I have devised two tests that pit punctuationalism against gradualism. The first is the Test of Adaptive Radiation, which I apply to families of middle Eocene Mammalia and Late Cretaceous Bivalvia. This test shows that species in both of these classes lasted much too long for evolution within them (phyletic evolution) to have produced the new families that arose during brief time intervals. This test would yield similar results for many other taxa. It supports the punctuational model, as does the Test of Living Fossils, which predicts that long, slender clades, having experienced little speciation, should have undergone little evolution. Limited largely to phyletic evolution, this is exactly what happened to them.

Several multivariate morphological studies of numerous fossil lineages have found little or no gradual evolution to have been the norm. One of these included 153 lineage traits and another, 250. Still another produced a rectangular stratophenetic phylogeny, with inferred horizontal speciation events connecting vertical lineages. Taken together these studies provide overwhelming support for the punctuational model.

Many studies have shown that rapid speciation events occur frequently and some are punctuational. Jellyfishes that have appeared recently in saltwater lakes on the Pacific island of Palau are remarkable examples of punctuational speciation, and so is the sudden appearance of the novel sand dollar family Dendrasteridae in the California Miocene.

The punctuational model shows that the value of sexual reproduction must be in producing long-lived adaptive radiations, whereas clones die out quickly.

Our ability to measure evolution by natural selection in the fossil record is limited by the near impossibility of estimating the fecundity and thus relative fitness of most fossil organisms. Neocheilostome bryozoans are an important exception, because they have calcified larval brood chambers known as ovicells that provide an approximate estimate of the colony’s sexual fecundity. This clade has a rich fossil record dating back ~100 million years, providing potential opportunities to observe changes in relative fitness and natural selection through many past intervals of environmental change. However, neocheilostome fossil specimens are often highly fragmented, and fragments are not necessarily randomized subsets of a colony. To make use of the majority of the neocheilostome fossil record, we need to test the effect colony organization has on our methods of inferring colony fecundity from fragmented specimens.

In this study, we measure colony fecundity in a population of Recent neocheilostome bryozoan specimens of the species Parasmittina eccentrica Winston & Jackson, 2021 and quantify the nonrandom spatial arrangement of ovicells due to colony organization. We then simulate fragmenting these specimens and test the statistical robustness of standard methods one might use to reconstruct fecundity from fossil specimens. We find that ovicells are clustered and concentrated at mid-distances from the ancestrula (the oldest part of the colony). As a result, estimates of a colony’s fecundity from a single fragment have higher variance than would be expected if ovicells were randomly distributed. When estimating average population fecundity, observed variance among fossil fragments is a better estimator of sample variance than methods that assume spatial independence (such as a binomial distribution), especially for fragment sizes of 8 mm or less. While there is much to be learned about neocheilostome ovicell arrangement across taxa and environments, we can robustly estimate fecundity from small fossil fragments even in extinct neocheilostome species.

Mammalian species richness is commonly highest at mid- to high elevations, but the accumulation of sediment that might bury and preserve skeletal remains generally occurs at lower elevations, leading to concerns that fossil assemblages are biased toward low-elevation taxa. Here, I use extant mammals as an analogue to test the basin-scale spatial overlap between species ranges and sediment sinks where burial and fossilization would be possible. Sediment sinks are estimated within five topographically complex regions in western North America by identifying areas with both a low slope and a high contributing area of runoff and are compared with point occurrences of mammals compiled from the Global Biodiversity Information Facility (GBIF). I find that, among the test areas, 82–96% of all species have occurrences that overlap with a sediment sink, despite common offsets in the elevations of maximum sink area and maximum species richness: summed across all test areas, 83% of species and 87% of total sediment sink area are found in the lowest 1000 m of the test areas. Although many other factors can act against the fossilization of terrestrial mammals, these results indicate that the spatial distribution of mammal species with respect to sediment sinks should not in itself impose a major bias at the basin scale.

In The Structure of Evolutionary Theory, Stephen Jay Gould observed that the theory of punctuated equilibria formed “the coordinating centerpiece” of his work in evolutionary biology. It occupied this position because it bridged several themes in Gould’s thought, including the necessity of understanding evolution in a hierarchical context and a critique of the adaptationist program in evolutionary biology. Yet this assessment concealed a historical puzzle. The puzzle arose from the fact that the Gould of “Eldredge and Gould (1972)” held several commitments that the older Gould did not. These included a preference for adaptationist explanations and, perhaps more surprising, a commitment to the central importance of “biological improvement” in the history of life. So, how did punctuated equilibria come to play a coordinating role within a view of evolution that differed starkly from the one Gould held in 1972? And why did it only begin to play this role after 1977? This article answers these questions, focusing on the aims of Gould’s early research program and its transformation in response to external stimuli. In so doing, it illuminates an important and frequently misunderstood episode in the history of paleobiology.

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.

The evolution of the mandible in mammalian carnivores is influenced by ecological demands that have changed over their phylogenetic history. We combined geometric morphometrics and biomechanical analysis (including beam analysis and finite element analysis, or FEA) to assess the interaction between form and function as the mandible has adapted independently to carnivorous diets in therian clades including Metatheria, Mesonychia, “Creodonta,” and Carnivoramorpha. Our goal was to determine the relative contributions of mechanical advantage, mandibular force, and mandibular resistance to bending and torsion, to the evolution of mandibular shape in these groups, as well as whether they produce differential rates of shape evolution in the horizontal and ascending rami, which respectively are the tooth-bearing and muscle-loading parts of the structure.

We found that the ascending ramus has higher rates of evolution than the horizontal ramus, making it the more rapidly evolvable portion of the mandible. Statistical evaluation supports this interpretation, as mechanical advantage and resistance to force explain more of the variance in shape than do the beam mechanic estimates that are heavily influenced by the mandibular body. Regression analysis shows that the evolution of specialized carnivory was associated with stronger mandibles in which mandibular shape changed by shortening and thickening of the mandible, increasing the areas of muscle attachment, and increasing the carnassial blade length. Principal component analysis of mandibular shape shows that different clades in Theria have been able to fill out similar specialized carnivorous niches with similar functional metrics despite having different mandibular morphologies.

Morphological characters are central to phylogenetic inference, especially for fossil taxa for which genomic data are unavailable. While Bayesian methods have gained popularity in recent years, they typically assume characters evolve independently, despite known correlations among characters. Here, we assess the impact of character correlation and evolutionary rate heterogeneity on Bayesian phylogenetic inference using extensive simulations of binary characters evolving under independent and correlated models. We find that Bayesian inference assuming character independence accurately recovers tree topologies even when characters are strongly correlated or evolve under heterogeneous rates. However, branch lengths or clock rates tend to be underestimated, particularly under extreme rate heterogeneity. These biases are partially corrected using models that integrate over character-state heterogeneity. Our results demonstrate that Bayesian methods are robust to violations of character independence in topological inference, supporting their continued use in morphological phylogenetics.

Linear state space models provide a useful framework for investigating phenotypic evolution in fossil lineages for a wide variety of models representing Brownian motion, Ornstein-Uhlenbeck processes, and the potential influence of environmental covariates. A state space framework also provides access to residuals for the predicted and observed values at each time point as well as improved numerical stability. We illustrate the value of the state space approach by reanalyzing a classic dataset of trait evolution in the diatom lineage Stephanodiscus yellowstonensis. A series of increasingly complex models were fit to these data, including a novel modification of an Ornstein-Uhlenbeck model in which a trait tracks an exogenous covariate. These model results suggest that the number of spines on the periphery of the diatom is best explained by adaptation to changing solar insolation over time.

While punctuated equilibrium is foundational to modern paleobiology, the degree to which paleontologists and evolutionary biologists understand its claims and implications is not clear. Many critiques of punctuated equilibrium are based on misinterpretations of the model, and these misconceptions are likely to be common in classrooms. To begin to understand how the paleontological and evolutionary biology communities, including students, educators, researchers, and museum staff, perceive punctuated equilibrium, we distributed a preliminary exploratory survey to assess how respondents use punctuated equilibrium in their research and teaching and how well they comprehend its core ideas. This pilot study was undertaken to identify possible areas for future research, as well as to assess initial patterns in the data that might indicate the need for a more rigorous follow-up investigation, for example, with a formal validated survey instrument. Among this exploratory sample of 122 respondents, a strong consensus emerged that punctuated equilibrium is important to both paleontology and evolutionary biology and should be included in textbooks. However, while punctuated equilibrium is taught in both introductory and upper-level courses, most instructors in the sample spend 1 week or less on the topic. Survey items designed to explore respondents’ understanding of core ideas within punctuated equilibrium revealed internally inconsistent responses, with a notable lack of consensus on many items. Response data suggest that both empirical (e.g., anagenesis is a common phenomenon) and conceptual (e.g., punctuated equilibrium states that morphological change occurs within just a few generations during speciation) misconceptions may be common. These potential misconceptions are held by the surveyed paleontologists and evolutionary biologists alike, in all career stages. Despite 50 years of discussion, our survey results suggest the lack of a shared understanding of punctuated equilibrium within this scientific community. We therefore provide some initial guidance and concrete strategies to improve teaching and learning about punctuated equilibrium and propose areas for further investigation.

Paleontology provides insights into the history of the planet, from the origins of life billions of years ago to the biotic changes of the Recent. The scope of paleontological research is as vast as it is varied, and the field is constantly evolving. In an effort to identify “Big Questions” in paleontology, experts from around the world came together to build a list of priority questions the field can address in the years ahead. The 89 questions presented herein (grouped within 11 themes) represent contributions from nearly 200 international scientists. These questions touch on common themes including biodiversity drivers and patterns, integrating data types across spatiotemporal scales, applying paleontological data to contemporary biodiversity and climate issues, and effectively utilizing innovative methods and technology for new paleontological insights. In addition to these theoretical questions, discussions touch upon structural concerns within the field, advocating for an increased valuation of specimen-based research, protection of natural heritage sites, and the importance of collections infrastructure, along with a stronger emphasis on human diversity, equity, and inclusion. These questions offer a starting point—an initial nucleus of consensus that paleontologists can expand on—for engaging in discussions, securing funding, advocating for museums, and fostering continued growth in shared research directions.

Fossil data are subject to inherent biological, geologic, and anthropogenic filters that can distort our interpretations of ancient life and environments. The inevitable presence of incomplete fossils thus requires a holistic assessment of how to navigate the downstream effects of bias on our ability to accurately reconstruct aspects of biology in deep time. In particular, we must assess how biases affect our capacity to infer evolutionary relationships, which are essential to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. In this study, we use an established completeness metric to quantify the effects of taphonomic filters on the amount of phylogenetic information available in the fossil record of 795 extinct squamate (e.g., lizards, snakes, amphisbaenians, and mosasaurs) species spanning 242 Myr of geologic time. This study found no meaningful relationship between spatiotemporal sampling intensity and fossil record completeness. Instead, major differences in squamate fossil record completeness stem from a combination of anatomy/body size and affinities of different squamate groups to specific lithologies and depositional environments. These results reveal that naturally occurring processes create structural megabiases that filter anatomical and phylogenetic data in the squamate fossil record, while anthropogenic processes play a secondary role.

The first geographically widespread metazoans form the Avalon assemblage (Ediacaran; 574–560 Ma). These early animals were regularly disturbed by sedimentation events such as ash flows and turbidites, leading to an apparent “resetting” of communities. However, it is not clear how biological legacies—remains or survivors of disturbance events—influenced community ecology in the Avalon. Here, we use spatial point process analysis on 19 Avalon paleocommunities to test whether two forms of biological legacy (fragmentary remains of Fractofusus and survivor fronds) impacted the recolonization dynamics of Avalon paleocommunities. We found that densities of Fractofusus were increased around the Fractofusus fragments, suggesting that they helped to recolonize the post-disturbance substrate, potentially contributing to the Fractofusus dominance found in 8 of the 19 paleocommunities. However, we found no such effects for survivor fronds. Our results suggest that the evolution of height was for long-distance dispersal rather than local recolonization. In modern deep-sea environments, there is a trade-off between local and long-distance dispersal, and our work demonstrates that this differentiation of reproductive strategies had already developed in the early animals of the Avalon.

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.

In whales, extreme modifications to the ancestral mammalian feeding apparatus facilitate novel modes of aquatic feeding. These modifications manifest in morphological diversity across a suite of characters, including the mandibular symphysis. Cetaceans span a range of symphyseal morphologies, with one lineage (crown mysticetes) evolving a highly mobile condition unique among mammals. Here, we use phylogenetic comparative methods to examine the evolution of symphyseal fusion and elongation across 206 extant and fossil cetacean taxa. Ancestral state reconstructions corroborate observations from the fossil record that suggest the ancestral condition for Cetacea was a fused, moderately elongated symphysis. Shifts in symphyseal morphology coincided with ocean restructuring and diversification of feeding modes. Evolutionary rates peaked in the middle–late Eocene and at the Eocene/Oligocene boundary as whales evolved shorter, unfused symphyses. During the Eocene, ankylosed mandibles became less common with the appearance of increasingly pelagic whales. Mysticetes evolved decoupled, highly mobile mandibles near the Eocene/Oligocene boundary. Several odontocete lineages underwent a trait reversal and converged on fully fused, elongated mandibles in the Miocene. Analyses evaluating the influence of ecological variables indicate strong correlations in feeding strategy, dentition, and prey type. The loss of prey-processing behavior and changes to masticatory loading regimes may explain concurrent trends in symphyseal morphology and tooth simplification. We suggest that the functional and morphological diversity of the symphysis in whales is a consequence of aquatic feeding imposing different mechanical constraints than those associated with feeding on land.

The present-day climate crisis is transforming coral reef communities, potentially undermining ecosystem functioning. Evolutionary trade-offs between species traits result in diverse life-history strategies, enabling corals to survive disturbance events through specific adaptive mechanisms. Trait–trait relationship networks offer insights into trait turnover and changing life-history strategies during environmental changes. Paleoecological insights from the fossil records can further illustrate how species adapt to environmental shifts, highlighting resilience traits.

We highlight coral traits that promote resilience in the Caribbean based on fossil occurrences and morphological traits, examining biological determinants of species and trait turnover across the Cenozoic. We use traits that underpin the survival of corals during disturbances, for example, corallite diameter, colony growth form, corallite integration, and budding type. We analyzed species turnover and extinctions with a bipartite network and explored trait turnover with trait–trait co-occurrence networks based on 4268 species records at 421 sites over ~40 Myr.

Our findings support existing evidence that species turnover coincided with major environmental and biogeographic changes across the Cenozoic. Additionally, our results provide new insight into functional changes throughout the Cenozoic. Past cooler climates favored corals with a fast growing and reproducing (competitive) life-history strategy, which boosts short-term success, but also increases susceptibility to diseases and thermal stress. Cenozoic species and trait turnover occurred during environmental change, corroborating expectations of such turnover in the future. We found trait co-occurrence modules associated with competitive and stress-tolerant life-history strategies. The transition from the “greenhouse” (Paleogene) to the “icehouse” (Neogene) climate over ~40 Myr favored competitive traits, which supported fast-growing, shallow reefs. With rising temperatures and declining Acropora in the Caribbean, future reefs may resemble Eocene reefs: dominated by stress-tolerant, slow-growing corals adapted to marginal environments.

Paleo-ecological niche modeling (paleoENM) estimates the niches and distributions of extinct species using fossil paleo-coordinates and local environmental data. While general circulation models (GCMs) have been used to estimate climate conditions in deep time, primarily for terrestrial vertebrates, variations in paleo-elevation models used in GCM construction can influence paleoENM outcomes. This study (1) examines the impact of the Cretaceous–Paleogene (K-Pg) mass extinction on the niche dimensions of the marine invertebrate group Turritellinae (Cerithoidea: Turritellidae) and (2) compares two paleo-elevation models’ effects on GCM-based species’ distribution predictions. Fossil occurrence data from the Maastrichtian and Danian periods were collected from the Paleobiology Database (PBDB), museum collections, and published literature. Environmental data were extracted from HadCM3L GCM simulations using Scotese- and Getech-based paleogeographic and pCO2 boundary conditions. We estimated the niche dimensions of turritellines using maximum entropy (MaxEnt) and performed ordination analysis using kernel density estimation. MaxEnt model metrics showed that the Getech-based GCM outperformed the Scotese-based GCM. Geographic projections revealed minor differences in suitable habitat between the Maastrichtian and Danian in the Getech-based GCM, but overinflated predictions in the Scotese-based GCM. Niche overlap between the Maastrichtian and Danian was high, with both GCMs supporting niche similarity and equivalency. Our results suggest that differences in elevation model boundary conditions affected predicted distribution and niche patterns. This study offers a novel approach to understanding ecological persistence in invertebrates after mass extinction events, examines the robustness of GCM boundary conditions in paleoENM studies, and provides a framework for future paleoecological research on fossil invertebrates.

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.

Species recognition is an essential part of biological and paleontological study. In gastropods, although species are genetic entities, shell morphology continues to be used as the primary source of information to recognize most species. While there are few directly tested cases, variations in conchological characters for modern species are expected to reflect underlying genetic differences that define a biological species, an assumption that is also applied to identify species in the fossil record. Additionally, how consistently shell shape differentiates gastropod species remains poorly understood. In this study, shell shape of Recent and Pliocene–Pleistocene fossil specimens of well-known intertidal gastropods (Littorinidae, periwinkles: †Littorina petricola, Littorina keenae, and the sister-species pair Littorina plena and Littorina scutulata) from the east Pacific was analyzed using landmark-based morphometrics and compared with published molecular data. For the extant species, there is a general positive relationship between shell shape and genetic differences. Discriminant function analyses indicate distantly related species can be more reliably recognized from their shells, while closely related species have a higher error. Fossils and recent specimens were classified with similar consistency. More work is needed to illuminate whether this case applies more widely.