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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.