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.

Sister groups (two clades sharing a common ancestor) often differ greatly in taxonomic, phenotypic, and ecologic diversity, but explanations for these differences remain elusive. One hypothesis is that mate choice involving display promotes genetic isolation and thus speciation. We test this and other hypotheses by analyzing individual-level phenotypes that evolved in one but not the other of the two great molluscan sister clades Aculifera (chitons and relatives) and the much more diverse Conchifera (snails, clams, squid, and their relatives). The key difference lies in the morphological relationship between body and shell, which in Aculifera are tightly coupled, greatly limiting locomotion, activity, and mate choice. In Conchifera (especially in the major subclade Megalopodifera), the body and shell are more decoupled, facilitating a wide range of activity, modular evolution, and ecological expansion. Contrary to the primacy of mate choice as an engine of diversification, display-related mate choice is part of a larger theme of evolutionary feedbacks among habitat (including mate) choice, locomotor and other activity, and speciation. Some conchiferan clades never diversified and remain phenotypically conservative, highlighting the fact that the only unifying feature of a clade is its retrospective monophyly.

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.

Ontogenetic change is a major source of phenotypic variation among members of a species and is often of greater magnitude than the anatomical differences that distinguish closely related species. Ontogeny has therefore become a problematic confounding variable in vertebrate paleontology, especially in study systems distant from extant crown clades, rendering taxonomic hypothesis testing (a fundamental process in evolutionary biology) rife with difficulty. Paleontologists have adopted quantitative methods to compensate for the perception that juvenile specimens lack diagnostic apomorphies seen in their adult conspecifics. Here, I critically evaluate these methods and the assumptions that guide their interpretation using a μCT dataset comprising growth series of American and Chinese alligator. I find that several widespread assumptions are scientifically unjustifiable and that two popular methods—geometric morphometrics and cladistic analysis of ontogeny—have unacceptably high rates of type II error and present numerous procedural difficulties. However, I also identify a suite of ontogenetically invariant characters that differentiate the living species of Alligator throughout ontogeny. These characters overwhelmingly correspond to anatomical systems that develop before (and play a signaling role in) the development of the cranial skeleton itself, suggesting that their ontogenetic invariance is a consequence of the widely conserved vertebrate developmental program. These observations suggest that the architecture of the cranium is fixed early in embryonic development and that ontogenetic remodeling does not alter the topological relationships of the cranial bones or the soft tissue structures they house. I propose a general model for future taxonomic hypothesis tests in the fossil record, in which the hypothesis that two specimens are different ontogenetic stages of a single species can be falsified by the discovery of character differences that cannot be attributed plausibly to ontogenetic variation.

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 mammalian skull plays important roles in sensing, communication, and obtaining and processing food. These diverse functions make the skull a natural target for investigating how developmental processes and selective pressures related to ecology interact to produce patterns of morphological evolution. Here, we investigate the evolution of the equid skull through the lens of craniofacial evolutionary allometry (CREA), a pattern of relative facial elongation in larger mammals that has been hypothesized to result from similar patterns of facial elongation over ontogeny. Using 3D geometric morphometrics and linear measurements, we describe the major axes of shape variation in the equid skull, test whether equids follow or deviate from the CREA pattern over the clade’s evolutionary history, and assess whether the evolution of high-crowned teeth (hypsodonty) is related to relative facial proportions, all in an explicitly phylogenetic context. We find that equids deviate from the CREA pattern and that the evolution of hypsodont dentition did not significantly influence facial proportions in the group. Importantly, these results are only apparent when using statistics appropriate for phylogenetic data. Comparison with previously published data on facial proportions from modern equids indicates that ontogenetic patterns of facial elongation do not scale to produce patterns of facial proportions observed at the intraspecific and evolutionary levels. Taken together, our results complicate the historic narrative that a single set of selective factors drove patterns of morphological evolution within the group.

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.

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.

Sauropodomorphs were the largest terrestrial animals to have ever existed on Earth.

While previous studies using skeletal remains and digital 3D models suggested that manus became more circular shape and relatively larger over time, this study uses trackways to test these hypotheses with a much larger sample size. In this study, we used the sauropodomorph trackway record from the Early Jurassic to the Late Cretaceous to analyze temporal changes in manus and pes shapes and their relationship with body size. We analyzed footprint measurements from 690 trackways and, for the first time, applied elliptic Fourier descriptors (EFDs) to sauropodomorph footprint outlines to quantitatively assess their morphology. Analyses revealed temporal and size-related changes in manus morphology, whereas no changes were observed in pedes. Specifically, manus shape became anteroposteriorly longer over time and in larger individuals. The relative manus area compared with pes area (the heteropody) also increased chronologically; however, manus areas showed negative allometry relative to pes areas. These results indicate that the temporal change toward circular or horseshoe-shaped manus morphology in sauropodomorphs represents an adaptation to gigantism, while the chronological increase in manus size relative to the pes reflects the radiation of a clade (Titanosauria) with proportionally large manus.

Living chondrichthyans comprise only a fraction of their historical diversity represented in the fossil record, but together they provide insights into the evolution of this ancient clade. Using a theoretical morphology approach, we sought the evolutionary drivers of mandible morphology, a key factor in the feeding ecology of the clade, across their more than 400 million year evolutionary history. Using an empirical sample of 122 extant and 95 extinct species across 35 orders, we created a theoretical morphospace that encompasses, and expands beyond, sampled variation. We sampled morphologies from this theoretical morphospace and subjected them to biomechanical analysis of speed and strength, deriving landscapes of functional performance and optimality into which we projected a phylomorphospace. We examined how the optimality landscape has been navigated by chondrichthyan evolution and how it has been occupied by taxa characterized according to habitat and trophic level. The empirical chondrichthyan morphospace occupation was dispersed from the trade-off optimality peaks. Early chondrichthyans occupy morphospace characterized by narrow, curved jaws before expanding to more robust morphologies through time. This move toward robust morphologies does not follow the most optimal trade-off morphologies, instead avoiding areas that are least optimal. Deep-water species occupy the largest morphospace area, while higher trophic level species stay closer to the trade-off optimality peaks. Our study shows that chondrichthyans, rather than being living fossils, have explored increasingly specialized jaw morphologies, likely related to shifts in ecology such as increased numbers of durophagous taxa, as opposed to a more generalist optimization of component biomechanical constraints.

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.

In whales, extreme modifications to the ancestral mammalian feeding apparatus facilitate novel modes of aquatic feeding. These modifications manifest in morphological diversity across a suite of characters, including the mandibular symphysis. Cetaceans span a range of symphyseal morphologies, with one lineage (crown mysticetes) evolving a highly mobile condition unique among mammals. Here, we use phylogenetic comparative methods to examine the evolution of symphyseal fusion and elongation across 206 extant and fossil cetacean taxa. Ancestral state reconstructions corroborate observations from the fossil record that suggest the ancestral condition for Cetacea was a fused, moderately elongated symphysis. Shifts in symphyseal morphology coincided with ocean restructuring and diversification of feeding modes. Evolutionary rates peaked in the middle–late Eocene and at the Eocene/Oligocene boundary as whales evolved shorter, unfused symphyses. During the Eocene, ankylosed mandibles became less common with the appearance of increasingly pelagic whales. Mysticetes evolved decoupled, highly mobile mandibles near the Eocene/Oligocene boundary. Several odontocete lineages underwent a trait reversal and converged on fully fused, elongated mandibles in the Miocene. Analyses evaluating the influence of ecological variables indicate strong correlations in feeding strategy, dentition, and prey type. The loss of prey-processing behavior and changes to masticatory loading regimes may explain concurrent trends in symphyseal morphology and tooth simplification. We suggest that the functional and morphological diversity of the symphysis in whales is a consequence of aquatic feeding imposing different mechanical constraints than those associated with feeding on land.

Abelisaurid dinosaurs display a remarkable diversity in cranial ornamentation, which includes several features such as rugosities, pits and grooves on the rostrum and orbital regions, midline knobs, and paired plus sculptured structures across the skull roof. To investigate macroevolutionary patterns that underlie this diversity, we tested the “species recognition” hypothesis using phylogenetic comparative methods. Our results indicate directional and ordered evolutionary patterns in cranial ornamentation that are more consistent with expectations of sexual selection than with the stochastic patterns predicted under the species recognition hypothesis. Moreover, sympatric species exhibited highly divergent ornamentation, and the degree of surface texturing and the development of certain structures (e.g., knobs) increased through ontogeny. These findings suggest that cranial ornamentation in Abelisaurids was influenced by mechanisms of sexual selection, sexual dimorphism, or mutual selection. Evolutionary modeling combined with evidence from the fossil record and phylogenetic correlation analysis reveals that the ornamentation of the rostrum and orbital regions was evolutionarily coupled and became canalized during the Early Cretaceous. In contrast, phylogenetic correlation analyses demonstrated that skull roof ornaments and rostral and orbital ornaments evolved decoupled. Neither discrete ornament traits nor the accumulation of traits over time showed significant associations with body size, indicating that ornament diversification in Abelisauridae was not constrained by allometric trends. During the Late Cretaceous, after refined ecological specialization, the subclades Carnotaurini and Majungasaurinae underwent further elaboration, acquiring features such as a prominent midline knobs, paired structures, and reinforced occipital and cervical regions. These derived morphologies may have facilitated more complex sociosexual behaviors.

Wing shape is integrally related to flight performance and function in extant animals. Analyzing this relationship in pterosaurs is complicated by the fragmentary nature of the fossil record and because the flight dimensions of wing membranes do not preserve. In the absence of fully extended pterosaur wing fossils, scientific reconstruction of the pterosaur Bauplan presents the clearest alternative for analysis. However, these wing shapes are subject to multiple conflicting scientific opinions and the artistic styles of the researchers and illustrators reconstructing them. Here we test the functional ramifications of different wing-shape reconstructions. We use theoretical morphospace analysis to establish whether modern reconstructions of pterosaur wings exhibit the diversification and functional performance expected of living animals. Pterosaur wing reconstructions show little by way of taxonomic separation either in shapespace or functional performance, with all pterosaur groups overlapping independent of time, size or proposed niche. This suggests that published pterosaur reconstructions underestimate the diversity of wing shapes expected of such a diverse group and are not reflective of flying animals. Stylistic approaches have little effect on the occupation and diversity of pterosaur reconstructions, suggesting that the underpinning issues lie in the lack of scientific consensus on the shape and structure of the wings, rather than how they are reconstructed.