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.

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.

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.

Polymorphism, the occurrence of different morphs of a trait within the population of a single species, plays a crucial role in species diversification, genetic variation, and adaptation. Detecting polymorphism in a single character helps us to understand population dynamics, particularly in species that inhabit diverse environments. However, detecting polymorphisms in fossil taxa is challenging due to the fragmentary and incomplete records. Dimorphism, defined as the occurrence of different morphs of a trait within the population of a single species, represents the simplest and most common form of polymorphism. This study focuses on dimorphism instead of polymorphism, which allows for a more streamlined analysis. We use computational simulation experiments to estimate the minimum sample size required to detect bimodal distribution in univariate morphological variables. We describe the morphological diversity of a measured variable (e.g., body mass or skeletal length) as a probability density distribution with specific parameter sets. Subsequently, we simulate the diversity of the measured variable with varying sample sizes and conduct resampling procedures to ensure the robustness. Four key parameters that characterize the probability distribution are identified as having significant influence on the minimum sample size for dimorphism recognition. According to the simulation experiments, a model is built to estimate the minimum sample size for dimorphism recognition based on these parameters. A dataset from extant avian and reptilian species is used to test the model. Furthermore, we calculate a reference for the minimal sample size required for assessing phenotypic dimorphism in fossil avian taxa by applying parameters derived from extant avian species.

Punctuated equilibria (PE) was presented 50 years ago as an alternative to the widespread assumption that most evolution proceeds by gradual phyletic change within lineages. Unfortunately, PE has been widely misunderstood, misrepresented, and unfairly dismissed since this first publication. We argue that much of this misunderstanding centers around a misinterpretation of the meaning of “mode” in evolution, and its significance, properly understood, for how we understand macroevolutionary processes. PE proposed that most morphospecies do not show significant anagenetic trends through their stratigraphic ranges, and that most new morphospecies that are recognized arise via cladogenesis. To the degree that this is true, most exploration of disparity space must be associated with cladogenesis.

We surveyed a sample of the recent paleontological literature to assess the frequency with which new morphospecies appear in the fossil record via anagenesis versus cladogenesis using a persistence of ancestor criterion and found the overwhelmingly dominant mode of species origin to be cladogenesis. This is a valuable but underutilized approach to this problem, which could be exploited with more studies of species-level phylogenies of fossil taxa. Combined with the conclusions of other studies that stasis or nondirectional change is common, this finding of the dominance of cladogenesis affirms that PE is very much alive and of substantial significance for understanding macroevolutionary patterns.

Multituberculate extinction is often cited as a classic case of competitive exclusion, coinciding with the first rodent arrivals in the late Paleocene. Analyzing 124 North American multituberculate last occurrence records during the Eocene from 56 to 34 million years ago, this study aimed to differentiate Eocene multituberculate and coeval rodent floral associations through geographic spatial analysis to understand niche overlap between the two groups. If competitive exclusion with rodents was a factor in multituberculate extinction, both multituberculates and rodents would be predicted to share similar forest habitat preferences and have competed for similar ecological niches regarding their forest associations. Using spatial analysis, this study found that Eocene rodents and multituberculates did not overlap in their forest associations. The findings indicate that multituberculates were unique in inhabiting a specific type of ancient forest habitat, favoring forests composed of Metasequoia, Glyptostrobus, and Alnus, and thus thrived in wetter northern temperate forest communities during the Eocene. Metasequoia and Glyptostrobus declined significantly in North America during the later Cenozoic, coinciding with multituberculate decline and extinction as the global climate shifted toward colder and drier climates around the Eocene/Oligocene boundary. In contrast, the success of rodents is attributed to their much broader forest affinity. These preferences align with the widespread distribution of rodents today, contributing to their modern success. The absence of any similar reconstructed forest habitat preferences between rodents and multituberculates suggests that changing forest structure, rather than competitive exclusion, drove multituberculate extinction.

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.

Over the interval 2008–2023 a large number of studies have been published testing various aspects of punctuated equilibria, including the prevalence of stasis, and also the extent to which most evolutionary change is concentrated at cladogenesis. In the vast majority of studies, punctuated equilibria continued to be strongly validated, as widespread evidence for stasis accumulated, with only some rare incidences of gradual change found. Support for the importance of cladogenetic change has increased, and new analytical approaches to study punctuated equilibria have been developed. Over this time period, there has also been an increase in the number of studies that have concentrated on extant taxa to test for punctuated equilibria, and these have also corroborated its widespread presence. In this respect, punctuated equilibria has served as an important bridge between neontological and paleontological approaches to evolutionary biology. From 2008 to 2023, there has also been some drift in how stasis is defined, such that, in certain studies, the definition diverged from the original 1972 definition in important respects. Notably, it is the few studies that have most changed the definition of what stasis constitutes that have most challenged the validity of punctuated equilibria, indicating it is morphing interpretations and definitions rather than the discovery of data compatible with phyletic gradualism that are most responsible for divergent results.