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.

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 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.

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 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 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.

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.

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.