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.

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.

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.

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.

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.

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 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.

Morphological characters are central to phylogenetic inference, especially for fossil taxa for which genomic data are unavailable. While Bayesian methods have gained popularity in recent years, they typically assume characters evolve independently, despite known correlations among characters. Here, we assess the impact of character correlation and evolutionary rate heterogeneity on Bayesian phylogenetic inference using extensive simulations of binary characters evolving under independent and correlated models. We find that Bayesian inference assuming character independence accurately recovers tree topologies even when characters are strongly correlated or evolve under heterogeneous rates. However, branch lengths or clock rates tend to be underestimated, particularly under extreme rate heterogeneity. These biases are partially corrected using models that integrate over character-state heterogeneity. Our results demonstrate that Bayesian methods are robust to violations of character independence in topological inference, supporting their continued use in morphological phylogenetics.

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.

Linear state space models provide a useful framework for investigating phenotypic evolution in fossil lineages for a wide variety of models representing Brownian motion, Ornstein-Uhlenbeck processes, and the potential influence of environmental covariates. A state space framework also provides access to residuals for the predicted and observed values at each time point as well as improved numerical stability. We illustrate the value of the state space approach by reanalyzing a classic dataset of trait evolution in the diatom lineage Stephanodiscus yellowstonensis. A series of increasingly complex models were fit to these data, including a novel modification of an Ornstein-Uhlenbeck model in which a trait tracks an exogenous covariate. These model results suggest that the number of spines on the periphery of the diatom is best explained by adaptation to changing solar insolation over time.

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.

The evolution of the mandible in mammalian carnivores is influenced by ecological demands that have changed over their phylogenetic history. We combined geometric morphometrics and biomechanical analysis (including beam analysis and finite element analysis, or FEA) to assess the interaction between form and function as the mandible has adapted independently to carnivorous diets in therian clades including Metatheria, Mesonychia, “Creodonta,” and Carnivoramorpha. Our goal was to determine the relative contributions of mechanical advantage, mandibular force, and mandibular resistance to bending and torsion, to the evolution of mandibular shape in these groups, as well as whether they produce differential rates of shape evolution in the horizontal and ascending rami, which respectively are the tooth-bearing and muscle-loading parts of the structure.

We found that the ascending ramus has higher rates of evolution than the horizontal ramus, making it the more rapidly evolvable portion of the mandible. Statistical evaluation supports this interpretation, as mechanical advantage and resistance to force explain more of the variance in shape than do the beam mechanic estimates that are heavily influenced by the mandibular body. Regression analysis shows that the evolution of specialized carnivory was associated with stronger mandibles in which mandibular shape changed by shortening and thickening of the mandible, increasing the areas of muscle attachment, and increasing the carnassial blade length. Principal component analysis of mandibular shape shows that different clades in Theria have been able to fill out similar specialized carnivorous niches with similar functional metrics despite having different mandibular morphologies.

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 rarity of preserved soft tissues in the fossil record has limited our understanding of the life appearance of extinct vertebrates. However, through examination of various osteological features and comparisons with extant ecomorphological analogues, we can predict some of the external characteristics of ancient taxa. Specifically, for the Cretaceous mosasaurians (a group of seagoing squamates), extant sharks serve as suitable modern analogues because of their comparable caudal vertebral morphologies and ecologies. In this study, we build a novel framework by combining two-block partial least squares (2B-PLS) regression analysis and geometric morphometrics to investigate the relationship between tail fin shape and the underlying musculoskeletal morphology in sharks and mosasaurians. Our analysis reveals a strong correlation between the “tail fin expanded soft tissue” (TFEST) and shape of the associated caudal skeleton/musculature. Moreover, the covariation pattern between these two structures is remarkably similar in sharks and mosasaurians. Based on these findings, we then develop a predictive model that reconstructs the tail fin in mosasaurian taxa without known soft tissues. Our model indicates that all hydropedal forms possessed a bilobed, hypocercal (downturned) fluke, while plesiopedal species lacked a well-developed fleshy dorsal lobe. The variation in fluke morphologies between the four different evolutionary lineages of derived mosasaurians (mosasaurines, halisaurines, plioplatecarpines, and tylosaurines) suggests multiple independent origins of a bilobed tail fin. This study thus highlights the complexity of aquatic adaptations in mosasaurians and demonstrates the utility of predictive models when reconstructing the life appearance of extinct animals.