ForCenS-LGM: a dataset of planktonic foraminifera species assemblage composition for the Last Glacial Maximum

Species assemblage composition of marine microfossils offers the possibility to investigate ecological and climatological change on time scales inaccessible using conventional observations. Planktonic foraminifera - calcareous zooplankton - have an excellent fossil record and are used extensively in palaeoecology and palaeoceanography. During the Last Glacial Maximum (LGM; 19,000 - 23,000 years ago), the climate was in a radically different state. This period is therefore a key target to investigate climate and biodiversity under different conditions than today. Studying LGM climate and ecosystems indeed has a long history, yet the most recent global synthesis of planktonic foraminifera assemblage composition is now nearly two decades old. Here we present the ForCenS-LGM dataset with 2,365 species assemblage samples collected using standardised methods and with harmonised taxonomy. The data originate from marine sediments from 664 sites and present a more than 50% increase in coverage compared to previous work. The taxonomy is compatible with the most recent global core top dataset, enabling direct investigation of temporal changes in foraminifera biogeography and facilitating seawater temperature reconstructions.

Climate change is an important predictor of extinction risk on macroevolutionary timescales

Anthropogenic climate change is increasing rapidly and already impacting biodiversity. Despite its importance in future projections, understanding of the underlying mechanisms by which climate mediates extinction remains limited. We present an integrated approach examining the role of intrinsic traits versus extrinsic climate change in mediating extinction risk for marine invertebrates over the past 485 million years. We found that a combination of physiological traits and the magnitude of climate change is necessary to explain marine invertebrate extinction patterns. Our results suggest that taxa previously identified as extinction resistant may still succumb to extinction if the magnitude of climate change is great enough.

Landscape dynamics and the Phanerozoic diversification of the biosphere

The long-term diversification of the biosphere responds to changes in the physical environment. Yet, over the continents, the nearly monotonic expansion of life started later in the early part of the Phanerozoic eon1 than the expansion in the marine realm, where instead the number of genera waxed and waned over time2. A comprehensive evaluation of the changes in the geodynamic and climatic forcing fails to provide a unified theory for the long-term pattern of evolution of life on Earth. Here we couple climate and plate tectonics models to numerically reconstruct the evolution of the Earth's landscape over the entire Phanerozoic eon, which we then compare to palaeo-diversity datasets from marine animal and land plant genera. Our results indicate that biodiversity is strongly reliant on landscape dynamics, which at all times determine the carrying capacity of both the continental domain and the oceanic domain. In the oceans, diversity closely adjusted to the riverine sedimentary flux that provides nutrients for primary production. On land, plant expansion was hampered by poor edaphic conditions until widespread endorheic basins resurfaced continents with a sedimentary cover that facilitated the development of soil-dependent rooted flora, and the increasing variety of the landscape additionally promoted their development.

Automatic identification and morphological comparison of bivalve and brachiopod fossils based on deep learning

Fossil identification is an essential and fundamental task for conducting palaeontological research. Because the manual identification of fossils requires extensive experience and is time-consuming, automatic identification methods are proposed. However, these studies are limited to a few or dozens of species, which is hardly adequate for the needs of research. This study enabled the automatic identification of hundreds of species based on a newly established fossil dataset. An available "bivalve and brachiopod fossil image dataset" (BBFID, containing >16,000 "image-label" data pairs, taxonomic determination completed) was created. The bivalves and brachiopods contained in BBFID are closely related in morphology, ecology and evolution that have long attracted the interest of researchers. We achieved >80% identification accuracy at 22 genera and ∼64% accuracy at 343 species using EfficientNetV2s architecture. The intermediate output of the model was extracted and downscaled to obtain the morphological feature space of fossils using t-distributed stochastic neighbor embedding (t-SNE). We found a distinctive boundary between the morphological feature points of bivalves and brachiopods in fossil morphological feature distribution maps. This study provides a possible method for studying the morphological evolution of fossil clades using computer vision in the future.

Impact of global climate cooling on Ordovician marine biodiversity

Global cooling has been proposed as a driver of the Great Ordovician Biodiversification Event, the largest radiation of Phanerozoic marine animal Life. Yet, mechanistic understanding of the underlying pathways is lacking and other possible causes are debated. Here we couple a global climate model with a macroecological model to reconstruct global biodiversity patterns during the Ordovician. In our simulations, an inverted latitudinal biodiversity gradient characterizes the late Cambrian and Early Ordovician when climate was much warmer than today. During the Mid-Late Ordovician, climate cooling simultaneously permits the development of a modern latitudinal biodiversity gradient and an increase in global biodiversity. This increase is a consequence of the ecophysiological limitations to marine Life and is robust to uncertainties in both proxy-derived temperature reconstructions and organism physiology. First-order model-data agreement suggests that the most conspicuous rise in biodiversity over Earth's history - the Great Ordovician Biodiversification Event - was primarily driven by global cooling.

The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education

There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.

Challenges and directions in analytical paleobiology

Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini)

North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.

A persistent influence of supernovae on biodiversity over the Phanerozoic

It is an open question what has constrained macroevolutionary changes in marine animal diversity on the time scale of the Phanerozoic. Here, we will show that supernovae appear to have significantly influenced the biodiversity of life. After normalizing diversity curves of major animal marine genera by the changes in the area of shallow marine margins, a close correlation between supernovae frequency and biodiversity is obtained. The interpretation is that supernovae influence Earth's climate, which controls the ocean and atmospheric circulation of nutrients. With this, supernovae influence ocean bioproductivity and are speculated to affect genera-level diversity. The implication is a surprisingly influential role of stellar processes on evolution.

Cortical Parvalbumin-Positive Interneuron Development and Function Are Altered in the APC Conditional Knockout Mouse Model of Infantile and Epileptic Spasms Syndrome

Infantile and epileptic spasms syndrome (IESS) is a childhood epilepsy syndrome characterized by infantile or late-onset spasms, abnormal neonatal EEG, and epilepsy. Few treatments exist for IESS, clinical outcomes are poor, and the molecular and circuit-level etiologies of IESS are not well understood. Multiple human IESS risk genes are linked to Wnt/β-catenin signaling, a pathway that controls developmental transcriptional programs and promotes glutamatergic excitation via β-catenin's role as a synaptic scaffold. We previously showed that deleting adenomatous polyposis coli (APC), a component of the β-catenin destruction complex, in excitatory neurons (APC cKO mice, APCfl/fl x CaMKIIαCre) increased β-catenin levels in developing glutamatergic neurons and led to infantile behavioral spasms, abnormal neonatal EEG, and adult epilepsy. Here, we tested the hypothesis that the development of GABAergic interneurons (INs) is disrupted in APC cKO male and female mice. IN dysfunction is implicated in human IESS, is a feature of other rodent models of IESS, and may contribute to the manifestation of spasms and seizures. We found that parvalbumin-positive INs (PV+ INs), an important source of cortical inhibition, were decreased in number, underwent disproportionate developmental apoptosis, and had altered dendrite morphology at P9, the peak of behavioral spasms. PV+ INs received excessive excitatory input, and their intrinsic ability to fire action potentials was reduced at all time points examined (P9, P14, P60). Subsequently, GABAergic transmission onto pyramidal neurons was uniquely altered in the somatosensory cortex of APC cKO mice at all ages, with both decreased IPSC input at P14 and enhanced IPSC input at P9 and P60. These results indicate that inhibitory circuit dysfunction occurs in APC cKOs and, along with known changes in excitation, may contribute to IESS-related phenotypes.SIGNIFICANCE STATEMENT Infantile and epileptic spasms syndrome (IESS) is a devastating epilepsy with limited treatment options and poor clinical outcomes. The molecular, cellular, and circuit disruptions that cause infantile spasms and seizures are largely unknown, but inhibitory GABAergic interneuron dysfunction has been implicated in rodent models of IESS and may contribute to human IESS. Here, we use a rodent model of IESS, the APC cKO mouse, in which β-catenin signaling is increased in excitatory neurons. This results in altered parvalbumin-positive GABAergic interneuron development and GABAergic synaptic dysfunction throughout life, showing that pathology arising in excitatory neurons can initiate long-term interneuron dysfunction. Our findings further implicate GABAergic dysfunction in IESS, even when pathology is initiated in other neuronal types.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

The hierarchy of factors predicting the latitudinal diversity gradient

The numerous explanations for why Earth's biodiversity is concentrated at low latitudes fail to explain variation in the strength and even direction of the gradient through deep time. Consequently, we do not know if today's gradient is representative of what might be expected on other planets or is merely an idiosyncrasy of Earth's history. We propose a hierarchy of factors driving the latitudinal distribution of diversity: (i) over geologically long time spans, diversity is largely predicted by climate; (ii) when climatic gradients are shallow, diversity tracks habitat area; and (iii) historical contingencies linked to niche conservatism have geologically short-term, transient influence at most. Thus, latitudinal diversity gradients, although variable in strength and direction, are largely predictable on our planet and possibly others.

Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth-death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.

Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the 'global' dataset may identify accurate local diversity trends.

An 80-million-year sulphur isotope record of pyrite burial over the Permian-Triassic

Despite the extensive use of sulphur isotope ratios (δ³⁴S) for understanding ancient biogeochemical cycles, many studies focus on specific time-points of interest, such as the end-Permian mass extinction (EPME). We have generated an 80 million-year Permian-Triassic δ³⁴S_evap curve from the Staithes S-20 borehole, Yorkshire, England. The Staithes δ³⁴S_evap record replicates the major features of the global curve, while confirming a new excursion at the Olenekian/Anisian boundary at ~ 247 million years ago. We incorporate the resultant δ³⁴S_evap curve into a sulphur isotope box model. Our modelling approach reveals three significant pyrite burial events (i.e. PBEs) in the Triassic. In particular, it predicts a significant biogeochemical response across the EPME, resulting in a substantial increase in pyrite burial, possibly driven by Siberian Traps volcanism. Our model suggests that after ~ 10 million years pyrite burial achieves relative long-term stability until the latest Triassic.

Breathless through Time: Oxygen and Animals across Earth's History

AbstractOxygen levels in the atmosphere and ocean have changed dramatically over Earth history, with major impacts on marine life. Because the early part of Earth's history lacked both atmospheric oxygen and animals, a persistent co-evolutionary narrative has developed linking oxygen change with changes in animal diversity. Although it was long believed that oxygen rose to essentially modern levels around the Cambrian period, a more muted increase is now believed likely. Thus, if oxygen increase facilitated the Cambrian explosion, it did so by crossing critical ecological thresholds at low O₂. Atmospheric oxygen likely remained at low or moderate levels through the early Paleozoic era, and this likely contributed to high metazoan extinction rates until oxygen finally rose to modern levels in the later Paleozoic. After this point, ocean deoxygenation (and marine mass extinctions) is increasingly linked to large igneous province eruptions-massive volcanic carbon inputs to the Earth system that caused global warming, ocean acidification, and oxygen loss. Although the timescales of these ancient events limit their utility as exact analogs for modern anthropogenic global change, the clear message from the geologic record is that large and rapid CO₂ injections into the Earth system consistently cause the same deadly trio of stressors that are observed today. The next frontier in understanding the impact of oxygen changes (or, more broadly, temperature-dependent hypoxia) in deep time requires approaches from ecophysiology that will help conservation biologists better calibrate the response of the biosphere at large taxonomic, spatial, and temporal scales.

Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time

What controls species diversity and diversification is one of the major questions in evolutionary biology and paleontology. Previous studies have addressed this issue based on various plant and animal groups, geographic regions, and time intervals. However, as most previous research focused on terrestrial or marine ecosystems, our understanding of the controls on diversification of biota (and particularly invertebrates) in freshwater environments in deep time is still limited. Here, we infer diversification rates of North American freshwater gastropods from the Late Triassic to the Pleistocene and explore potential links between shifts in speciation and extinction and major changes in paleogeography, climate, and biotic interactions. We found that variation in the speciation rate is best explained by changes in continental fragmentation, with rate shifts coinciding with major paleogeographic reorganizations in the Mesozoic, in particular the retreat of the Sundance Sea and subsequent development of the Bighorn wetland and the advance of the Western Interior Seaway. Climatic events in the Cenozoic (Middle Eocene Climate Optimum, Miocene Climate Optimum) variably coincide with shifts in speciation and extinction as well, but no significant long-term association could be detected. Similarly, no influence of diversity dependence was found across the entire time frame of ~ 214 Myr. Our results indicate that short-term climatic events and paleogeographic changes are relevant to the diversification of continental freshwater biota, while long-term trends have limited effect.

Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

Resilience of infaunal ecosystems during the Early Triassic greenhouse Earth

The Permian-Triassic mass extinction severely depleted biodiversity, primarily observed in the body fossil of well-skeletonized animals. Understanding how whole ecosystems were affected and rebuilt following the crisis requires evidence from both skeletonized and soft-bodied animals; the best comprehensive information on soft-bodied animals comes from ichnofossils. We analyzed abundant trace fossils from 26 sections across the Permian-Triassic boundary in China and report key metrics of ichnodiversity, ichnodisparity, ecospace utilization, and ecosystem engineering. We find that infaunal ecologic structure was well established in the early Smithian. Decoupling of diversity between deposit feeders and suspension feeders in carbonate ramp-platform settings implies that an effect of trophic group amensalism could have delayed the recovery of nonmotile, suspension-feeding epifauna in the Early Triassic. This differential reaction of infaunal ecosystems to variable environmental controls thus played a substantial but heretofore little appreciated evolutionary and ecologic role in the overall recovery in the hot Early Triassic ocean.

Life rather than climate influences diversity at scales greater than 40 million years

The diversity of life on Earth is controlled by hierarchical processes that interact over wide ranges of timescales¹. Here, we consider the megaclimate regime² at scales ≥1 million years (Myr). We focus on determining the domains of 'wandering' stochastic Earth system processes ('Court Jester'³) and stabilizing biotic interactions that induce diversity dependence of fluctuations in macroevolutionary rates ('Red Queen'⁴). Using state-of-the-art multiscale Haar and cross-Haar fluctuation analyses, we analysed the global genus-level Phanerozoic marine animal Paleobiology Database record of extinction rates (E), origination rates (O) and diversity (D) as well as sea water palaeotemperatures (T). Over the entire observed range from several million years to several hundred million years, we found that the fluctuations of T, E and O showed time-scaling behaviour. The megaclimate was characterized by positive scaling exponents-it is therefore apparently unstable. E and O are also scaling but with negative exponents-stable behaviour that is biotically mediated. For D, there were two regimes with a crossover at critical timescale [Formula: see text] ≈ 40 Myr. For shorter timescales, D exhibited nearly the same positive scaling as the megaclimate palaeotemperatures, whereas for longer timescales it tracks the scaling of macroevolutionary rates. At scales of at least [Formula: see text] there is onset of diversity dependence of E and O, probably enabled by mixing and synchronization (globalization) of the biota by geodispersal ('Geo-Red Queen').

Avoiding ocean mass extinction from climate warming

Global warming threatens marine biota with losses of unknown severity. Here, we quantify global and local extinction risks in the ocean across a range of climate futures on the basis of the ecophysiological limits of diverse animal species and calibration against the fossil record. With accelerating greenhouse gas emissions, species losses from warming and oxygen depletion alone become comparable to current direct human impacts within a century and culminate in a mass extinction rivaling those in Earth's past. Polar species are at highest risk of extinction, but local biological richness declines more in the tropics. Reversing greenhouse gas emissions trends would diminish extinction risks by more than 70%, preserving marine biodiversity accumulated over the past ~50 million years of evolutionary history.

Do species factories exist? Detecting exceptional patterns of evolution in the mammalian fossil record

A species factory refers to the source that gives rise to an exceptionally large number of species. However, what is it exactly: a place, a time or a combination of places, times and environmental conditions, remains unclear. Here we search for species factories computationally, for which we develop statistical approaches to detect origination, extinction and sorting hotspots in space and time in the fossil record. Using data on European Late Cenozoic mammals, we analyse where, how and how often species factories occur, and how they potentially relate to the dynamics of environmental conditions. We find that in the Early Miocene origination hotspots tend to be located in areas with relatively low estimated net primary productivity. Our pilot study shows that species first occurring in origination hotspots tend to have a longer average longevity and a larger geographical range than other species, thus emphasizing the evolutionary importance of the species factories.

Fossil coleoid cephalopod from the Mississippian Bear Gulch Lagerstätte sheds light on early vampyropod evolution

We describe an exceptionally well-preserved vampyropod, Syllipsimopodi bideni gen. et sp. nov., from the Carboniferous (Mississippian) Bear Gulch Lagerstätte of Montana, USA. The specimen possesses a gladius and ten robust arms bearing biserial rows of suckers; it is the only known vampyropod to retain the ancestral ten-arm condition. Syllipsimopodi is the oldest definitive vampyropod and crown coleoid, pushing back the fossil record of this group by ~81.9 million years, corroborating molecular clock estimates. Using a Bayesian tip-dated phylogeny of fossil neocoleoid cephalopods, we demonstrate that Syllipsimopodi is the earliest-diverging known vampyropod. This strongly challenges the common hypothesis that vampyropods descended from a Triassic phragmoteuthid belemnoid. As early as the Mississippian, vampyropods were evidently characterized by the loss of the chambered phragmocone and primordial rostrum-traits retained in belemnoids and many extant decabrachians. A pair of arms may have been elongated, which when combined with the long gladius and terminal fins, indicates that the morphology of the earliest vampyropods superficially resembled extant squids.

Colonial history and global economics distort our understanding of deep-time biodiversity

Sampling biases in the fossil record distort estimates of past biodiversity. However, these biases not only reflect the geological and spatial aspects of the fossil record, but also the historical and current collation of fossil data. We demonstrate how the legacy of colonialism and socioeconomic factors, such as wealth, education and political stability, impact the global distribution of fossil data over the past 30 years. We find that a global power imbalance persists in palaeontology, with researchers in high- or upper-middle-income countries holding a monopoly over palaeontological knowledge production by contributing to 97% of fossil data. As a result, some countries or regions tend to be better sampled than others, ultimately leading to heterogeneous spatial sampling across the globe. This illustrates how efforts to mitigate sampling biases to obtain a truly representative view of past biodiversity are not disconnected from the aim of diversifying and decolonizing our discipline.

Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification

Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life.

This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.

The Deep-Time Digital Earth program: data-driven discovery in geosciences

Current barriers hindering data-driven discoveries in deep-time Earth (DE) include: substantial volumes of DE data are not digitized; many DE databases do not adhere to FAIR (findable, accessible, interoperable and reusable) principles; we lack a systematic knowledge graph for DE; existing DE databases are geographically heterogeneous; a significant fraction of DE data is not in open-access formats; tailored tools are needed. These challenges motivate the Deep-Time Digital Earth (DDE) program initiated by the International Union of Geological Sciences and developed in cooperation with national geological surveys, professional associations, academic institutions and scientists around the world. DDE’s mission is to build on previous research to develop a systematic DE knowledge graph, a FAIR data infrastructure that links existing databases and makes dark data visible, and tailored tools for DE data, which are universally accessible. DDE aims to harmonize DE data, share global geoscience knowledge and facilitate data-driven discovery in the understanding of Earth's evolution.

Shared patterns in body size declines among crinoids during the Palaeozoic extinction events

Crinoids were among the most abundant marine benthic animals throughout the Palaeozoic, but their body size evolution has received little attention. Here, we compiled a comprehensive database on crinoid calyx biovolumes throughout the Palaeozoic. A model comparison approach revealed contrasting and complex patterns in body size dynamics between the two major crinoid clades (Camerata and Pentacrinoidea). Interestingly, two major drops in mean body size at around two mass extinction events (during the late Ordovician and the late Devonian respectively) are observed, which is reminiscent of current patterns of shrinking body size of a wide range of organisms as a result of climate change. The context of some trends (marked declines during extinctions) suggests the cardinal role of abiotic factors (dramatic climate change associated with extinctions) on crinoid body size evolution; however, other patterns (two intervals with either relative stability or steady size increase in periods between mass extinctions) are more consistent with biotic drivers.

Biodiversity across space and time in the fossil record

The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.

Increase in marine provinciality over the last 250 million years governed more by climate change than plate tectonics

Amidst long-term fluctuations of the abiotic environment, the degree to which life organizes into distinct biogeographic provinces (provinciality) can reveal the fundamental drivers of global biodiversity. Our understanding of present-day biogeography implies that changes in the distribution of continents across climatic zones have predictable effects on habitat distribution, dispersal barriers and the evolution of provinciality. To assess marine provinciality through the Phanerozoic, here we (a) simulate provinces based on palaeogeographic reconstructions and global climate models and (b) contrast them with empirically derived provinces that we define using network analysis of fossil occurrences. Simulated and empirical patterns match reasonably well and consistently suggest a greater than 15% increase in provinciality since the Mesozoic era. Although both factors played a role, the simulations imply that the effect of the latitudinal temperature gradient has been twice as important in determining marine provinciality as continental configuration.

Thresholds of temperature change for mass extinctions

Climate change is a critical factor affecting biodiversity. However, the quantitative relationship between temperature change and extinction is unclear. Here, we analyze magnitudes and rates of temperature change and extinction rates of marine fossils through the past 450 million years (Myr). The results show that both the rate and magnitude of temperature change are significantly positively correlated with the extinction rate of marine animals. Major mass extinctions in the Phanerozoic can be linked to thresholds in climate change (warming or cooling) that equate to magnitudes >5.2 °C and rates >10 °C/Myr. The significant relationship between temperature change and extinction still exists when we exclude the five largest mass extinctions of the Phanerozoic. Our findings predict that a temperature increase of 5.2 °C above the pre-industrial level at present rates of increase would likely result in mass extinction comparable to that of the major Phanerozoic events, even without other, non-climatic anthropogenic impacts.

Productivity, niche availability, species richness, and extinction risk: Untangling relationships using individual-based simulations

It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology.

Dinosaur biodiversity declined well before the asteroid impact, influenced by ecological and environmental pressures

The question why non-avian dinosaurs went extinct 66 million years ago (Ma) remains unresolved because of the coarseness of the fossil record. A sudden extinction caused by an asteroid is the most accepted hypothesis but it is debated whether dinosaurs were in decline or not before the impact. We analyse the speciation-extinction dynamics for six key dinosaur families, and find a decline across dinosaurs, where diversification shifted to a declining-diversity pattern ~76 Ma. We investigate the influence of ecological and physical factors, and find that the decline of dinosaurs was likely driven by global climate cooling and herbivorous diversity drop. The latter is likely due to hadrosaurs outcompeting other herbivores. We also estimate that extinction risk is related to species age during the decline, suggesting a lack of evolutionary novelty or adaptation to changing environments. These results support an environmentally driven decline of non-avian dinosaurs well before the asteroid impact.

The Boltysh impact structure: An early Danian impact event during recovery from the K-Pg mass extinction

Both the Chicxulub and Boltysh impact events are associated with the K-Pg boundary. While Chicxulub is firmly linked to the end-Cretaceous mass extinction, the temporal relationship of the ~24-km-diameter Boltysh impact to these events is uncertain, although it is thought to have occurred 2 to 5 ka before the mass extinction. Here, we conduct the first direct geochronological comparison of Boltysh to the K-Pg boundary. Our ⁴⁰Ar/³⁹Ar age of 65.39 ± 0.14/0.16 Ma shows that the impact occurred ~0.65 Ma after the mass extinction. At that time, the climate was recovering from the effects of the Chicxulub impact and Deccan trap flood volcanism. This age shows that Boltysh has a close temporal association with the Lower C29n hyperthermal recorded by global sediment archives and in the Boltysh crater lake sediments. The temporal coincidence raises the possibility that even a small impact event could disrupt recovery of the Earth system from catastrophic events.

Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data

Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.

Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton

Many ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient, i.e. the increase in species richness from the poles to the tropics. Among the evolutionary hypotheses, the 'out of the tropics' (OTT) hypothesis has received considerable attention. The OTT posits that the tropics are both a cradle and source of biodiversity for extratropical regions. To test the generality of the OTT hypothesis, we explored the spatial biodiversity dynamics of unicellular marine plankton over the Cenozoic era (the last 66 Myr). We find large-scale climatic changes during the Cenozoic shaped the diversification and dispersal of marine plankton. Origination was generally more likely in the extratropics and net dispersal was towards the tropics rather than in the opposite direction, especially during the warmer climates of the early Cenozoic. Although migration proportions varied among major plankton groups and climate phases, we provide evidence that the extratropics were a source of tropical microplankton biodiversity over the last 66 Myr.

Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton

The latitudinal diversity gradient (LDG)-the decline in species richness from the equator to the poles-is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.

Impacts of speciation and extinction measured by an evolutionary decay clock

The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution^1,2. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates the simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events², seven additional mass extinctions, two combined mass extinction-radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations^1,3, we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions⁴, evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay⁴ (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.

Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient

Global biodiversity currently peaks at the equator and decreases toward the poles. Growing fossil evidence suggest this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar diversity across latitudes flattening out the LDG during past greenhouse periods. However, when and how diversity declined at high latitudes to generate the modern LDG remains an open question. Although diversity-loss scenarios have been proposed, they remain mostly undemonstrated. We outline the "asymmetric gradient of extinction and dispersal" framework that contextualizes previous ideas behind the LDG under a time-variable scenario. Using phylogenies and fossils of Testudines, Crocodilia, and Lepidosauria, we find that the hump-shaped LDG could be explained by (1) disproportionate extinctions of high-latitude tropical-adapted clades when climate transitioned from greenhouse to icehouse, and (2) equator-ward biotic dispersals tracking their climatic preferences when tropical biomes became restricted to the equator. Conversely, equivalent diversification rates across latitudes can account for the formation of an ancient flat LDG. The inclusion of fossils in macroevolutionary studies allows revealing time-dependent extinction rates hardly detectable from phylogenies only. This study underscores that the prevailing evolutionary processes generating the LDG during greenhouses differed from those operating during icehouses.

Flat latitudinal diversity gradient caused by the Permian-Triassic mass extinction

The latitudinal diversity gradient (LDG) is recognized as one of the most pervasive, global patterns of present-day biodiversity. However, the controlling mechanisms have proved difficult to identify because many potential drivers covary in space. The geological record presents a unique opportunity for understanding the mechanisms which drive the LDG by providing a direct window to deep-time biogeographic dynamics. Here we used a comprehensive database containing 52,318 occurrences of marine fossils to show that the shape of the LDG changed greatly during the Permian-Triassic mass extinction from showing a significant tropical peak to a flattened LDG. The flat LDG lasted for the entire Early Triassic (∼5 My) before reverting to a modern-like shape in the Middle Triassic. The environmental extremes that prevailed globally, especially the dramatic warming, likely induced selective extinction in low latitudes and accumulation of diversity in high latitudes through origination and poleward migration, which combined together account for the flat LDG of the Early Triassic.

The spatial structure of Phanerozoic marine animal diversity

The global fossil record of marine animals has fueled long-standing debates about diversity change through time and the drivers of this change. However, the fossil record is not truly global. It varies considerably in geographic scope and in the sampling of environments among intervals of geological time. We account for this variability using a spatially explicit approach to quantify regional-scale diversity through the Phanerozoic. Among-region variation in diversity is comparable to variation through time, and much of this is explained by environmental factors, particularly the extent of reefs. By contrast, influential hypotheses of diversity change through time, including sustained long-term increases, have little explanatory power. Modeling the spatial structure of the fossil record transforms interpretations of Phanerozoic diversity patterns and their macroevolutionary explanations. This necessitates a refocus of deep-time diversification studies.

A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity

One great challenge in understanding the history of life is resolving the influence of environmental change on biodiversity. Simulated annealing and genetic algorithms were used to synthesize data from 11,000 marine fossil species, collected from more than 3000 stratigraphic sections, to generate a new Cambrian to Triassic biodiversity curve with an imputed temporal resolution of 26 ± 14.9 thousand years. This increased resolution clarifies the timing of known diversification and extinction events. Comparative analysis suggests that partial pressure of carbon dioxide (Pco2) is the only environmental factor that seems to display a secular pattern similar to that of biodiversity, but this similarity was not confirmed when autocorrelation within that time series was analyzed by detrending. These results demonstrate that fossil data can provide the temporal and taxonomic resolutions necessary to test (paleo)biological hypotheses at a level of detail approaching those of long-term ecological analyses.

Marine Biodiversity and Geographic Distributions Are Independent on Large Scales

Fundamental ecological and evolutionary theories, such as community saturation and diversity-dependent diversification, assume that biotic competition restricts resource use, and thus limits realized niche breadth and geographic range size [1-3]. This principle is called competitive exclusion. The corollary (ecological release) posits that, after competitors disappear from a region, species that were previously excluded will invade. Hundreds of field experiments have demonstrated ecological release in living populations. However, few of these studies were conducted in marine environments, and almost no work extended beyond 10 years and 1,000 km2 [4, 5]. In limited investigation of marine taxa at larger spatiotemporal scales, macroecologists and paleobiologists have observed little evidence of competitive exclusion [6-9]. Here, we quantified spatial trends in the rich and densely sampled fossil history of brachiopods and bivalves, while accounting for inconsistent sampling coverage through time using a new method of spatial standardization. The number of potential competitors in a region did not explain the geographic distribution of constituent species or genera. Furthermore, although ecological release predicts species to expand after extinction events, survivors of intervals with net species loss expanded as rarely as species in other intervals. Regression model estimates indicated different spatial responses of brachiopods and bivalves, and of habitat specialists and generalists, but no effect from changes in number of potential competitors. Biotic competition may control the distribution of populations, but, on larger spatiotemporal scales, non-competitive factors may have driven biogeographic patterns of brachiopods and bivalves.

Impacts of spatial and environmental differentiation on early Palaeozoic marine biodiversity

The unprecedented diversifications in the fossil record of the early Palaeozoic (541-419 million years ago) increased both within-sample (α) and global (γ) diversity, generating considerable ecological complexity. Faunal difference (β diversity), including spatial heterogeneity, is thought to have played a major role in early Palaeozoic marine diversification, although α diversity is the major determinant of γ diversity through the Phanerozoic. Drivers for this Phanerozoic shift from β to α diversity are not yet resolved. Here, we evaluate the impacts of environmental and faunal heterogeneity on diversity patterns using a global spatial grid. We present early Palaeozoic genus-level α, β and γ diversity curves for molluscs, brachiopods, trilobites and echinoderms and compare them with measures of spatial lithological heterogeneity, which is our proxy for environmental heterogeneity. We find that α and β diversity are associated with increased lithological heterogeneity, and that β diversity declines over time while α increases. We suggest that the enhanced dispersal of marine taxa from the Middle Ordovician onwards facilitated increases in α diversity by encouraging the occupation of narrow niches and increasing the prevalence of transient species, simultaneously reducing spatial β diversity. This may have contributed to a shift from β to α diversity as the major determinant of γ diversity increase over this critical evolutionary interval.

FosSahul 2.0, an updated database for the Late Quaternary fossil records of Sahul

The 2016 version of the FosSahul database compiled non-human vertebrate megafauna fossil ages from Sahul published up to 2013 in a standardized format. Its purpose was to create a publicly available, centralized, and comprehensive database for palaeoecological investigations of the continent. Such databases require regular updates and improvements to reflect recent scientific findings. Here we present an updated FosSahul (2.0) containing 11,871 dated non-human vertebrate fossil records from the Late Quaternary published up to 2018. Furthermore, we have extended the information captured in the database to include methodological details and have developed an algorithm to automate the quality-rating process. The algorithm makes the quality-rating more transparent and easier to reproduce, facilitating future database extensions and dissemination. FosSahul has already enabled several palaeoecological analyses, and its updated version will continue to provide a centralized organisation of Sahul's fossil records. As an example of an application of the database, we present the temporal pattern in megafauna genus richness inferred from available data in relation to palaeoclimate indices over the past 180,000 years.