Mesozoic marine ecosystems were dominated by several clades of reptiles, including sauropterygians, ichthyosaurs, crocodylomorphs, turtles, and mosasaurs, that repeatedly invaded ocean ecosystems. Previous research has shown that marine reptiles achieved great taxonomic diversity in the Middle Triassic, as they broadly diversified into many feeding modes in the aftermath of the Permo-Triassic mass extinction, but it is not known whether this initial phase of evolution was exceptional in the context of the entire Mesozoic. Here, we use a broad array of disparity, morphospace, and comparative phylogenetic analyses to test this. Metrics of ecomorphology, including functional disparity in the jaws and dentition and skull-size diversity, show that the Middle to early Late Triassic represented a time of pronounced phenotypic diversification in marine reptile evolution. Following the Late Triassic extinctions, diversity recovered, but disparity did not, and it took over 100 Myr for comparable variation to recover in the Campanian and Maastrichtian. Jurassic marine reptiles generally failed to radiate into vacated functional roles. The signatures of adaptive radiation are not seen in all marine reptile groups. Clades that diversified during the Triassic biotic recovery, the sauropterygians and ichthyosauromorphs, do show early diversifications, early high disparity, and early burst, while less support for these models is found in thalattosuchian crocodylomorphs and mosasaurs. Overall, the Triassic represented a special interval in marine reptile evolution, as a number of groups radiated into new adaptive zones.

The mid-late Ediacaran Period (~579–541 Ma) is characterized by globally distributed marine soft-bodied organisms of unclear phylogenetic affinities colloquially called the “Ediacara biota.” Despite an absence of systematic agreement, previous workers have tested for underlying factors that may control the occurrence of Ediacaran macrofossils in space and time. Three taxonomically distinct “assemblages,” termed the Avalon, White Sea, and Nama, were identified and informally incorporated into Ediacaran biostratigraphy. After ~15 years of new fossil discoveries and taxonomic revision, we retest the validity of these assemblages using a comprehensive database of Ediacaran macrofossil occurrences. Using multivariate analysis, we also test the degree to which taphonomy, time, and paleoenvironment explain the taxonomic composition of these assemblages. We find that: (1) the three assemblages remain distinct taxonomic groupings; (2) there is little support for a large-scale litho-taphonomic bias present in the Ediacaran; and (3) there is significant chronostratigraphic overlap between the taxonomically and geographically distinct Avalonian and White Sea assemblages ca. 560–557 Ma. Furthermore, both assemblages show narrow bathymetric ranges, reinforcing that they were paleoenvironmental–ecological biotopes and spatially restricted in marine settings. Meanwhile, the Nama assemblage appears to be a unique faunal stage, defined by a global loss of diversity, coincident with a noted expansion of bathymetrically unrestricted, long-ranging Ediacara taxa. These data reinforce that Ediacaran biodiversity and stratigraphic ranges of its representative taxa must first statistically account for varying likelihood of preservation at a local scale to ultimately aggregate the Ediacaran macrofossil record into a global biostratigraphic context.

The sizes and shapes of marine organisms often vary systematically across latitude and water depth, but the environmental factors that mediate these gradients in morphology remain incompletely understood. A key challenge is isolating the individual contributions of many, often correlated, environmental variables of potential biological significance. Benthic foraminifera, a diverse group of rhizarian protists that inhabit nearly all marine environments, provide an unparalleled opportunity to test statistically among the various potential controls on size and volume–to–surface area ratio. Here, we use 7035 occurrences of 541 species of Rotallid foraminifera across 946 localities spanning more than 60 degrees of latitude and 1600 m of water depth around the North American continental margin to assess the relative influences of temperature, oxygen availability, carbonate saturation, and particulate organic carbon flux on their test volume and volume–to–surface area ratio. For the North American data set as a whole, the best model includes temperature and dissolved oxygen concentration as predictors. This model also applies to data from the Pacific continental margin in isolation, but only temperature is included in the best model for the Atlantic. Because these findings are consistent with predictions from the first principles of cell physiology, we interpret these statistical associations as the expressions of physiological selective pressures on test size and shape from the physical environment. Regarding existing records of temporal variation in foraminiferal test size across geological time in light of these findings suggests that the importance of temperature variation on the evolution of test volume and volume–to–surface area ratio may be underappreciated. In particular, warming may have played as important a role as reduced oxygen availability in causing test size reduction during past episodes of environmental crisis and is expected to inflict metabolic stress on benthic foraminifera over the next century due to anthropogenic climate change.

Understanding the evolution of a Bauplan starts with discriminating phylogenetic signal from adaptation and the latter from exaptation in the observed biodiversity. Whether traits have predated, accompanied, or followed evolution of particular functions is the basic inference to establish the type of explanations required to determine morphological evolution. To accomplish this, we focus in a particular group of vertebrates, the anurans. Frogs and toads have a unique Bauplan among vertebrates, with a set of postcranial features that have been considered adaptations to jumping locomotion since their evolutionary origin. This interpretation is frequently stated but rarely tested in scientific literature. We test this assumption reconstructing the locomotor capabilities of the earliest known salientian, Triadobatrachus massinoti. This extinct taxon exhibits a mosaic of features that have traditionally been considered as representing an intermediate stage in the evolution of the anuran Bauplan, some of which were also linked to jumping skills. We considered T. massinoti in an explicit evolutionary framework by means of multivariate analyses and comparative phylogenetic methods. We used length measurements of major limb bones of 188 extant limbed amphibians (frogs and salamanders) and lizards as a morphological proxy of observed locomotor behavior. Our findings show that limb data correlate with locomotion, regardless of phylogenetic relatedness, and indicate that salamander-like lateral undulatory movements were the main mode of locomotion of T. massinoti. These results contrast with recent hypotheses and indicate that derived postcranial features that T. massinoti shared with anurans might have been later co-opted as exaptations in jumping frogs.

The highly elongated necks, and often tails, of sauropod dinosaurs were composed of concavo-convex vertebrae that provided stability without compromising mobility. Polarities of these concavo-convex joints in the neck and tail are anatomically opposite one another but mechanically equivalent. Opisthocoelous cervical vertebrae and procoelous caudal vertebrae have the convex articular face directed away from the body and the concave articular face directed toward the body. This “sauropod-type” polarity is hypothesized to be (1) more resistant to fracturing of the cotylar rim and (2) better stabilized against joint failure by rotation than the opposite polarity. We used physical models to test these two functional hypotheses. Photoelastic analysis of model centra loaded as cantilevers reveals that neither polarity better resists fracture of the cotylar rim; strain magnitude and localization are similar in both polarities. We assessed the rotational stability of concavo-convex joints using pairs of concavo-convex centra loaded near the joint. Sauropod-type joints withstood significantly greater weight before failure occurred, a pattern we interpret to be dependent on the position of the center of rotation, which is always within the convex part of the concavo-convex joint. In sauropod-type joints, the free centrum rotates about a center of rotation that lies within the more stable proximal centrum. In contrast, the opposite polarity results in a free centrum that rotates about an internal point; when the condyle rotates down and out of joint, the distal end rotates back toward the body, unopposed by ligamentous support. Sauropod-type joints remained stable with greater mobility, more mechanically advantageous tensile element insertions, and greater distal loads than the opposite polarity. The advantages conferred by this joint polarity would have facilitated the evolution of hyperelongated necks and tails by sauropods. Polarity of concavo-convex joints of the appendicular skeleton (e.g., hip, shoulder) is also consistent with the demands of rotational stability.

Paleecological data allow not only the study of trends along deep-time chronological transects but can also be used to reconstruct ecological gradients through time, which can help identify causal factors that may be strongly correlated in modern ecosystems. We have applied such an analysis to Bergmann’s rule, which posits a causal relationship between temperature and body size in mammals. Bergmann’s rule predicts that latitudinal gradients should exist during any interval of time, with larger taxa toward the poles and smaller taxa toward the equator. It also predicts that the strength of these gradients should vary with time, becoming weaker during warmer periods and stronger during colder conditions. We tested these predictions by reconstructing body-mass trends within canid and equid genera at different intervals of the Oligo-Miocene along the West Coast of North America. To allow for comparisons with modern taxa, body mass was reconstructed along the same transect for modern Canis and Odocoileus. Of the 17 fossil genera analyzed, only two showed the expected positive relationship with latitude, nor was there consistent evidence for a relationship between paleotemperature and body mass. Likewise, the strength of body-size gradients does not change predictably with climate through time. The evidence for clear gradients is ambiguous even in the modern genera analyzed. These results suggest that, counter to Bergmann’s rule, temperature alone is not a primary driver of body size and underscore the importance of regional-scale paleoecological analyses in identifying such drivers.

Diet and body mass are highly important factors in mammalian ecology, and they have also proven to be powerful paleoecological indicators. Our previous research has proposed a new classification scheme for mammals with more dietary divisions that emphasizes the primary resource in a given diet. We analyzed a database summarizing the dietary preferences of 139 species of marsupial and placental terrestrial mammals (including 14 orders) and their average body masses in order to explore whether this new classification better highlights ecomorphological differences between species. Additionally, the dietary diversity of every species in the data set was quantified by applying the inverse Simpson index to stomach content percentages. We observed a decrease in maximum dietary diversity with increasing body mass. Having lower requirements for energy and nutrients per unit of body weight or ecological advantages such as larger home ranges allows larger mammals to feed on less nutritive feeding resources (i.e., structural plant material). Our results also suggest that body-size ranges are different across dietary specializations. Smaller mammals (<1 kg) are mainly insectivores, granivores, or mixed feeders, while bigger animals (>30 kg) are usually either carnivores or herbivores that feed specifically on grasses and leaves. The medium-size range (1–30 kg) is mostly composed of frugivorous species that inhabit tropical and subtropical rain forests. Thus, the near absence of medium-sized mammals in open environments such as savannas can be linked to the decreasing density of fruit trees needed to support a pure frugivorous diet year-round. In other words, seasonality of precipitation prevents species from specializing on a totally frugivorous diet. Our results suggest that this new classification scheme correlates well with body mass, one of the most studied morphological variables in paleoecology and ecomorphology. Therefore, the classification should serve as a useful basis for future paleoclimatological studies.

Few methods exist that put a posterior probability on the hypothesis that a thing is gone forever given its sighting history. A recently proposed Bayesian method is highly accurate but aggressive, generating many near-zero or near-one probabilities of extinction. Here I explore a Bayesian method called the agnostic equation that makes radically different assumptions and is much more conservative. The method assumes that the overall prior probability of extinction is 50% and that slices of the prior are exponentially distributed across the time series. The conditional probability of the data given survival is based on a simple, long-known combinatorial expression that captures the chance all presences would fall at random before or within the last sighting’s interval (L) given that they could fall anywhere. The same equation is used to compute the conditional probability given extinction at the start of each interval i, that is, the chance that all sightings would fall before or within L given that none could equal or postdate i. The conditional probability is zero for all hypothesized extinction intervals through L. Bayes’s theorem is then used to compute the posterior extinction probability. It is noted that recycling the mean posterior for a population as a prior improves the method’s accuracy. The agnostic equation differs from an earlier, related one, because it explicitly includes a term to represent the hypothesis of survival, and it therefore does not assume that the species has necessarily gone extinct within the sampling window. Simulations demonstrate that the posterior extinction probabilities are highly accurate when considered as a suite but individually indecisive, rarely approaching one. This property is advantageous whenever inferring extinction would have dangerous consequences. The agnostic method is therefore advocated in cases where conservative estimates are desired.

As paleontological studies are generally distorted by gaps and biases in the fossil record, it is important to assess its completeness. Here we address the fossil record of Parareptilia, a Permian–Triassic amniote clade, applying two measures of specimen completeness: the skeletal completeness metric (SCM) and the character completeness metric (CCM). The SCM quantifies how much of the skeletal material of a taxon is preserved, whereas the CCM measures the amount of phylogenetic information available. The latter was implemented using two different approaches. In this study, we compare three completeness metrics. Two CCM implementations show a strong correlation with each other, but only the second implementation of the CCM correlates significantly with the SCM, possibly due to character selection in phylogenetic data sets. There is no correlation between diversity of parareptiles and their completeness, implying that the observed fluctuations in diversity are not driven by the completeness of the fossils. The mean completeness of parareptiles through time is consistently high compared with previously studied tetrapod clades, suggesting that most parareptile taxa are based on reasonably complete specimens. Clade-specific differences reveal no link between body size and completeness. However, the analyses confirm the impact of ecology, with aquatic mesosaurids being better preserved than terrestrial taxa.

One important and sometimes contentious challenge in paleobiology is discriminating between species, which is increasingly accomplished by comparing specimen shape. While lengths and proportions are needed to achieve this task, finer geometric information, such as concavity, convexity, and curvature, plays a crucial role in the undertaking. Nonetheless, standard morphometric methodologies such as landmark analysis are not able to capture in a quantitative way these features and other important fine-scale geometric notions.

Here we develop and implement state-of-the-art techniques from the emerging field of computational geometry to tackle this problem with the Mississippian blastoid Pentremites. We adapt a previously known computational framework to produce a measure of dissimilarity between shapes. More precisely, we compute “distances” between pairs of 3D surface scans of specimens by comparing a mix of global and fine-scale geometric measurements. This process uses the 3D scan of a specimen as a whole piece of data incorporating complete geometric information about the shape; as a result, scans used must accurately reflect the geometry of whole, undamaged, undeformed specimens. Using this information we are able to represent these data in clusters and ultimately reproduce and refine results obtained in previous work on species discrimination. Our methodology is landmark free, and therefore faster and less prone to human error than previous landmark-based methodologies.

Occupancy statistics in ecology and paleontology are biased upward by the fact that we generally do not have solid data on species that exist but are not found. The magnitude of this bias increases as the average occupancy probability decreases and as the number of sites sampled decreases. A maximum-likelihood method is developed to estimate the underlying distribution of occupancy probabilities of all species based only on the sample of observed species with nonzero occupancy. The method is based on determining the probability that the number of occupied sites will take on any specific value for a given occupancy probability, integrated over the entire distribution of occupancy probabilities. If the shape of the underlying distribution is well modeled, the resulting occupancy estimates circumvent the bias inherent in failing to observe some species and the fact that this bias depends on the number of sites. For occupancy data on marine animal genera drawn from the Paleobiology Database, the underlying distribution is reasonably approximated as a right-truncated log-normal, but the methods developed can be extended to any distribution. Examples are presented to illustrate some observations that are robust and others that need to be revised in light of this bias correction. The method is compared to a recently developed, distribution-free approach to the same problem.