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Phanerozoic biodiversity in space and time

Lead Research Organisation: UNIVERSITY OF OXFORD
Department Name: Earth Sciences

Abstract

Different numbers of species are found in different regions of the globe and in different environments. The tropics house incredible numbers of species, whereas polar environments house far fewer. This pattern of decreasing number of species from the equator to the poles is referred to as the latitudinal biodiversity gradient. The spatial distribution of life on Earth is well characterised today, but we know relatively little about how spatial patterns of biodiversity have varied over millions of years, during times in which Earth's climate and continents were dramatically different to today. This knowledge gap prevents us from understanding the causes of variation in richness among regions and environments, leaving a fundamental and unanswered question at the heart of biodiversity studies. We will characterise how latitudinal biodiversity gradients in the oceans have varied during the past 545 million years, using the rich fossil record of skeletonising marine invertebrates. This will allow us to ask what environmental factors control the distribution of biodiversity among regions and environments. These deep time patterns will provide important historical context for understanding the distribution of life on Earth, yielding unprecedented insight into the generation and maintenance of marine biodiversity. It will also help us to understand the long-term effects of major shifts in climate state, such as those occurring today, on biodiversity.
 
Description The number of species found at any given location on Earth today varies spatially, with more species packed into tropical regions at low latitudes. Before work on this grant, little was known about whether spatial biodiversity patterns were similar millions of years ago. We quantified spatial biodiversity patterns in deep time for marine invertebrate species and found evidence for an inverse biodiversity gradient, wherein biodiversity is highest at low latitudes and declines towards the poles, just like today. We also find that biodiversity in environments supporting reefs is higher than environments without reefs for 100's of millions of years. To characterise these patterns, we developed a new spatial software tool for the R programming language, called divvy.
Exploitation Route The software developed as part of this grant will be of broad use to the scientific community to investigate how the Earth and life have co-evolved over time. We have hosted a workshop for researchers to learn these new spatial subsetting skills (March 2024), which has built research in the UK and internationally. Our research on deep time spatial biodiversity patterns has provided a platform for further research on the genesis of modern biodiversity patterns.
Sectors Education

Environment
 
Description New spatial methods workshop
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Title development of a new R package - divvy 
Description This new R package will help with spatially standardising biological and palaeobiological samples, which can be used in numerous research endeavours, including understanding how communities respond to global change. 
Type Of Material Improvements to research infrastructure 
Year Produced 2023 
Provided To Others? Yes  
Impact This new research tool will be available and used widely in the biological and palaeobiological communities for research on ecological and evolutionary questions. We hope that this tool will allow us to better understand how species respond to climate change. 
URL https://cran.r-project.org/web/packages/divvy/index.html
 
Title Data from: Evaluating migration hypotheses for the extinct Glyptotherium using Ecological Niche Modeling 
Description The formation of the Isthmus of Panama allowed for migrations between the once separated continents of North and South America. This led to one of the greatest documented interchanges of biota in Earth history, wherein an array of species across many groups migrated between the continents. Glyptotherium, a giant extinct armadillo-like grazer, is an example of a taxon that likely originated in South America and migrated to North America. Here we use Ecological Niche Modeling to test the extent of suitable conditions for Glyptotherium in Central America and surrounding regions during the intervals when the taxa is thought to have dispersed, allowing for assessment of plausible migration routes and the hypothesis that the genus migrated from North America back to South America during the Rancholabrean (14,000 to 240,000 years ago). Our niche modeling results show suitable abiotic conditions for Glyptotherium in Central America and the surrounding area throughout the Plio-Pleistocene, with western South America (the "high road") suggested as their ancestors' route northwards. Depending on the extent of suitable conditions, it may have been possible for Glyptotherium to return to South America during the Rancholabrean. The results support previous hypotheses that the range of Glyptotherium was constrained by the need for warm, wet environments. 
Type Of Material Database/Collection of data 
Year Produced 2025 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.ghx3ffc08
 
Title Data from: Marine animal diversity across latitudinal and temperature gradients during the Phanerozoic 
Description The latitudinal biodiversity gradient (LBG) is a fundamental biological pattern seen across taxa and ecosystems today, but its drivers remain uncertain despite intense theoretical and empirical study. Palaeontological studies may add valuable evidence from diversity distributions during intervals when Earth system configurations were different from today, including potential analogues of future climate regimes. However, accurately characterising these distributions is challenging because the geographic scope of fossil record coverage varies through time, introducing biases that have not been quantified by most previous studies. Here, we attempt a comprehensive documentation of latitudinal biodiversity distributions for marine invertebrates through the past 540 million years, explicitly accounting for regional variation in diversity and sampling. We demonstrate large uncertainties when using current fossil data at this scale. Nevertheless, some signals are detectable. We show that marine animal biodiversity declined with increasing palaeolatitude and with decreasing temperature during at least some intervals from the Permian onwards (298.9 Ma). Additionally, we find that the LBG was shallower, on average, when Earth's climate was hotter, although this signal is weak. We also document a strong, systematic bias due to intense sampling of the fossil record in North America and especially Europe, which may have led previous studies to incorrectly infer a mid-latitude diversity peak during hot intervals of Earth history. Our results provide a baseline for what current fossil databases might tell us about Phanerozoic LBGs of marine animals, and suggest that quantitative consideration of uncertainties will be central to advancing knowledge of geographic variation in diversity through Earth's history. 
Type Of Material Database/Collection of data 
Year Produced 2025 
Provided To Others? Yes  
URL https://datadryad.org/dataset/doi:10.5061/dryad.6djh9w1bx
 
Title Dataset S1 from Human brains preserve in diverse environments for at least 12 000 years 
Description Archive of human brains preserved in the archaeological record. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Dataset_S1_from_Human_brains_preserve_in_diverse_environmen...
 
Title Global climate model comparisons of niche evolution in Turritelline gastropods across the end-Cretaceous mass extinction 
Description Paleo-Ecological Niche Modeling (PaleoENM) aims to map the distributions of extinct species using paleo-coordinates of fossils and local environmental data. While General Circulation Models (GCMs) have been widely used to estimate climate conditions in deep time, they have primarily been applied to the terrestrial vertebrate record. Furthermore, variations in paleo-elevation models used in GCM construction can significantly influence the outcomes of PaleoENM. This study addresses two main objectives: (1) to investigate whether changing climatic factors drove niche shifts following the end-Cretaceous mass extinction in the shelly marine invertebrate group, the tower snails (Turritellidae: Turritellinae), and (2) to compare the effects of two different paleo-elevation models on the results of GCM-based predictions of species distribution. Fossil occurrence data from the Maastrichtian and Danian time periods were obtained from the Paleobiology Database, supplemented by museum collections and published literature. Environmental data were extracted from atmosphere-ocean General Circulation Model (GCM) simulations using the HadCM3L model, applying two different sets of paleogeographic and CO2 boundary conditions: Scotese-based and Getech-based. Additional sedimentology and depositional environment data were sourced from the Paleobiology Database (PBDB). We predicted the distributions of Turritellines using the maximum entropy (MaxentMaxEnt) algorithm and performed niche similarity analysis using principal component analysis and kernel density estimation. We found significant differences in the spatial arrangement of suitable habitats between the Maastrichtian and Danian time periods across GCMs. The results also showed that the Getech-based GCM outperformed the Scotese-based GCM in terms of model metrics. Niche overlap across both time periods was high, with niche similarity and equivalency being higher than expected by chance within both GCMs. Our results also suggest that differences in elevation model boundary conditions led to variations in the predicted distribution and niche patterns. This study provides a novel approach to understanding ecological resilience and niche change in invertebrate taxa after mass extinction events. It also explores the robustness of varying GCM boundary conditions on PaleoENM studies and offers a framework for future paleoecological research on fossil invertebrate taxa. 
Type Of Material Database/Collection of data 
Year Produced 2025 
Provided To Others? Yes  
URL https://datadryad.org/dataset/doi:10.5061/dryad.w9ghx3g17
 
Title Origination of the modern-style diversity gradient 15 million years ago 
Description Supplementary figures, data files, and code to accompany the paper. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Origination_of_the_modern-style_diversity_gradi...
 
Title PaleoReefs Database (PARED) 
Description PARED has been developed by Prof. Wolfgang Kiessling since 1995 with the aim to collect data on Phanerozoic reefs in a standardized format and to use those data for tracing patterns and processes in reef development. PARED currently holds data on more than 4300 Phanerozoic reef sites with geological, geographical, and paleontological information on every reef. While mostly developed for research, the database is useful for tracing reefal oil reservoirs through time and space. This upload is a simplified version with only the main reef builders, their age, coordinates, paleocoordinates, and the primary reference. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact The distribution of reefs will help to better constrain the distribution of marine biodiversity 
URL https://zenodo.org/record/6037852
 
Title Paleobiogeographic insights gained from ecological niche models: progress and continued challenges 
Description The spatial distribution of individuals within ecological assemblages, and their associated traits and behaviors, are key determinants of ecosystem structure and function. Consequently, determining the spatial distribution of species, and how distributions influence patterns of species richness across ecosystems today and in the past, helps us understand what factors act as fundamental controls on biodiversity. Here, we explore how ecological niche modeling has contributed to understanding the spatiotemporal distribution of past biodiversity, and past ecological and evolutionary processes. We first perform a semi-quantitative literature review to capture studies that applied ecological niche models (ENMs) in the past, identifying 668 studies. We coded each study according to focal taxonomic groups and whether and how the study used fossil evidence, whether it relied on evidence or methods in addition to ENMs, and spatial scale and temporal intervals. We used trends in publication patterns across categories to anchor discussion of recent technical advances in niche modeling, focusing on paleobiogeographic ENM applications. We then explored the contributions of ENMs to paleobiogeography, with a particular focus on examining patterns and associated drivers of range dynamics; phylogeography and within-lineage dynamics; macroevolutionary patterns and processes, including niche change, speciation, and extinction; drivers of community assembly; and conservation paleobiogeography. Overall, ENMs are powerful tools for elucidating paleobiogeographic patterns. ENMs are most commonly used to understand Quaternary dynamics, but an increasing number of studies use ENMs to gain important insight into both ecological and evolutionary processes in pre-Quaternary times. Deeper integration with traits and phylogenies may further extend those insights. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.m37pvmd9n
 
Description Christmas STEM talk to school children 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact PI Saupe gave a lecture on the research being undertaken in this grant to school children at the Oxford Museum of Natural History about 'Using the past to conserve species today'
Year(s) Of Engagement Activity 2022
 
Description Work featured in a temporary museum exhibit - Connected Planet - OUMNH 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Erin Saupe, PI, was featured talking about her research as part of the new 'Connected Planet' exhibit in the Oxford Museum of Natural History. The public can click on questions and hear PI Saupe respond to them. Her discussions focus on work completed for this grant. The exhibit is estimated to reach around 200,000 visitors.
Year(s) Of Engagement Activity 2023