Digenean trematodes are parasites with a complex life cycle that often infest shell-bearing mollusks and produce distinct traces on the host skeleton that are recognizable in the fossil record. Here, three bivalve species (Transennella conradina, Abra segmentum, and Chamelea gallina) from Pleistocene and Holocene deposits of Florida and Italy were used to evaluate the hypothesis that trematode infestation affects shell morphology. The morphological effects of infestation were evaluated using geometric morphometrics and the pallial sinus index (PSI = pallial sinus length/shell length). For all three host species: (1) large size classes possess higher trematode prevalence (i.e., proportion of specimens possessing trematode-induced pits within a population) and higher per-specimen frequency of trematode-induced scars when compared with smaller size classes, suggesting ontogenetic accumulation of parasites; and (2) infested and non-infested specimens significantly differ in shell landmark-based morphology. Geometric morphometric analyses indicate that in two out of three species (Transennella conradina, Abra segmentum): (1) PSI and thin-plate spline analyses suggest significant pallial sinus reduction in infested specimens relative to non-infested; and (2) overall morphospace range, estimated by sample-standardized principal component (PC) hypervolume, was inflated with the inclusion of infested specimens. Consistent with previous studies, results indicate that trematode-induced morphological changes may influence the burrowing capabilities of the studied bivalves, affecting their ecological functioning and fitness. Changes in morphospace induced by trematode parasites hamper species delineation and confound morphometric and disparity patterns in the fossil record of infestation-prone species. Excluding fossil specimens with trematode traces can mitigate those confounding effects. Conversely, comparative morphometric analyses of infested and non-infested host specimens may allow us to investigate host responses to parasites over evolutionary timescales.

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.

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.

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.

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.

Sexual dimorphism, a widespread phenomenon, has been extensively researched in extant and fossil crustaceans. However, identifying sexual dimorphism in phyllocarid fossils preserved as isolated parts is often challenging, except in cases where the specimens are exceptionally well preserved, including those with soft tissues. This study proposes a novel approach by introducing the use of geometric morphometric techniques to identify sexual dimorphism in phyllocarid fossils based on carapace morphology. It presents a comprehensive re-analysis of Soomicaris ordosensis Liu et al., 2023a, carapaces from the Upper Ordovician in North China and Tarim Plates. Elliptic Fourier analysis was applied to quantify the size and shape variation in nearly 100 specimens. The results demonstrate the presence of significant sexual dimorphism in the length and shape of the S. ordosensis carapace. The carapace shape exhibited variation between the sexes: the posterodorsal margin of one group of carapaces gradually extends backward to form a posterodorsal spine; the carapaces of the other group have a convex posterior margin and lack a posterodorsal spine. Additionally, both types manifest an overall allometric growth pattern, albeit with distinct growth coefficients. Furthermore, the observed approximately 1:1 ratio between the two forms suggests that the population of S. ordosensis may have exhibited a dioecious mating system. Geometric morphometrics are a highly effective method for elucidating the subtle variations in the carapace morphology of S. ordosensis, thereby underscoring the cryptic dimorphism characteristics of fossil animals. This finding offers the first indirect evidence for egg-brooding behavior within the extinct order Archaeostraca.

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.

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.

An important question in evolutionary biology and macroecology is whether taxa show systematic trajectories in occupancy, the proportion of geographic area occupied, over macroevolutionary timescales. Past studies have used fossils to document these trajectories, showing a symmetric rise and fall. In this study, I focus on several biases in the analyses of fossil occupancy trajectories that have been unaccounted for. First, better sampling of boundary bins in a taxon’s stratigraphic range, paradoxically, results in lower mean occupancy of taxa in those bins. This is because better sampling allowed more taxa with low occupancies to be included in the mean occupancies of those bins compared with intermediate bins. Second, the possibility that taxa may have incomplete durations within boundary bins could also lower occupancies in those bins. Finally, a bias can also exist when the number of sampled sites is not constant throughout a taxon’s stratigraphic range. I use simulations to show that the first bias can be corrected by conditioning these boundary bins to be sampled in the same way as intermediate bins. To mitigate the second bias, I use higher-resolution time bins to constrain the intervals over which taxa’s occupancies are measured so that they are comparable between boundary and intermediate time bins. I also present an approach that can correct for the last bias by subsampling geographic sites, testing its impact in a simulation. Considering these factors, the occupancy trajectories of marine animal genera look to be a relatively gradual rise post-origination with a sudden decline before extinction.

Orthoceratoid cephalopods had straight or slightly curved shells that often contained enigmatic calcareous structures in their chambers. These cameral deposits have been interpreted as counterweights, allowing these cephalopods to assume postures other than a default, downward-facing orientation. These animals must have balanced the proportions of their soft body, cameral deposits, and air-filled chambers to maintain a condition near neutral buoyancy. Lower body chamber ratios (BCRs) allow more mass to be dedicated to cameral deposits, increasing their influence over the total mass distribution. Using 43 computer reconstructions, we calculated the proportion of chamber contents that satisfy a neutrally buoyant condition across different BCRs. Furthermore, we explored the limits of cameral deposit distributions inside the shell to better understand their influence over orientation, stability, and maneuverability. Cephalopods with 40% BCR cannot accommodate any deposits and assume stable, downward-facing orientations. Cephalopods with 30% BCR allow some cameral deposits, which negligibly reduce stability. A slight reduction in BCR to 25% can considerably improve maneuverability, allowing these cephalopods to assume a wider range of postures while swimming. While our results are most relevant to some subset of orthocone cephalopods (Pseudorthoceratida), we also highlight similar constraints faced by broader orthocone groups. Swimming capabilities are extremely sensitive to BCR, which likely constrains the life habits and ecology of these animals. Our results add context to (1) the physical constraints of orthocone cephalopods, (2) their functional complexity in Paleozoic ecosystems, and (3) how these early swimmers navigated physical trade-offs between stability and maneuverability.

Bones preserved in fluvial sediments make up the majority of the terrestrial vertebrate fossil record, and unsteady flows (overbank floods, levee breaches, debris flows, etc.) are often invoked as agents of bone transport and burial. Experiments exploring transport of mammal bones under steady-state flow led to the development of Voorhies Groups, which are used as indicators of winnowing and transport at fossil sites. Some studies have raised concerns about the use of transport groups beyond the scope of the original experiments, especially regarding untested taxa and flow conditions. Here we investigate transport of hadrosauroid dinosaur bone models and modern sheep bones in experimental sheet floods. We find that evolving flow dynamics in unsteady flows can influence bone mobility behaviors. Factors such as bedforms and interactions with other bones caused shorter transport distances than might be expected in some elements, which would be heightened in real flooding situations where trapping mechanisms are common. Our hadrosauroid bones sorted into two statistically significant groups and one overlapping intermediate group based on transport distance. However, those groups could not be identified among sheep bones. Distributions of transport distances in both taxa do not fully match predictions based on Voorhies Groups. Our results indicate that Voorhies Groups do not quantitatively apply to all potential fluvial settings and taxa, and we thus advise caution in interpretations of fossil site taphonomic history based on Voorhies Groups. Further exploration of variables underlying bone transport and burial may allow for more broadly comparative examinations of fluvial biostratinomy.

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.

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.

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.