Our ability to measure evolution by natural selection in the fossil record is limited by the near impossibility of estimating the fecundity and thus relative fitness of most fossil organisms. Neocheilostome bryozoans are an important exception, because they have calcified larval brood chambers known as ovicells that provide an approximate estimate of the colony’s sexual fecundity. This clade has a rich fossil record dating back ~100 million years, providing potential opportunities to observe changes in relative fitness and natural selection through many past intervals of environmental change. However, neocheilostome fossil specimens are often highly fragmented, and fragments are not necessarily randomized subsets of a colony. To make use of the majority of the neocheilostome fossil record, we need to test the effect colony organization has on our methods of inferring colony fecundity from fragmented specimens.

In this study, we measure colony fecundity in a population of Recent neocheilostome bryozoan specimens of the species Parasmittina eccentrica Winston & Jackson, 2021 and quantify the nonrandom spatial arrangement of ovicells due to colony organization. We then simulate fragmenting these specimens and test the statistical robustness of standard methods one might use to reconstruct fecundity from fossil specimens. We find that ovicells are clustered and concentrated at mid-distances from the ancestrula (the oldest part of the colony). As a result, estimates of a colony’s fecundity from a single fragment have higher variance than would be expected if ovicells were randomly distributed. When estimating average population fecundity, observed variance among fossil fragments is a better estimator of sample variance than methods that assume spatial independence (such as a binomial distribution), especially for fragment sizes of 8 mm or less. While there is much to be learned about neocheilostome ovicell arrangement across taxa and environments, we can robustly estimate fecundity from small fossil fragments even in extinct neocheilostome species.

With the growing application of artificial intelligence (AI) and machine learning (ML), great potential exists to leverage these technologies in paleontology. Relative to many other scientific fields, a challenge of ML applied to paleontology is small sample sizes, particularly for fossil vertebrates. Shark teeth, abundant in the fossil record, provide a model system to use ML across varying sample sizes. Here we use six classes (taxa) of Neogene shark teeth for taxonomic identification, including a curated dataset of 3150 images. Each class was evaluated using an 80% training and 20% validation split, with a separate, external test set of 25 samples per class. Pretrained models perform well (accuracy > 90%), providing a strong baseline for classification. However, enabling fine-tuning of the ML model to identify fossil shark teeth improves performance considerably. Likewise, sample size per class also affects the accuracy of the models’ classifications. Smaller sample sizes (n = 50 individuals per class) yielded a mean accuracy of 93.4%, but plateaued at ~99% between 200 and 500 images per class. Confidence likewise increases with larger samples, from 81.8% (n = 50 individuals per class) to >90% (n = 300 to 500 individuals per class). Misidentifications followed consistent patterns, reflecting morphological similarities and/or poor preservation. Artificially increasing the training datasets using data augmentation improves the confidence of identifications. This research indicates that relatively small samples of vertebrate species (~50 to 500 individuals per class) can effectively train an ML model to identify these shark teeth with high levels of accuracy.

Richard Bambach was a leading figure in the “paleobiology revolution” of the late 1960s and 1970s, keeping the movement grounded with his keen geological and ecological insights. With interests ranging from the functional biology of individual organisms to the largest macroevolutionary trends in the history of life, he was especially adept at linking paleoecological and macroevolutionary patterns across spatiotemporal scales. He authored seminal publications during five different decades and was recognized with both the Moore Medal from the Society for Sedimentary Geology and the Paleontological Society Medal.

The fossil record is subject to multiple biases that can distort macroevolutionary and paleoecological inferences. Although temporal and spatial sampling biases have received substantial attention, other sources of fossil sampling heterogeneity remain less well quantified. Using the Triton database of planktonic foraminifera, we assess the influence of geographic, ecological, morphological, and methodological factors on fossil recovery rates. We first apply a temporal subsampling method to standardize fossil occurrences over geologic time, validating this approach against an expert-curated lineage-through-time trajectory. After subsampling, the occurrences remain unevenly distributed throughout species’ lifetimes and inhomogeneously distributed across species, reflecting biological signal and/or persistent sampling biases.

We then investigate this residual sampling heterogeneity with a generalized additive model incorporating relevant predictors from Triton. Our results reveal that, after correcting for temporal biases, geographic predictors (paleolatitude, paleolongitude, longitudinal spread) explain nearly a third of sampling variation. Species-specific ecological and morphological attributes contribute an additional fraction, among which mean relative abundance emerges as the main factor. Additional predictors of fossil sampling rates include age-calculation methods and biostratigraphic sampling biases. Despite accounting for multiple sources of variation, 37% of the deviance remains unexplained, suggesting unmodeled biological, stratigraphic, diagenetic, or taxonomic drivers of sampling heterogeneity.

Overall, observed recovery rates question the validity of the homogeneous-sampling assumption used in most diversification models, and this heterogeneity cannot be reduced to a single dominant factor. This conclusion reinforces the need for integrated subsampling approaches and process-based models that explicitly account for heterogeneous fossilization rates to improve the reliability of macroevolutionary analyses.

Polymorphism, the occurrence of different morphs of a trait within the population of a single species, plays a crucial role in species diversification, genetic variation, and adaptation. Detecting polymorphism in a single character helps us to understand population dynamics, particularly in species that inhabit diverse environments. However, detecting polymorphisms in fossil taxa is challenging due to the fragmentary and incomplete records. Dimorphism, defined as the occurrence of different morphs of a trait within the population of a single species, represents the simplest and most common form of polymorphism. This study focuses on dimorphism instead of polymorphism, which allows for a more streamlined analysis. We use computational simulation experiments to estimate the minimum sample size required to detect bimodal distribution in univariate morphological variables. We describe the morphological diversity of a measured variable (e.g., body mass or skeletal length) as a probability density distribution with specific parameter sets. Subsequently, we simulate the diversity of the measured variable with varying sample sizes and conduct resampling procedures to ensure the robustness. Four key parameters that characterize the probability distribution are identified as having significant influence on the minimum sample size for dimorphism recognition. According to the simulation experiments, a model is built to estimate the minimum sample size for dimorphism recognition based on these parameters. A dataset from extant avian and reptilian species is used to test the model. Furthermore, we calculate a reference for the minimal sample size required for assessing phenotypic dimorphism in fossil avian taxa by applying parameters derived from extant avian species.

Continuous morphological traits play a crucial role in phylogenetic inference, yet they are often discretized due to limited software support and challenges of handling missing data efficiently. We present a new implementation of the Brownian motion model for continuous trait evolution in the Bayesian phylogenetics software MrBayes. Our approach efficiently accommodates any proportion of missing data and supports evolutionary rate variation across characters and data partitions. It is compatible with both non-clock and relaxed clock models. We validate the implementation through simulations and apply it to empirical datasets of pterosaurs and ancient humans, demonstrating that continuous traits can improve phylogenetic resolution. This development expands the methodological tool kit for morphological and total-evidence phylogenetics and is applicable across diverse taxonomic groups.

We use new macroevolutionary rate estimates to resolve the dynamics of severe versus background extinction through the history of a major, globally distributed, Paleozoic zooplankton clade, the graptoloids. Our data span one of the “Big Five” mass extinctions, the Late Ordovician Mass Extinction (LOME), and several secondary, severe extinction events. We use cohort survivorship curves to derive both “instantaneous” rates and smoothed rates based on “natural” time-bin intervals that honor the structure of the data. We avoid the approximation of many approaches that average rate estimates within essentially arbitrary time bins.

We find that 63% of graptoloid extinctions lie within intervals classified previously as “background” extinction; only 7% lie within the LOME, and the remainder lie within the spans of 15 other secondary extinction events spread through the Ordovician and Silurian. Extinction rate magnitudes define a continuous, unimodal distribution. Background extinction in the graptoloids is not stochastically uniform but includes many more high-rate pulses than expected under a null model of uniform, memoryless extinction. Our results support the inference of pulsed extinction in the marine realm, with pulses occurring on timescales much finer than the standard age divisions of the Ordovician and Silurian periods. The LOME and secondary extinction events are not characterized by instantaneous extinction rates that are higher than so-called background. Instead, extinction events are distinguished from background by increased duration of their component, short-lived pulses of elevated extinction, and the LOME represents a protracted interval with multiple such pulses and little time for faunal recovery.

Our results are consistent with the notion that, whereas a mass or severe extinction may have an exceptional or singular initial trigger, the effects of that trigger propagate out to global-scale species loss via a complex web of processes that are common to many extinction episodes and may take significant time.

Over the past half century, paleobiologists have advanced the estimation of phylogenetic relationships among fossil taxa to explore evolutionary patterns in deep time. This study employs a breadth of phylogenetic analyses, specifically divergence time estimations and character rate evolution, within three blastozoan echinoderm clades: Diploporita, Eublastoidea, and Paracrinoidea. Utilizing reversible jump Markov chain Monte Carlo (rjMCMC) and fossilized birth–death (FBD) models, we investigated evolutionary rates through anatomical subunit partitioning. Results suggest similar rates among the three groups, although Paracrinoidea exhibits elevated rates in several anatomical subunits. The inferred trees largely agree with other recently published analyses, in that the current taxonomy of the group does not reflect true evolutionary relationships. Thus, this study adds to a growing body of literature that highlights the need to revise echinoderm taxonomy. We tested different clock models for each group and found that model choice had strong effects on resulting trees; our findings suggest linked clocks (i.e., the same clocks for all character partitions) had more support than unlinked clocks (i.e., different clocks for different character partitions). These findings indicate a need to carefully consider model choice and rates of evolution when utilizing these types of analyses.

Multituberculate extinction is often cited as a classic case of competitive exclusion, coinciding with the first rodent arrivals in the late Paleocene. Analyzing 124 North American multituberculate last occurrence records during the Eocene from 56 to 34 million years ago, this study aimed to differentiate Eocene multituberculate and coeval rodent floral associations through geographic spatial analysis to understand niche overlap between the two groups. If competitive exclusion with rodents was a factor in multituberculate extinction, both multituberculates and rodents would be predicted to share similar forest habitat preferences and have competed for similar ecological niches regarding their forest associations. Using spatial analysis, this study found that Eocene rodents and multituberculates did not overlap in their forest associations. The findings indicate that multituberculates were unique in inhabiting a specific type of ancient forest habitat, favoring forests composed of Metasequoia, Glyptostrobus, and Alnus, and thus thrived in wetter northern temperate forest communities during the Eocene. Metasequoia and Glyptostrobus declined significantly in North America during the later Cenozoic, coinciding with multituberculate decline and extinction as the global climate shifted toward colder and drier climates around the Eocene/Oligocene boundary. In contrast, the success of rodents is attributed to their much broader forest affinity. These preferences align with the widespread distribution of rodents today, contributing to their modern success. The absence of any similar reconstructed forest habitat preferences between rodents and multituberculates suggests that changing forest structure, rather than competitive exclusion, drove multituberculate extinction.

Mammalian species richness is commonly highest at mid- to high elevations, but the accumulation of sediment that might bury and preserve skeletal remains generally occurs at lower elevations, leading to concerns that fossil assemblages are biased toward low-elevation taxa. Here, I use extant mammals as an analogue to test the basin-scale spatial overlap between species ranges and sediment sinks where burial and fossilization would be possible. Sediment sinks are estimated within five topographically complex regions in western North America by identifying areas with both a low slope and a high contributing area of runoff and are compared with point occurrences of mammals compiled from the Global Biodiversity Information Facility (GBIF). I find that, among the test areas, 82–96% of all species have occurrences that overlap with a sediment sink, despite common offsets in the elevations of maximum sink area and maximum species richness: summed across all test areas, 83% of species and 87% of total sediment sink area are found in the lowest 1000 m of the test areas. Although many other factors can act against the fossilization of terrestrial mammals, these results indicate that the spatial distribution of mammal species with respect to sediment sinks should not in itself impose a major bias at the basin scale.

The extinction of clades outside mass extinction events remains an understudied aspect of evolutionary dynamics. This study examines the Dactylioceratidae, an ammonite family that disappeared during the Early Jurassic, outside a recognized mass extinction event. By using high-resolution taxonomic (species-level) and temporal (subchronozone) data, we assess its evolutionary trajectory, from diversification to extinction. Our analysis reveals that Dactylioceratidae experienced an initial expansion in diversity and geographic range, followed by increased specialization. Morphological disparity and diversity peaked before a sharp decline, suggesting a possible link between ecological specialization and extinction risk. This pattern aligns with hypotheses proposing that overspecialization limits adaptability, leading to extinction under background conditions. In contrast to mass extinctions driven by sudden catastrophic events, background extinctions may be influenced by gradual ecological changes and evolutionary constraints. By comparing the case of Dactylioceratidae with broader ammonoid trends, this study provides insights into long-term extinction mechanisms. These findings are relevant for understanding both past and present biodiversity crises, shedding light on how species’ evolutionary strategies impact their survival over time.

Body-mass evolution in extinct mammals is an important factor in understanding their diversification and niche occupation dynamics over geological time. To know how Macraucheniidae, South American native ungulates, diversified over 30 Myr, we estimated body mass for 15 genera within this family and investigated which evolutionary process best explains body-mass evolution in this lineage. For this purpose, we applied a set of body-mass estimation equations and conducted comparative phylogenetic analyses to assess the presence of phylogenetic signals and identify the best-fitting model of trait evolution. Our results show that all Macraucheniidae genera can be classified as megafauna (i.e., mammals weighing more than 44 kg). The evolutionary model that best explains body-mass diversification in this family is a directional, gradual increase over time. The subfamilies Cramaucheniinae and Macraucheniinae did not differ significantly in body-mass evolutionary rates; however, the negative relationship between body mass and temperature, together with the most parsimonious evolutionary scenario, supports temperature as the primary ecological driver of body-mass evolution in macraucheniids.

The fossil record offers a unique window into patterns of extinction and biodiversity recovery over deep time, and recent advances in analytical methods have significantly enhanced this research field. Our analysis of an updated dataset that includes 50 terminal taxa and 175 fossil occurrences of Ophiacodontidae, Edaphosauridae, and Sphenacodontidae (OES grade hereafter) using a recent implementation of the skyline fossilized birth–death model (FBD hereafter) confirms our previous conclusion that the OES grade diversified during the latter half of the Pennsylvanian but waned thereafter. However, our new results differ in several important points compared with our previous study (published in 2024). Notably, the transition between these two diversification regimes seems to have occurred earlier (at 298.9 Ma, at the Carboniferous/Permian transition), and it appears to have been marked by a moderate (0.527 survival probability), previously unreported extinction event. Also, the OES grade seems to have experienced a much more severe mass extinction event in the mid-Kungurian, with an estimated survival rate of only 0.113, which left very few surviving OES grade lineages. Climatic instability that started around the Carboniferous/Permian boundary and lasted throughout the Cisuralian, plausibly caused by intense volcanism of the Tarim Large Igneous Province and the Panjal Traps, may explain this pattern, which consists of a stagnating biodiversity followed by a brief, severe extinction event. This is reminiscent of the press–pulse model proposed by Arens and West in 2008, but if there was indeed an end-Carboniferous crisis, it could also be viewed as a new, more complex, pulse–press–pulse pattern.

The first geographically widespread metazoans form the Avalon assemblage (Ediacaran; 574–560 Ma). These early animals were regularly disturbed by sedimentation events such as ash flows and turbidites, leading to an apparent “resetting” of communities. However, it is not clear how biological legacies—remains or survivors of disturbance events—influenced community ecology in the Avalon. Here, we use spatial point process analysis on 19 Avalon paleocommunities to test whether two forms of biological legacy (fragmentary remains of Fractofusus and survivor fronds) impacted the recolonization dynamics of Avalon paleocommunities. We found that densities of Fractofusus were increased around the Fractofusus fragments, suggesting that they helped to recolonize the post-disturbance substrate, potentially contributing to the Fractofusus dominance found in 8 of the 19 paleocommunities. However, we found no such effects for survivor fronds. Our results suggest that the evolution of height was for long-distance dispersal rather than local recolonization. In modern deep-sea environments, there is a trade-off between local and long-distance dispersal, and our work demonstrates that this differentiation of reproductive strategies had already developed in the early animals of the Avalon.

Over the past 10 million years, coastal-marine settings along the Peruvian Margin have undergone profound geographic and oceanographic transformations, resulting in extensive changes in coastal-marine communities. While mollusk taxonomy research is slowly being integrated into ecosystem-wide analyses, which have historically centered on vertebrates, a long-term chronostratigraphically controlled analysis of molluscan diversity and compositional changes has not been undertaken for this region. We compiled a database covering 152 species, 97 genera, and 51 families of mollusk fossils from the Peruvian Margin (13–16°S) to assess long-term diversification patterns and faunal turnover from the late Miocene to the present. We identified two distinctive molluscan assemblages. The first, dating to the late Miocene (10–6 Ma), underwent a substantial shift during the Mio-Pliocene transition (6–4 Ma), culminating in a second assemblage more akin to modern counterparts. This shift resulted in an increase in diversity, with the younger assemblage (6–0 Ma) exhibiting greater genus richness than the former late Miocene assemblage. The turnover at 6–4 Ma was driven by peaks in bivalve origination (6–5 Ma) along with elevated extinction rates for gastropods (6–5 Ma) and bivalves (5–4 Ma). Ecological analyses revealed that no single ecological trait consistently changed during this interval, indicating that the turnover resulted from a broad reorganization of ecological strategies. We propose that the major molluscan turnover during the late Miocene–early Pliocene is associated with geomorphological changes related to the Andean uplift, the disappearance of semi-embayments, and a sea-level rise.

Traditional approaches to studying paleontological biodiversity have focused on richness, that is, the number of taxa at a given level in the Linnaean hierarchy. While valuable, this approach does not capture the phylogenetic dimension of biodiversity as reflected by its taxonomic structure. This paper introduces a novel perspective in the study of past biodiversity by applying taxonomic distinctness (TD) metrics, average taxonomic distinctness (AvTD) and variation in taxonomic distinctness (VarTD), to investigate the rediversification of marine bivalves following the Permian–Triassic mass extinction. Using a dataset of 59 fossil faunas, we explore the dynamics of the taxonomic tree during the Triassic and along paleolatitudinal gradients. Subtropical assemblages show higher AvTD and lower VarTD than tropical ones, suggesting ecological and biogeographic influences on the taxonomic structure. In the temporal dimension, our data reveal an Early Triassic decrease in AvTD and an increase in VarTD, followed by a long-term trend of increasing AvTD and decreasing VarTD that persisted until the Norian. This pattern suggests that vacant ecospace after the end-Permian mass extinction did not stimulate the immediate appearance of a disproportional number of supraspecific taxa, possibly due to the unusual biotic and abiotic environment of the early postextinction time. In contrast, the long-term increase in AvTD that followed this Early Triassic lag phase indicates a low but steady surplus of supraspecific taxa relative to newly evolved species. This observation supports macroevolutionary scenarios in which evolutionary rates correlate with ecological opportunity. However, the long duration of this phase is unexpected, particularly when compared with conventional indicators for “complete” recovery. Based on TD metrics, recovery from the greatest Phanerozoic mass extinction went on at least until the end of the Norian, nearly 50 Ma after the crisis.

The patterns by which ancestral species give rise to descendants offer critical insights into the processes governing evolutionary and ecological change through time. One such pattern, predicted by both theoretical models and empirical studies, is the persistence of long-lived ancestral species that give rise to multiple descendants. While models such as the birth–death process long employed by paleobiologists predict the occurrence of such “super-progenitors,” the extent to which they should appear in fossil clades remains unknown. To address this, I apply a birth–death-sampling model to four marine clades to evaluate the expected prevalence of super-progenitors and the distribution of sampled descendants. I also explore through analytical and simulation-based predictions how variation in preservation, turnover, and net diversification rate influences these expectations. The model predicts that super-progenitors should be common across nearly all of the clades examined, provided that sampling completeness exceeds approximately 50% at the taxon level. Although the threshold excludes some poorly sampled terrestrial groups, my findings suggest that super-progenitors should be expected across a broad array of clades. Continued integration of super-progenitors into phylogenetic inference and models of diversification may thus contribute to a more complete understanding of macroevolutionary pattern and process.

Species recognition is an essential part of biological and paleontological study. In gastropods, although species are genetic entities, shell morphology continues to be used as the primary source of information to recognize most species. While there are few directly tested cases, variations in conchological characters for modern species are expected to reflect underlying genetic differences that define a biological species, an assumption that is also applied to identify species in the fossil record. Additionally, how consistently shell shape differentiates gastropod species remains poorly understood. In this study, shell shape of Recent and Pliocene–Pleistocene fossil specimens of well-known intertidal gastropods (Littorinidae, periwinkles: †Littorina petricola, Littorina keenae, and the sister-species pair Littorina plena and Littorina scutulata) from the east Pacific was analyzed using landmark-based morphometrics and compared with published molecular data. For the extant species, there is a general positive relationship between shell shape and genetic differences. Discriminant function analyses indicate distantly related species can be more reliably recognized from their shells, while closely related species have a higher error. Fossils and recent specimens were classified with similar consistency. More work is needed to illuminate whether this case applies more widely.

The chances that existing taxa are replaced by new taxa decreases over Phanerozoic time, and older taxa persist for longer and longer. This long-term trend has been interpreted as resulting from repeated culling and non-replacement of groups with high turnover or, in other words, from long-term selection for extinction resistance. It is therefore assumed that taxon-specific properties are critical for this trend. However, taxa are part of higher-level ecological genealogical units that represent shared genealogies and histories of ecological interactions. Structural aspects such as the composition of the evolving eco-genealogical units as a possible explanation have received little attention.

Here we analyzed the temporal change within Phanerozoic benthic marine mega-assemblages (PMAs). PMAs are groups of marine animal genera delineated through hierarchical modular partitioning of a multilayer spatiotemporal network and interpreted as eco-genealogical units. For each higher-level PMA, we calculated how its median genus age, its richness, the evolutionary rates, and the spatial β-diversity changed over time. The resulting estimates support the assumption that the assemblages are meaningful eco-evolutionary units, because their temporal patterns differ from those of randomly chosen Phanerozoic time intervals.

PMAs differ from randomly chosen intervals in that the increase of genus age is associated with a decline in origination proportions and with increasing β-diversities. This contradicts the hypothesis of a simple Phanerozoic sorting toward extinction resistance and generalization. The observed pattern can be explained as a process of eco-evolutionary entrenchment resulting from conditioned assembly and weak within-lineage directionality toward specialization and geographic restriction.

The Lilliput Effect, wherein assemblages decrease in mean individual body size after mass extinctions, has not been documented at a wide geographic scale in any of the Late Devonian mass extinction pulses in invertebrate taxa. Based on a dataset of 800 scolecodonts (polychaete jaw elements) from the literature, museum collections, and newly presented data from the Appalachian Basin, we find that scolecodont size distribution per temporal bin decreases across the Frasnian/Famennian Kellwasser Events from a median length of 500 μm before the Kellwasser Events to a median length of 196 μm during the Kellwasser Events. The majority of the small scolecodonts documented during the extinction interval are newly measured specimens from the Kellwasser Events of the Appalachian Basin, although this size change is not unique to the Appalachian Basin. We interpret the reduction in body size as a hypoxia-driven occurrence of the Lilliput Effect because of the susceptibility of benthic invertebrates to hypoxia and the association of this extinction event with hypoxia. While previous studies have shown that polychaete community biomass decreases in response to oxygen stress, our study provides fossil evidence of individual size reduction, plausibly due to oxygen stress.