Biomechanical models illustrate how the principles of physics and physiology determine function in organisms, allowing ecological inferences and functional predictions to be based on morphology. Dynamic lever and linkage models of the mechanisms of the jaw and skull during feeding in fishes predict function from morphology and have been used to compare the feeding biomechanics of diverse fish groups, including fossil taxa, and to test ideas in ecological morphology. Here we perform detailed computational modeling of the four-bar linkage mechanism in the skull and jaw systems of Dunkleosteus terrelli, using software that accepts landmark morphological data to simulate the movements and mechanics of the skull and jaws during prey capture. The linkage system is based on the quadrate and cranio-thoracic joints: Cranial elevation around the cranio-thoracic joint forces the quadrate joint forward, which, coupled with a jaw depressor muscle connecting the jaw to the thoracic shield, causes the jaw to rotate downward during skull expansion. Results show a high speed transmission for jaw opening, producing a rapid expansion phase similar to that in modern fishes that use suction during prey capture. During jaw closing, the model computes jaw and skull rotation and a series of mechanical metrics including effective mechanical advantage of the jaw lever and kinematic transmission of the skull linkage system. Estimates of muscle cross-sectional area based on the largest of five specimens analyzed allow the bite force and strike speed to be estimated. Jaw-closing muscles of Dunkleosteus powered an extraordinarily strong bite, with an estimated maximal bite force of over 6000 N at the jaw tip and more than 7400 N at the rear dental plates, for a large individual (10 m total length). This bite force capability is among the most powerful bites in animals. The combination of rapid gape expansion and powerful bite meant that Dunkleosteus terrelli could both catch elusive prey and penetrate protective armor, allowing this apex predator to potentially eat anything in its ecosystem, including other placoderms.

Fossil species of the family Hyaenidae represent a wide range of ecomorphological diversity not observed in living representatives of this carnivoran group. Among them, the cursorial meat-and-bone specialists are of particular interest not only because they were the most cursorial of the hyaenids, but also because they were the only members of this family to spread into the New World. Here we conduct a functional morphological analysis of the cranium of the cursorial meat-and-bone specialist Chasmaporthetes lunensis by using finite element modeling to compare it with the living Crocuta crocuta, a well-known bone-cracking carnivoran. As found with previous finite element studies on hyaenid crania, the cranium of C. lunensis is not differentially adapted for stress dissipation between the bone-cracking and meat-shearing teeth. A smaller occlusal surface on the more slender P3 cusp of C. lunensis allowed this species to use less bite force to crack a comparably-sized bone relative to C. crocuta, but higher muscle masses in the latter probably allow it to process larger food items. We use two indices, the stress slope and the bone-cracking index, to show that C. lunensis has a well-adapted cranium for stress dissipation given its size, but the main stresses placed on its cranium might have been more from subduing prey and less from cracking bones. Throughout the Cenozoic, other carnivores besides hyaenids convergently evolved similar morphologies, including domed frontal regions, suggesting an adaptive value for a repetitive mosaic of features. Our analyses add support to the hypothesis that bone-cracking adaptations are a complex model that has evolved convergently several times across different carnivoran families, and these predictable morphologies may evolve along a common gradient of functionality that is likely to be under strong adaptive control.

Determining whether a species has gone extinct is a central problem in both paleobiology and conservation biology. Past literature has mostly employed equations that yield confidence intervals around the endpoints of temporal ranges. These frequentist methods calculate the chance of not having seen a species lately given that it is still alive (a conditional probability). However, any reasonable person would instead want to know the chance that a species is extinct given that it has not been seen (the posterior probability). Here, I present a simple Bayesian equation that estimates posteriors. It uninterestingly assumes that the sampling probability equals the frequency of sightings within the range. It interestingly sets the prior probability of going extinct during any one time interval (E) by assuming that extinction is an exponential decay process and there is a 50% chance a species has gone extinct by the end of its observed range. The range is first adjusted for undersampling by using a routine equation. Bayes' theorem is then used to compute the posterior for interval 1 (ε1), which becomes the prior for interval 2. The following posterior ε2 again incorporates E because extinction might have happened instead during interval 2. The posteriors are called “creeping-shadow-of-a-doubt values” to emphasize the uniquely iterative nature of the calculation. Simulations show that the method is highly accurate and precise given moderate to high sampling probabilities and otherwise conservative, robust to random variation in sampling, and able to detect extinction pulses after a short lag. Improving the method by having it consider clustering of sightings makes it highly resilient to trends in sampling. Example calculations involving recently extinct Costa Rican frogs and Maastrichtian ammonites show that the method helps to evaluate the status of critically endangered species and identify species likely to have gone extinct below some stratigraphic horizon.

Standard techniques of energy exchange analysis are applied to modelling the thermal regimes of several species of sailback pelycosaurs. Of particular interest is the role played by the sail in thermoregulation. Although the sail did increase the rate at which the model could warm up in the morning, its effectiveness fell short of previous estimates. The sail increased the daytime internal temperature by typically 3°C to 6°C. The more massive subjects had the highest temperature increases owing partly to their higher thermal inertia and partly to their disproportionately large sails. The sail had no impact upon the nocturnal minimums in temperature.

Overheating does not appear to have been a significant problem in the Permian environment, particularly in view of the high thermal inertia of the subjects modeled. When overheating occurred, the sail was of limited value for dumping excess heat.

A computer simulation was developed which estimates the effects of differential preservation on the value of taxonomic diversity in fossil assemblages. Taxonomic diversity was measured with the Shannon-Weaver index, H′ and with evenness, J. Preservation markedly alters quantitative measurements of taxonomic diversity. The degree of alteration can, however, be predicted on the basis of the species-abundance distribution and on the distributions of species of varying preservability. The indices of diversity H′ and J measure different aspects of diversity, but respond to differential preservation in a similar manner. Evenness, J, is recommended for paleoecologic use. The computer model can be used to revise fossil diversity data. A simple form of such a model has been used, and suggests that some previous interpretations of paleoecologic diversity may be in error.

Edge-drilling is an unusual predation pattern in which a predatory gastropod drills a hole on the commissure between the valves of a bivalve. Although it is faster than wall drilling, it involves the potential risk of amputating the drilling organ. We therefore hypothesize that this risky strategy is advantageous only in environments where predators face high competition or predation pressure while feeding. The high frequency of edge-drilling (EDF, relative to the total number of drilled valves) in a diverse Recent bivalve assemblage from the Red Sea enables us to test this hypothesis, predicting (1) a low EDF in infaunal groups, (2) a high EDF in bivalves with elongated shape, (3) high incidence of edge-drilling in groups showing a high wall-drilling frequency, and (4) high EDF in shallow habitats. We evaluate these predictions based on >15,000 bivalve specimens. Among ecological attributes, we found substrate affinity and predation intensity of a species to be good predictors of edge-drilling incidence. Infaunal taxa with high length/width ratio have a low EDF, in accordance with our predictions. Predation intensity is also a significant predictor of edge-drilling; groups with high predation intensity show higher incidence of edge-drilling, confirming our prediction. Although water depth fails to show any significant effect on EDF, this analysis generally supports the high-risk hypothesis of edge-drilling incidence because shallow depths have considerable microhabitat variability. Classically the drill hole site selection has often been linked to predatory behavior. Our study indicates that prey attributes are also crucial in dictating the behavioral traits of a driller such as site selection. This calls for considering such details of the prey to fully understand predation in modern and fossil habitats. Moreover, this perspective is important for tackling the longstanding riddle of the limited temporal and spatial distribution of edge-drilling.

The origins and maintenance of morphological diversity through the Phanerozoic have been documented in several groups of invertebrates. By using shape analysis of the ventral valve, we quantify morphological diversity within the inarticulate brachiopods, which have a species-rich lower Paleozoic history followed by low richness through the rest of the Phanerozoic. Morphological diversity peaked during the Cambrian, and was subsequently maintained despite significant decreases in richness at all taxonomic levels. The loss of morphological diversity, associated with late-Paleozoic decreases in the number of orders and the Permo-Triassic mass extinction, was followed by rapid morphological rediversification without concordant taxonomic diversification. Any limits upon the generation of diverse morphologies were established early in the Cambrian and were maintained and approached through the history of this group.

Cases of convergent evolution, particularly within ecomorphological contexts, are instructive in identifying universally adaptive morphological features across clades. Tracing of evolutionary pathways by which ecomorphological convergence takes place can further reveal mechanisms of adaptation, which may be strongly influenced by phylogeny. Ecomorphologies of carnivorous mammals represent some of the most outstanding cases of convergent evolution in the Cenozoic radiation of mammals. This study examined patterns of cranial shape change in the dog (Canidae) and hyena (Hyaenidae) families, in order to compare the evolutionary pathways that led to the independent specialization of bone-cracking hypercarnivores within each clade. Geometric morphometrics analyses of cranial shape in fossil hyaenids and borophagine canids provided evidence for deep-time convergence in morphological pathways toward the independent evolution of derived bone-crackers. Both clades contained stem members with plesiomorphic generalist/omnivore cranial shapes, which evolved into doglike species along parallel pathways of shape change. The evolution of specialized bone-crackers from these doglike forms, however, continued under the constraint of a full cheek dentition and restriction on rostrum length reduction in canids, but not hyaenids. Functionally, phylogenetic constraint may have limited borophagine canids to crack bones principally with their carnassial instead of the third premolar as in hyaenids, but other cranial shape changes associated with durophagy nevertheless evolved in parallel in the two lineages. Size allometry was not a major factor in cranial shape evolution in either lineage, supporting the interpretation of functional demands as drivers for the observed convergence. The comparison between borophagines and hyaenids showed that differential effects of alternative functional “solutions” that arise during morphological evolution may be multiplied with processes of the “macroevolutionary ratchet” already in place to further limit the evolutionary pathways available to specialized lineages.

Amino acid analyses of undecalcified samples of fossil crocodile and rhinoceros enamel and dentin from mature teeth revealed that the total protein content of these mineralized fossil tissues varied from ~0.01–0.007% by weight. Except in one instance, amino acid analyses of the enamel proteins revealed them to be free of collagen and to have an amino acid composition similar to the proteins obtained from the enamel of mature modern vertebrates. Molecular sieving of the acid soluble enamel proteins demonstrated that the components consisted principally of small peptides and free amino acids, as in the enamel of modern vertebrates.

Based on the presence of hydroxyproline (hyp) and hydroxylysine (hyl), collagen was detected in undecalcified mature dentin of fossil rhinoceros, but not in undecalcified crocodile dentin. It was only by sequential extraction procedures that the presence of collagen in the dentin of fossil crocodile was established, emphasizing the utility and importance of analyzing the soluble components in specific extracts of the fossil. Based on these data and the concentrations of hyp and hyl in the material solubilized by the various solvents, the dentin of fossil rhinoceros contained considerably more collagen per weight and as a percentage of the total protein in the dentin than did the dentin of fossil crocodile.

As with modern dentin, EDTA and dilute acid solubilize the noncollagenous proteins and peptides found in fossil enamel and dentin, some of which contain O-phosphoserine [Ser(P)], an amino acid unique to mineralized connective tissues. Similar to recent reported findings from fossil bone, less of the original content of the noncollagenous proteins, including those phosphorylated, is degraded and removed from the enamel and dentin during fossilization than the percentage of dentinal collagen and the nonphosphorylated domains of the enamel proteins which are removed. This selective resistance to degradation and removal of the noncollagenous proteins, including phosphoproteins, may reflect the strong interaction of these proteins with the mineral phase of fossilized tissues. The amount and close packing of the inorganic crystals may also inhibit the interaction of the proteins in the interior of the enamel and dentin with the geochemical environment.

The geographic distribution of brachiopod genus occurrences over the Phanerozoic shows that secular declines in origination and extinction rates were paralleled by increases in invasion and extirpation rates. Origination and extinction rates declined in two phases, the first from the Cambrian to latest Permian Periods and the second from the latest Permian Period to the present, which were accompanied by concomitant increases in invasion and extirpation rates. In addition to the temporal correlation, an inverse correlation was also weakly evident among time-averaged latitudinal gradients of rates. Compared with faunas at higher latitudes, low-latitude faunas experienced higher origination and extinction rates, and lower invasion and extirpation rates. We suggest that progressive increases in migration ability lowered origination and extinction rates because species that were better equipped to track a preferred habitat, for example, by the ability to disperse larvae over large distances, were less likely to evolve or become extinct in response to local environmental changes. The two phases were separated by the end-Permian mass extinction, which reset to high levels the origination and extinction rates of a taxonomically and ecologically altered global brachiopod fauna. Our data also allow us to quantify the relative contributions of origination, extinction, invasion, and extirpation to regional diversity (quantified as 10° latitudinal zones) more generally. Overall, invasion and extirpation explained slightly more variation in diversity than in situ origination and extinction. The four variables usually occurred in combinations that maintained rather than altered the shape of the latitudinal diversity gradient. For most of the Phanerozoic Eon, the gradient was not the product of continuous renewal, but rather existed as a holdover from a previous interval.

Studies of extinction in the fossil record commonly involve comparisons of taxonomic extinction rates, often expressed as the percentage of taxa (e.g., families or genera) going extinct in a time interval. Such extinction rates may be influenced by factors that do not reflect the intrinsic severity of an extinction trigger. Two identical triggering events (e.g., bolide impacts, sea level changes, volcanic eruptions) could lead to different taxonomic extinction rates depending on factors specific to the time interval in which they occur, such as the susceptibility of the fauna or flora to extinction, the stability of food webs, the positions of the continents, and so on. Thus, it is possible for an extinction event with a higher taxonomic extinction rate to be caused by an intrinsically less severe trigger, compared to an event with a lower taxonomic extinction rate.

Here, we isolate the effects of taxonomic susceptibility on extinction rates. Specifically, we quantify the extent to which the taxonomic extinction rate in a substage is elevated or depressed by the vulnerability to extinction of classes extant in that substage. Using a logistic regression model, we estimate that the taxonomic susceptibility of marine fauna to extinction has generally declined through the Phanerozoic, and we adjust the observed extinction rate in each substage to estimate the intrinsic extinction severity more accurately. We find that mass extinctions do not generally occur during intervals of unusually high susceptibility, although susceptibility sometimes increases in post-extinction recovery intervals. Furthermore, the susceptibility of specific animal classes to extinction is generally similar in times of background and mass extinction, providing no evidence for differing regimes of extinction selectivity. Finally, we find an inverse correlation between extinction rate within substages and the evenness of diversity of major taxonomic groups, but further analyses indicate that low evenness itself does not cause high rates of extinction.

Ptychopariid trilobites from the Marjumiid biomere of Laurentia underwent a statistically significant morphological diversification that is concordant with proposed adaptive radiations of trilobites in each of the Cambrian biomeres. An analysis of a subset consisting of the biomere's most characteristic taxa, the Asaphiscacea, Raymondinacea, and Marjumiacea, also illustrates this morphological diversification. In detail, the total data set and subset show a limited range of morphologies near the base of the biomere and a large increase in range in the upper portion of the biomere.

Regional assemblages from the Appalachians, Great Basin, and Texas were also studied to determine if they too show the larger-scale macroevolutionary patterns of trilobites from Laurentia as a whole. The regional assemblages illustrate similar, but not identical, morphological diversifications, which are also similar to the overall Laurentian pattern. Subsets of the characteristic taxa also show this diversification. These results suggest that regional assemblages can be used to investigate these larger-scale macroevolutionary patterns.

Causal mechanisms for the diversification patterns are not clear. Potential mechanisms include: (1) endemic evolution of new morphologies in Laurentia; (2) migration of new morphologies, including intra- and inter-continental migrations; and (3) environmental controls over the distribution of morphologies. Likely causes for the morphological diversification and its similarity among regions probably include aspects of all three mechanisms.

The organic matrix components of a fossil ammonoid shell from the Upper Cretaceous, can be separated into sub-fractions which are generally comparable to those found in extant Nautilus, using ion exchange chromatography. This suggests that at least portions of these components are sufficiently well preserved to interact characteristically with the ion exchange resin. Amino acid compositions of these sub-fractions, however, do not resemble Nautilus organic matrix sub-fractions, indicating that considerable diagenetic alteration of this material has taken place.

Genera by their very nature are expected to be monotypic and geographically and environmentally restricted at their origin, and most genera do not endure past their stage of first appearance. At the same time, those genera that do endure have a capacity to expand greatly in geographic range, environmental breadth, and species richness. Here we ask what it is that allows some genera and not others to survive past their inception. Using occurrence data from the Paleobiology Database, we find that initial geographic range has the strongest effect on survival, followed by environmental breadth, with the effect of species richness weaker on average. The effect of geographic range is strongest if measured as the distances spanned by the occurrences of a genus rather than the number of distinct areas in which a genus lives. We document substantial secular variation in selectivity of early survival. The most striking aspect of this variation is that survival is only weakly selective among genera that first appear during the Mesozoic. By following genera beyond their stage of first appearance, we find that selectivity with respect to all factors becomes systematically stronger as cohorts age and genera become more differentiated in range, breadth, and richness. This may help account for a previously identified statistical effect of genus age on the chances of survival.

Taxon-age distributions were compiled for families of marine animals surviving or becoming extinct in each stage of the Phanerozoic. I demonstrate, through the use of a modified bootstrap analysis, that there is no difference between the longevity of families becoming extinct during times of background extinction and times of mass extinction. In both mass and background extinction intervals the mean age of families that become extinct is 2 standard deviations below the geometric mean taxon age of families available for extinction. Young families are more susceptible to extinction, perhaps as the result of lower species richness or of occupying a smaller geographic range. There is no tendency during mass extinctions toward loss of families with different taxon ages other than those that become extinct during background times. Thus, in terms of family survival, mass extinction appears to be an exaggeration of processes of background extinction.

Distributions of brachiopods from low-latitude paleogeographic settings, primarily in the Tethyan Ocean of southern Europe, with additional data from North America allow some observations on the bathymetric distribution of early Mesozoic brachiopod orders. Norian and latest Triassic (Rhaetian) brachiopod biofacies are dominated in shallowest waters by short-looped terebratulids (Terebratulidina) while spire-bearing athyrids (Athyrida) are common components of deeper-water environments in the latest Triassic. In the late Early Jurassic (Pliensbachian), shallow-water brachiopod faunas are dominated by rhynchonellids, short-looped terebratulids are commoner in relatively deeper shelf waters, and spiriferids and long-looped terebratulids (Terebratellidina) are abundant in deeper-water shelf environments.

Following the end-Triassic extinction event there appears to be niche-replacement in deep-water shelf environments of Late Triassic athyrids by spiriferids and long-looped terebratulids in the Early Jurassic. Rhynchonellids appear to have diversified into shallowest water environments; specialized short-looped terebratulids may have occupied deeper-water niches that resulted ultimately in the success of the enigmatic Pygopidae later in the Jurassic and Cretaceous.

Subcolony boundaries within Paleozoic bryozoan colonies, not otherwise easily observable, can be located precisely by computer mapping of variables derived from Fourier series. The monticule-centered subcolonies were maintained by morphogenetic gradients that controlled zooecial size and form, zooidal degeneration (producing brown bodies), and the spacing of monticules with respect to each other. These gradients were probably determined by the release of a budding inhibitor from polymorphic zooids within the monticule. In colonies with active monticular budding the morphogenetic gradients represent ontogenetic series, as the zooids that arose in the monticule gradually migrated outward along modified spiral pathways. Polymorphism, including reproductive functions, is probably reflected in the spatial order of zooids away from a monticule. In subcolonies with monticular budding, polymorphs represent different stages in the life history of a single zooid, with gradual transitions in zooecial form between castes.

The structural similarity between monticules and oghurd dunes supports the idea that they also functioned as excurrent water outlets, possibly with reproductive polymorphs clustered near the outflow. The variability of monticular size and spacing in some colonies indicates that hydrodynamic efficiency was compromised by the need for developmental plasticity. The development of active budding within monticules is considered an ecophenotypic response to the external environment, suggesting that all monticules within the Stenolaemata were potential budding sites. Monticules were successful adaptations in bryozoans because they performed a multiplicity of functions. While regulating the morphogenesis of the colony, they simultaneously served the metabolic functions of waste removal, feeding and reproduction.

An early Pliocene fossil locality in the Canadian High Arctic preserves the remains of the extinct beaver Dipoides sp. (Castoridae, Rodentia) in association with an assemblage of fossil beaver-cut wood. The wood assemblage presents a first opportunity to investigate woodcutting behavior and ecological performance in an extinct castorid genus. This study compares woodcutting in Dipoides sp. with that of the modern beaver, Castor canadensis, using evidence from small-diameter cut sticks (i.e., sticks transected by parallel series of cut marks) in combination with behavioral observations of Castor woodcutting. During woodcutting both Castor and Dipoides used their incisors unilaterally; the upper incisor was pressed against the stick while the corresponding lower incisor cut. Cut marks were relatively larger for Castor than Dipoides (scaled to incisor size). Compared with Dipoides, Castor more frequently used a cutting strategy that minimized the number of cuts needed to transect a stick (e.g., clipping as opposed to chip removal). Taken together, the behavioral evidence suggests that ecological cutting performance was lower for Dipoides than Castor.

Examination of organismal characteristics which promote survivorship through both background and mass extinctions may reveal general ecological principles potentially critical to modern conservation efforts. This study explores survivorship of brachiopods, a highly diverse and abundant Paleozoic clade, through the mid-Permian to mid-Triassic interval, which includes the greatest mass extinction in the history of metazoan life. This interval of time separates two of the major Phanerozoic evolutionary faunas. In this regard, survivorship across any one extinction during the interval would not have been relevant if the survivor went extinct shortly after the extinction event; surviving background extinction is as important as surviving a mass extinction. Similarly, taxa that survived but failed to rediversify also were not major elements of the Mesozoic evolutionary fauna. Thus, the analysis aims to analyze survivorship not just across a single extinction but across the entire mid-Permian to mid-Triassic; only survivors through the entire interval can be the ancestors of the Mesozoic clades.

Fewer brachiopod genera survived the interval than did brachiopod clades, suggesting that pseudoextinction or insufficient sampling could be a problem in analyzing these extinctions; thus, survivorship analysis should be conducted at the clade level. Nine characteristics were examined for generic representatives of 20 North American brachiopod clades, five of which survived both Permian extinctions and the subsequent earliest Triassic transitional interval. Characteristics include both those that operate on global scales and those that operate on the higher-resolution scales of individuals and populations.

Survivors were significantly smaller and occurred less frequently than victims. Mean diversity of communities in which survivors were present was significantly greater. The finding that rare taxa belonging to high-diversity communities were more likely to survive runs counter to traditional predictions. However, these results are consistent with recent studies suggesting that higher diversity within a trophic level may create a buffer, as surviving taxa quickly occupy the vacant niche space of the victims. As size, abundance, and community diversity are all statistically related, the small size of survivors may be an artifact of reduced biovolume per taxon in a diverse community.

No significant relationship exists between global-scale processes and survivorship of brachiopods through the mid-Permian to mid-Triassic. The results suggest that ecological processes can strongly influence global extinction patterns.

Species abundance data are of vital importance in paleontology, but fossil accumulations invariably represent a biased subset of original source communities. Efforts to quantify taphonomic biases are typically prevented by a lack of independent data on the ecological composition of prehistoric faunas. However, analysis of the continental Holocene record can provide a rare opportunity for independent calibration of fossil abundance patterns. We analyzed a comprehensive data set available for the Holocene avifauna of Sweden to investigate the relationship between species abundance in the recent fossil and zooarchaeological records and in prehistoric source communities, and to characterize the importance of different ecological factors in determining terrestrial vertebrate fossil abundances. The number of assemblages in which species occurred was compared with modern-day species abundance, annual residence, body mass, and ecological realm. Modern-day abundance is only one of several significant predictors of fossil abundance; the strongest predictor is body mass, and Holocene species abundance can be interpreted as a measure of species abundance in source communities for a given size class only. Our study represents one of the only direct attempts to quantify species abundance biases between fossil faunas and source communities, and has general applicability for a wide range of terrestrial vertebrate faunas.