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 common-cause hypothesis says that factors regulating the sedimentary record also exert macroevolutionary controls on speciation, extinction, and biodiversity. I show through computational modeling that common cause factors can, in principle, also control microevolutionary processes of trait evolution. Using Bermuda and its endemic land snail Poecilozonites, I show that the glacial–interglacial sea-level cycles that toggle local sedimentation between slow pedogenesis and rapid eolian accumulation could also toggle evolution rates between long slow phases associated with large geographic ranges and short rapid phases associated with small, fragmented ranges and “genetic surfing” events. Patterns produced by this spatially driven process are similar to the punctuated equilibria patterns that Gould inferred from the fossil record of Bermuda, but without speciation or true stasis. Rather, the dynamics of this modeled system mimic a two-rate Brownian motion process (even though the rate parameter is technically constant) in which the contrast in rate and duration of the phases makes the slower one appear static. The link between sedimentation and microevolution in this model is based on a sediment-starved island system, but the principles may apply to any system where physical processes jointly control the areal extents of sedimentary regimes and species’ distributions.

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.

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.

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.

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.

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.

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.

Humans have dramatically transformed ecosystems over the previous millennia and are potentially causing a mass extinction event comparable to the others that shaped the history of life. However, only a fraction of these impacts has been directly recorded, limiting conservation actions. Conservation paleobiology leverages geohistorical records to offer a long-term perspective on biodiversity change in the face of anthropogenic stressors. Nevertheless, the field's on-the-ground contributions to conservation outcomes are still developing. Here, we present an overview of directions in which paleobiological research could progress to aid conservation in the coming decades using elasmobranchs (sharks, rays, and skates)—a highly threatened group with a rich fossil record—as a model. These research directions are guided by areas of overlap between an expert-led list of current elasmobranch conservation priorities and available fossil and historical records. Four research topics emerged for which paleobiological research could address open questions in elasmobranch science and conservation: (1) baselines, (2) ecological roles, (3) threats, and (4) conservation priorities. Increasingly rich datasets and novel analytical frameworks present exciting opportunities to apply the elasmobranch fossil record to conservation practice. A similar approach could be extended to other clades. Given the synthetic nature of these research topics, we encourage collaboration across timescales and with conservation practitioners to safeguard the future of our planet's rapidly disappearing species.

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.

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.

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.