Lewis Alan Jones

The latitudinal diversity gradient (LDG)—a decline in taxonomic richness from the Equator to the poles—is a fundamental biogeographic pattern on Earth today, yet its primary regulators remain debated. Whereas many of the proposed climatic and environmental drivers covary with latitude in the present day, these variables have fluctuated substantially over millions of years. The fossil record therefore offers a unique perspective on the response of diversity and, by extension, the LDG, to global climatic change. We test the hypothesis that Earth's long-term climate state controls LDG strength, determining the conditions under which steep, ‘modern-type’ gradients with low-latitude-centred diversity peaks emerge. By analysing sampling-standardized marine invertebrate diversity across the past 500 million years, we reveal a systematic link: ‘modern-type’ LDGs typically prevail during coldhouse–coolhouse intervals, whereas flattened LDGs or temperate diversity peaks occur predominantly within transitional, warmhouse and hothouse climates. This robust phenomenon demonstrates that long-term climate exerts a primary control on global biodiversity patterns, whereas palaeogeography, including the distribution of shallow-marine habitat and continental configuration, modulates the regional expression of the LDG, including hemispheric variation. As anthropogenic warming pushes Earth towards hothouse conditions, our results offer a critical geohistorical perspective on the impending restructuring of global biodiversity.

The fossil record is key to elucidating past biodiversity dynamics, yet it remains incomplete and non-uniform, governed by factors such as sedimentation rates, species’ range and body size, and sampling effort. How these biases distort inferences on evolutionary trends remains poorly understood. Here, we simulate a future fossil record of present-day land mammals to quantify the extent to which real evolutionary patterns can be recovered from fragmentary fossil data. Species are filtered according to sediment availability, species’ range and body size, and spatial and taxonomic sampling biases under three preservation rates, and then systematically pruned from a baseline mammal phylogeny before analyses of body mass and diet evolution through phylogenetic comparative methods. We find that biological and taxonomic filters strongly skew these inferences, while spatial filters do not significantly distort them. Our results provide first-order estimates of how fossil record incompleteness can bias our interpretation of deep-time biodiversity change.

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.

Worldwide, coral reefs are declining due to a combination of local and global stressors. In the Red Sea, these pressures have affected hard coral cover, altered community composition, and reduced coral colony size. However, the lack of long-term historical data in this region makes it difficult to accurately quantify the extent of reef degradation. Establishing regional baselines that represent pre-anthropogenic, pristine reef conditions is therefore essential. Pleistocene reefs provide a unique opportunity in this regard, offering insights into reef community structure and composition in the absence of recent anthropogenic disturbance. In this study, we conduct, for the first time, a quantitative comparison between a Pleistocene (Marine Isotope Stage 5e; ~125,000 years ago) fossil reef and an adjacent modern reef in northern Egypt to assess the current state of the modern reef. Our results show that the fossil reef had larger colony size in four of the five most abundant genera and the overall community composition differed significantly between the fossil and modern reef. Our findings also suggest that massive corals may be more suitable than branching corals for comparisons of coral colony size distributions due to their better preservation potential in the fossil record. While some observed differences may stem from taphonomic processes, time-averaging and environmental differences, we argue that most of the disparity reflects genuine degradation in the modern reef.

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.

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 finalising 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.

Coral reefs provide habitat for approximately 25% of all extant marine species, including 845 species of scleractinian corals. These rich ecosystems are becoming increasingly degraded in many regions by a range of anthropogenic factors, including recurrent bleaching episodes associated with rising sea surface temperatures. Within the northern Red Sea, coral reef communities appear to be faring relatively better than global trends and continue to exhibit remarkable diversity and thermal tolerance. However, recent reports of coral bleaching in the region highlight the urgent need for comprehensive ecological surveys to provide a baseline for long-term monitoring of biodiversity and potential species loss. This field report aims to support the tracking of diversity and growth form distributions of scleractinian corals at two reef sites at Mangrove Bay, El Qoseir, Egypt. Over time, it is our hope that such reports will contribute to broader databases and analyses focused on the biodiversity of reef-building coral species in the northern Red Sea. This study presents the first comprehensive checklist of scleractinian coral species (Scleractinia Bourne, 1900) in Mangrove Bay, El Qoseir, Egypt. As a result of our 2023 field survey, we identified a total of 68 species across 29 genera and 14 families, spanning six reef habitats — three per study site — at two study locations (sheltered and current-exposed), with depths ranging from 0 to 9.5 m. We found that both scleractinian coral diversity and coral growth forms varied amongst the six habitats. Branching corals were found in each habitat, but were particularly abundant at the current-exposed reef edge, where they covered 67% of the habitat. Encrusting and massive corals became more prevalent with increasing depth at both study sites, with massive corals covering 72% at the sheltered deeper reef slope and encrusting corals covering 24% at the current-exposed deeper reef slope. Species of the genus Porites dominated the sheltered site at all depths and the deeper reef slope at the current-exposed site, while Pocillopora verrucosa was most abundant at the exposed site’s reef edge and shallow slope. We provide photographs confirming these new records and access to the raw data on the abundance, distribution and conservation status of these taxa. Forty-three percent of the scleractinian species are classified as "Least Concern," but six are identified as "Vulnerable" (9%). Reef cover analyses revealed algae as the dominant group in most habitats, while scleractinian coral cover ranged between approximately 17% at the current-exposed reef edge and almost 35% at the current-exposed shallow reef slope. Millepora contributed the most at the exposed reef edge with nearly 28% cover, but was scarce elsewhere; soft corals exhibited their highest abundance on the deeper slope. Our observations serve as a critical baseline for future research and conservation efforts at Mangrove Bay by presenting an initial inventory of the local scleractinian communities and emphasise the importance of detailed species data in understanding and preserving coral reef ecosystems.

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.

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.