Lungfishes are known for, and indeed take their name from, their bimodal respiratory abilities. All three extant genera can use their lungs to extract oxygen from the atmosphere, although their reliance upon this capability differs among taxa. Lungs are considered primitive for the Osteichthyes, however the distinctive buccal pump mode of air gulping exhibited by extant lungfishes appears to be a specialization. It is associated with a number of derived skeletal characters (cranial ribs, long parasphenoid stalk, midline gap between palatal tooth plates) that first appeared during the Devonian. These have been described individually, but in no Devonian lungfish has their three-dimensional (3D) spatial relationship been reconstructed and analyzed. Here we present the 3D morphology of Rhinodipterus, a Mid-Late Devonian lungfish from Australia and Europe, based on synchrotron tomography and conventional microtomography scans.

Unlike less crownward contemporaneous lungfishes such as Griphognathus and Chirodipterus, Rhinodipterus has a full set of skeletal buccal pump components that can be directly compared to those of extant lungfishes, suggesting that it made more extensive use of air breathing than other Gogo or Bergisch Gladbach genera. This is interesting in relation to the environmental context as Gogo and Bergisch Gladbach are both marine, contrasting with the frequently hypoxic tropical to subtropical fresh water environments inhabited by modern lungfishes. The evolution of buccal pump-supported lung ventilation was evidently not necessarily associated with a transition to non-marine habitats.

One of the major evolutionary transitions of the mammaliaform lineage was the origin of a typically mammalian pattern of growth. This is characterized by rapid juvenile growth followed by abrupt cessation of growth at adult size and may be linked with other important mammaliaform apomorphies of dental replacement and morphology. Investigation of growth patterns in the tritylodontid cynodont Oligokyphus and the basal mammaliaform Morganucodon provides insight into this crucial transition. We collected mandibular depth measurements from large samples of Morganucodon and Oligokyphus and constructed distributions of mandibular depth versus frequency for each species. These were compared with distributions from species from three different growth classes of extant amniote: testudines + crocodilians, mammals + birds, and lepidosaurs. Discriminant function analysis was used to differentiate between known growth classes by using different combinations of three measures of mandibular depth distribution shape (skew, kurtosis, and coefficient of variation) as proxies for different juvenile and adult growth patterns. Classification of the fossil species showed that Morganucodon closely resembled extant placental mammals in having rapid juvenile growth followed by truncated, determinate adult growth. Oligokyphus showed intermediate growth patterns, with more extended adult growth patterns than Morganucodon and slightly slower juvenile growth. This suggests a gradual evolution of mammalian growth patterns across the cynodont to mammaliaform transition, possibly with the origin of rapid juvenile growth preceding that of truncated, determinate adult growth. In turn, acquisition of both these aspects of mammalian growth was likely necessary for the evolution of diphyodont tooth replacement in the mammaliaform lineage.

Dental microwear analyses of ungulates and other large herbivores rely on correlations of diet and microwear among extant ungulates, primarily ruminants. Microwear is considered a ‘taxon-free’ method of paleodietary analysis. The properties of food are associated with causality of microwear, but the possibility that heritable properties of the consumer (tooth morphologies, masticatory dynamics, enamel mechanical properties, digestive physiologies) may introduce bias is not considered. Using an observer blind method of light microscopy, we examined the distribution of microwear features on the molars of eight species of ruminants and perissodactyls. Grazing and browsing ruminants had statistically different numbers of scratches forming discrete data clusters. Perissodactyls differ in the numbers of scratches and pits but without discrete browser and grazer clusters. Microwear features were distributed homogeneously across ruminant molars and strongly predictive of diet from the labial edge of the molar to the lingual edge. Microwear was heterogeneously distributed across perissodactyl molars with more pits on the labial edge and more scratches on the lingual edge. In perissodactyls, microwear sampled from the labial edge was strongly predictive of diet, while microwear sampled from other areas were not. Discriminant function analyses of microwear assigned individual molars to diets (browser and grazer) and clades (ruminant and perissodactyl) with similar success (70–73%) indicating that phylogeny and diet influence microwear equally. Rhino microwear was more sensitive to clade membership while other perissodactyl microwear was more sensitive to diet. Although it is not clear what heritable variables may phylogenetically bias dental microwear, extant ruminants may not be appropriate models for the microwear of other large herbivores.

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.

New growth rate estimates for nine species from three genera of New Zealand Crassatellidae (Mollusca: Bivalvia), combined with existing morphometric ontogenetic descriptions, allow identification of heterochronic processes in the evolution of these genera. Both paedomorphosis (progenesis and neoteny) and peramorphosis (hypermorphosis and acceleration) have occurred within the clade. Overall, morphological variability and response to environmental pressure in this nonsiphonate group is restricted by the interplay of anatomical and life habit constraints. Stability in the substrate, predator avoidance, sluggish burrowing speed, and inability to escape by deep burial are suggested as key drivers of, or constraints on, morphological change. Two groups of shell characters are identified: heavy, armored “anchors” and elongate “snorkels,” which combine juvenile and adult traits in shells of different sizes and ages, produced by heterochronic variation in developmental timing. Anchors and snorkels both represent different “solutions” to the problems of life as a nonsiphonate, infaunal bivalve.

Most of the mammalian diversity is known only from fossils, and only a few of these fossils are well preserved or abundant. This undersampling poses serious problems for understanding mammalian phenotypic evolution under a quantitative genetics framework, since this framework requires estimation of a group’s additive genetic variance–covariance matrix (G matrix), which is impossible, and estimating a phenotypic variance–covariance matrix (P matrix) requires larger sample sizes than what is often available for extinct species. One alternative is to use G or P matrices from extant taxa as surrogates for the extinct ones. Although there are reasons to believe this approach is usually safe, it has not been fully explored. By thoroughly determining the extant and some extinct Xenarthra (Mammalia) cranium P matrices, this study aims to explore the feasibility of using extant G or P matrices as surrogates for the extinct ones and to provide guidelines regarding the reliability of this strategy and the necessary sample sizes. Variance–covariance and correlation P matrices for 35 cranium traits from 16 xenarthran genera (12 extant and 4 extinct) were estimated and compared between genera. Results show xenarthran P-matrix structures are usually very similar if sample sizes are reasonable. This study and others developed with extant therian mammals suggest, in general, that using extant G or P matrices as an approximation to extinct ones is a valid approach. Nevertheless, the accuracy of this approach depends on sample size, selected traits, and the type of matrix being considered.

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.

The Early Jurassic Toarcian Oceanic Anoxic Event is considered one of the most dramatic environmental perturbations of the Mesozoic. An elevated extinction rate among marine invertebrates accompanied rapid environmental changes, but effects on large vertebrates are less understood. We examined changes in ichthyosaur body size in the Posidonia Shale of the Southwest German Basin spanning the extinction interval to assess how environmental changes and biotic crisis among prey species affected large reptiles. We report no species-level extinction among the ichthyosaurs coinciding with peak invertebrate extinction. Large ichthyosaurs were absent from the fauna during the extinction interval, but became more abundant in the immediate aftermath. Stenopterygius quadriscissus, the most abundant species during the extinction interval, increased in body size after the biotic event. Rapid invasion by large taxa occurred immediately following the extinction event at the end of the first ammonite zone of the early Toarcian. Greater mobility permitting exploitation of ephemeral resources and opportunistic feeding behavior may minimize the impacts of environmental change on large vertebrates.

Graphoglyptids are deep-marine trace fossils, often found preserved as casts in positive relief on the base of turbidites. Previous analyses of the behavioral evolution of graphoglyptids suggested they were slowly diversifying, becoming optimized, and getting smaller over time until the Late Cretaceous, when a sudden increase in diversification occurred. This current study quantifies the morphology of approximately 400 different graphoglyptid specimens, ranging in age from the Cambrian to the present, in order to evaluate the behavioral evolutionary interpretations made previously. Results from this study indicate that although some general evolutionary patterns can be discerned, they are not as straightforward as previously reported.

Different topological categories of trace fossils represent organisms’ responses to evolutionary pressures in unique ways. While burrow widths of meandering traces were becoming smaller over time, as predicted by previous workers, the burrow widths of the network traces were becoming smaller only until the Late Cretaceous, when they started to get larger again. The times of significant evolutionary changes in behavior were not consistent among various topological categories, with some morphological features being affected in the Late Cretaceous and others during the beginning of the Eocene. It is likely that the behavioral evolution of graphoglyptids was influenced by deep-marine global influences linked to climate change, glaciation, and deep-ocean warming. These influences affected each topological group uniquely, suggesting that different species or genera of trace makers were creating each of the topological categories. This is contrary to the hypothesis that all graphoglyptids were created by closely related species.

Carnivore-rich fossil sites are uncommon in the fossil record and, accordingly, provide valuable opportunities to study predators from vantages that are rarely applied to ancient faunas. Through stable isotopes of carbon and a Bayesian mixing model, we analyze time-successive (nearly contemporaneous), late Miocene carnivoran populations from two fossil sites (Batallones-1 and Batallones-3) from central Spain. Stable isotopes of carbon in tooth enamel provide a reliable and direct methodology to track ancient diets. These two carnivoran-dominated fossil sites display differences in the composition and abundance of the carnivoran species, with some species present at both sites and some present only at one site. This disparity has been interpreted as the consequence of habitat differences between Batallones-1, the older site, and Batallones-3, the younger site. However, carbon isotope values of carnivore and herbivore tooth enamel suggest a common habitat of C3 woodland originally present at both sites. The differences in the carnivoran faunas rather may be the consequence of the dynamics of species entrance and exit from the Madrid Basin during the time elapsed between Batallones-1 and Batallones-3 and changes in population densities due to biotic factors. We infer higher levels of interspecific competition in Batallones-3 than in Batallones-1 because of the larger number of similar-sized, sympatric predators; the clear overlap in their δ13C values (except for the amphicyonid Magericyon anceps); and similarity of their preferred prey: the hipparionine horses. Finally, carbon stable isotopic composition of Indarctos arctoides teeth implies that this ursid was a carnivorous omnivore rather than a herbivorous omnivore. This work demonstrates the insights that stable isotopes can provide in characterizing the feeding ecology and trophic interactions of ancient carnivoran taxa.

The small size of Early Triassic marine organisms has important implications for the ecological and environmental pressures operating during and after the end-Permian mass extinction. However, this “Lilliput Effect” has only been documented quantitatively in a few invertebrate clades. Moreover, the discovery of Early Triassic gastropod specimens larger than any previously known has called the extent and duration of the Early Triassic size reduction into question. Here, we document and compare Permian-Triassic body size trends globally in eight marine clades (gastropods, bivalves, calcitic and phosphatic brachiopods, ammonoids, ostracods, conodonts, and foraminiferans). Our database contains maximum size measurements for 11,224 specimens and 2,743 species spanning the Late Permian through the Middle to Late Triassic. The Permian/Triassic boundary (PTB) shows more size reduction among species than any other interval. For most higher taxa, maximum and median size among species decreased dramatically from the latest Permian (Changhsingian) to the earliest Triassic (Induan), and then increased during Olenekian (late Early Triassic) and Anisian (early Middle Triassic) time. During the Induan, the only higher taxon much larger than its long-term mean size was the ammonoids; they increased significantly in median size across the PTB, a response perhaps related to their comparatively rapid diversity recovery after the end-Permian extinction. The loss of large species in multiple clades across the PTB resulted from both selective extinction of larger species and evolution of surviving lineages toward smaller sizes. The within-lineage component of size decrease suggests that only part of the size decrease can be related to the end-Permian kill mechanism; in addition, Early Triassic environmental conditions or ecological pressures must have continued to favor small body size as well. After the end-Permian extinction, size decrease occurred across ecologically and physiologically disparate clades, but this size reduction was limited to the first part of the Early Triassic (Induan). Nektonic habitat or physiological buffering capacity may explain the contrast of Early Triassic size increase and diversification in ammonoids versus size reduction and slow recovery in benthic clades.

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.

Thylacoleo carnifex, or the “pouched lion” (Mammalia: Marsupialia: Diprotodontia: Thylacoleonidae), was a carnivorous marsupial that inhabited Australia during the Pleistocene. Although all present-day researchers agree that Thylacoleo had a hypercarnivorous diet, the way in which it killed its prey remains uncertain. Here we use geometric morphometrics to capture the shape of the elbow joint (i.e., the anterior articular surface of the distal humerus) in a wide sample of extant mammals of known behavior to determine how elbow anatomy reflects forearm use. We then employ this information to investigate the predatory behavior of Thylacoleo. A principal components analysis indicates that Thylacoleo is the only carnivorous mammal to cluster with extant taxa that have an extreme degree of forearm maneuverability, such as primates and arboreal xenarthrans (pilosans). A canonical variates analysis confirms that Thylacoleo had forearm maneuverability intermediate between wombats (terrestrial) and arboreal mammals and a much greater degree of maneuverability than any living carnivoran placental. A linear discriminant analysis computed to separate the elbow morphology of arboreal mammals from terrestrial ones shows that Thylacoleo was primarily terrestrial but with some climbing abilities. We infer from our results that Thylacoleo used its forelimbs for grasping or manipulating prey to a much higher degree than its supposed extant placental counterpart, the African lion (Panthera leo). The use of the large and retractable claw on the semiopposable thumb of Thylacoleo for potentially slashing and disemboweling prey is discussed in the light of this new information.

Thalattosuchians are crocodylomorphs mainly known from marine strata of Early Jurassic to Early Cretaceous age. They represent the earliest crocodylomorph radiation to an aquatic habitat and their evolutionary history offers very few records from freshwater settings. Here, we report several exquisitely preserved thalattosuchian skulls attributed to a derived teleosaurid from a pedogenic horizon located at the base of a fluvial series of alternating silts and sandstones of the Phu Kradung Formation (Upper Jurassic) of northeastern Thailand. Using laser ablation multicollector inductively coupled mass spectrometry (MC-ICP-MS) on tooth enamel and dentine, we measured isotopic ratios of strontium (87Sr/86Sr) to test the habitat of these teleosaurids. In addition, Sr concentrations of the dental tissues were estimated from the calibrated signal intensities of the Sr isotope measurements. The dataset includes bioapatite (teeth or scales) of eight terrestrial and five aquatic vertebrates. Theropods exhibit lower Sr concentrations both in enamel and dentine compared to others groups, a pattern in accordance with the calcium biopurification process, which predicts that Sr concentrations in the body of vertebrates decrease up the trophic chain. It also excludes the possibility that diagenesis has completely overprinted the Sr isotope compositions of the fossil assemblage, which exhibits a homogeneous 87Sr/86Sr signature above the Late Jurassic seawater value. Values for teleosaurid teeth are in the range of other values for vertebrates in the continental assemblage and imply that these crocodylomorphs did not migrate between freshwater and marine habitats at least in the time constraint of the mineralizing tooth. This result represents the first demonstration that a population of teleosaurids was established for a prolonged time in a freshwater environment. Whether the ability of teleosaurids to inhabit freshwater habitats is a secondary adaptation or whether it is plesiomorphic and inherited from freshwater ancestors is discussed.

The late Paleozoic ice age (LPIA) had a profound effect on the biota. Despite much research having been focused on paleotropical regions or global-scale analyses, regional ecological changes have seldom been studied in ice-proximal basins. Here, I study the compositional turnover and diversity structure across the main Carboniferous glacial event recorded in western Argentina and the subsequent nonglacial interval. Brachiopod and bivalve data from western Argentina suggest that the transition from glacial to nonglacial climates caused major compositional changes. Turnover, however, was not uniform across the bathymetric gradient, being higher in deep environments. Because extirpation was concentrated in brachiopods, but immigration was similar in both clades, the taxonomic structure of the region was significantly modified. Although regional hierarchical diversity structure and occupancy distributions remained stable, dissecting the analysis in brachiopods and bivalves underscores that both clades had different responses to climate change. Brachiopods, on the one hand, show stability in the diversity structure and a very slight decrease in occupancies of intermediate genera, while bivalves show an important rise in diversity, both at the environment and regional scale, and an increase in genera with intermediate occupancies. The bathymetric diversity gradient was also modified from hump shaped with maximum diversity in the deep subtidal to a linear gradient with maximum values toward the offshore. However, relative compositional differences within environments remained stable, with maximum values at intermediate depths both in glacial and nonglacial intervals. Moreover, local-scale coexistence between brachiopods and bivalves changed in the nonglacial interval, showing significant segregation, which indicates relevant modifications in community assembly dynamics. Results from western Argentina highlight the magnitude of regional-scale ecological changes during the LPIA in ice-proximal regions, suggesting that the waxing and waning of glaciers was able to cause regional taxonomic turnover and medium-scale ecological changes even during intervals of relative macroevolutionary quiescence.

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.

This study uses a comprehensive, revised, and updated global bivalve dataset combining information from two major databases available to study temporal trends in Phanerozoic bivalve richness: the Sepkoski Compendium and the Paleobiology Database. This compilation results in greater taxonomic and stratigraphic coverage than possible with either of the two databases alone. However, there are challenges in directly comparing these two sources due to differences in their taxonomic designations and stratigraphic range information. Moreover, both of these datasets are fraught with a number of taxonomic errors, which can significantly bias the overall richness estimate. Additionally, a substantial number of taxonomic corrections were made before a new Phanerozoic bivalve richness curve was produced. The new generic taxonomic curve is comparable with the trajectory of the Sepkoski’s modern fauna and shows rapid and substantial diversification through the Ordovician, followed by a Paleozoic plateau, a Mesozoic high, and Cenozoic diversification after a small reduction in richness associated with the K/Pg extinction. The steep Cenozoic rise documented in the raw richness curve derived from the new dataset is likely real, and reflects the overall robustness and completeness of the bivalve fossil record.

Large body size in Keen’s mouse, Peromyscus keeni, has been regarded as a relictual character that developed in times of geographic separation from P. maniculatus. However, body-size changes in Keen’s mouse have not been studied in detail. To address this problem the present paper compares the size of ancient and modern Peromyscus specimens from Vancouver Island. Results indicate that Late Pleistocene Peromyscus from Arch-2 Cave and early Holocene Peromyscus from Pellucidar Cave are significantly larger than those of modern P. maniculatus and P. keeni. Morphology and linear discriminant analyses support tentative assignment of several ancient specimens to P. keeni. Radiocarbon age estimates of 11,960±45 BP (14,004–13,637 cal BP) on a small mammal bone and 12,370±35 BP (14,695–14,148 cal BP) on Ursus arctos from Arch-2 Cave place these faunas on the island as relative sea level fell from a postglacial highstand, suggesting a local source for faunas with limited over-water dispersal capacities. Results of this study are consistent with insular relictual gigantism in Keen’s mouse, although some modification of the original hypothesis is needed to explain the smaller size of modern than ancient mice.