Extant species of the genus Equus (e.g., horses, asses, and zebras) have a widespread distribution today on all continents except Antarctica. Extinct species of Equus represented by fossils were likewise widely distributed in the Pliocene and even more so during the Pleistocene. In order to understand the efficacy of “big data” for (paleo)biogeographic analyses, location records (latitude, longitude) and fossil occurrences for the genus Equus were mined and further explored from six databases, including iDigBio, Paleobiology Database, VertNet, BISON, Neotoma, and GBIF. These were chosen from a priori knowledge of where relevant data might be aggregated. We also realized that these databases have different objectives and data sources and therefore would provide a useful comparative study of the widespread taxon Equus in space and time.

The mining of Equus data from these six sources yielded a combined total of 123.8 K location records, including 116.2K fossil specimens. These include individual points that are unique, that is, only occurring in one of these databases, and those that are duplicated in multiple databases. Of the six databases, three (iDigBio, Paleobiology Database, and GBIF) were judged to be the most useful in the Equus use case. Most of the databases are biased toward North American records, thus limiting the reconstruction of the actual distribution of the genus Equus in space and time outside of this continent. Although Equus has a large number of digitally accessible records, fundamentally interesting questions pertaining to evolutionary dynamics and extinction geography are still a challenge for these kinds of biodiversity databases due primarily to the lack of sufficiently dense and precise temporal data.

Morphological responses of nonmammalian herbivores to external ecological drivers have not been quantified over extended timescales. Herbivorous nonavian dinosaurs are an ideal group to test for such responses, because they dominated terrestrial ecosystems for more than 155 Myr and included the largest herbivores that ever existed. The radiation of dinosaurs was punctuated by several ecologically important events, including extinctions at the Triassic/Jurassic (Tr/J) and Jurassic/Cretaceous (J/K) boundaries, the decline of cycadophytes, and the origin of angiosperms, all of which may have had profound consequences for herbivore communities. Here we present the first analysis of morphological and biomechanical disparity for sauropodomorph and ornithischian dinosaurs in order to investigate patterns of jaw shape and function through time. We find that morphological and biomechanical mandibular disparity are decoupled: mandibular shape disparity follows taxonomic diversity, with a steady increase through the Mesozoic. By contrast, biomechanical disparity builds to a peak in the Late Jurassic that corresponds to increased functional variation among sauropods. The reduction in biomechanical disparity following this peak coincides with the J/K extinction, the associated loss of sauropod and stegosaur diversity, and the decline of cycadophytes. We find no specific correspondence between biomechanical disparity and the proliferation of angiosperms. Continual ecological and functional replacement of pre-existing taxa accounts for disparity patterns through much of the Cretaceous, with the exception of several unique groups, such as psittacosaurids that are never replaced in their biomechanical or morphological profiles.

As a label for a distinct category of life, “living fossil” is controversial. The term has multiple definitions, and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective in which a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: Does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed among species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model in which the probability of speciation and extinction is a function of a tip’s ED. We simulated thousands of trees in which the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations in which the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor–descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor–descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.

A priori choices in the detail and breadth of a study are important in addressing scientific hypotheses. In particular, choices in the number and type of characters can greatly influence the results in studies of morphological diversity. A new character suite was constructed to examine trends in the disparity of early Paleozoic crinoids. Character-based rarefaction analysis indicated that a small subset of these characters (~20% of the complete data set) could be used to capture most of the properties of the entire data set in analyses of crinoids as a whole, noncamerate crinoids, and to a lesser extent camerate crinoids. This pattern may be the result of the covariance between characters and the characterization of rare morphologies that are not represented in the primary axes in morphospace. Shifting emphasis on different body regions (oral system, calyx, periproct system, and pelma) also influenced estimates of relative disparity between subclasses of crinoids. Given these results, morphological studies should include a pilot analysis to better examine the amount and type of data needed to address specific scientific hypotheses.

Although extinction risk has been found to have a consistent negative relationship with geographic range across wide temporal and taxonomic scales, the effect has been difficult to disentangle from factors such as sampling, ecological niche, or clade. In addition, studies of extinction risk have focused on benthic invertebrates with less work on planktic taxa. We employed a global set of 1114 planktic graptolite species from the Ordovician to lower Devonian to analyze the predictive power of species’ traits and abiotic factors on extinction risk, combining general linear models (GLMs), partial least-squares regression (PLSR), and permutation tests. Factors included measures of geographic range, sampling, and graptolite-specific factors such as clade, biofacies affiliation, shallow water tolerance, and age cohorts split at the base of the Katian and Rhuddanian stages.

The percent variance in durations explained varied substantially between taxon subsets from 12% to 45%. Overall commonness, the correlated effects of geographic range and sampling, was the strongest, most consistent factor (12–30% variance explained), with clade and age cohort adding up to 18% and other factors <10%. Surprisingly, geographic range alone contributed little explanatory power (<5%). It is likely that this is a consequence of a nonlinear relationship between geographic range and extinction risk, wherein the largest reductions in extinction risk are gained from moderate expansion of small geographic ranges. Thus, even large differences in range size between graptolite species did not lead to a proportionate difference in extinction risk because of the large average ranges of these species. Finally, we emphasize that the common practice of determining the geographic range of taxa from the union of all occurrences over their duration poses a substantial risk of overestimating the geographic scope of the realized ecological niche and, thus, of further conflating sampling effects on observed duration with the biological effects of range size on extinction risk.

Placodontia were a group of marine reptiles that lived in shallow nearshore environments during the Triassic. Based on tooth morphology it has been inferred that they were durophagous, but tooth morphology differs among species: placodontoid placodonts have teeth described as hemispherical, and the teeth of more highly nested taxa within the cyamodontoid placodonts have been described as flat. In contrast, the sister taxon to the placodonts, Palatodonta bleekeri, like many other marine reptiles, has tall pointed teeth for eating soft-bodied prey. The goals of this paper are to quantify these different tooth morphologies and compare tooth shape among taxa and with a functionally “optimal” tooth. To quantify tooth morphology we measured the radius of curvature (RoC) of the occlusal surface by fitting spheres to 3D surface scans or computed microtomographic scans. Large RoCs correspond to flatter teeth, while teeth with smaller RoCs are pointier; positive RoCs have convex occlusal surfaces, and a negative RoC indicates that the occlusal surface of the tooth is concave. We found the placodontoid taxa have teeth with smaller RoCs than more highly nested taxa, and palatine teeth tend to be flatter and closer to the optimal morphology than maxillary teeth. Within one well-nested clade, the placochelyids, the rearmost palatine teeth have a more complex morphology than the predicted optimal tooth, with an overall concave occlusal surface with a small, medial cusp. These findings are in keeping with the hypothesis that placodonts were specialized durophagous predators with teeth modified to break hard prey items while resisting tooth failure.

The robusticity of the weight-bearing limbs of large terrestrial animals is expected to increase at a more rapid rate than in their smaller relatives. This scaling has been hypothesized to allow large species to maintain stresses in the limb bones that are similar to those seen in smaller ones. Curvilinear scaling has previously been found in mammals and nonavian theropods but has not been demonstrated in birds. In this study, polynomial regressions of leg-bone length and circumference in terrestrial flightless birds were carried out to test for a relationship similar to that seen in nonavian theropods. Flightless birds exhibit curvilinear scaling, with the femora of large taxa becoming thicker relative to length at a greater rate than in smaller taxa. Evidence was found for nonlinear scaling in the leg bones of nonavian theropods. However, unlike in avians, there is also phylogenetic variation between taxonomic groups, with tyrannosaur leg bones in particular scaling differently than other groups. Phylogenetically corrected quadratic regressions and separate analyses of taxonomic groupings found little phylogenetic variation in flightless birds. It is suggested here that the nonlinear scaling seen in avian femora is due to the need to maintain the position of the knee under a more anterior center of mass, thereby restricting femoral length. The femur of nonavian theropods is not so constrained, with greater variability of the linear scaling relationships between clades. Phylogenetic variation in limb-bone scaling may broaden the errors for mass-predictive scaling equations based on limb-bone measurements of nonavian theropods.

Our knowledge of the diversity, ecology, and phylogeny of Mesozoic birds has increased significantly during recent decades, yet our understanding of their flight competence remains poor. Wing loading (WL) and aspect ratio (AR) are two aerodynamically relevant parameters, as they relate to energy costs of aerial locomotion and flight maneuverability. They can be calculated in living birds (i.e., Neornithes) from body mass (BM), wingspan (B), and lift surface (S L). However, the estimates for extinct birds can be subject to biases from statistical issues, phylogeny, locomotor adaptations, and diagenetic compaction. Here we develop a sequential approach for generating reliable multivariate models that allow estimation of measurements necessary to determine WL and AR in the main clades of non-neornithine Mesozoic birds. The strength of our predictions is supported by the use of those variables that show similar scaling patterns in modern and stem taxa (i.e., non-neornithine birds) and the similarity of our predictions with measurements obtained from fossils preserving wing outlines. In addition, although our WL and AR values are based on estimates (BM, B, and S L) that have an associated error, there is no cumulative error in their calculation, and both parameters show low prediction errors. Therefore, we present the first taxonomically broad, error-calibrated estimation of these two important aerodynamic parameters in non-neornithine birds. Such estimates show that the WL and AR of the non-neornithine birds here analyzed fall within the range of variation of modern birds (i.e., Neornithes). Our results indicate that most modern flight modes (e.g., continuous flapping, flap and gliding, flap and bounding, thermal soaring) were possible for the wide range of non-neornithine avian taxa; we found no evidence for the presence of dynamic soaring among these early birds.