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.

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.

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.

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

Analysis of length-frequency data using the ELEFAN (Electronic Length-Frequency Analysis) approach and software is widely used to quantify the growth, mortality, longevity, and related parameters of Recent marine animals. Here we analyze a sample (n = 211) of the Ediacaran metazoan Parvancorina minchami Glaessner, 1958, from the Vendian siliciclastic marine deposits of the southeastern White Sea region, Russia. The results fit a von Bertalanffy equation with the parameters L∞ = 2 cm, K = yr−1 (with t0 not estimated) and an instantaneous rate of mortality (M) of 1.44 yr−1, implying M/K ≈ 2, as commonly occurs in Recent small invertebrates. These parameter values also imply a longevity for P. minchami of about 4 yr. The concepts and approach used here, previously applied to an Ordovician trilobite and a Cambrian radiodont, suggest that inferences on growth, mortality, longevity, and related parameters can be obtained from suitable size-frequency samples of long-extinct metazoans, opening new vistas on their growth dynamics and functional roles in ancient ecosystems.

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.

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

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.

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.

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.

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.

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.

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

Mass extinctions are natural experiments on the short- and long-term consequences of pushing biotas past breaking points, often with lasting effects on the structure and function of biodiversity. General properties of mass extinctions—exceptionally severe, taxonomically broad, global losses of taxa—are starting to come into focus through comparisons among dimensions of biodiversity, including morphological, functional, and phylogenetic diversity. Notably, functional diversity tends to persist despite severe losses of taxonomic diversity, whereas taxic and morphological losses may or may not be coupled. One of the biggest challenges in synthesizing and extracting general consequences of these events has been that they are often driven by multiple, interacting pressures, and the taxa and their traits vary among events, making it difficult to link single stressors to specific traits. Ongoing improvements in the taxonomic and stratigraphic resolution of these events for multiple clades will sharpen tests for selectivity and help to isolate hitchhiking effects, whereby organismal traits are carried by differential survival or extinction of taxa owing to other organismal or higher-level attributes, such as geographic-range size. Direct comparative analyses across multiple extinction events will also clarify the impacts of particular drivers on taxa, functional traits, and morphologies. It is not just the extinction filter that deserves attention, as the longer-term impact of extinctions derives in part from their ensuing rebounds. More work is needed to uncover the biotic and abiotic circumstances that spur some clades into re-diversification while relegating others to marginal shares of biodiversity. Combined insights from mass extinction filters and their rebounds bring a macroevolutionary view to approaching the biodiversity crisis in the Anthropocene, helping to pinpoint the clades, functional groups, and morphologies most vulnerable to extinction and failed rebounds.

We analyzed the oxygen isotope composition of biogenic apatite phosphate (δ18Op) in fossil tooth enameloid to investigate the paleoecology of Late Cretaceous sharks in the Gulf Coastal Plain of Alabama, USA. We analyzed six different shark taxa from both the Mooreville Chalk and the Blufftown Formation. We compared shark δ18Op with the δ18Op of a co-occurring poikilothermic bony fish Enchodus petrosus as a reference for ambient conditions. Enchodus petrosus tooth enamel δ18Op values are similar between formations (21.3‰ and 21.4‰ Vienna Standard Mean Ocean Water [VSMOW], respectively), suggesting minimal differences in water δ18O between formations. Most shark taxa in this study are characterized by δ18Op values that overlap with E. petrosus values, indicating they likely lived in similar habitats and were also poikilothermic. Ptychodus mortoni and Cretoxyrhina mantelli exhibit significantly lower δ18Op values than co-occurring E. petrosus (P. mortoni δ18Op is 19.1‰ VSMOW in the Mooreville Chalk; C mantelli δ18Op is 20.2‰ VSMOW in the Mooreville Chalk and 18.1‰ VSMOW in the Blufftown Formation). Excursions into brackish or freshwater habitats and thermal water-depth gradients are unlikely explanations for the lower P. mortoni and C. mantelli δ18Op values. The low P. mortoni δ18Op value is best explained by higher body temperature relative to surrounding temperatures due to active heating (e.g., mesothermy) or passive heating due to its large body size (e.g., gigantothermy). The low C. mantelli δ18Op values are best explained by a combination of mesothermy (e.g., active heating) and migration (e.g., from the Western Interior Seaway, low-latitude warmer waters, or the paleo–Gulf Stream), supporting the hypothesis that mesothermy evolved in lamniform shark taxa during the Late Cretaceous. If the anomalous P. mortoni δ18Op values are also driven by active thermoregulation, this suggests that mesothermy evolved independently in multiple families of Late Cretaceous sharks.

The Cretaceous/Paleogene (K/Pg) mass extinction was a pivotal event in Earth history, the latest among five mass extinctions that devastated marine and terrestrial life. Whereas much research has focused on the global demise of dominant vertebrate groups, less is known about changes among plant communities during the K/Pg mass extinction. This study investigates a suite of 11 floral assemblages leading up to and across the K/Pg boundary in northeastern Montana constrained within a well-resolved chronostratigraphic framework. We evaluate the impact of the mass extinction on local plant communities as well as the timing of post-K/Pg recovery. Our results indicate that taxonomic composition changed significantly from the Late Cretaceous to Paleocene; we estimate that 63% of latest-Cretaceous plant taxa disappeared across the K/Pg boundary, on par with other records from North America. Overall, taxonomic richness dropped by ~23–33% from the Late Cretaceous to the Paleocene, a moderate decline compared with other plant records from this time. However, richness returned to Late Cretaceous levels within 900 kyr after the K/Pg boundary, significantly faster than observed elsewhere. We find no evidence that these results are due to preservational bias (i.e., differences in depositional environment) and instead interpret a dramatic effect of the K/Pg mass extinction on plant diversity and ecology. Overall, plant communities experienced major restructuring, that is, changes in relative abundance and unseating of dominant groups during the K/Pg mass extinction, even though no major (e.g., family-level) plant groups went extinct and communities in Montana quickly recovered in terms of taxonomic diversity. These results have direct bearing on our understanding of vegetation change during diversity crises, the differing responses of plant groups (e.g., angiosperms vs. gymnosperms), and spatial variation in extinction and recovery timing.

Ancient changes in the biosphere, from organismic traits to wholesale ecosystem changes, can be aligned with climate forcing across the Phanerozoic. Clear examples of abrupt climate warming causing biodiversity crises are primarily found between the Permian and Paleogene periods. During these times, catastrophic events occurred, resembling the extreme climate scenarios projected for the near future. The paleobiologic literature around these events generally supports the hypothesis that abrupt climate change was a dominant trigger of extinction and/or ecological crisis. When climate change and climate history are considered, virtually all post-Paleozoic global biotic events can be confidently attributed to climatic change, with abrupt warming (hyperthermal events) leaving the most consistent fingerprint. The combined stress of deoxygenation and warming are sufficient to explain marine extinction patterns across most hyperthermal events. Although ocean acidification may have contributed, the direct role of pH on the extinction toll of organisms is not consistently demonstrated. Future research can enhance the correspondence between the magnitudes of climatic changes and their biological impacts, even though observed rates of change cannot currently be compared across different timescales. Mimicking multi-scale approaches in modern ecology, paleontological approaches to climate impact research will benefit from specifically targeting scaling relationships.

Geometric morphometrics facilitates the quantification and visualization of variation in shape and proportion through the comparison of homologous features. Eublastoidea, a Paleozoic echinoderm clade with a conservative body plan, is an ideal group for morphometric analysis, because their plate junctions are homologous and identifiable on all species. Eublastoids have previously been grouped taxonomically by generalized shape types (e.g., globose). These shapes are often used in taxonomic descriptions and as characters in phylogenetic analyses. The underlying homology of these broad shape types has never been explored. Herein we apply the first comprehensive use of three-dimensional geometric morphometrics (3D GMM) on fossil echinoderms to investigate taxonomic assignments, temporal distribution, and whether the varying proportions of skeletal elements that produce the gross thecal morphology are distinguishable. Taxonomic assignments specifically at the ordinal and family levels show varying amounts of overlap in morphospace, suggesting that many assignments may not be reevaluated. Our results suggest that none of the generalized shape types are distinct in morphospace and, therefore, likely do not capture the homologous changes in taxa. The plate circlet ratios showed trends specifically relating to the deltoid plate circlet, which has the most variability. We reanalyzed previous work and subsetted our data to be more comparable and found that there are key differences between methodologies and landmarks that will require future evaluation. Applying modern technological methods to previously explored questions allows for an updated understanding of this important fossil clade and provides a framework for others to assess fossil clades in a similar manner.

Preserved records of tooth–bone interactions, known as tooth marks, can yield a wealth of information regarding organismal behavior and ecology. For this reason, workers in a wide range of disciplines, but particularly paleontology, have inspected and interpreted these features for decades. Although previous studies have gleaned invaluable insights, they have also described tooth marks using terminological frameworks that have been incompletely defined, have incorporated behavioral hypotheses in definitions, and/or have been inconsistently applied. To address these problems, we introduce the category-modifier (CM) system, the first system to both sort tooth marks into clearly defined main categories and use descriptive modifiers to characterize their appearance more precisely. The CM system is designed to apply to a wide range of vertebrates, to enable comparisons across disciplines and studies, and to help researchers keep their investigations into behavioral hypotheses free of circular reasoning.