The Ediacaran/Cambrian transition (ECT; ~575–500 Ma) captures the early diversification of animals, including the oldest crown-group taxa of most major animal phyla alive today. Key to understanding the drivers underneath the ECT macroevolutionary patterns are the interactions of animals with one another and their environment, and how these interactions scale up to global diversity patterns. Understanding the ecology of ECT organisms is enabled by the abundance of Lagerstätten over this time period, with a relatively large proportion of soft-bodied organisms preserved, often within the communities in which they lived. Here, we review our understanding of organismal, community, and macroecology of the ECT, and how these different scales of ecological analyses relate to the macroevolutionary diversification patterns we see over this 75 Myr time period. Across all ecological scales, we find clear trends, starting with stochastic ecosystem dynamics dominated by generalist taxa in the first Ediacaran communities, to more structured, niche-driven specialist dynamics by Cambrian Epoch 2. These trends are reflected in organism functional morphology, the complexity and strength of organisms’ interactions within their communities, and large-scale metacommunity, biogeographic, and biodiversity patterns. Yet there is often a time delay between the origination of a new type of ecological interaction and when it is observed to impact the ecosystem as a whole. As such, while many modern ecological innovations were in place by the end of the Cambrian, the knock-on effects and complexity of these interactions continued to build up throughout the Phanerozoic, leading to the complex biosphere we have today.

The recent proliferation of quantitative models for assessing anatomical character evolution all assume that character change happens continuously through time. However, the punctuated equilibrium model posits that character change should be coincide with cladogenetic events, and thus should be tied to origination rates. Rates of cladogenesis are important to quantitative phylogenetics, but typically only for establishing prior probabilities in the tree model component of phylogenetic analyses. Here, we modify existing character-likelihood models to use the local cladogenesis rates from Bayesian analyses to generate amounts of character change over time dependent on origination rates, as expected under the punctuated equilibrium model. In the case of strophomenoid brachiopods from the Ordovician, Bayesian analyses strongly favor punctuated models over continuous-time models, with elevated rates of cladogenesis early in the clade’s history inducing frequencies of change despite constant rates of change per speciation event. This corroborates prior work proposing that the early burst in strophomenoid disparity simply reflects elevated speciation rates, which in turn has implications for seemingly unrelated macroevolutionary theory about whether early bursts reflect shifts in intrinsic constraints or empty ecospace. Future development of punctuated character evolution models should account for the full durations of species, which will provide a test of continuous change rates. Ultimately, continuous change versus punctuated change should become part of phylogenetic paleobiology in the same way that we currently test other models of character evolution.

Genome size (GS) is thought to be a key life-history trait and important for controlling plant distributions and evolutionary dynamics, but a full understanding of GS variation through evolutionary history requires proxy measurements from fossils. Here, we compare two potential GS proxies: guard cell length (GCL) and sporomorph size. We generated GCL and pollen size data from angiosperms growing in the University of Münster Botanical Garden, compiled sporomorph size data from the literature, and related these to GS using phylogenetic regression models. We also fit evolutionary models to the botanical garden data and used a published dataset to validate GCL as a GS proxy. The majority of the analyses conducted revealed a positive relationship between GS and sporomorph size, but in most cases, the explanatory power of the regressions was low. GCL showed a stronger and more consistent relationship with GS, and independent validation of the relationship showed a generally good match between predicted and observed GS. Sporomorph size is not suitable as a cross-taxon GS proxy, but some specific taxa (e.g., Pinus) may contain useful GS information. GCL has much more potential for measuring paleo-GS, but requires further research for us to better understand possible environmental controls on cell size variation.

The Paleocene–Eocene thermal maximum (PETM) was the largest early Cenozoic hyperthermal event, one of a series of carbon cycle and climate perturbations marked by massive releases of carbon into the atmosphere and spikes in global temperature. Previous studies have documented major changes in the composition of terrestrial plant and animal communities during the PETM, as well as changes in arthropod herbivory. Here, we examine possible changes in pollination mode during the PETM in the Bighorn Basin, Wyoming, USA, as inferred from three lines of evidence: (1) the prevalence of fossil pollen preserved as clumps, (2) the pollination mode of nearest living relatives (NLR), and (3) angiosperm pollen morphological diversity. These suggest animal pollination became more common and wind pollination less common during the PETM. The decrease in wind pollination during the PETM reflects the basin-scale extirpation of wind-pollinated lineages and their replacement by dominantly animal-pollinated lineages concomitant with rapid warming and drying. The hotter and seasonally drier climates not only facilitated the northward range shift of plant taxa, but likely their insect and/or vertebrate pollinators as well. The dramatic floral changes during the PETM in the Bighorn Basin may also have changed available resources for insect and/or vertebrate pollinators.

The Paleozoic evolution of a complex terrestrial biota has been among the most important events in Earth history. Here, we synthesize paleontological and neontological information across the different threads of the biota—including microbial life, fungi, animals, and plants—addressing discrepancies between the fossil record and time-calibrated molecular phylogenies. Four fundamental patterns are emphasized: (1) Most terrestrial animal lineages consist of diminutive inhabitants of soil and litter, with the soil fauna exhibiting remarkable continuity between the Paleozoic and present. (2) Faunal evolution tracks the ecological opportunities afforded by the evolution of the land flora. Flora and fauna alike were initially confined to the thin interface between soil and air, but animals explored both flight and burrowing as vascular plant size increased to encompass tree stature and deep rooting. (3) Skewed nutrient ratios of land plants present a fundamental challenge for animals that are accommodated through contrasting size-based dietary strategies. Detritivory and cell-by-cell herbivory are the diets most readily available for primary consumers but impose limits on the largest possible body sizes; only with subsequent evolution of herbivory in insects and then vertebrates could the dramatic increases in size in the Permian and Mesozoic have been achieved. (4) A second pulse of animal terrestrializations is apparent in the Cretaceous and Cenozoic that might be attributed to increased terrestrial productivity associated with angiosperm evolution. However, environmental changes to nutrient availability earlier in the Mesozoic prevent an unambiguous causal attribution, and the pulse may just be an artifact of our modern vantage point.

A primary tenet of punctuated equilibria (PE) is that stasis, that is, little to no net morphological change, characterizes the histories of species. In the past ~50 years since PE was proposed, stasis has been recognized in the evolutionary histories of many species, but consensus has not been reached concerning its causes.

One unresolved issue is whether viable ecological mechanisms for stasis exist. We argue that a promising potential ecological explanation for stasis is coevolutionary alternation, which addresses how antagonists (e.g., predators or parasites and their groups of victims) coevolve over eco-evolutionary time across broad spatial scales. Coevolutionary alternation predicts different patterns of predator preferences and prey defenses within different populations and alternation of high and low levels of prey defenses as predator preferences evolve. The geographic structure of populations experiencing different environmental pressures and coevolutionary dynamics can yield stasis in such traits on the scale of entire species. We suggest that predator–prey coevolutionary alternation could be modeled using coupled stochastic differential equations (SDEs), which have been used to study correlative and causal connections among time series. SDEs can handle irregular sampling intervals, measurement uncertainty, and feedback loops between time series and can incorporate environmental proxies and time series from multiple geographic locations. We advocate developing this approach further to test the role of coevolutionary alternation in stasis and make recommendations for how SDEs might be used to model the coevolutionary feedback of predator(s) and multiple prey populations evolving in response to one another across space in a constantly changing environment.

Organismal morphology was at the core of study of biodiversity for millennia before the formalization of the concept of evolution. In the early to mid-twentieth century, a strong theoretical framework was developed for understanding both pattern and process of morphological evolution, and the 50 years since the founding of this journal capture a transformational period in the quantification of morphology and in analytical tools for estimating how morphological diversity changes through time. We are now at another inflection point in the study of morphological evolution, with the availability of vast amounts of high-resolution data sampling extant and extinct diversity allowing “omics”-scale analysis. Artificial intelligence is accelerating the pace of phenomic data acquisition even further. This new reality, in which the ability to obtain data is quickly outpacing the ability to analyze it with robust, realistic evolutionary models, brings a new set of challenges. Phylogenetic comparative methods have provided new insights into the processes generating morphological diversity, but the reliance on molecular data and resultant exclusion of fossil data from most large phylogenetic trees has well-established negative impacts on evolutionary analyses, as we demonstrate with examples of standard single-rate evolutionary models, mode- and rate-shift models, and a recently described Ornstein-Uhlenbeck climate model. Further development of methods for phylogenetic comparative analysis of high-dimensional data is needed, but existing tools can refine our understanding and expectations of morphological evolution and the generation of morphological diversity under different scenarios, as we demonstrate with analyses of placental skull evolution through the Cenozoic. Fully transitioning the study of morphological evolution into the omics era will involve the development of tools to automate the extraction of meaningful, comparable morphometric data from images, integrate fossil data into large phylogenetic trees and downstream evolutionary analyses, and generate robust models that accurately reflect the complexity of evolutionary processes and are well-suited for high-dimensional data. Combined, these advancements will solidify the emerging field of evolutionary phenomics and appropriately center it around the analysis of deep-time data.

Documenting patterns of evolution and stasis has been a major focus of paleobiology. However, despite substantial knowledge gleaned on this topic, many questions related to the underlying environmental processes that determine the dynamics of evolution and stasis remain unresolved. Therefore, this study focuses on examining these evolutionary patterns framed within an environmental context. Specifically, we test Sheldon’s “Plus ça change” model, which predicts that morphological change is associated with more stable environments, such as in tropical latitudes or greenhouse climates, whereas stasis is linked to less stable environments, like those found in temperate latitudes or during icehouse climates. We examine the role that broadscale climatic variation exerts on evolutionary dynamics by documenting morphological change among nuculid bivalves in shallow-shelf settings from three different climate regimes: (1) the stable Late Cretaceous greenhouse climate; (2) the moderately stable Neogene transitional climate; and (3) the less stable Quaternary icehouse climate. Morphological changes over time were assessed using both bivalve size and outline shape. Comparison among changes in size and outline-shape patterns for Late Cretaceous and Neogene–Quaternary Nucula indicates that morphological change over time and stasis, respectively, dominated these different time intervals. In all cases, morphological change over time coincided with the more stable and less climatically variable greenhouse conditions, whereas stasis was associated with the more variable regimes characteristic of icehouse climates. These data provide strong support for the need to consider broad environmental factors—in this case climate—when assessing evolutionary modes. Furthermore, they point to the relevance of the Plus ça change model to explain patterns of evolution and stasis.

The common-cause hypothesis says that factors regulating the sedimentary record also exert macroevolutionary controls on speciation, extinction, and biodiversity. I show through computational modeling that common cause factors can, in principle, also control microevolutionary processes of trait evolution. Using Bermuda and its endemic land snail Poecilozonites, I show that the glacial–interglacial sea-level cycles that toggle local sedimentation between slow pedogenesis and rapid eolian accumulation could also toggle evolution rates between long slow phases associated with large geographic ranges and short rapid phases associated with small, fragmented ranges and “genetic surfing” events. Patterns produced by this spatially driven process are similar to the punctuated equilibria patterns that Gould inferred from the fossil record of Bermuda, but without speciation or true stasis. Rather, the dynamics of this modeled system mimic a two-rate Brownian motion process (even though the rate parameter is technically constant) in which the contrast in rate and duration of the phases makes the slower one appear static. The link between sedimentation and microevolution in this model is based on a sediment-starved island system, but the principles may apply to any system where physical processes jointly control the areal extents of sedimentary regimes and species’ distributions.

Incorporating paleontological data into phylogenetic inference can greatly enrich our understanding of evolutionary relationships by providing insights into the diversity and morphological evolution of a clade over geological timescales. Phylogenetic analysis of fossil data has been significantly aided by the introduction of the fossilized birth–death (FBD) process, a model that accounts for fossil sampling through time. A decade on from the first implementation of the FBD model, we explore its use in more than 170 empirical studies, summarizing insights gained through its application. We identify a number of challenges in applying the model in practice: it requires a working knowledge of paleontological data and their complex properties, Bayesian phylogenetics, and the mechanics of evolutionary models. To address some of these difficulties, we provide an introduction to the Bayesian phylogenetic framework, discuss important aspects of paleontological data, and finally describe the assumptions of the models used in paleobiology. We also present a number of exemplar empirical studies that have used the FBD model in different ways. Through this review, we aim to provide clarity on how paleontological data can best be used in phylogenetic inference. We hope to encourage communication between model developers and empirical researchers, with the ultimate goal of developing models that better reflect the data we have and the processes that generated them.

Although the theory of punctuated equilibria has stood the test of time, critics have sometimes highlighted the lack of a complementary molecular mechanism. The developmental gene hypothesis (DGH) provides just such a mechanism and is reviewed and significantly expanded in the present paper, taking advantage of concepts of active and passive evolvability, genetic drift, and the nearly neutral theory of molecular evolution, and compensatory adaptation in the face of weakly deleterious genetic variation. In addition, with the use of game theory, the author models the behavior of developmental regulatory (DevReg) genes, which are integral to the proposed hypothesis, in order to better understand their roles in stasis and speciation.

In the last 50 years, the field of paleobiology has undergone a computational revolution that opened multiple new avenues for recording, storing, and analyzing vital data on the history of life on Earth. With these advances, the amount of data available for research has grown, but so too has our responsibility to ensure that our data tools and infrastructures continue to innovate in order to best serve our diverse community. This review focuses on data equity in paleobiology, an aspirational goal, wherein data in all forms are collected, stored, shared and analyzed in a responsible, equitable, and sustainable manner. While there have been many advancements across the last five decades, inequities persist. Our most significant challenges relate to several interconnected factors, including ethical data collection, sustainable infrastructure, socioeconomic biases, and global inequalities. We highlight the ways in which data equity is critical for paleobiology and stress the need for collaborative efforts across the paleobiological community to urgently address these data equity challenges. We also provide recommendations for actions from individuals, teams, academic publishers, and academic societies in order to continue enhancing data equity and ensuring an equitable and sustainable future for our field.

The theory of punctuated equilibria, introduced in paleobiology, postulates enduring morphological stability in species interrupted by rapid phenotypic change at speciation events. It played a pivotal role in evolutionary biology, reshaping perspectives and triggering a conceptual shift by redefining species as discrete and enduring entities, and paving the way for a hierarchical model of the organic world. This hierarchical approach initially faced limited attention but experienced a resurgence in the new millennium. The revived interest in hierarchical models, integrating genomics, computational methodologies, and complex systems sciences, has provided a more comprehensive theoretical foundation for understanding biological evolution. This resurgence has fueled empirical studies across various disciplines, from genomics to paleobiology, offering a potential unifying theory within the biological sciences.

This paper posits the efficacy of the hierarchy theory of biology as a comprehensive, unifying framework for understanding the organic world. Despite its generality, the theory remains agnostic to specific mechanisms, allowing flexibility to accommodate diverse biological models. Through its application to speciation analysis, the hierarchy theory unveils causal processes, identifies entities and interactions, and bridges the economic and genealogical hierarchies. Acknowledging its potential for refinement based on empirical data, the hierarchy theory of biology stands as a paradigm, shaping interdisciplinary exploration and inspiring investigations across disciplines.

Punctuated equilibria argue for intervals of long-term net stasis and comparatively abrupt change in the morphology of individual species lineages resulting from the process of allopatric speciation as recorded in the stratigraphic and fossil record. The concept of coordinated stasis extends punctuated equilibria to posit that not only individual species, but groups of coexisting lineages within a basin, display concurrent morphological and ecological stability over the same extended intervals of geologic time (105 to 106 yr). These blocks of stability termed ecological–evolutionary subunits (EESUs) are separated by shorter-lived (on the order of 103 to 104 yr) episodes of change characterized by varying combinations of speciation, extinction, immigration, and emigration. The result is a pattern of evolutionary and ecological stasis and change that is coincident and highly punctuational.

Here, we assess the connections among environment, evolution, and ecology by documenting patterns of stability, geographic extent, and synchronous turnover during medium-scale bioevents in the Middle Devonian of the eastern United States, and we briefly compare these with patterns of EESUs across the Late Ordovician mass extinction (LOME) based on ongoing work. We quantify the geographic extent and stability of faunas originally documented in the Appalachian Basin and identify their likely places of origin and refugia during turnovers. Faunas are geographically widespread during times of stability and border comparably stable faunas in adjacent provinces. During geologically brief intervals, assemblages display near-synchronous shifts involving local extirpation/extinction and coordinated migration of biogeographic boundaries over very long distances. Allopatric speciation in small, locally isolated populations along the edges of basins during brief windows of dramatically altered environmental conditions is more consistent with the geological record, emphasizes the role of environment and biogeography in driving evolutionary change, and confirms the prevalence of punctuated equilibria.