Paleobiology was founded 50 years ago to provide an outlet for biological paleontology, with an emphasis on investigating evolutionary patterns and processes that could apply generally across the history of life. While the intellectual and financial prospects for Paleobiology were uncertain in the beginning (Sepkoski 2012; Valentine 2009), this 50th anniversary issue testifies to its overwhelming success. Fifty years of anything well done deserves a celebration. These moments are a time for reflection and a time for imagining future directions. With this introduction, we outline briefly the start of the journal and two landmark anniversary issues, the 10th and the 25th. No special issue can adequately survey all research themes in a field as intellectually rich as paleobiology. However, these anniversary issues offer a snapshot of research directions, and they can trace the shift and expansion of established fields and mark the emergence of new ones. We end by outlining the contributions to the 50th anniversary issue that summarize current themes and future directions for the field.

Paleontologists Niles Eldredge and Stephen Jay Gould introduced punctuated equilibria (PE) to the scientific community in 1972 (Eldredge and Gould 1972). Since then, the concept has been debated and tested, misunderstood and clarified, applied, extended, and integrated into evolutionary thought. To celebrate PE’s semicentennial, we and Paleobiology’s editors have produced this special issue. Our goal has been to bring together paleontologists, evolutionary biologists, and historians of science to reflect on the concept of PE, how it has been tested, the underlying mechanisms for stasis and punctuated change, and the broader impacts of PE for paleontology, biology, and macroevolution. In this introduction, we highlight the key components and implications of PE, briefly review the history surrounding its emergence and reception, and outline how PE expands evolutionary theory. We explain the organization of the papers included in this special issue, providing brief summaries to guide the interested reader. Finally, we conclude with a call for paleobiologists to “rediscover” PE and consider how the concept and its implications can be applied to their own work. In this endeavor, we are aware that a great many authors have contributed significant data, insight, and perspective to these issues over the years. As our purpose in this introduction is not to provide a comprehensive review, we do not cite and recognize them all individually, but we applaud all of those who have weighed in on this important topic.

Prospective and early-career paleontologists deserve an accurate assessment of employment opportunities in their chosen field of study. Drawing on a wide range of sources, we have produced an admittedly incomplete analysis of the current status and recent trends of permanent academic employment in the discipline. Obtaining more complete longitudinal data on employment trends is a major difficulty; this is a challenge that needs to be addressed. The number of job seekers is far in excess of available positions. There has been a clear erosion in the number of academic paleontologists in the United States, a trend exacerbated in recent years. The decline, in constant dollars, of federal funding for paleontological research has potential strong negative impacts on future hiring. The loss of paleontology positions has also had a deleterious effect on our professional societies, which have seen a loss of regular (professional) membership, although student membership remains strong. These trends also potentially negatively impact efforts to diversify the field. Professional societies need to better coordinate their efforts to address these serious issues. Individual paleontologists also must become more effective advocates for the importance and relevance of our science.

Fossil pollen analysis is an “open-world” problem in paleontology for which there is a long-standing need for automated identification and classification. In the open world, categorical classes are imbalanced, test classes are not known a priori, and test data are captured across different domains. Pollen samples capture large numbers of specimens that include both common and abundant types and rare and sometimes novel taxa. Pollen is diverse morphologically and features can be altered during fossilization. Additionally, there is little standardization in the imaging of pollen samples. Therefore, generalized workflows for automated pollen analysis require techniques that are robust to these differences and can work with microscope images. We focus on a critical first step, the initial detection of pollen specimens on a palynological slide and review how existing methods can be employed to build robust and generalizable analysis pipelines. First, we demonstrate how a mixture-of-experts approach—the fusion of a general pollen detector with an expert model trained on minority classes—can be used to address taxonomic biases in detections, particularly the missed detections of rarer pollen types. Second, we demonstrate the efficiency of domain fine-tuning in addressing domain gaps—differences in image magnification and resolution across microscopes and of taxa across different sample sources. Third, we demonstrate the importance of continual learning workflows, which integrate expert feedback, in training detection models from incomplete data. Finally, we demonstrate how cutting-edge segmentation models can be used to refine and clean detections for downstream deep learning classification models.

The spatial distribution of individuals within ecological assemblages and their associated traits and behaviors are key determinants of ecosystem structure and function. Consequently, determining the spatial distribution of species, and how distributions influence patterns of species richness across ecosystems today and in the past, helps us understand what factors act as fundamental controls on biodiversity. Here, we explore how ecological niche modeling has contributed to understanding the spatiotemporal distribution of past biodiversity and past ecological and evolutionary processes. We first perform a semiquantitative literature review to capture studies that applied ecological niche models (ENMs) to the past, identifying 668 studies. We coded each study according to focal taxonomic group, whether and how the study used fossil evidence, whether it relied on evidence or methods in addition to ENMs, spatial scale of the study, and temporal intervals included in the ENMs. We used trends in publication patterns across categories to anchor discussion of recent technical advances in niche modeling, focusing on paleobiogeographic ENM applications. We then explored contributions of ENMs to paleobiogeography, with a particular focus on examining patterns and associated drivers of range dynamics; phylogeography and within-lineage dynamics; macroevolutionary patterns and processes, including niche change, speciation, and extinction; drivers of community assembly; and conservation paleobiogeography. Overall, ENMs are powerful tools for elucidating paleobiogeographic patterns. ENMs are most commonly used to understand Quaternary dynamics, but an increasing number of studies use ENMs to gain important insight into both ecological and evolutionary processes in pre-Quaternary times. Deeper integration with traits and phylogenies may further extend those insights.

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.

It is a pleasure to be invited to contribute to the celebration of the publication of “punctuated equilibria” (“punk eek”) 50 years ago—the canonical version I did with Steve Gould (Eldredge and Gould 1972) at the behest of Tom Schopf for his visionary project to inject more thought, more interpretation and theory, into the working lives of paleontologists.

Life-history traits such as dispersal affect population attributes like gene flow, which can have consequences for speciation and extinction rates over macroevolutionary timescales. Here we use the Cheilostomatida, a monophyletic order of marine bryozoans, to test whether a life-history trait, larval brooding, affected the origination and extinction rates of genera throughout their fossil record. Cheilostome lineages that brood their larvae have shorter larval dispersal distances than non-brooding lineages, which has led to the hypothesis that the evolution of larval brooding decreased gene flow, increased origination, and drove their Cretaceous diversification. Brooding cheilostomes are far more diverse than non-brooding cheilostomes today, but it remains to be shown that brooding lineages have a higher origination rate than non-brooders. We fit time-varying Pradel seniority capture–mark–recapture models to look at the effect of brooding on origination and extinction rates during the Cretaceous cheilostome diversification, the Cretaceous/Paleogene mass extinction and recovery, and through the Cenozoic. Our results support the hypothesis that brooding affects origination rate, but only in the Cenomanian to Campanian. Extinction rates do not differ between brooding and non-brooding genera, and there is no regime shift specific to the Cretaceous/Paleogene mass extinction. Our work illustrates the importance of using fossil occurrences and time-varying models, which can detect interval-specific diversification differentials.

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.

Over the last 50 years, paleobiology has made great strides in illuminating organisms and ecosystems in deep time through study of the often-curious nature of the fossil record itself. Among fossil deposits, none are as enigmatic or as important to our understanding of the history of life as Konservat-Lagerstätten, deposits that preserve soft-bodied fossils and thereby retain disproportionately large amounts of paleobiological information. While Konservat-Lagerstätten are often viewed as curiosities of the fossil record, decades of study have led to a better understanding of the environments and circumstances of exceptional fossilization.Whereas most types of exceptional preservation require very specific sets of conditions, which are rare but can occur at any time, Seilacher noted the problem of “anactualistic” modes of exceptional preservation, defined as modes of fossilization that are restricted in time and that no longer occur. Here, we focus on anactualistic preservation and the widely recognized overrepresentation of Konservat-Lagerstätten in the Ediacaran and early Paleozoic. While exceptional fossil deposits of Ediacaran, Cambrian, and Early Ordovician age encompass a number of modes of fossilization, the signal of exceptional preservation is driven by only two modes, Ediacara-type and Burgess Shale–type preservation. Both are “extinct” modes of fossilization that are no longer present in marine environments. We consider the controls that promoted widespread anactualistic preservation in the Ediacaran and early Paleozoic and their implications for the environmental conditions in which complex life first proliferated in the oceans.

Body mass is an important facet of reconstructing the paleobiology of fossil species and has, historically, been estimated from individual skeletal measurements. This paper demonstrates the potential advantages of estimating body mass using 3D geometric morphometrics on limb bones, which allows size to be explicitly contextualized within the functional morphology of the animal. Geometric morphometrics of the humerus and femur is used to estimate body mass in domestic dogs and wild canids, and the resulting estimates are compared with estimates made using limb bone dimensions and centroid size. In both groups, 3D methods produced more accurate estimates of body mass than linear dimensions. Additionally, centroid size was a poor predictor of body mass and should not be preferred over linear measurements. The use of 3D methods also reveals specific aspects of shape that are associated with different sizes. In general, relatively heavier individuals were associated with more robust bones and wider articulation sites, as well as larger attachment sites for muscles related to flexion and extension of the shoulder and hip joints. The body-mass equations constructed based on dogs were further evaluated on wild canids, as a test of their potential efficacy on fossil canids. With some adjustments, the body-mass estimation equations made for domestic dogs were able to reliably predict the mass of wild canids. These equations were then used to estimate body mass for a selection of fossil canids: Canis latrans, 16 kg; Aenocyon dirus, 67 kg; Phlaocyon multicuspus, 8 kg; and Hesperocyon gregarius, 2.5 kg.

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.

The evolution of mammalian innovations like elevated growth rates, endothermy, and live birth has been the subject of paleobiological work for decades. Bone histology provides one of the best lines of evidence for assessing growth rates and life-history traits in the fossil record. However, little ontogenetic information is available for nonmammalian cynodonts, the stock lineage that eventually gave rise to mammals. Here, I report the bone histology of two traversodontid cynodonts from the Triassic Manda Formation of Tanzania. Using two femoral size series, I correlate bone tissue composition and limb size in Scalenodon angustifrons and Luangwa drysdalli. Fifteen individuals were analyzed from seven penecontemporaneous localities to assess intraspecific histovariation within traversodontid ontogenetic development for the first time. My results show that Scalenodon and Luangwa have disparate life histories despite being similarly sized contemporaries. Luangwa is characterized by parallel-fibered bone that transitions to woven-parallel bone early in ontogeny, interpreted as a growth spurt. This increase in growth rate is seen in small- and middle-sized individuals but is resorbed and remodeled in the largest, skeletally mature individual. By contrast, Scalenodon is characterized by woven-parallel tissue in early ontogeny. However, femur size is not correlated with changes in bone tissue composition, as multiple individuals show peripheral slower-growing tissue regardless of size, interpreted as highly developmentally plastic growth. Together, these results demonstrate that coeval members of Traversodontidae show disparate life histories. The underlying mechanisms to explain different life histories in these taxa are likely due to (1) intrinsic differences in growth rates and (2) varying degrees of developmentally flexible growth. The implication of this work is that intraspecific variation in growth dynamics may be more widespread than currently understood in cynodonts and that size is not a good indicator of maturity for some species.

Stratigraphic paleobiology uses a modern understanding of the construction of the stratigraphic record—from beds to depositional sequences to sedimentary basins—to interpret patterns and guide sampling strategies in the fossil record. Over the past 25 years, its principles have been established primarily through forward numerical modeling, originally in shallow-marine systems and more recently in nonmarine systems. Predictions of these models have been tested through outcrop-scale and basin-scale field studies, which have also revealed new insights. At multi-basin and global scales, understanding the joint development of the biotic and sedimentary records has come largely from macrostratigraphy, the analysis of gap-bound packages of sedimentary rock. Here, we present recent advances in six major areas of stratigraphic paleobiology, including critical tests in the Po Plain of Italy, mass extinctions and recoveries, contrasts of shallow-marine and nonmarine systems, the interrelationships of habitats and stratigraphic architecture, large-scale stratigraphic architecture, and the assembly of regional ecosystems. We highlight the potential for future research that applies stratigraphic paleobiological concepts to studies of climate change, geochemistry, phylogenetics, and the large-scale structure of the fossil record. We conclude with the need for more stratigraphic thinking in paleobiology.

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.

A central goal in ecology is investigating the impact of major perturbations, such as invasion, on the structure of biological communities. One promising line of inquiry is using co-occurrence analyses to examine how species’ traits mediate coexistence and how major ecological, climatic, and environmental disturbances can affect this relationship and underlying mechanisms. However, present communities are heavily influenced by anthropogenic behaviors and may exhibit greater or lesser resistance to invasion than communities that existed before human arrival. Therefore, to disentangle the impact of individual disturbances on mammalian communities, it is important to examine community dynamics before humans. Here, we use the North American fossil record to evaluate the co-occurrence structure of mammals across the Great American Biotic Interchange. We compiled 126 paleocommunities from the late Pliocene (4–2.5 Ma) and early Pleistocene (2.5–1 Ma). Genus-level co-occurrence was calculated to identify significantly aggregated (co-occur more than expected) and segregated (co-occur less than expected) genus pairs. A functional diversity analysis was used to calculate functional distance between genus pairs to evaluate the relationship between pair association strength and functional role. We found that the strength distribution of aggregating and segregating genus pairs does not significantly change from the late Pliocene to the early Pleistocene, even with different mammals forming the pairs, including immigrant mammals from South America. However, we did find that significant pairs, both aggregations and segregations, became more similar in their functional roles following the Plio-Pleistocene transition. Due to different mammals and ecological roles forming significant associations and the stability of co-occurrence structure across this interval, our study suggests that mammals have fundamental ways of assembling that may have been altered by humans in the present.

The fitness of groups is often considered to be the average fitness among constituent members. This assumption has been useful for developing models of multilevel selection, but its uncritical adoption has held back our understanding of how multilevel selection actually works in nature. If group fitness is only equal to mean member fitness, then it is a simple task to erode the importance of group-level selection in all multilevel scenarios—species selection could then be reduced to organismal selection as easily as group selection can. Because selection from different levels can act on a single trait, body size, for example, there must be a way to translate one level of fitness to another. This allows the calculation of the contributions of selection at each level. If high-level fitness is not a simple function of member fitness, then how do they interlace? Here we reintroduce Leigh Van Valen’s argument for the inclusion of expansion as a component of fitness. We show that expansion is an integral part of fitness even if one does not subscribe to the energetic view of fitness from which Van Valen originally derived it. From a hierarchical perspective, expansion is the projection of demographic fitness from one level to the next level up; differential births and deaths at one level produce differential expansion one level above. Including expansion in our conceptual tool kit helps allay concerns about our ability to identify the level of selection using a number of methods as well as allowing for the various forms of multilevel selection to be seen as manifestations of the same basic process.

Organismal metabolic rate is linked to environmental temperature and oxygen consumption, and as such, may be a useful predictor of extinction risk. This is especially true during major climate-driven extinctions, given the tightly linked stressors of warming and hypoxia. However, metabolic attributes can be quantified in different ways, highlighting differing aspects of organisms’ ecology. Here, we estimate resting whole-body and mass-specific metabolic rates in post-Carboniferous bivalve taxa using body size, seawater paleotemperature, and a taxon-specific adjustment factor to assess how metabolic rate correlates with survival both during and outside intervals of rapid climate warming, or “hyperthermals.” Accounting for the effects of geographic range size, we find a pattern of preferential extinction of bivalves with lower total calorific needs, consistent with increasing body size and the postulated ramping up of ecosystem energetics over the Meso-Cenozoic. Contrary to expectations, extinction selectivity based on total calorific needs, which emphasizes body size, does not differ between hyperthermals and other time intervals. However, a higher metabolic rate per gram of tissue—which is more strongly determined by environmental temperature than by body size—consistently increases the probability of extinction during hyperthermals relative to baseline conditions, particularly within the paleotropics. This serves to highlight the potential significance of environmental temperature on metabolic performance, particularly in organisms that are already living close to their thermal limits. In tandem with previously documented patterns of extinction selectivity based on relative activity levels, including motility and feeding style, these results enhance our understanding of the role of metabolic rate through time and during climate-driven extinctions. When standardized by mass, metabolic rate may represent a useful metric through which to predict the effects of anthropogenic climate change on modern marine faunas.

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.