The intersection of paleontology and biomechanics can be reciprocally illuminating, helping to improve paleobiological knowledge of extinct species and furthering our understanding of the generality of biomechanical principles derived from study of extant species. However, working with data gleaned primarily from the fossil record has its challenges. Building on decades of prior research, we outline and critically discuss a complete workflow for biomechanical analysis of extinct species, using locomotor biomechanics in the Triassic theropod dinosaur Coelophysis as a case study. We progress from the digital capture of fossil bone morphology to creating rigged skeletal models, to reconstructing musculature and soft tissue volumes, to the development of computational musculoskeletal models, and finally to the execution of biomechanical simulations. Using a three-dimensional musculoskeletal model comprising 33 muscles, a static inverse simulation of the mid-stance of running shows that Coelophysis probably used more upright (extended) hindlimb postures and was likely capable of withstanding a vertical ground reaction force of magnitude more than 2.5 times body weight. We identify muscle force-generating capacity as a key source of uncertainty in the simulations, highlighting the need for more refined methods of estimating intrinsic muscle parameters such as fiber length. Our approach emphasizes the explicit application of quantitative techniques and physics-based principles, which helps maximize results robustness and reproducibility. Although we focus on one specific taxon and question, many of the techniques and philosophies explored here have much generality to them, so they can be applied in biomechanical investigation of other extinct organisms.

Beta diversity quantifies the spatial structuring of ecological communities and is a fundamental partition of biodiversity, central to understanding many macroecological phenomena in modern biology and paleobiology. Despite its common application in ecology, studies of beta diversity in the fossil record are relatively limited at regional spatial scales that are important for understanding macroevolutionary processes. The spatial scaling of beta diversity in the fossil record is poorly understood, but has significant implications due to temporal variation in the spatial distribution of fossil collections and the large spatiotemporal scales typically employed. Here we test the spatial scaling of several common measures of beta diversity using the Cenozoic shallow-marine molluscan fossil record of New Zealand and derive a spatially standardized time series of beta diversity. To measure spatial scaling, we use and compare grid-cell occupancy based on an equal-area grid and summed minimum spanning tree length, both based on reconstructed paleocoordinates of fossil collections. We find that beta diversity is spatially dependent at local to regional scales, regardless of the metric or spatial scaling utilized, and that spatial standardization significantly changes apparent temporal trends of beta diversity and, therefore, inferences about processes driving diversity change.

Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily “quiescent” times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of “sluggish” evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatiotemporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance before their extinction but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19–25 Myr) during which standard macroevolutionary rules did not apply.

A key question in paleoecology and macroevolution is whether assemblages of species (paleocommunities) are persistent entities that endure over millions of years. While community turnover in the face of abiotic change is the presumed norm, paleocommunities have been shown to persist for long time periods and regardless of environmental disruption. It remains an open question, however, as to what processes allow for this. We investigate these questions by analyzing the Carboniferous brachiopod paleocommunities from the Midcontinent of North America. These diverse communities were subjected to repeated and geologically rapid changes in sea level. Using a suite of statistical techniques, we characterize the nature and scope of changes in these paleocommunities over time. We find that, at the paleocommunity scale, there is no evidence for obdurate ecological stasis, with fluctuations in both taxonomic composition and the associated abundance of taxa. However, at a higher ecological scale, stability is manifest, as diversity patterns remain stable across time, with a consistent number of species that can exist in any given paleocommunity. This suggests ecological rules such as taxon packing are in effect, resulting in a form of ecological stability even in the face of constant disequilibrium, and parallels ecological patterns of disruption and recovery previously observed for invertebrate communities from modern marine systems. Based on these results, we advocate for consideration of different hierarchical entities and scales when interpreting the ecological dynamics of fossil assemblages, as focusing exclusively on changes in taxon identity/abundance or diversity levels can lead to very different results.

Brachiopods dominated the seafloor as a primary member of the Paleozoic fauna. Despite the devastating effects of the end-Permian extinction, the group recovered during the early Mesozoic only to gradually decline from the Jurassic to today. This decline likely had multiple causes, including increased predation and bioturbation-driven substrate disruption, but the role of changing substrate is not well understood. Given the importance of substrate for extant brachiopod habitat, we documented Mesozoic–Cenozoic lithologic preferences and morphological changes to assess how decreasing firm-substrate habitat may have contributed to the brachiopod decline. Compared with bivalves, Mesozoic brachiopods occurred more frequently and were disproportionately abundant in carbonate lithologies. Although patterns in glauconitic or ferruginous sediments are equivocal, brachiopods became more abundant in coarser-grained carbonates and less abundant in fine-grained siliciclastics. During the Jurassic, brachiopod species rarely had abraded beaks but tended to be more convex with a high beak, potentially consistent with a non-analogue lifestyle resting on the seafloor. However, those highly convex morphotypes largely disappeared by the Cenozoic, when more terebratulides had abraded beaks, suggesting closer attachment to hard substrates. Rhynchonellides disproportionately declined to become a minor component of Cenozoic faunas, perhaps because of less pronounced morphological shifts. Trends in lithologic preferences and morphology are consistent with bioturbation-driven substrate disruption, with brachiopods initially using firmer carbonate sediments as refugia before adapting to live primarily attached to hard surfaces. This progressive habitat restriction likely played a role in the final brachiopod decline, as bioturbating ecosystem engineers transformed benthic habitats in the Mesozoic and Cenozoic.

Troodon formosus, a theropod from the Late Cretaceous, is one of the few species of dinosaurs with multiple nest sites uncovered. It has been consistently demonstrated that eggs within these nests would have been partially buried in life—an exceedingly rare state in modern vertebrates. There has been debate over Troodon's capacity to engage in thermoregulatory contact incubation, especially regarding an adult's ability to efficiently supply partially buried eggs with energy. An actualistic investigation was undertaken to determine the thermodynamic efficiency of contact incubating partially buried eggs. An efficient system would keep eggs at temperatures closer to the surrogate parent than the ambient, without prohibitively high energy input. For the experiment, a surrogate dinosaur was created and used in both indoor controlled ambient temperature trials and in an outdoor variant. Even with ambient temperatures that were likely cooler than Cretaceous averages, the results showed that contact incubating partially buried eggs did seem to confer an energetic advantage; egg temperatures remained closer to the surrogate than ambient in both indoor and outdoor tests. Still, critics of contact incubating partially buried eggs are correct in that there is a depth at which adult energy would fail to make much of an impact—perhaps more relevant to buried eggs, as partially buried eggs would be in contact with an adult and likely above the thermal input threshold. Additionally, results from this experiment provide evidence for a possible evolutionary path from guarding behavior to thermoregulatory contact incubation.

Heterochrony describes acceleration, displacement, and/or retardation of descendants’ development events compared with ancestral states and has often been cited as an important process to bring about morphological novelty. It was coined one-and-a-half centuries ago and has been discussed by both paleobiologists and biologists frequently ever since. Many types of fossil organisms preserve aspects of their development histories in their bones or shells that have been used for heterochrony analyses, with body size being used as a developmental age indicator, despite questions being raised regarding this practice. For organisms whose hard structures consist of multiple chambers, or that contain growth lines, age information suggested by these structures independently can facilitate ontogenetic modeling. In this way, relations among size, shape, and age can be established to document patterns of morphological development.

Morphological analysis of pseudoschwagerine fusulinids, a fossil foraminifera group that developed a morphologically novel spherical shell, along with their presumptive triticitid ancestors illustrates this approach to heterochrony analysis. Ontogenetic trajectory comparisons of four major pseudoschwagerine genera, as well as those of triticitids, document relations between their shapes, sizes, and developmental ages. A complex of heterochronic patterns, including peramorphic predisplacement, hypermorphosis, and acceleration, characterize pseudoschwagerine development and appear to be responsible for the novel appearance of large, inflated fusiform and spherical tests in these late Paleozoic benthic foraminifera. The morphometric approach employed in this investigation could be applied widely in the quantitative morphological studies of development histories in a variety of other fossil groups.

Inferences on the development and morphology of extinct brachiopods must be informed by the ontogeny and shell ornamentation of extant brachiopods. Although the adult shells of extant brachiopods are well studied, detailed descriptions of the embryonic and juvenile shells of extant lingulides are lacking. Here, we describe in detail the shells of juveniles of Lingula anatina Lamarck, 1801 from Vietnam and the Republic of the Philippines. The following previously unknown properties of the lingulide shell are described: (1) a distinct border between the protegulum and the brephic shell; (2) drapes that develop on both the protegulum and brephic shell; and (3) the notched anterior margin of the brephic shell. The drapes and cogs on the brephic shell may be caused by the formation of setal follicles during the planktonic stage. Specimens of L. anatina from the Philippines have larger brephic shells than those from Vietnam, probably because the former have a longer planktonic stage. Based on comparisons of the first-formed shells of extant brachiopods with published data on fossil brachiopods, we suggest that the life cycle of extant lingulides, in which planktotrophic juveniles with a shell hatch from the egg envelope, is the most evolutionarily advanced brachiopod life cycle and appeared in the early Silurian. We suggest criteria for determining the type of life cycle based on the structure of the first-formed shell of brachiopods. Finally, we consider hypothetical scenarios of life cycles of fossil brachiopods, including true planktotrophic larvae in the Cambrian linguliforms.

Extant and extinct terebratulide brachiopod species have been defined primarily on the basis of morphology. What is the fidelity of morphological species to biological species? And how can we test this fidelity with fossils? Taxonomically and phylogenetically, the most informative internal feature in the brachiopod suborder Terebratellidina is the geometrically complex long-looped brachidium, which is highly fragile and only rarely preserved in the fossil record. Given this, it is essential to test other sources of morphological data, such as valve outline shape, when trying to recognize and identify species. We analyzed valve outlines and brachidia in the genus Laqueus to explore the utility of shell shape in discriminating extant and fossil species. Using geometric morphometric methods, we quantified valve outline variability using elliptical Fourier methods and tested whether long-looped brachidial morphology correlates with shell outline shape. We then built classification models based on machine learning algorithms using outlines as shape variables to predict fossil species’ identities. Our results demonstrate that valve outline shape is significantly correlated with long-looped brachidial shape and that even relatively simple outlines are sufficiently morphologically distinct to enable extant Laqueus species to be identified, validating current taxonomic assignments. These are encouraging results for the study and delimitation of fossil terebratulide species, and their recognition as biological species. In addition, machine learning algorithms can be successfully applied to help solve species recognition and delimitation problems in paleontology, especially when morphology can be characterized quantitatively and analyzed statistically.