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.

Echinoderms have long been characterized by the presence of ambulacra that exhibit pentaradiate symmetry and define five primary body axes. In reality, truly pentaradial ambulacral symmetry is a condition derived only once in the evolutionary history of echinoderms and is restricted to eleutherozoans, the clade that contains most living echinoderm species. In contrast, early echinoderms have a bilaterally symmetrical 2-1-2 arrangement, with three ambulacra radiating from the mouth. Branching of the two side ambulacra during ontogeny produces the five adult rays. During the Cambrian Explosion and Ordovician Radiation, some 30 clades of echinoderms evolved, many of which have aberrant ambulacral systems with one to four rays. Unfortunately, no underlying model has emerged that explains ambulacral homologies among disparate forms. Here we show that most Paleozoic echinoderms are characterized by uniquely identifiable ambulacra that develop in three distinct postlarval stages. Nearly all “aberrant” echinoderm morphologies can be explained by the paedomorphic ambulacra reduction (PAR) model through the loss of some combination of these growth stages during ontogeny. Superficially similar patterns of ambulacral reduction in distantly related clades have resulted from the parallel loss of homologous ambulacra during ontogeny. Pseudo-fivefold symmetry seen in Blastoidea and the true fivefold symmetry seen in Eleutherozoa result from great reduction and total loss, respectively, of the 2–1–2 symmetry early in ontogeny. These ambulacral variations suggest that both developmental and ecological constraints affect the evolution of novel echinoderm body plans.

Despite extensive paleoecological analyses of spatial and temporal turnover in species composition, the fidelity with which time-averaged death assemblages capture variation in species composition and diversity partitioning of living communities remains unexplored. Do death assemblages vary in composition between sites to a lesser degree than do living assemblages, as would be predicted from time-averaging? And is the higher number of species observed in death relative to living assemblages reduced with increasing spatial scale? We quantify the preservation of spatial and temporal variation in species composition using 11 regional data sets based on samples of living molluscan communities and their co-occurring time-averaged death assemblages. (1) Compositional dissimilarities among living assemblages (LA) within data sets are significantly positively rank-correlated to dissimilarities among counterpart pairs of death assemblages (DA), demonstrating that pairwise dissimilarity within a study area has a good preservation potential in the fossil record. Dissimilarity indices that downplay the abundance of dominant species return the highest live-dead agreement of variation in species composition. (2) The average variation in species composition (average dissimilarity) is consistently smaller in DAs than in LAs (9 of 11 data sets). This damping of variation might arise from DAs generally having a larger sample size, but the reduction by ∼10–20% mostly persists even in size-standardized analyses (4 to 7 of 11 data sets, depending on metric). Beta diversity expressed by the number of compositionally distinct communities is also significantly reduced in death assemblages in size-standardized analyses (by ∼25%). This damping of variation and reduction in beta diversity is in accord with the loss of temporal resolution expected from time-averaging, without invoking taphonomic bias (from differential preservation or postmortem transportation) or sample-size effects. The loss of temporal resolution should directly reduce temporal variation, and assuming time-for-space substitution owing to random walk within one habitat and/or temporal habitat shifting, it also decreases spatial variation in species composition. (3) DAs are more diverse than LAs at the alpha scale, but the difference is reduced at gamma scales because partitioning of alpha and beta components differs significantly between LAs and DAs. This indicates that the effects of time-averaging are reduced with increasing spatial scale. Thus, overall, time-averaged molluscan DAs do capture variation among samples of the living assemblage, but they tend to damp the magnitude of variation, making them a conservative means of inferring change over time or variation among regions in species composition and diversity. Rates of temporal and spatial species turnover documented in the fossil record are thus expected to be depressed relative to the turnover rates that are predicted by models of community dynamics, which assume higher temporal resolution. Finally, the capture by DAs of underlying variation in the LA implies little variation in the net preservation potential of death assemblages across environments, despite the different taphonomic pathways suggested by taphofacies studies.

The ability of paleobiologists to draw paleoecological inferences based on spatial faunal variability within a single stratigraphic interval depends ultimately on the spatial resolving power of the fossil record. This paper evaluates the potential spatial resolution of fossil assemblages by examining modern skeletal remains of molluscs on a benthic transect, along which there is a marked decrease in seagrass cover, in Smuggler's Cove, St. Croix, U.S. Virgin Islands. The sampling transect began in a Thalassia-covered area approximately three meters deep, extended into slightly deeper water with lighter seagrass cover, and ended on an open, bioturbated sandy tract at a depth of nearly six meters.

Two-way cluster analysis and polar ordination of 37 samples of molluscan remains, taken at 10-meter intervals along the 360-meter transect, reveal patterns of variation that are shown by correlation analyses and consideration of the autecologies of individual species to be related to measured changes in vegetation. There is a transition from dominance primarily by epifaunal gastropods living on seagrass blades to dominance by infaunal, burrowing bivalves as grass cover becomes lighter. Some non-systematic variability exists in faunal distributional patterns within areas where the environment does not vary systematically, but this does not mask the regular faunal transitions related to environmental changes. Correspondence between the dead and live faunas is difficult to ascertain because of the scarcity of live fauna in collected samples.

The results suggest that spatial faunal transitions in fossil remains at even the fine scale evaluated in this study are potentially preservable in the fossil record.

The 18 m.y. history of the subfamily Equinae (exclusive of Archaeohippus and “Parahippus”) in North America consisted of a 3-m.y. radiation phase, a 9-m.y. steady-state diversity phase, and a 6-m.y. reduction phase. During the steady-state phase, species richness varied between 14 and 20, with two maxima at about 13.5 and 6.5 Ma. Species richness of the tribes Hipparionini and Equini was about equal through the middle Miocene, but hipparionines consistently had more species in the late Miocene and early Pliocene. Overall mean species duration was 3.2 m.y. (n = 50), or an average extinction rate of 0.31 m.y.-1 During the radiation phase, speciation rates were very high (0.5 to 1.4 m.y.-1), while extinction rates were low (<0.10 m.y.-1). Speciation and extinction rates both averaged about 0.15 m.y.-1 during the steady-state phase, with extinction rates having more variation. Extinction rates increased fourfold during the reduction phase, while speciation rates declined slightly. Late Hemphillian extinctions affected both tribes severely, not just the three-toed hipparionines, and were correlated with global climatic change.

Occurrence data from the Paleobiology Database are used to analyze the waxing and waning of genera over time. Irrespective of whether we tabulate species richness, frequency of occurrence, geographic range, or other measures, the average rise and fall of genera is remarkably symmetrical. Genera tend already to be in a state of decline when they become extinct. Genera that last appear in the major mass extinction stages, however, are more frequently truncated while they are holding steady or even increasing. This need not imply that mass extinctions are qualitatively different from other events; it is consistent with the expected effects of simply increasing the magnitude of extinction. For reasons that are not completely clear, post-Paleozoic genera show less of a rise and fall on average and tend to be less symmetrical than do Paleozoic genera.

Taxonomic survivorship curves may reflect stratigraphic as well as biologic factors. The approximately lognormal distribution of lengths of Phanerozoic time intervals produces an error in the estimation of taxonomic durations that is also lognormally distributed. As demonstrated by several simulated examples, this error may cause concave taxonomic survivorship curves to appear linear, especially if the maximum durations involved are relatively short. The error of estimation also makes highly concave taxonomic survivorship curves virtually unrecognizable. Incomplete sampling of the fossil record, on the other hand, may not be a serious problem in survivorship analysis. Simulated paleontological sampling employing a simple model suggests that survivorship curves tend to retain their original shapes even when as few as 20% of the taxa have been discovered. However, concave taxonomic survivorship curves tend to lose their concavity as efficiency of sampling declines.

Paleotectonic reconstructions for the late Proterozoic have differed over the timing of the Cordilleran rifting between Laurentia and the East Gondwana cratons. Parsimony Analysis of Endemism (PAE) and phenetic clustering of the “Ediacara biota” were carried out, for comparison with competing paleotectonic hypotheses. All analyses show a common pattern of similarities among biotas. The biotas of Charnwood Forest and Newfoundland consistently group together, while the south Australian biota is closest to those of Baltica, northern Laurentia, and Siberia. The biota of southwest North America, though still poorly known, strikingly resembles that of Namibia—not that of northwestern Canada. This pattern is not obviously due to facies-related or preservational bias and is very different from Cambrian biogeographic patterns. The overall pattern is most consistent with the hypothesis that the western margin of Laurentia was in close contact with East Gondwana, with rifting taking place either during or just before the Vendian. This arrangement has been previously proposed as a paleotectonic hypothesis; however, most recent paleomagnetic and structural studies support the alternate hypothesis that this rifting took place more than 100 million years before the Vendian. Resolving this contradiction will require much more data on both organismal distribution and cratonal position.

Cohort analysis is used to investigate survivorship of trilobites originating during the Cambrian and Ordovician. Using a time-homogeneous branching model, it is estimated that trilobite genera and species originating during the Ordovician survived three times longer than Cambrian genera and species. Monte Carlo simulation of survivorship is used to show that (1) Cambrian and Ordovician survivorship are significantly different, (2) Ordovician cohorts conform more closely to the time-homogeneous model than do Cambrian cohorts, and (3) deviations from temporal homogeneity are more often produced by extraordinary extinction than by unusually slow turnover.

When Early Ordovician cohorts are decomposed into genera within families that originated in the Cambrian versus the Ordovician, no evidence that Cambrian and Ordovician survivorship differences are clade-specific can be found. Ordovician genera of Cambrian affinity and of Ordovician affinity become extinct at similar rates.

Some of the ultimate causes of these differences in survivorship include (1) taxonomic inconsistency, (2) greater environmental stability in the Ordovician, and (3) more highly structured ecosystems in the Ordovician that may have led to the weeding out of extinction-prone taxa.

Evolutionary paleontologists seek explanations of form and pattern in a diversity of contexts. A review of this diversity is presented to underscore the difficulty of producing a general model of the factors controlling the morphology of real organisms. A model specific to the marine prosobranch gastropod radula identifies seven factors contributing to form and pattern: (1) phylogenetic, (2) mechanical, (3) ecological, (4) programmatic, (5) maturational, (6) degenerative, and (7) constructional. Aspects of radular morphology attributable to each factor are illustrated in scanning electron micrographs of radulae of marine prosobranch gastropods. Applications of and extrapolations from the radular model are made to promote recognition of a broader range of interacting factors in other systems. Some aspects of form and pattern convey important information about non-evolutionary processes and phenomena and are best examined outside of the evolutionary framework.

The claw equipped forelimbs have been shown to be an important hunting weapon for modern felids. In light of its functional importance, the claw retractile mechanism for modern felids was compared with that of the saber-toothed felids. In this regard, the functional anatomy of claw retraction for saber-toothed felids was found to be the same as that of modern forms. Body proportions of modern felids were also compared with saber-toothed felids and the relationship of their morphology to habitat structure and habitat utilization were studied. It was found that the relative body proportions for Hoplophoneus and Smilodon were similar to modern forest felids (dwellers of high structured dense forest), while Dinictis and Machairodus could probably compete in more open terrain (open woodland, meadow). It is postulated that saber-toothed felids used their claw equipped forelimbs to grasp and hold their prey as do modern felids. In this fashion, the enlarged upper canines could then be used to kill the victim, and this was probably done by a stab to the nape of the neck. It is also thought that Smilodon, like the modern lion, adapted to open habitats by forming prides.

The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the only direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time. The software PyRate implements a Bayesian framework to analyze fossil occurrence data to estimate the rates of preservation, origination, and extinction while incorporating several sources of uncertainty. Building upon this framework, we present a suite of methodological advances including more complex and realistic models of preservation and the first likelihood-based test to compare the fit across different models. Further, we develop a new reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, which provides more reliable results and includes an explicit estimation of the number and temporal placement of statistically significant rate changes. Finally, we implement a new C++ library that speeds up the analyses by orders of magnitude, therefore facilitating the application of the PyRate methods to large data sets. We demonstrate the new functionalities through extensive simulations and with the analysis of a large data set of Cenozoic marine mammals. We compare our analytical framework against two widely used alternative methods to infer origination and extinction rates, revealing that PyRate decisively outperforms them across a range of simulated data sets. Our analyses indicate that explicit statistical model testing, which is often neglected in fossil-based macroevolutionary analyses, is crucial to obtain accurate and robust results.

While the importance of allopatric speciation in the fossil record has long been underestimated, phyletic change within single unbranching lineages also occurs. The 50% increase in thoracic width observed in the radiolarian species Pseudocubus vema from an Antarctic deep-sea core is a clear example of a long-term phyletic trend in a continuous fossil sequence. Phyletic change in P. vema occurred at varying rates, but changes in the morphologic rate of evolution do not correspond to any obvious breaks in the fossil record such as would be indicated by missing segments of the core's magnetic stratigraphy. Variation in thoracic width, as measured by the coefficient of variation, does not depend on the morphologic rate of evolution, proportional rate of evolution, nor the amount of time required for the width to change by one standard deviation, so much as it depends on whether change was accomplished by addition or removal of extreme phenotypes to or from the population.

The presumed affinities of the Terminal Neoproterozoic Ediacara biota have been much debated. However, even in the absence of concrete evidence for phylogenetic affinity, numerical paleoecological approaches can be effectively used to make inferences about organismal biology, the nature of biotic interactions, and life history. Here, we examine the population structure of three Ediacaran rangeomorph taxa (Fractofusus, Beothukis, and Pectinifrons), and one non-rangeomorph taxon (Thectardis) across five fossil surfaces around the Avalon Peninsula, Newfoundland, through analysis of size-frequency distributions using Bayesian Information Criterion (BIC). Best-supported models resolve communities of all studied Ediacaran taxa at Mistaken Point as single cohorts with wide variance. This result is best explained in terms of a “continuous reproduction” model, whereby Ediacaran organisms reproduce aseasonally, so that multiple size modes are absent from preserved communities. Modern benthic invertebrates (both as a whole and within specific taxonomic groups) in deeper-water settings reproduce both seasonally and aseasonally; distinguishing between biological (i.e., continuous reproductive strategies) and environmental (lack of a seasonal trigger) causes for this pattern is therefore difficult. However, we hypothesize that the observed population structure could reflect the lack of a trigger for reproduction in deepwater settings (i.e., seasonal flux of organic matter), until the explosive appearance of mesozooplankton near the base of the Cambrian.

High-resolution stratigraphic analysis of 18 sections spanning the Cenomanian–Turonian Stage boundary in the western interior of the United States has allowed determination of the magnitude and pattern of molluscan extinction and disruption. Composite range data from all sections show that the faunal turnover across the stage boundary occurs in a series of narrow stratigraphic zones, defined by multiple first and last occurrences, separated by intervals displaying little or no taxonomic turnover. Two of the apparent extinction steps (bottom and top of the Neocardioceras juddii Zone) may be intercontinentally developed. The additional steps apparently reflect cyclic changes in water mass and substrate characteristics in the western interior basin produced in response to orbital forcing of climate. An interval (ca. 10-100 k.y. duration) of changing community structure and general biotic deterioration is found below each of the two potentially intercontinentally developed extinction steps. The most affected mollusks were those having intercontinental distributions (ammonites and inoceramid bivalves), suggesting that disruption of planktotrophic larval dispersal may have played a role in increasing extinction and speciation rates near the C–T boundary. The nekto-benthic ammonites were affected earlier and to a greater degree than the pelagic forms, implying progressive upward expansion of the oxygen minimum zone preceding the stage boundary.

A combination of historical, functional, and biomechanical constraints has shaped the masticatory apparatus of fossil and extant xenarthrans. Among the more notable features are the teeth: hypselodont; commonly reduced in size, complexity, and number; separated by short diastema; and composed of osteodentine. Enamel is absent, as are the cuspal patterns of other mammals. A comprehensive revision of teeth and other features of the masticatory apparatus of xenarthrans reveals that previous generalizations underestimate the morphological diversity and adaptive possibilities developed within the clade. The great diversity of forms suggests several such possibilities ranging from specialized myrmecophagous species to carrion feeders or predators among animalivores; selective browsers to bulk grazers among herbivores; and omnivores. In some cases xenarthrans represent less extreme versions of patterns developed in other major clades of mammals (marsupials, afrotheres, euarchontoglires, and laurasiatheres) clearly predetermined by a tribosphenic dental morphology, whereas in others they represent unique novelties indicative of particular biological roles. The combination of tooth features that characterize xenarthrans might be seen as the key innovation for the ecologic diversity developed at least since the Oligocene, breaking the mold of the tribosphenic condition that constrained the evolution of the other major clades of mammals.

In both jaw geometry and molar morphology, eutherian carnivores (order Carnivora) as a whole display greater diversity (plasticity in evolution from the primitive type) than marsupial carnivores (order Dasyurida). This is related to the difference in tooth replacement between the two taxa. In Carnivora, the permanent carnassial is preceded by a deciduous carnassial; the permanent tooth can erupt in its (geometrically) permanent position, and the post-carnassial molars are free to evolve for specialized functions or be reduced. In Dasyurida, there is relative molar progression, each erupting molar in turn functioning as a carnassial, and subsequently being pushed forwards in the jaw by the next erupting molar. Thus, all molars have carnassiform morphology, and none are free to develop for other functions. The greater plasticity of Carnivora has led to their adaptive zone being broader (as a group they are relatively more eurytopic than Dasyurida), which in turn has led to greater taxonomic diversity within Carnivora than Dasyurida. The resulting pattern from a macroevolutionary point of view is that, even in the absence of direct competition, Carnivora have had greater evolutionary “success” than Dasyurida.

Analysis of post-mortem buoyancy loss in Nautilus shells suggests that extensive nekroplanktonic drifting occurs infrequently. Most shells do not reach the surface but settle to the sea floor, after a short period of ascent. This occurs because the rate of water influx into the phragmocone due to ambient hydrostatic pressure is sufficiently rapid in most cases to overcome positive buoyancy before the shell reaches the surface. The resulting geographic distribution of Nautilus shells would therefore mirror the distribution of the live animals. Thus, post-mortem drift in Nautilus cannot be used as a basis for questioning the validity of cephalopod paleobiogeography. Estimate of influx rates in ammonoid siphuncles indicates that many, if not most, ammonoid shells also would not become nekroplanktonic. This is especially true for small (<5 cm diameter) shells. Cephalopod paleobiogeographic investigation appears less subject to criticism stemming from the supposed obfuscating effects of post-mortem drift than previously thought.

This paper proposes a simple, unorthodox model for use in the study of vertebrate jaw mechanics. Central to the new “bifulcral model” is the assumption that the bite point may be regarded as a distinct and independent “occlusal fulcrum” equal in status to the jaw articulation or “joint fulcrum” of more traditional biomechanical models. The bifulcral model allows all mechanical forces acting on the feeding system to be evaluated in terms of their purely rotational and purely translational components defined relative to the occlusal and joint fulcra. The major benefit of this analytical approach is that it permits a new and substantially different perspective on the functional consequences of morpho-geometric organization in feeding systems. The bifulcral model clearly establishes the dynamic relationships among muscle alignment, bite point and the resultant patterns of mechanical stress at the craniomandibular joint (CMJ). It also reveals potentially important modes of competitive interaction between otherwise seemingly synergistic jaw muscles. Further, the bifulcral model encourages preliminary investigations into the possible contribution of intramuscular dynamics to the overall operational plasticity of the feeding machinery.

Specific application of the new model to structural and functional problems concerning the origin of the mammalian feeding complex lead to the following tentative conclusions. (1) Contrary to current opinion, the CMJ of most cynodont therapsids probably did not experience positive vertical loads (= compressive) when the cheek teeth were utilized for mastication. Instead, net CMJ loads were either neutral or somewhat negative (= tensile). (2) The development of a pronounced coronoid process in cynodonts was more directly related to promoting the differentiation of the masseter complex than to either improving the mechanical advantage or prehensile capacity of the temporalis muscle. (3) Differential motor activity within the complex temporalis musculature of cynodonts could have resulted in “derived lines of action” markedly different from the reconstructed lines of action employed in previous analyses of feeding mechanics in these reptiles. Such derived lines of action may have been optimal configurations for the integrated activity of the temporalis and masseter musculature. (4) Selection in cynodonts favored the evolution of a superficial masseter rather than the elaboration of the preexisting and geometrically similar pterygoideus musculature. This occurred because the masseter held the greater potential for improving bite force, motor control and facilitating the reduction of the postdentary bones of the mandible while still preserving the basic spatial economy of the cranial region. (5) The rearward growth of the condylar process of the dentary in cynodonts promoted the reduction of the postdentary unit primarily by shifting the point of load application between the dentary and postdentary units, thereby reducing bending stresses in the postdentary unit. (6) The enlarged squamosal sulcus of cynodonts was occupied mainly by a hypertrophied depressor mandibulae muscle; an auditory tube was also present in the sulcus deep to the muscle. (7) The depressor mandibulae played a major role in CMJ stabilization in therapsids; this was possibly its only function in later cynodonts. The peculiar downturned retroarticular process of the mandible in therapsids appears to have been related to this same function.