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

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

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.

Most species exhibit morphological stasis following speciation, and this is a key feature of the concept of punctuated equilibria. Stasis results in species often having long durations on geological timescales. Durational data are fundamental to many types of paleobiological analyses and are ideally based on occurrence data represented by specimens in museum collections. Often, however, durational data are presented without supporting information about voucher specimens that document stratigraphic ranges, including first and last appearances. We use the iconic Devonian trilobite Eldredgeops rana to demonstrate that durational data can be challenging to determine at multiple taxonomic levels. Further, we show that different datasets—including Sepkoski’s published databases, the Paleobiology Database, and iDigBio—give discordant results concerning first and last occurrences. We argue that paleontologists should adopt two general best practices to help address these problems. First, systematists should clearly identify voucher specimens that represent stratigraphic occurrences of species. Second, we recommend that high-quality photographs of occurrence vouchers be placed in open access websites and be assigned public domain licensing before being paywalled by journals. Such voucher images also have a role to play in training artificial intelligence (AI) systems that will be applied to future paleobiological questions.

The Pleistocene/Holocene transition furnishes a classic example of apparent evolutionary stasis during a period of major environmental change, where observed environmental clines might predict evolutionary change. We have previously attempted to assess whether or not body size and shape were static in the extensive Quaternary vertebrate fauna of Rancho La Brea (RLB). However, the validity of time-series studies depends on dating, and there are indications that previous approaches based on pit mean radiocarbon ages may be misleading. Here we have compiled and recalibrated all available RLB radiocarbon ages, reanalyzed our morphometric data using a novel method for bootstrap resampling of calibrated C age distributions to estimate a time series of populations, and fit the time series with a range of simple evolutionary time-series models.

Although the shortness of our time series tends to favor nondirectional models and is insufficient to allow reliable discrimination between punctuated and gradual change, the results can still be clearly interpreted. The population means for most anatomical elements in most species at RLB do genuinely appear to be static through the Pleistocene/Holocene transition, as previously published. Some species exhibit previously undetected changes in population mean size and shape, including Smilodon, Gymnogyps, and Equus. However, the timing of change is variable among the non-static species and generally does not correspond to changes in temperature, and thus resists a Bergmann’s rule interpretation. Considering the species by ecological category may reveal more about the effects of climate regime shifts.

Ichthyosauria, Plesiosauria, and Metriorhynchidae were apex predators in Mesozoic oceanic trophic networks. Previous stable oxygen isotope studies suggested that several taxa belonging to these groups were endothermic and that some of them were homeothermic organisms. However, these conclusions remain contentious owing to the associated uncertainties regarding the δ18O value and oxygen isotope fractionation relative to environmental seawater. Here, we present new bioapatite phosphate δ18O values (δ18Op) of Ichthyosauria, Plesiosauria, and Metriorhynchidae (Middle Jurassic to Early Cretaceous) recovered from mid- to high paleolatitudes to better constrain their thermophysiology and investigate the presence of regional heterothermies. The intraskeletal δ18Op variability failed to reveal distinct heterothermic patterns within any of the specimens, indicating either intrabody temperature homogeneity or an overriding diagenetic overprint of the original biological δ18Op bone record. Body temperature estimates have been reassessed from new and published δ18Op values of well-preserved isolated teeth, recently revised Mesozoic latitudinal δ18O oceanic gradients, and 18O-enrichment factors of fully aquatic air-breathing vertebrates. Our results confirm that Ichthyosauria were homeothermic endotherms (31°C to 41°C), while Plesiosauria were likely poikilothermic endotherms (27°C to 34°C). The new body temperature estimates of the Metriorhynchidae (25°C to 32°C) closely follow ambient temperatures and point to poikilothermic strategy with no or little endothermic ability. These results improve our understanding of Mesozoic marine reptile thermoregulation and indicate that due to their limited body temperature variations, the δ18Op values from Ichthyosauria fossil remains could be used as valuable archives of Mesozoic oceans δ18Osw values that may help improve paleoenvironmental and paleoclimatic reconstructions.

The Neotropics host the highest diversity of plants on the Earth today and have done since at least the late Paleogene (~58 Ma). Several mechanisms have been proposed to explain this elevated diversity, but the empirical patterns of Neotropical plant diversification that would test key aspects of those mechanisms are still unclear. We use an extensive palynological database from northern South America to characterize patterns of extinction, origination, and diversity and their possible drivers since the Paleogene. The foreland Llanos basin of Colombia preserves the evolutionary history of Neotropical vegetation as well as the geological evolution of northern South America, offering a unique opportunity to study the relationship between the geological and fossil records. The palynological record of the Llanos basin has been intensely studied mainly for oil exploration, and we use this information to infer the evolutionary history of Neotropical vegetation in Colombia during the Cenozoic. There is no straightforward relationship between global temperature and Neotropical plant diversity. Nevertheless, environmental change had an important influence on the dynamics of diversification, especially during volatile climate intervals such as the Paleocene–Eocene and the Pleistocene. Pulses of regional extinction were driven by large-scale temperature excursions, including both warming and cooling phases. Time-lagged origination pulses results in rapid floral replacement on a timescale of 1 Myr. Origination and extinction are essentially balanced on long timescales, leading to a near-zero long-term net diversification rate. Regional geological events, like the uplift of the Andean Cordillera, and changes in paleogeography also played an important role in Neotropical plant diversification.

The first compilations of Proterozoic eukaryote diversity, published in the 1980s showed a dramatic peak in the Tonian Period (1000–720 Ma), interpreted as the initial radiation of eukaryotes in the marine realm. Over the decades, new discoveries filled in the older part of the record and the peak diminished, but the idea of a Tonian radiation of eukaryotes has remained strong, and is now widely accepted as fact. We present a new diversity compilation based on 181 species and 713 species occurrences from 145 formations ranging in age from 1890 Ma to 720 Ma and find a significant increase in diversity in the Tonian. However, we also find that the number of eukaryotic species through time is highly correlated with the number of formations in our dataset (i.e. eukaryote-bearing formations) through time. This correlation is robust to interpretations of eukaryote affinity, bin size, and bin boundaries. We also find that within-assemblage diversity—a measure thought to circumvent sampling bias—is related to the number of eukaryote-bearing formations through time. Biomarkers show a similar pattern to body fossils, where the rise of eukaryotic biosignatures correlates with increased sampling. We find no evidence that the proportion of eukaryote-bearing versus all fossiliferous formations changed through the Proterozoic, as might be expected if the correlation reflected an increase in eukaryote diversity driving an increase in the number of eukaryote-bearing formations. Although the correlation could reflect a common cause such as changes in sea level driving both diversification and an increase in sedimentary rock volume, we favor the explanation that the pattern of early eukaryote diversity is driven by variations in paleontological sampling.

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 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.

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

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

Every organism interacts with a host of other organisms of the same and different species throughout its life. These biotic interactions have varying influences on the reproduction and dispersal of the organism, and hence also the population and species lineage to which the organism belongs. By extension, biotic interactions must contribute to the macroevolutionary patterns that we observe in the fossil record, but exactly how, when, and why are research questions we have been asking before the start of the journal Paleobiology. In this contribution for Paleobiology’s 50th anniversary, we present a brief overview of how paleobiologists have studied biotic interactions and their macroevolutionary consequences, recognizing paleontology’s unique position to contribute data and insights to the topic of interspecies interactions. We then explore, in a semi-free-form manner, what promising avenues might be open to those of us who use the fossil record to understand biotic interactions. In general, we emphasize the need for increased effort surrounding the understanding of ecological details, integration of different types of information, and model-based approaches.

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.

Despite advances in understanding planktonic foraminifera environmental interactions, their role as prey remains elusive, often inferred from indirect evidence such as drill holes. Bioerosional traces offer valuable insights into fossil assemblages, although knowledge for planktonic foraminifera remains limited compared with benthic species. This study addresses this gap by analyzing bioerosional site selectivity in late Quaternary planktonic foraminifera from the western South Atlantic. We examined 2588 specimens from eight species to map trace patterns using kernel density estimation, sector-based, and hotspot mapping approaches. Drilling traces were located, transposed to graphical representations, and transformed into x,y coordinates. We analyzed specimen frequency per trace quantity and trace frequency, sectoring them per chamber and test regions. Correspondence analysis and exact test of goodness of fit assessed groupings among the species and preferential regions. Frequencies revealed that spinose species had more multiple-drilled specimens than non-spinose ones. Bioerosional traces were prevalent in the final whorl, decreasing toward earlier chambers. However, when normalized by surface area, the penultimate whorl had higher trace frequencies, particularly for spinose species, while the ultimate whorl had higher trace density for some non-spinose ones. Spinose species are preferentially drilled in the early chambers, likely due to their thinner walls. Thus, bioeroders prioritize regions with a higher cost–benefit ratio, which is evident in the prevalence of successful–failed traces in early chambers of spinose species, but not in thicker-walled, non-spinose ones. Our study reveals distinct bioerosion patterns, highlighting strategic site selectivity and suggesting that morphological differences between spinose and non-spinose species contribute to varying vulnerability to bioerosion.

Variation in observed global generic richness over the Phanerozoic must be partly explained by changes in the numbers of fossils and their geographic spread over time. The influence of sampling intensity (i.e., the number of samples) has been well addressed, but the extent to which the geographic distribution of samples might influence recovered biodiversity is comparatively unknown. To investigate this question, we create models of genus richness through time by resampling the same occurrence dataset of modern global biodiversity using spatially explicit sampling intensities defined by the paleo-coordinates of fossil occurrences from successive time intervals. Our steady-state null model explains about half of observed change in uncorrected fossil diversity and a quarter of variation in sampling-standardized diversity estimates. The inclusion in linear models of two additional explanatory variables associated with the spatial array of fossil data (absolute latitudinal range of occurrences, percentage of occurrences from shallow environments) and a Cenozoic step increases the accuracy of steady-state models, accounting for 67% of variation in sampling-standardized estimates and more than one-third of the variation in first differences. Our results make clear that the spatial distribution of samples is at least as important as numerical sampling intensity in determining the trajectory of recovered fossil biodiversity through time and caution against the overinterpretation of both the variation and the trend that emerge from analyses of global Phanerozoic diversity.

Planktonic foraminifera are extremely well suited to studying evolutionary change in the fossil record due to their abundant deposits and global distribution. Species are typically conservative in their shell morphology, with the same geometric shapes appearing repeatedly through iterative evolution, but the mechanisms behind the architectural limits on foraminiferal shell shape are still not well understood. To determine how these developmental constraints arise, we study morphological change leading up to the origination of the unusually ornate species Globigerinoidesella fistulosa. We measured the size and circularity of more than 900 specimens of G. fistulosa, its ancestor the Trilobatus sacculifer plexus, and intermediate forms from a site in the western equatorial Pacific. Our results show that the origination of G. fistulosa from the T. sacculifer plexus involved a combination of two heterochronic expressions: earlier onset of protuberances (pre-displacement) and a steeper allometric slope (acceleration) as compared with its ancestor. Our work provides a case study of the complex morphological and developmental changes required to produce unusual shell shapes and highlights the importance of developmental deviations in evolutionary origination.