Phylogenetic inferences using combined datasets of both extant and extinct species have grown increasingly popular, in part thanks to the development of the fossilized birth–death (FBD) process. The FBD process provides a powerful model for the evolution of past and present lineages and can be used for both inference and simulation. Simulations in particular are very helpful for new users to gain better understanding of the model and its different components. In this work, we present FossilSimShiny, a visual application for simulating phylogenies, fossil samples, and fossil taxonomies under the FBD process. The app integrates a wide range of simulation models and presents the simulation results in clear, customizable figures. As a teaching tool, FossilSimShiny allows lecturers to create illustration plots and students to directly experiment with the model. For research applications, the app can help researchers save time and effort by testing and calibrating simulation setups before running them on a large scale.

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.

In 1980, Steven J. Gould published an essay on the emergence of paleobiology as a nomothetic discipline (Gould 1980), nomothetism referring to the search for general laws or principles. Gould contrasted this with the foundation of paleontology, the idiographic tradition of detailing the history of life from the description of new fossil taxa to the elucidation of the long-term patterns of change through time. Among the pioneers of this nomothetic expansion was Jim Valentine. Here I pay tribute to Jim as one of the first paleobiologists, a colleague, coauthor, and friend, emphasizing his intellectual style and insights as much as his lasting contributions. I have written this in part as a eulogy, a remembrance for those who knew him, but also as an introduction to the continuing relevance of his work for those who may be unfamiliar with it.

Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases like the Paleobiology Database (PBDB) enable assessment of patterns and processes spanning millions of years, up to global scale. The status quo for data citation creates an imbalance wherein publications drawing data from the PBDB receive significantly more citations (median: 4.3 ± 3.5 citations/year) than the publications producing the data (1.4 ± 1.3 citations/year). By accounting for data reuse where citations were neglected, the projected citation rate for data-provisioning publications approached parity (4.2 ± 2.2 citations/year) and the impact factor of paleontological journals (n = 55) increased by an average of 13.4% (maximum increase = 57.8%) in 2019. Without rebalancing the distribution of scientific credit, emerging “big data” research in paleontology—and science in general—is at risk of undercutting itself through a systematic devaluation of the work that is foundational to the discipline.

In modern nonmarine settings, previous studies have demonstrated the importance of elevation-correlated ecological gradients, but such studies tend to focus on relatively small areas and only one higher taxon. Here, we analyze Global Biodiversity Information Facility occurrence records from a wide variety of taxa across the southeastern U.S. coastal plain. Many taxa display ecological gradients (gradients in proportional or relative abundance) correlated with elevation, distance to the coast, and latitude. These gradients tend to be steepest within a few tens of kilometers near the coast and at elevations less than 25 m. Some taxa, notably terrestrial mammals, do not display gradients correlated with elevation and distance to the coast. The small sample sizes of these groups and their heterogeneous sampling raise concerns about whether sufficient data exist. Coupled with previous studies of these ecological gradients, their common presence over distances of tens to hundreds of kilometers and elevations of tens to hundreds of meters suggests they are likely important in the nonmarine fossil record. Because elevation and distance to the coast change predictably with cycles of accommodation and sediment flux, these ecological gradients are predicted to occur in the nonmarine stratigraphic record, especially through intervals that record transgression or regression. Such gradients will affect the local composition of species associations and occurrences, even in the absence of regional species origination, immigration, and extinction and of regional change in the structure of ecological gradients. The ordination of taxon counts in stratigraphically limited samples has great potential for establishing their existence.

The fossil record is spatiotemporally heterogeneous: taxon occurrence data have patchy spatial distributions, and this patchiness varies through time. Large-scale quantitative paleobiology studies that fail to account for heterogeneous sampling coverage will generate uninformative inferences at best and confidently draw wrong conclusions at worst. Explicitly spatial methods of standardization are necessary for analyses of large-scale fossil datasets, because nonspatial sample standardization, such as diversity rarefaction, is insufficient to reduce the signal of varying spatial coverage through time or between environments and clades. Spatial standardization should control both geographic area and dispersion (spread) of fossil localities. In addition to standardizing the spatial distribution of data, other factors may be standardized, including environmental heterogeneity or the number of publications or field collecting units that report taxon occurrences. Using a case study of published global Paleobiology Database occurrences, we demonstrate strong signals of sampling; without spatial standardization, these sampling signatures could be misattributed to biological processes. We discuss practical issues of implementing spatial standardization via subsampling and present the new R package divvy to improve the accessibility of spatial analysis. The software provides three spatial subsampling approaches, as well as related tools to quantify spatial coverage. After reviewing the theory, practice, and history of equalizing spatial coverage between data comparison groups, we outline priority areas to improve related data collection, analysis, and reporting practices in paleobiology.

Women are underrepresented in paleontology. Despite more women students, representation at senior levels remains low. To advance professionally, scientists must disseminate their research through peer-reviewed publications. We examine gendered authorship patterns in Paleobiology to ask whether the publishing infrastructure supports the Paleontological Society's gender-equity goals. We reviewed all papers published in Paleobiology from its inception in 1975 through 2021. For each paper, we recorded each author, the author's position in the author list, and the total number of authors on each paper. We coded gender based on a combination of personal communication and pronouns used in publicly available information. We compared author demographics with anonymized membership data from the Paleontological Society. Over the journal's run, the number of authors per paper increased due to cultural shifts toward collaborative work and acknowledging student contributions with coauthorship. These trends contribute to proportionally more women authors, beginning in the early 2000s. Despite these increases, women remain chronically underrepresented. In 2018, 2019, and 2021, the proportion of women authors in Paleobiology paralleled membership in the Paleontological Society. However, in 2020, Paleobiology published fewer women authors than expected based on society membership. This echoes declines in women's scholarly productivity in the first year of the COVID-19 pandemic observed across many disciplines. We offer four recommendations: (1) practice double-anonymous peer review; (2) recruit editors from diverse backgrounds who invite reviewers with diverse backgrounds; (3) democratize manuscript review by selecting reviewers from a disaggregated reviewer database; and (4) gather and analyze demographic data for both submissions and publications.

The trace fossil record provides important insights into the evolution of early animals during the Ediacaran/Cambrian transition, with changes in ichnodiversity through time and between environments informing on the diversification of major body plans, behaviors, and niches. To quantify variation in the diversity of trace fossils across this critical interval, we propose a measure of trace fossil dissimilarity (ichnodissimilarity) based on vector calculation. Furthermore, by comparing discrepancies between the angular bisector and mean vector of two sets of vectorized fossil data, we are able to weigh the relative contribution of increases and decreases in the variation of occurrences of taxa. We used this metric to analyze an expansive dataset of Ediacaran/Cambrian trace fossils. The results allowed us to quantify the diversification of traces across this transition, informing on the timing of first appearance of different behaviors (e.g., foraging, grazing, and resting) and functional groups. By interpreting the results in the context of environmental changes and advancements in motility and sensory capabilities, we were able to pinpoint the onset and sequence of the Fortunian diversification event, Cambrian information revolution, and agronomic revolution, shedding light on the evolution of organismal body plans, behaviors, and locomotion during the Ediacaran/Cambrian transition. We identified two phases of origination and expansion during the divergence of early animal traces. Furthermore, by analyzing shallow- and deep-marine trace fossils, we were able to uncover evidence for a more rapid diversification of traces in shallow-marine environments, with progressive niche partitioning through the Ediacaran to Cambrian.

Bioturbation can increase time averaging by downward and upward movements of young and old shells within the entire mixed layer and by accelerating the burial of shells into a sequestration zone (SZ), allowing them to bypass the uppermost taphonomically active zone (TAZ). However, bioturbation can increase shell disintegration concurrently, neutralizing the positive effects of mixing on time averaging. Bioirrigation by oxygenated pore-water promotes carbonate dissolution in the TAZ, and biomixing itself can mill shells weakened by dissolution or microbial maceration, and/or expose them to damage at the sediment–water interface. Here, we fit transition rate matrices to bivalve age–frequency distributions from four sediment cores from the southern California middle shelf (50–75 m) to assess the competing effects of bioturbation on disintegration and time averaging, exploiting a strong gradient in rates of sediment accumulation and bioturbation created by historic wastewater pollution. We find that disintegration covaries positively with mixing at all four sites, in accord with the scenario where bioturbation ultimately fuels carbonate disintegration. Both mixing and disintegration rates decline abruptly at the base of the 20- to 40-cm-thick, age-homogenized surface mixed layer at the three well-bioturbated sites, despite different rates of sediment accumulation. In contrast, mixing and disintegration rates are very low in the upper 25 cm at an effluent site with legacy sediment toxicity, despite recolonization by bioirrigating lucinid bivalves. Assemblages that formed during maximum wastewater emissions vary strongly in time averaging, with millennial scales at the low-sediment accumulation non-effluent sites, a centennial scale at the effluent site where sediment accumulation was high but bioturbation recovered quickly, and a decadal scale at the second high-sedimentation effluent site where bioturbation remained low for decades. Thus, even though disintegration rates covary positively with mixing rates, reducing postmortem shell survival, bioturbation has the net effect of increasing the time averaging of skeletal remains on this warm-temperate siliciclastic shelf.

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.

Biological variation fuels evolutionary change. Across longer timescales, however, polymorphisms at both the genomic and phenotypic levels often persist longer than would be expected under standard population genetic models such as positive selection or genetic drift. Explaining the maintenance of this variation within populations across long time spans via balancing selection has been a major triumph of theoretical population genetics and ecology. Although persistent polymorphisms can often be traced in fossil lineages over long periods through the rock record, paleobiology has had little to say about either the long-term maintenance of phenotypic variation or its macroevolutionary consequences. I explore the dynamics that occur when persistent polymorphisms maintained over long lineage durations are filtered into descendant lineages during periods of demographic upheaval that occur at speciation. I evaluate these patterns in two lineages: Ectocion, a genus of Eocene mammals, and botryocrinids, a Mississippian cladid crinoid family. Following origination, descendants are less variable than their ancestors. The patterns by which ancestral variation is sorted cannot be distinguished from drift. Maintained and accumulated polymorphisms in highly variable ancestral lineages such as Barycrinus rhombiferus Owen and Shumard, 1852 may fuel radiations as character states are sorted into multiple descendant lineages. Interrogating the conditions under which trans-specific polymorphism is either maintained or lost during periods of demographic and ecological upheaval can explain how population-level processes contribute to the emergent macroevolutionary dynamics that shape the history of life as preserved in the fossil record.

The process of evolution and the structures it produces are best understood in the light of hierarchy theory. The biota traditionally is described by either the genealogical Linnaean hierarchy or economic hierarchies of communities or ecosystems. Here we describe the Bretskyan hierarchy—a hybrid eco-genealogical hierarchy that consists of nested sets of different-sized, usually polyphyletic communities of interacting individuals separated from other such communities in space and time at multiple scales. The Bretskyan hierarchy consists of elements that have both genealogical and economic properties and functions—situated between, and connecting the elements of, the economic hierarchies (Vernadskyan) and the genealogical (Linnaean) hierarchy. The described hierarchy at lower tiers is populated by holobionts, individuals composed of multiple polyphyletic lineages integrated by functional interactions or biotically fabricated structures, such as membranes. At larger spatial tiers and longer time scales, the members of the Bretskyan hierarchy are of a more diffuse nature, partially due to the small size and relatively short duration of us as observers of larger and longer-lasting structures, here described as geobiomes. Their individuality is externally forced and directly tied to the spatial and temporal physical structures of our planet. These are sub-bioprovinces and bioprovinces—large and effectively isolated spatiotemporal structures of biota integrated internally by coevolution and individuated externally by a hierarchy of barriers. Gaia is here understood as the largest eco-genealogical individual compartmentalized by the outer space of the Earth and integrated at long time scales by biotic interactions and plate tectonic mixing of biota. The existence of a hierarchy of barriers and multilevel allopatry suggests that geographic isolation takes part not only in individuating species lineages, but also in producing coherent complexes of separate lineages forming bioprovinces at multiple space and time scales. The sizes, configurations, and durations of Bretskyan units are directly tied to geodynamics, demonstrating the central role of the physical planet in the processes of individuation and merging of geobiomes and the control of coevolution, and all its ramifications, at multiple space and time scales. The Bretskyan hierarchy also allows the integration of previously unconnected themes—“egalitarian” major transitions in individuality (e.g., eukaryogenesis) and some of the megatrajectories in the history of life—into a single theoretical framework of spatial and temporal scaling of eco-genealogy. The pervasive scaling of geodynamical processes and the direct connection of geodynamics to the dynamics of Bretskyan units allows us to formulate conjectures on the scales and limits of spatial and temporal contingency and competitiveness of biotas in evolution.

Phacopid trilobites are well documented during the Paleozoic. Nevertheless, while 2D quantitative analyses have advanced our understanding of the morphological relationships among trilobites, the quantification of their morphological traits in 3D remains rarely documented. Based on two sets of morphological data (head and tail), 2D versus 3D shape quantification approaches were used to explore shape allometries as well as to explore how the shape variations can be explained by the phylogenetic relationships among phacopid trilobite species for the first time. We demonstrate that (1) there are similar patterns of morphological variability across taxa in 3D and 2D; (2) there are rather congruent results between 3D and 2D to discriminate taxa; (3) 2D and 3D landmarks capture different levels of detail, and the third dimension in 3D is very important for making taxonomic distinctions at the genus level; (4) there is congruity between 2D and 3D datasets for allometric patterns with results showing similar allometric slopes among species exhibiting a glabellar length decrease during growth leading to wider cephala; (5) the phylomorphospaces show tree branches that do not intersect, suggesting possible phylogenetic constraints on morphospace occupation for each species and supporting the idea that the Austerops and Morocops groups are sister clades that experienced different modes of morphological evolution; and (6) the morphological descriptors in morphometric analyses in 2D and 3D throughout phacopid evolution are effective.

We know the fossil record is incomplete, but just how much biodiversity does it miss? We produce the first geographically controlled estimate by comparing the geographic ranges of 34,266 modern tetrapods with a map of the world's sedimentary basins. By modeling which tetrapods live within sedimentary basins, we produce a first-order estimate of what might be found in the fossil record of the future. In this record, nearly 30% of tetrapod species have almost no chance of fossilizing, and more stringent criteria for fossilization exclude far more diversity. This geographically structured fossil record preserves disparate patterns of taxonomic and phylogenetic diversity in different tetrapod groups and underpreserves projected extinctions. For the globally threatened amphibians, the magnitude of the extinction of all endangered species would be underestimated by 66–98% in our future record. These results raise profound questions about the structure of the fossil record. Is it capable of recording major origination and extinction events on land? Have swaths of terrestrial diversity gone unrecorded based on geography alone? There are chapters of Earth history that paleontologists can never hope to know, but what is missing, and why?

The trend of global cooling across the Cenozoic transformed the North American landscape from closed forest to more open grasslands, resulting in dietary adaptations in herbivores in response to shifting resources. In contrast, the material properties of the predator food source (muscle, skin, and bone) have remained constant over this transition, suggesting a corresponding lack of change in predator dietary adaptations. We investigated the North American mammalian predator fossil record using a tooth-shape metric and body mass, predicting that the former would exhibit stability. Instead, we found that mean molar morphology became more blade-like, with our tooth-shape metric sharply increasing in the late Eocene and remaining high from the Oligocene onward. Subsequent tests in extant carnivorans reveal taxa with more bladelike teeth are prevalent in more open environments. Our results reveal an unexpected functional shift among North American predators in response to large-scale environmental changes across the Cenozoic.

The first size reduction (FSR) in the Reticulofenestra-Gephyrocapsa-Emiliania (RGE) lineage (order Isochrysidales), which occurred in the early Oligocene (~32 Ma), is of great significance for understanding the Lilliput effect that has affected coccolithophore communities from the late Eocene to this day. We conducted a morphologic analysis on the coccoliths of Reticulofenestra species that lived during the late middle Eocene to early Oligocene (~40–31 Ma), using marine sediments from the South Atlantic Ocean. Our data show increasing size and decreasing abundance of the large species during the late Eocene, leading to their disappearance at the FSR, and a concurrent decrease in the size variability of the small- to medium-sized coccoliths whose central opening diameter had become very reduced. Although the cosmopolitan late Paleogene through Neogene size decrease in coccolithophores has been linked to the concomitant long-term decline in global pCO2, we suggest here that the FSR was the result of environmental destabilization caused by the expansion of eutrophic environments following the late Eocene establishment of overturning circulation associated with ice buildup on Antarctica. This study also leads us to propose a hypothetical model that links coccolith morphology of species of the RGE lineage and trophic resources in the upper ocean: the small- to medium-sized, r-selected coccolithophores with smaller coccolith central openings live in nutrient-rich waters where they rely mostly on photosynthesis and little on mixotrophy, whereas the larger, K-selected species with larger coccolith central openings live in oligotrophic waters where they are more dependent on mixotrophy.

The Fezouata Shale Formation has dramatically impacted our understanding of Early Ordovician marine ecosystems before the great Ordovician biodiversification event (GOBE), thanks to the abundance and quality of exceptionally preserved animals within it. Systematic work has noted that the shelly fossil subassemblages of the Fezouata Shale biota are typical of open-marine deposits from the Lower Ordovician, but no studies have tested the quantitative validity of this statement. We extracted 491 occurrences of recalcitrant fossil genera from the Paleobiology Database to reconstruct 31 subassemblages to explore the paleoecology of the Fezouata Shale and other contemporary, high-latitude (66°S–90°S) deposits from the Lower Ordovician (485.4–470 Ma) and test the interpretation that the Fezouata Shale biota is typical for an Ordovician open-marine environment. Sørensen's dissimilarity metrics and Wilcoxon tests indicate that the subassemblages of the Tremadocian-aged lower Fezouata Shale are approximately 20% more heterogenous than the Floian-aged upper Fezouata Shale. Dissimilarity metrics and visualization suggest that while the lower Fezouata and upper Fezouata share faunal components, the two sections have distinct faunas. We find that the faunal composition of the lower Fezouata Shale is comparable with other Tremadocian-aged subassemblages from high latitudes, suggesting that it is typical for an Early Ordovician open-marine environment. We also find differences in faunal composition between Tremadocian- and Floian-aged deposits. Our results corroborate previous field-based and qualitative systematic studies that concluded that the shelly assemblages of the Fezouata Shale are comparable with those of other Lower Ordovician deposits from high latitudes. This establishes the first quantitative baseline for examining the composition and variability within the assemblages of the Fezouata Shale and will be key to future studies attempting to discern the degree to which it can inform our understanding of marine ecosystems just before the start of the GOBE.

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.

Corallite sizes reflect a continuum in the efficacy of photosymbiosis in colonial reef corals, with smaller corallite sizes generally associated with higher autotrophy. Using a large compilation of reef-coral traits and corallite diameters as a proxy, we test here the hypothesis that photosymbiotic efficacy has increased over the evolutionary history of scleractinian corals. To gain a more comprehensive understanding of the evolutionary versus ecological patterns of corallite sizes of reef corals, we used three analytical methods: (1) occurrences-weighted within-bin analyses as a proxy for abundance or ecological dominance to depict ecological patterns; (2) unweighted range-through analyses; and (3) unweighted sampled-in-bin analyses to represent diversity in terms of taxonomic richness, enabling us to trace evolutionary patterns. By-genus, range-through analysis indicates a slightly positive trend of corallite sizes toward the Recent. However, the occurrences-weighted assessment shows a pronounced negative trend of corallite sizes in colonial corals since the Mesozoic. Random walk and directional evolution are both statistically supported to explain this long-term decrease. A driven trend is evolutionarily plausible, giving reef corals a selective advantage in the oligotrophic environments they largely occupy today.

Caryocaridids are a unique representative of pelagic arthropods from the Ordovician period. They are typically found as flattened carapaces in mudstones and shales. This study reports on a species of caryocaridids, Soomicaris cedarbergensis, discovered in the Lower Ordovician of northwestern Xinjiang, NW China. The species shows the rare enrolled carapaces with a preserved cuticular ultrastructure. These specimens of caryocaridids from Xinjiang are the first reported in the Yili Block, and provide the substantial evidence that the paleogeographic distribution of caryocaridid phyllocarids could extend to the Central Asian Orogenic Belt. This species existed from the late Tremadocian until the end of the Ordovician (Hirnantian), making it the longest-ranging known species of caryocaridids. The carapace cuticle of S. cedarbergensis is composed of carbonate-fluorapatite and can be divided into three mineralized lamellae: outer, middle, and inner. The outer and inner lamellae each consist of three layers that correspond to the epicuticle, exocuticle, and endocuticle of extant crustacean carapaces. Moreover, the polygonal reticulation structure of the carapace in archaeostracans appears to be similar in shape and size to the hemolymph sinuses of leptostracans. This unique ultrastructure of the carapace cuticle in caryocaridids is believed to be better suited for a pelagic lifestyle.