrics were not driven by changes in species richness across time, nor were they driven by climate change. The degree of node overlap and connectance also shifted dramatically across the Pleistocene-Holocene transition and was significantly different from null model expectations in the Holocene but not in the Pleistocene. Main Conclusions: These results suggest that the transition from a diverse and compartmentalised network to a network of less complexity with an overlap of interacting species may have been driven by other factors that altered the food web. This implies that the change in mammal food web structure of the Edwards Plateau was mainly a consequence of the megafauna extinctions and not coupled with climate change.

Data visualization is a key component of any scientific data analysis workflow and is vital for the summarization and dissemination of complex ideas and results. One common hurdle across the Earth Sciences and other scientific fields remains the reproducibility of many types of visualizations of data over long time intervals (>10,000 years). This paper introduces the R package deeptime, which provides easy-to-use functions to facilitate a wide array of fully reproducible visualizations of geological data. The package facilitates streamlined access to geological reference data, such as geological timescales and lithostratigraphic patterns, and includes novel functionality to incorporate these data into a wide range of existing visualizations. By leveraging the existing framework of the ggplot2 R package, deeptime allows for these visualizations to be highly customizable. The open-source and constantly evolving package is accompanied by exhaustive documentation about the myriad options available to users and several tutorials demonstrating the available functionality. It is anticipated that deeptime will reduce the amount of time and experience needed to make reproducible and professional data visualizations, giving scientists more time to ensure that these visualizations are more accessible and engaging.

Understanding the role of humans as 'ecosystem engineers' requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no conceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional definitions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term - 'Earth system engineering' - to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate this framework using the fossil record, and show how it can be applied across the tree of life, and throughout Earth history.

The latitudinal gradient of declining species richness from the Equator towards the poles is one of the most pervasive macroecological patterns on Earth today. However, the ubiquity of this trend over geological timescales remains unclear. One reason for this uncertainty is that palaeobiologists need Global Plate Models (GPMs) to estimate the latitudinal position of organisms' remains at time of deposition. However, as GPMs constitute hypotheses for how tectonic plates have moved over Earth's history, reconstructions of the latitudinal biodiversity gradient (LBG) might also vary based on the GPM used. Here, using the fossil record of five major marine invertebrate groups, we evaluate the impact of GPM choice on reconstructions of the LBG over the Phanerozoic. Our results show that GPM choice can lead to different conclusions about the shape and strength of LBGs in deep time, even at a coarse spatial scale. These findings suggest additional caution is needed when reconstructing deep-time biogeographic patterns and macroevolutionary events, such as the origin of the present-day LBG. We therefore advocate for future palaeobiogeographic studies to conduct sensitivity analyses investigating the impact of GPM choice on their conclusions, and for greater interdisciplinary collaboration between palaeobiologists and palaeogeographic modellers to avoid common issues in the use of GPMs. ### Competing Interest Statement The authors have declared no competing interest.

We analysed fossil mammal assemblages from over 350 Late Pleistocene and Holocene sites worldwide to test whether human activities, such as agriculture, domestication and intensified land use, restructured global patterns of mammal co-occurrence. Using presence-absence data, we contrasted a novel iterative 'chase clustering' method, which is compositionally driven, against a traditional spatially constrained Ward's clustering approach. Both methods recovered continental-scale groupings in the Pleistocene, consistent with known biogeographic boundaries. Holocene land use and domestication reconfigured these historical patterns, creating novel assemblages independent of previous biogeographic constraints. Faunal turnover at the local scale varied substantially across regions, being especially pronounced in the Americas, whereas other areas showed relative stability. Even moderate expansion of domesticates altered how communities grouped, highlighting their disproportionate ecological influence. Our findings demonstrate that human-driven niche modification, beyond earlier megafaunal extinctions, profoundly reshaped mammal communities on a global scale. Recognizing these anthropogenic legacies provides essential context for anticipating how current and future human pressures might further transform biodiversity.

The geological record is a vast archive of information that provides the only empirical data about the evolution of the Earth. In recent years, concentrated efforts have been made to compile macrostratigraphic data into the online centralized database Macrostrat. Macrostrat is a global stratigraphic database containing information regarding surface and subsurface rock units and their respective ages, lithologies, geographic extents, and various other associated metadata. However, these raw data are currently directly accessible only through the Macrostrat application programming interface, which is a barrier to potential users that are less familiar with such services. This data accessibility hurdle currently prevents full capitalization of the value offered by Macrostrat, particularly its potential to improve understanding of the geological and biological evolution of the Earth. Here, we introduce rmacrostrat, an R package that interfaces with the Macrostrat database to access and retrieve a variety of geological, paleontological, and economic data directly into the R programming environment. In this article, we provide details about how the package can be installed, its implementation, and potential use cases. For the latter, we showcase how rmacrostrat can be used to visualize regional stratigraphic columns, produce regional geologic outcrop maps, and investigate temporal trends in macrostratigraphic units. We hope that this package will make geological data more readily accessible and in turn will facilitate new research utilizing Earth system data.

Collecting data for use in constructing phylogenies is a valuable but time- and resource-consuming pursuit. As a result, indicators of the potential value of including certain species in a phylogeny a priori could prove useful when planning this stage of research. Here, we used a simulation approach to investigate whether there are trends in the ability for phylogenetic comparative methods to recover the correct model of trait evolution based on certain characteristics of the phylogeny. First, we used multiple diversification rates to simulate phylogenies containing varying proportions of fossil and extant tips. We then simulated the evolution of a single trait across each phylogeny using multiple continuous trait evolution models. We then compared the fit of the correct and incorrect models to the simulated traits. This quantitative evaluation allows us to discern whether there are certain tip characteristics associated with identifying the correct trait evolution models. Our results indicate that the inclusion of fossils can be highly beneficial to reconstructing certain trait histories (e.g., Ornstein-Uhlenbeck and ACDC) but not to others (e.g., Brownian motion). In fact, in many cases, increasing the proportion of fossils in a phylogenetic dataset is far more beneficial, and perhaps more time- and resource-efficient, than increasing the number of extant taxa in the dataset. Our results corroborate previous findings that the inclusion of fossil tips can vastly improve the reconstruction of trait histories, but also show that this effect is often stronger for older fossils.

Aim: The species that compose local communities possess unique sets of functional and ecological traits that can be used as indicators of biotic and abiotic variation across space and time. Body size is a particularly relevant trait because species with different body sizes typically have different life history strategies and occupy distinct niches. Here we used the body sizes of non- volant (i.e., non- flying) terrestrial mammals to quantify and compare the body size disparity of mammal communities across the globe. Location: Global. Time Period: Present. Major Taxa Studied: Non- volant terrestrial mammals. Methods: We used IUCN range maps of 3982 terrestrial mammals to identify 1876 communities. We then combined diet data with data on climate, elevation and anthropogenic pressures to evaluate these variables' relative importance on the observed body size dispersion of these communities and its deviation from a null model. Results: Dispersion for these communities is significantly greater than expected in 54% of communities and significantly less than expected in 30% of communities. The number of very large species, continent, range sizes, diet disparity and annual temperature collectively explain > 50% of the variation in observed dispersion, whereas continent, the number of very large species, and precipitation collectively explain > 30% of the deviation from the null model. Main Conclusions: Climate and elevation have minimal predictive power, suggesting that biotic factors may be more important for explaining community body size distributions. However, continent is consistently a strong predictor of dispersion, likely due to it capturing the combined effects of climate, size- selective human- induced extinctions and more. Overall, our results are consistent with several plausible explanations, including, but not limited to, competitive exclusion, unequal distribution of resources, within- community environmental heterogeneity, habitat filtering and ecosystem engineering. Further work focusing on other confounding variables, at finer spatial scales and/or within more causal frameworks is required to better understand the driver(s) of these patterns.

Despite a global distribution throughout the tropics and sub-tropics, the order Schizomida (Arachnida) is heavily understudied and the phylogeny of the group is poorly understood. Identification keys are only available for some regions or genera but not for the entire order. ([1][1]) comprehensively reviewed the entire schizomid fauna and established a suite of characters to define all genera known at this time. This suite of characters still depicts the foundation of modern descriptions, supplemented by recently established characters, most of them documenting setation patterns on pedipalps, flagellum and chelicerae. In this paper, we present the Schizomida Trait Data Base (STDB) containing data for 25 characters based on the entire body of schizomid literature. Characters were chosen based on their use for modern taxonomic description and availability of the data. The STDB is a powerful tool that can be used by both amateurs and experienced researchers to categorise newly found specimens, both extant and fossil, down to genus level easily. Analysis using the new database gives insight into biogeographical patterns of characters. Furthermore, we are describing a new species, †Annazomus jamesi, a fossil specimen from Burmese (Kachin) amber and investigate a small collection of extant schizomids from Ecuador, which includes the previously unrecorded female of Surazomus palenque, herein described for the first time. The taxonomic assignment of both specimens is based on the STDB, highlighting the utility of the new data base approach to schizomid systematics. Arachnids, biogeography, Cretaceous, data base, fossil, new species, palaeontology, Schizomida, statistics, taxonomy ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1

1. The open-source programming language ‘R’ has become a standard tool in the palaeobiologist’s toolkit. Its popularity within the palaeobiology 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 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 the future plans for the broader palaeoverse project.4. palaeoverse is the first community-driven R package in 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.

Abstract Effective data visualisation is vital for data exploration, analysis and communication in research. In ecology and evolutionary biology, data are often associated with various taxonomic entities. Graphics of organisms associated with these taxa are valuable for framing results within a broader biological context. However, acquiring and using such resources can be challenging due to availability and licensing constraints. The PhyloPic database solves many of these issues by making organism silhouettes freely available. Tools that integrate this database with existing research workflows are needed to remove hurdles associated with data visualisation in the biological sciences. Here, we introduce rphylopic, an R package for fetching, transforming and visualising silhouettes of organisms from the PhyloPic database. In addition to making over 8000 organism silhouettes available within the R programming language, rphylopic empowers users to modify the appearance of these silhouettes for ultimate customisability when coding production–quality visualisations in both base R and ggplot2 workflows. In this work, we provide details about how the package can be installed, its implementation and potential use cases. For the latter, we showcase three examples across the ecology and evolutionary biology spectrum. Our hope is that rphylopic will make it easier for biologists to develop more accessible and engaging data visualisations by making external resources readily accessible, customisable and usable within R. In turn, by integrating into existing workflows, rphylopic helps to ensure that science is reproducible and accessible.