The excellent fossil record of conodonts represents an ideal, yet underutilized, resource for resolving fundamental issues of pattern and process in evolutionary theory. However, this potential has not been exploited because the quantitative understanding of the evolution of conodont element morphology is limited. This work applies standardized morphometric protocols to skeletal elements belonging to the conodont Pterospathodus, derived from a densely sampled section from Estonia. It has established a robust quantitative framework for morphological variation in Pterospathodus, permitting statistical analysis of the current qualitative hypotheses of evolutionary pattern within this genus for the first time. Apparent directional trends were statistically compared with patterns expected for directional evolution, an unbiased random walk and stasis, using maximum-likelihood model fitting, rescaled range analysis, and the runs test. Results confirmed the presence of trends in size and shape change through time, providing an example of convincing directional morphological change in a fossil lineage. The morphometric analyses have also allowed quantitative investigation of ontogenetic processes in Pterospathodus, suggesting that allometric repatterning was the proximal mechanism responsible for mediating the observed shifts in morphology through time. The results have demonstrated that conodonts represent an important resource for understanding evolutionary pattern and process in the fossil record.

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.

The marine faunas of tropical America underwent substantial evolutionary turnover in the past 3 to 4 million years in response to changing environmental conditions associated with the rise of the Isthmus of Panama, but the ecological signature of changes within major clades is still poorly understood. Here we analyze the paleoecology of faunal turnover within the family Pectinidae (scallops) over the past 12 Myr. The fossil record for the southwest Caribbean (SWC) is remarkably complete over this interval. Diversity increased from a low of 12 species ca. 10–9 Ma to a maximum of 38 species between 4 and 3 Ma and then declined to 22 species today. In contrast, there are large gaps in the record from the tropical eastern Pacific (TEP) and diversity remained low throughout the past 10 Myr. Both origination and extinction rates in the SWC peaked between 4 and 3 Ma, and remained high until 2–1 Ma, resulting in a 95% species level turnover between 3.5 and 2 Ma. The TEP record was too incomplete for meaningful estimates of origination and extinction rates. All living species within the SWC originated within the last 4 Myr, as evidenced by a sudden jump in Lyellian percentages per faunule from nearly zero up to 100% during this same interval. However, faunules with Lyellian percentages near zero occurred until 1.8 Ma, so that geographic distributions were extraordinarily heterogeneous until final extinction occurred. There were also striking differences in comparative diversity and abundance among major ecological groups of scallops. Free-swimming scallops constituted the most diverse guild throughout most of the last 10 Myr in the SWC, and were always moderately to very abundant. Leptopecten and Argopecten were also highly diverse throughout the late Miocene and early Pliocene, but declined to very few species thereafter. In contrast, byssally attaching scallops gradually increased in both diversity and abundance since their first appearance in our samples from 8–9 Ma and are the most diverse group today. Evolutionary turnover of scallops in the SWC was correlated with strong ecological reorganization of benthic communities that occurred in response to declining productivity and increased development of corals reefs.

Radiocarbon-calibrated amino acid racemization ages of 428 individually dated shells representing four molluscan taxa are used to quantify time-averaging and shell half-lives with increasing burial depth in the shallow-water carbonate lagoon of Rib Reef, central Great Barrier Reef, Australia. The top 20 cm of sediment contains a distinct, essentially modern assemblage. Shells recovered at depths from 25 to 125 cm are age-homogeneous and significantly older than the surface layer. Taxon age distributions within sedimentary layers indicate that the top 125 cm of lagoonal sediment is thoroughly mixed on a sub-century scale. The age distributions and shell half-lives of four taxa (Ethalia, Natica, Tellina, and Turbo) are found to be largely distinct. Shell half-lives do not coincide with any single morphological characteristic thought to infer greater durability, but they are strongly related to a combined durability score based on shell density, thickness, and shape. These results illustrate the importance of bioturbation in tropical sedimentary environments, indicate that age estimates in this depositional setting are sensitive to taxon choice, and quantify a taxon-dependent bias in shell longevity and death assemblage formation.

Stable carbon and oxygen isotope ratios were measured for carbonate in samples of hadrosaurid tooth enamel and dentine, and gar scale ganoine and dentine from five geologically “contemporaneous“ (two-million-year resolution) and geographically distant late Campanian formations (Two Medicine, Dinosaur Park, Judith River, Kaiparowits, and Fruitland) in the Western Interior Basin. In all cases, isotopic offsets were observed between enamel and dentine from the same teeth, with dentine being characterized by higher and more variable carbon and oxygen isotope ratios. Isotopic offsets were also observed between gar ganoine and hadrosaur enamel in all sites analyzed. Both of these observations indicate that diagenetic overprinting of enamel isotope ratios did not entirely obfuscate primary signals. Decreases in carbon and oxygen isotope ratios were observed in hadrosaur enamel from east to west, and overlap in isotope ratios occurred only between two of the sampled sites (Dinosaur Park and Judith River Formations).

The lack of isotopic overlap for enamel among localities could be due to diagenetic resetting of isotope ratios such that they reflect local groundwater effects rather than primary biogenic inputs. However, the large range in carbon isotope ratios, the consistent taxonomic offsets for enamel/ganoine data, and comparisons of enamel-dentine data from the same teeth all suggest that diagenesis is not the lone driver of the signal. In the absence of major alteration, the mostly likely explanation for the isotopic patterns observed is that hadrosaurids from the targeted formations were eating plants and drinking waters with distinct isotopic ratios. One implication of this reconstruction is that hadrosaurids in the Late Cretaceous of the Western Interior did not migrate to an extent that would obscure local isotopic signatures.

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

Pterosaurs were the first flying vertebrates and formed important components of terrestrial and marginal marine ecosystems during the Mesozoic. They became extinct during the latest Cretaceous (latest Maastrichtian), at, or near, the Cretaceous/Paleogene boundary, following an apparent decline in diversity in the Late Cretaceous. This reduction in species richness has been linked to the ecological radiation of birds in the Early Cretaceous and the proposal that birds competitively excluded pterosaurs from many key niches. However, although competition is often posited as a causal mechanism for many of the clade-clade replacements observed in the fossil record, these hypotheses are rarely tested. Here we present a detailed examination of pterosaur diversity through time, including both taxic and phylogenetically corrected diversity estimates and comparison of these estimates with a model describing temporal variation in the number of pterosaur-bearing formations (a proxy for rock availability). Both taxic and phylogenetic diversity curves are strongly correlated with numbers of pterosaur-bearing formations, suggesting that a significant part of the signal contained within pterosaur diversity patterns may be controlled by geological and taphonomic megabiases rather than macroevolutionary processes. There is no evidence for a long-term decline in pterosaur diversity through the Cretaceous, although a reduction in morphological, ecological, and phylogenetic diversity does appear to have occurred in the latest Cretaceous. Competitive replacement of pterosaurs by birds is difficult to support on the basis of diversity patterns.

The subfamily Equinae in the Great Plains region of North America underwent a dramatic radiation and subsequent decline as climate changed from warm and humid in the middle Miocene to cooler and more arid conditions during the late Miocene. Here we use ecological niche modeling (ENM), specifically the GARP (Genetic Algorithm using Rule-set Prediction) modeling system, to reconstruct the geographic distribution of individual species during two time slices from the middle Miocene through early Pliocene. This method combines known species occurrence points with environmental parameters inferred from sedimentological variables to model each species' fundamental niche. The geographic range of each species is then predicted to occupy the geographic area within the study region wherever the set of environmental parameters that constrain the fundamental niche occurs. We analyze changes in the predicted distributions of individual species between time slices in relation to Miocene/Pliocene climate change. Specifically, we examine and compare distribution patterns for two time slices that span the period from the mid-Miocene (Barstovian) Climatic Optimum into the early Pliocene (Blancan) to determine whether habitat fragmentation led to speciation within the clade and whether species survival was related to geographic range size. Patchy geographic distributions were more common in the middle Miocene when speciation rates were high. During the late Miocene, when speciation rates were lower, continuous geographic ranges were more common. Equid species tracked their preferred habitat within the Great Plains region as well as regionally throughout North America. Species with larger predicted ranges preferentially survived the initial cooling event better than species with small geographic ranges. As climate continued to deteriorate in the late Miocene, however, range size became irrelevant to survival, and extinction rates increased for species of all range sizes. This is the first use of ENM and GARP in the continental fossil record. This powerful quantitative biogeographic method offers great promise for studies of other taxa and geologic intervals.

Numerous methods have been developed to estimate the position of a mass extinction boundary while accounting for the incompleteness of the fossil record. Here we describe the point estimator and confidence interval for the extinction that are optimal under the assumption of uniform preservation and recovery potential, and independence among taxa. First, one should pool the data from all taxa into one combined “supersample.” Next, one can then apply methods proposed by Strauss and Sadler (1989) for a single taxon. This gives the optimal point estimator in the sense that it has the smallest variance among all possible unbiased estimators. The corresponding confidence interval is optimal in the sense that it has the shortest average width among all possible intervals that are invariant to measurement scale. These optimality properties hold even among methods that have not yet been discovered. Using simulations, we show that the optimal estimators substantially improve upon the performance of other existing methods. Because the assumptions of uniform recovery and independence among taxa are strong ones, it is important to assess to what extent they are satisfied by the data. We demonstrate the use of probability plots for this purpose. Finally, we use simulations to explore the sensitivity of the optimal point estimator and confidence interval to nonuniformity and lack of independence, and we compare their performance under these conditions with existing methods. We find that nonuniformity strongly biases the point estimators for all methods studied, inflates their standard errors, and degrades the coverage probabilities of confidence intervals. Lack of independence has less effect on the accuracy of point estimates as long as recovery potential is uniform, but it, too, inflates the standard errors and degrades confidence interval coverage probabilities.

Although only a few studies have explicitly evaluated live-dead agreement of species and community responses to environmental and spatial gradients, paleoecological analyses implicitly assume that death assemblages capture these gradients accurately. We use nine data sets from modern, relatively undisturbed coastal study areas to evaluate how the response of living molluscan assemblages to environmental gradients (water depth and seafloor type; “environmental component” of a gradient) and geographic separation (“spatial component”) is captured by their death assemblages. We find that:

1. Living assemblages vary in composition either in response to environmental gradients alone (consistent with a species-sorting model) or in response to a combination of environmental and spatial gradients (mass-effect model). None of the living assemblages support the neutral model (or the patch-dynamic model), in which variation in species abundance is related to the spatial configuration of stations alone. These findings also support assumptions that mollusk species consistently differ in responses to environmental gradients, and suggest that in the absence of postmortem bias, environmental gradients might be accurately captured by variation in species composition among death assemblages. Death assemblages do in fact respond uniquely to environmental gradients, and show a stronger response when abundances are square-root transformed to downplay the impact of numerically abundant species and increase the effect of rare species.

2. Species' niche positions (position of maximum abundance) along bathymetric and sedimentary gradients in death assemblages show significantly positive rank correlations to species positions in living assemblages in seven of nine data sets (both square-root-transformed and presence-absence data).

3. The proportion of compositional variation explained by environmental gradients in death assemblages is similar to that of counterpart living assemblages. Death assemblages thus show the same ability to capture environmental gradients as do living assemblages. In some instances compositional dissimilarities in death assemblages show higher rank correlation with spatial distances than with environmental gradients, but spatial structure in community composition is mainly driven by spatially structured environmental gradients.

4. Death assemblages correctly identify the dominance of niche metacommunity models in mollusk communities, as revealed by counterpart living assemblages. This analysis of the environmental resolution of death assemblages thus supports fine-scale niche and paleoenvironmental analyses using molluscan fossil records. In spite of taphonomic processes and time-averaging effects that modify community composition, death assemblages largely capture the response of living communities to environmental gradients, partly because of redundancy in community structure that is inherently associated with multispecies assemblages. The molluscan data sets show some degree of redundancy as evidenced by the presence of at least two mutually exclusive subsets of species that replicate the community structure, and simple simulations show that between-sample relationships can be preserved and remain significant even when a large proportion of species is randomly removed from data sets.

Previous analyses of the history of Phanerozoic marine biodiversity suggested that the post-Paleozoic increase observed at the family level and below was caused, in part, by an increase in global provinciality associated with the breakup of Pangea. Efforts to characterize the Phanerozoic history of provinciality, however, have been compromised by interval-to-interval variations in the methods and standards used by researchers to calibrate the number of provinces. With the development of comprehensive, occurrence-based data repositories such as the Paleobiology Database (PaleoDB), it is now possible to analyze directly the degree of global compositional disparity as a function of geographic distance (geo-disparity) and changes thereof throughout the history of marine animal life. Here, we present a protocol for assessing the Phanerozoic history of geo-disparity, and we apply it to stratigraphic bins arrayed throughout the Phanerozoic for which data were accessed from the PaleoDB. Our analyses provide no indication of a secular Phanerozoic increase in geo-disparity. Furthermore, fundamental characteristics of geo-disparity may have changed from era to era in concert with changes to marine venues, although these patterns will require further scrutiny in future investigations.

The significant impact of extant carnivores, particularly spotted hyenas, on the depositional history and physical characteristics of archaeofaunal and paleontological assemblages is well recognized. We focus on the behavioral ecology of extant spotted hyenas (Crocuta crocuta) in relation to bone accumulations produced by one East African clan at communal dens. Limbs and skulls of prey animals more frequently appear at dens than do other carcass portions. These items reflect the relative abundance of prey species near dens; carnivore remains are poorly represented. Comparative analysis reveals that bones are deposited far more slowly (<7 carcass portions per month) and accumulations tend to be smaller at Crocuta dens than at dens of either brown (Parahyaena brunnea) or striped (Hyaena hyaena) hyenas. We propose that extant Crocuta bone accumulation rates and sizes are likely affected by prey species abundance, clan size, social interactions within the clan, and the type and availability of den sites. We also suggest that the potential for intraspecific behavioral variability in bone accumulation patterns is important when comparisons are made among spotted hyena populations and across hyena species. For example, accumulation patterns may be dramatically influenced by the temporal span, potentially ranging from days to hundreds or thousands of years, in which bones are collected, depending on the species-specific history of occupation at a given site. Understanding the behavioral and ecological variability likely to influence bone accumulation patterns at dens used by different hyaenids will allow taphonomists and zooarchaeologists to refine their knowledge of mechanisms underlying site formation processes and potential causes of variability in deeper-time den assemblages.

Abundance is one of the primary factors believed to influence extinction yet little is known about its relationship to extinction rates over geologic time. Using data from the Paleobiology Database we show that abundance was an important factor in the extinction dynamics of marine bivalve genera over the post-Paleozoic. Contrary to expectations, our analyses reveal a nonlinear relationship between abundance and extinction rates, with rare and abundant genera exhibiting rates elevated over those of genera of moderate abundance. This U-shaped pattern is a persistent feature of the post-Paleozoic history of marine bivalves and provides one possible explanation for why we find strong support for heterogeneous extinction rates among genera grouped by similarity in abundance yet effectively no net relationship among these rates when using models of directional selection on abundance.

Paleobiological phylogenies often contain contrasting biological information to phylogenies based on extant species. Available software is primarily based on a present-day view of the world, however. Here, we present freeware to visualize phylogenies that is more suitable for the needs of paleobiologists, providing flexibility in how stratigraphic uncertainty, the geological timescale, and ancestor-descendant relationships are depicted.

Since David Raup's seminal 1976 work, paleontologists have been aware of the relationship between outcrop area and diversity. By incorporating lithologic data derived from Alexander Ronov and coworkers into our own data on areas of mapped outcrops from worldwide geologic maps, we are able to establish a quantitative connection between area of sedimentary rock exposure and diversity from the same general depositional environments. Significant power-law relations are observed at both global and continental scales of consideration. The addition of data on areas of habitable area estimated from paleogeographic maps does not substantially affect these correlations between outcrop area and diversity, indicating that the relation between outcrop area and diversity is primarily a function of sampling and not a common cause such as sea level. We observe a significant diversity-area effect, first noted by Jack Sepkoski in the marine realm. Unlike Sepkoski's, however, our diversity-area effect appears to play a substantial role in influencing diversity through time; a true global diversity signal appears to be contained in the rock record despite the impacts of variable sampling.

Greater outcrop area can serve to increase estimated diversity by increasing both the sample size and the range of habitats and biogeographic provinces sampled. After standardizing for pure sampling intensity by rarefying the number of taxon occurrences, outcrop area continues to explain a substantial portion of global marine diversity. This indicates that coverage, or sampling from multiple habitats and biogeographic provinces, is even more important than sampling intensity. If we remove the effect of outcrop area from our estimate of global biodiversity, we do not observe a net increase in diversity toward the present, lending support to other studies that have not supported a substantial, long-term global increase in biodiversity during the Phanerozoic.