Integrating information from the fossil record allows us to obtain accurate age estimates for important events in the evolutionary history of living species and to study the dynamics of speciation and extinction in more detail. The fossilized birth–death (FBD) process is a widely used model for the diversification of both extinct and extant species. Understanding the behavior of this model and the influence of its different parameters is thus very important for researchers interested in reconstructing the evolutionary history of species through time. Here, we present a web application built around the FBD process that allows users to simulate diversification and fossil sampling and visualize the results. The app can be used as a demonstration and teaching tool, allowing users to experiment with the different components of the model and observe their effect on the results of the simulation. It also helps researchers in designing simulation studies and testing their simulation choices.

Phylogenetic inferences using combined datasets of both extant and extinct species have grown increasingly popular, in part thanks to the development of the fossilized birth–death (FBD) process. The FBD process provides a powerful model for the evolution of past and present lineages and can be used for both inference and simulation. Simulations in particular are very helpful for new users to gain better understanding of the model and its different components. In this work, we present FossilSimShiny, a visual application for simulating phylogenies, fossil samples, and fossil taxonomies under the FBD process. The app integrates a wide range of simulation models and presents the simulation results in clear, customizable figures. As a teaching tool, FossilSimShiny allows lecturers to create illustration plots and students to directly experiment with the model. For research applications, the app can help researchers save time and effort by testing and calibrating simulation setups before running them on a large scale.

Over geologic time, shorelines build seaward and retreat landward, causing the elevation o coastal areas to change. Sediments deposited in rivers record these changes in elevation and distance to the coast, and organisms living in these environments may be preserved a fossils. If species vary among these environments, this variation might be preserved in the fos sil record, yet paleontologists have seldom documented this phenomenon. This absence raise the question of how commonly species distributions are related to elevation and distance to the coast. Here, we investigate the distributions of many plants, invertebrates, and vertebrate along the coastal plain of the southeastern United States, compiled from a community sourced public database. Statistical evaluation shows that many coastal communities vary pri marily with elevation and distance to the coast and to a lesser degree with latitude. Severa poorly documented groups display no detectable pattern of geographic variation, but it i unclear whether this is a true lack of variation or a lack of adequate data. The widespread occurrence of this pattern suggests that it is present in the fossil record yet has gone largely unnoticed.

In modern nonmarine settings, previous studies have demonstrated the importance of elevation-correlated ecological gradients, but such studies tend to focus on relatively small areas and only one higher taxon. Here, we analyze Global Biodiversity Information Facility occurrence records from a wide variety of taxa across the southeastern U.S. coastal plain. Many taxa display ecological gradients (gradients in proportional or relative abundance) correlated with elevation, distance to the coast, and latitude. These gradients tend to be steepest within a few tens of kilometers near the coast and at elevations less than 25 m. Some taxa, notably terrestrial mammals, do not display gradients correlated with elevation and distance to the coast. The small sample sizes of these groups and their heterogeneous sampling raise concerns about whether sufficient data exist. Coupled with previous studies of these ecological gradients, their common presence over distances of tens to hundreds of kilometers and elevations of tens to hundreds of meters suggests they are likely important in the nonmarine fossil record. Because elevation and distance to the coast change predictably with cycles of accommodation and sediment flux, these ecological gradients are predicted to occur in the nonmarine stratigraphic record, especially through intervals that record transgression or regression. Such gradients will affect the local composition of species associations and occurrences, even in the absence of regional species origination, immigration, and extinction and of regional change in the structure of ecological gradients. The ordination of taxon counts in stratigraphically limited samples has great potential for establishing their existence.

Bioturbation (biological mixing of solid particles and bioirrigation of burrows with water and solutes) should promote time averaging, shifting young shells downward into sedimentary increments with older shells and moving older shells upward where they can be mixed with newly produced shells. However, bioturbation is a double-edged sword for shell preservation, and also influences time averaging. On the one hand, bioirrigation of sediments promotes acid-producing reoxidation processes that dissolve carbonate shells; biomixing exhumes shells back into this taphonomically active zone (TAZ) and even up to the sediment–water interface, where they can be reexposed to physical damage and bioerosion, and the physical jostling, especially within siliciclastic sediments, can further damage weakened shells. On the other hand, biomixing can accelerate burial of shells well below the TAZ, advecting them into a sequestration zone faster than permitted by sediment accumulation alone; they achieve a time-out from aggressive disintegration in the TAZ and may become diagenetically stabilized. We assessed these competing effects of bioturbation on the disintegration and time averaging of bivalve shells in a modern-day, open-shelf siliciclastic setting (warm-temperate southern California shelf) relevant to shallow-marine fossil records, using a gradient in wastewater pollution that created conditions of both high and low sediment accumulation and high and low bioturbation, conditions that are beyond the scope and ethics of experimental manipulation. We found that bioturbation ultimately increases the time averaging of skeletal remains on this shelf, even though mixing and disintegration rates covary positively. Sediment (fine-matrix) accumulation remains the first-order control on the scale of time averaging: high rates limit time averaging regardless of bioturbation. However, a decline in bioturbation, either over space or through time (both explored here), also reduces time averaging. The well-documented increase of burrowing depth and intensity over the Phanerozoic, established independently by others, is thus probably associated with a secular increase in time averaging.

Bioturbation can increase time averaging by downward and upward movements of young and old shells within the entire mixed layer and by accelerating the burial of shells into a sequestration zone (SZ), allowing them to bypass the uppermost taphonomically active zone (TAZ). However, bioturbation can increase shell disintegration concurrently, neutralizing the positive effects of mixing on time averaging. Bioirrigation by oxygenated pore-water promotes carbonate dissolution in the TAZ, and biomixing itself can mill shells weakened by dissolution or microbial maceration, and/or expose them to damage at the sediment–water interface. Here, we fit transition rate matrices to bivalve age–frequency distributions from four sediment cores from the southern California middle shelf (50–75 m) to assess the competing effects of bioturbation on disintegration and time averaging, exploiting a strong gradient in rates of sediment accumulation and bioturbation created by historic wastewater pollution. We find that disintegration covaries positively with mixing at all four sites, in accord with the scenario where bioturbation ultimately fuels carbonate disintegration. Both mixing and disintegration rates decline abruptly at the base of the 20- to 40-cm-thick, age-homogenized surface mixed layer at the three well-bioturbated sites, despite different rates of sediment accumulation. In contrast, mixing and disintegration rates are very low in the upper 25 cm at an effluent site with legacy sediment toxicity, despite recolonization by bioirrigating lucinid bivalves. Assemblages that formed during maximum wastewater emissions vary strongly in time averaging, with millennial scales at the low-sediment accumulation non-effluent sites, a centennial scale at the effluent site where sediment accumulation was high but bioturbation recovered quickly, and a decadal scale at the second high-sedimentation effluent site where bioturbation remained low for decades. Thus, even though disintegration rates covary positively with mixing rates, reducing postmortem shell survival, bioturbation has the net effect of increasing the time averaging of skeletal remains on this warm-temperate siliciclastic shelf.

Understanding how predators respond to climate change is crucial given their disproportionate impact on ecosystems from their place atop the food chain. Past studies, which relied on simply keeping track of the number of species though time, concluded that predators were largely unaffected by climate change. However, our research challenges this notion by examining how tooth shape changed in North American mammalian predators over the Cenozoic (65 million years ago to the present). In our study, we collected and analyzed body-mass and tooth-shape data for both living and fossil mammalian predators. From our analysis on living mammalian predators, we found those with bladelike molars were more commonly found in open habitats. When we applied this result to our fossil mammalian predators, we found evidence for a similar relationship occurring in the past. Throughout the Cenozoic, the North America landscape transitioned from tropical forests to a patchwork of both larger open areas and smaller forests as the climate began to cool. Our study found that in response to this transition, fossil predator molars became more blade-like, demonstrating a response to a changing habitat. This discovery challenges the traditional belief that predators remained unaffected by climate change in the past and highlights the importance of accurately understanding historical responses to habitat change in predators.

The trend of global cooling across the Cenozoic transformed the North American landscape from closed forest to more open grasslands, resulting in dietary adaptations in herbivores in response to shifting resources. In contrast, the material properties of the predator food source (muscle, skin, and bone) have remained constant over this transition, suggesting a corresponding lack of change in predator dietary adaptations. We investigated the North American mammalian predator fossil record using a tooth-shape metric and body mass, predicting that the former would exhibit stability. Instead, we found that mean molar morphology became more blade-like, with our tooth-shape metric sharply increasing in the late Eocene and remaining high from the Oligocene onward. Subsequent tests in extant carnivorans reveal taxa with more bladelike teeth are prevalent in more open environments. Our results reveal an unexpected functional shift among North American predators in response to large-scale environmental changes across the Cenozoic.

Caryocaridids are a unique representative of the pelagic arthropod group during the Ordovician and stand out from other arthropods (ostracods, trilobites, etc.) for their remarkable pelagic abilities. Herein, we report on a species of caryocaridids, Soomicaris cedarbergensis, from the Lower Ordovician in northwestern Xinjiang, NW China, which shows the rare enrolled carapaces with the evidence of cuticular ultrastructure preserved. These caryocaridid specimens from Xinjiang provides the substantial evidence for the presence of caryocaridids in the Central Asian Orogenic Belt. This discovery suggests that S. cedarbergensis appeared as early as the Early Ordovician (late Tremadocian) and persisted until the end-Ordovician (Hirnantian) and is the longest-ranging species of known caryocaridids. The cuticle of the carapace in S. cedarbergensis is preserved in carbonate-fluorapatite, which can be divided into three mineralized lamellae (outer, middle, and inner). The outer and inner lamellae both consist of three layers, which seem to correspond to the epicuticle, exocuticle, and endocuticle of extant crustacean carapaces, respectively. The particular ultrastructure of the carapace of Ordovician caryocaridids (thin cuticle; thickened inner lamella cuticle; and large, complex oxygen supply system) probably represents an adaptation to the pelagic lifestyle during the Ordovician plankton revolution.

Caryocaridids are a unique representative of pelagic arthropods from the Ordovician period. They are typically found as flattened carapaces in mudstones and shales. This study reports on a species of caryocaridids, Soomicaris cedarbergensis, discovered in the Lower Ordovician of northwestern Xinjiang, NW China. The species shows the rare enrolled carapaces with a preserved cuticular ultrastructure. These specimens of caryocaridids from Xinjiang are the first reported in the Yili Block, and provide the substantial evidence that the paleogeographic distribution of caryocaridid phyllocarids could extend to the Central Asian Orogenic Belt. This species existed from the late Tremadocian until the end of the Ordovician (Hirnantian), making it the longest-ranging known species of caryocaridids. The carapace cuticle of S. cedarbergensis is composed of carbonate-fluorapatite and can be divided into three mineralized lamellae: outer, middle, and inner. The outer and inner lamellae each consist of three layers that correspond to the epicuticle, exocuticle, and endocuticle of extant crustacean carapaces. Moreover, the polygonal reticulation structure of the carapace in archaeostracans appears to be similar in shape and size to the hemolymph sinuses of leptostracans. This unique ultrastructure of the carapace cuticle in caryocaridids is believed to be better suited for a pelagic lifestyle.

Tribrachidium heraldicum is among the first large and structurally complex animals, appearing in the fossil record 550 million years ago. By using engineering software to simulate fluid flow around digital models of this organism, we recreate details of how it lived, including how it fed and the likely functions of its bizarre anatomy.

Tribrachidium heraldicum is an Ediacaran body fossil characterized by triradial symmetry. Previous work has suggested that the anatomy of Tribrachidium was conducive to passive suspension feeding; however, these analyses used an inaccurate model and a relatively simple set of simulations. Using computational fluid dynamics, we explore the functional morphology of Tribrachidium in unprecedented detail by gauging how the presence or absence of distinctive anatomical features (e.g., apical pits and arms) affects flow patterns. Additionally, we map particle pathways, quantify deposition rates at proposed feeding sites, and assess gregarious feeding habits to more fully reconstruct the lifestyle of this enigmatic taxon. Our results provide strong support for interpreting Tribrachidium as a macroscopic suspension feeder, with the apical pits representing loci of particle collection (and possibly ingestion) and the triradial arms representing morphological adaptations for interrupting flow and inducing settling. More speculatively, we suggest that the radial grooves may represent ciliated pathways through which food particles accumulating in the wake of the organism were transported toward the apical pits. Finally, our results allow us to generate new functional hypotheses for other Ediacaran taxa with a triradial body plan. This work refines our understanding of the appearance of suspension feeding in shallow-water paleoenvironments, with implications for the radiation of Metazoa across the Ediacaran/Cambrian boundary.

The horned dinosaurs underwent great changes throughout their evolution, including a shift in the locomotor mode (from bipedal to quadrupedal posture), enlargement of horns and frills, and increase in body size. Endocast reconstruction also suggests a decrease of olfactory acuity, hearing frequency, and the reptile encephalization quotient in derived horned dinosaurs. However, it is still unclear how these endocranial structures changed in early ceratopsian taxa due to a lack of information from the earliest horned dinosaurs. Here, we use virtual analytical methods to reconstruct the endocast of extinct dinosaurs and examine the evolution of the endocasts of horned dinosaurs that display some unique structures associated with auditory sense and smell. Based on the dataset and analytical detail on endocranial structures, we found that early-diverging horned dinosaurs (e.g., Yinlong and Psittacosaurus) had a high olfactory acuity and were adapted to hearing high frequencies, whereas the late-diverging horned dinosaurs (e.g., Triceratops) possessed lower olfactory acuity and hearing frequency. The early horned dinosaurs bear relatively large brain volumes, even higher than most extant reptiles. Head posture in ceratopsians displays a transition from forward facing to a downward tilt, indicating their different feeding preferences. These results are valuable for understanding the evolution of horned dinosaurs as well as extant tetrapods.

Ceratopsian dinosaurs underwent great changes, including a shift of locomotion mode, enlarged horns and frills, and increased body size. These changes occur alongside the evolution of endocranial morphology and physiology such as the size and shape of the flocculus, hearing range, olfactory ratio, and the reptile encephalization quotient (REQ). However, the evolution of endocranial structures in early ceratopsians is still unclear because of a lack of information on the earliest ceratopsians. Here, we reconstructed the endocasts of three early-diverging ceratopsians including the Late Jurassic Yinlong, and the Early Cretaceous Liaoceratops and Psittacosaurus. These ceratopsians display obvious flocculi, large and separate olfactory bulbs, long and high anterior semicircular canals, and relatively long cochlear ducts. In the evolution of the earliest ceratopsians to early neoceratopsians, changes include the increasing size of the flocculus (which is reduced or absent in late-diverging ceratopsids), the attenuation of the semicircular canals, and the heightening of the anterior semicircular canal (which is shortened in late-diverging ceratopsids). The endocranial structures suggest early-diverging ceratopsians had a higher olfactory acuity and were adapted to hearing higher frequencies than late-diverging ceratopsians. Furthermore, the REQ suggests that Yinlong and Psittacosaurus were more highly encephalized than late-diverging ceratopsians and most extant reptiles. The angle of the lateral semicircular canal suggests that heads in ceratopsians display a transition from a forward posture to a more downward posture. Our new findings are significant for understanding the physiological changes during ceratopsian evolution and also have implications for the evolution of physiology in extant tetrapods.

This study proposes a new computational method using a 3D digital model to understand how the zone of contact between cranial bones (namely sutures) works mechanically. In cranial mechanics, only movements in which the bones remain in constant contact are allowed. Therefore, we reproduced all these movements in four cranial models using different contact properties to validate the new methodology. The results obtained suggest that first, when the skull allows less movement between bones, stress is concentrated on certain points of the skull; and second, when the skull allows more movement between cranial bones, the stress tends to be dispersed in other bones, protecting the skull's physical integrity. Finally, we used these computational models to reproduce different types of predatory feeding behavior observed in animals such as crocodiles and alligators. We conclude that the new method to model the contact between bones can be applied to fossils of extinct animals that do not preserve soft tissue as cranial sutures.

Understanding cranial sutures and how they relieve and dissipate stress is essential to assess their role in cranial biomechanics and to develop highly accurate predictive models. This involves examining how ontogeny affects cranial sutures, as well as their morphology and function, and how these changes through time may impact essential biomechanical loadings such as chewing or direct biting. In this work, we study the cranial sutures of Crocodylus niloticus in detail using contact elements under finite element analysis. Contact elements permit the creation of a physical relationship between two bones that are in contact and even the configuration of these relationships, for example, in terms of movement or flexibility. The definition of bone contacts may require linear and/or nonlinear computational solutions to attain higher accuracy. Herein, skull geometry is tested to determine how bones may be altered by different types of contacts under various conditions. As predicted, the absence of sutures or cranial kinesis leads to a reduction in stress distribution across the skull, whereas sutures and cranial kinesis help the skull relieve stress and prevent certain bones from sustaining high stress levels. The type of contact used in individual sutures has a significant effect on model outcomes. Additionally, feeding behaviors significantly impact cranial biomechanics, reflecting the influence of other variables that may be applied to the models. As highlighted by the results, in order to obtain accurate results when analyzing fossil taxa, the nature of the cranial sutures should be taken into account. Therefore, developing predictive models based on living taxa is invaluable, because it facilitates the study of extinct taxa for which there is a lack of information on the fibrous joints due to poor or no preservation in the fossil record.