In this paper we present a method for estimating soil pCO2 in ancient environments using the measured carbon-isotope values of pedogenic carbonates and plant-derived organic matter. The validity of soil pCO2 estimates proves to be highly dependent on the organic δ13C values used in the calculations. Organic matter should be sourced from the same paleosol profiles as sampled carbonates to yield the most reliable estimates of soil pCO2. In order to demonstrate the potential use of soil pCO2 estimates in paleoecological and paleoenvironmental studies, we compare samples from three Upper Jurassic localities. Soil pCO2 estimates, interpreted as a qualitative indicator of primary paleoproductivity, are used to rank the Late Jurassic terrestrial environments represented by the Morrison Formation in western North America, the informally named Lourinhã formation in Western Europe, and the Stanleyville Group in Central Africa. Because modern terrestrial environments show a positive correlation between primary productivity and faunal richness, a similar relationship is expected in ancient ecosystems. When the relative paleoproductivity levels inferred for each study area are compared with estimates of dinosaur generic richness, a positive correlation emerges. Both the Morrison and Lourinhã formations have high inferred productivity levels and high estimated faunal richness. In contrast, the Stanleyville Group appears to have had low primary productivity and low faunal richness. Paleoclimatic data available for each study area indicate that both productivity and faunal richness are positively linked to water availability, as observed in modern terrestrial ecosystems.

Electron microprobe analyses of platform (pectiniform Pa) elements of Permian conodonts reveal detailed and systematic chemical element distributions. The crown of the conodont element is more densely mineralized than the basal body and shows evidence of less dense mineralization in areas of rapid growth. Patterns in sodium and sulfur concentrations indicate oral to aboral differentiation within conodont elements. These chemical element patterns support oral exposure during life and functional use as a tooth, and they approximate the erupted and embedded positions of the conodont tooth when the animal was alive. Previously unrecognized spatial distributions of geochemically important chemical elements warrant consideration in future geochemical studies of conodonts.

A basic hypothesis in extinction theory predicts that more abundant taxa have an evolutionary advantage over less abundant taxa, which should manifest as increased survivorship during major extinction events and longer fossil-record durations. Despite this, various paleontologic studies have found conflicting patterns, indicating a more complex relationship between abundance and extinction in the geologic past. This study tests the relationship between abundance and extinction among brachiopod genera within seven third-order depositional sequences spanning the Late Ordovician to Early Silurian (Katian–Aeronian) of the Cincinnati Arch.

Contrary to predictions, abundance is not positively correlated with duration in this study. Abundance and duration range from strongly negatively correlated to uncorrelated depending on the spatial scale of analysis and the geologic intervals included, but correlations never indicate that abundance is an evolutionary advantage. In contrast, abundance was an advantageous trait prior to the Ordovician/Silurian extinction, and brachiopods with higher abundances were more likely to survive the event than less abundant brachiopods. While this result is in keeping with common models of extinction, it has not been observed previously at a mass extinction boundary. This may be further evidence that the Ordovician/Silurian extinction was not accompanied by a shift in the macroevolutionary selectivity regime.

Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation.

Improvements in the perceived completeness of the fossil record may be driven both by new discoveries and by reinterpretation of known fossils, but disentangling the relative effects of these processes can be difficult. Here, we propose a new methodology for evaluating historical trends in the perceived completeness of the fossil record, demonstrate its implementation using the freely available software ASCC (version 4.0.0), and present an example using crown-group birds (Aves). Dates of discovery and recognition for the oldest fossil representatives of 75 major lineages of birds were collected for the historical period ranging from 1910 to 2010. Using a comprehensive phylogeny, we calculated minimum implied stratigraphic gaps (MIG range) across these 75 lineages. Our results show that a reduction in global MIG values of 1.35 Ga (billion years) occurred over the past century in avian paleontology. A pronounced increase in the average rate of global MIG reduction is noted in the post-1970s interval (290.5 Myr per decade) compared to the pre-1970s interval (31.9 Myr per decade). Although the majority of the improvement in the fossil record of birds has come from new discoveries, substantial improvement (∼22.5%) has resulted from restudy and phylogenetic revision of previously described fossils over the last 40 years. With a minimum estimate indicating that at least 1.34 Gyr of gaps remain to be filled between the predicted and observed first appearances of major lineages of crown Aves, there is much progress to be made. However, a notable tapering off in the rate of global MIG reduction occurs between 1990 and 2010, suggesting we may be approaching an asymptote of oldest record discoveries for birds. Only future observations can determine whether this is a real pattern or a historical anomaly. Either way, barring the discovery of fossils that substantially push back the minimum age for the origin of crown-clade Aves, new discoveries cannot continue to reduce global MIG values at the average post-1970s rate over the long term.

The fossil record provides an important source of data on adaptive radiations, and indeed some of the earliest theoretical insights on the nature of these radiations were made by paleontologists. Here we focus on the diverse Devonian Metacryphaeus group calmoniid trilobites, known from the Malvinokaffric Realm, which have been considered a classic example of an adaptive radiation preserved in the fossil record. We use a geometric morphometric analysis in conjunction with phylogenetic and biogeographic patterns and data on speciation rates. Using ancestral character state reconstruction during speciation events, we quantify patterns of morphological change in order to assess the role ecological and geographical factors may have played in mediating this radiation. We found no significant differences between the amount of morphological change that occurred during speciation events when ancestors and descendants were in the same area as opposed to when they occupied different areas. Further, the magnitude of morphological divergence did not change through time or with cladogenetic rank. These patterns, in conjunction with the fact that the radiation occurs in a geographically heterogeneous region subjected to repeated episodes of sea-level rise and fall, suggest that at the macroevolutionary scale this radiation may have been motivated more by phenomena that facilitated geographic isolation than by competition.

The potential of the ichnofossil record for exploring the evolution of behavior has never been fully realized. Some of this is due to the nature of the trace fossil record itself. Equally responsible is the separation of ichnology from the relevant areas of modern behavioral biology. The two disciplines have virtually no concepts, methods, or literature in common. The study of animal behavior and its evolution is thus bereft of the rich data and insights of ichnologists.

One potential pathway forward is for ichnologists to adopt and adapt the movement ecology paradigm proposed several years ago by Ran Nathan and colleagues. This approach views movement as resulting from interactions of the organism's internal state, its movement abilities, and its sensory capabilities with each other and with the external environment. These interactions produce a movement path. The adoption of this paradigm would place trace fossil studies in a far wider common context for the study of movement, while providing the dimension of the evolution of movement behavior in deep time to neontological studies.

A second component of this integration would be for paleontologists to develop a taphonomy of behavior that places in a phylogenetic context the range of possible behaviors that organisms can carry out and assesses the potential of each of these behaviors in leaving a diagnostic trace. Parallel to other taphonomic concepts, this approach assesses the preservation potential of particular behaviors; behavioral fidelity is the extent to which trace fossils preserve these original behavioral signals.

Analysis of dental wear and damage is becoming an increasingly important tool in unraveling the trophic ecology of a wide range of vertebrates, and when applied to fossils it can provide evidence of both diet and feeding kinematics that is independent of morphological analysis. Conodonts have the best fossil record among vertebrates and their skeletal elements are known to exhibit surface wear and damage generated in vivo as a consequence of their function as teeth. We report the results of the first systematic survey and analysis of the frequency and extent of this wear and damage in conodonts (based on P1 elements from a range of Carboniferous genera). This has revealed that wear and damage are remarkably common, present in all conodont elements sampled. Multivariate analysis reveals that patterns of wear and damage differ significantly among different conodont taxa, and exploratory ANOVA and linear discriminant analyses show that wear and damage differ according to the position of taxa in an onshore-offshore gradient, and whether they are likely to have had a benthic or pelagic mode of life. The incidence of denticle tip spalling in particular is higher in more-offshore environments and in taxa likely to have had a pelagic mode of life. Aspects of the data also reflect the occlusal kinematics of the elements, providing a means of testing hypotheses of element function. Our results have wide-ranging implications for unlocking the fossil record of conodonts, by, for example, furnishing direct evidence of the diet-mediated processes that may have driven observed patterns of evolutionary change, and reducing the confounding effects of depth segregation when using conodonts in isotope-based paleotemperature studies.

A developmental model, based upon murine rodents, has been proposed by Kavanagh et al. (2007) to explain lower molar proportions in mammals. We produce a clade-wide macroevolutionary test of the model using the dental evolutionary trends in a unique radiation of extinct mammals endemic to South America (“Meridiungulata”) that comprise a diverse array of molar morphologies. All of the South American ungulate groups examined follow the inhibitory cascade model with the exception of two groups: Interatheriidae (Notoungulata) and Astrapotheria. For most taxa studied, ratios between lower molar areas are greater than 1.0, indicating a weak inhibition by m1 on the subsequent molars in the tooth row, and a trend to greater absolute size of the posterior molars. Comparisons of mean ratios between clades indicate that a significant phylogenetic signal can be detected, particularly between the two groups within Notoungulata— Typotheria and Toxodontia. Body mass estimates were found to be significantly correlated with both m3/m1 and m2/m1 ratios, suggesting that the larger body size achieved the weaker inhibition between the lower molars. Molar ratio patterns are examined and discussed in relation to the independent and numerous acquisitions of hypsodonty that are characteristic of dental evolution in “Meridiungulata.”

One of the best-recognized patterns in the evolution of organismal size is the tendency for mean and maximum size within a clade to decrease following a major extinction event and to increase during the subsequent recovery interval. Because larger organisms are typically thought to be at higher extinction risk than their smaller relatives, it has commonly been assumed that size reduction mostly reflects the selective extinction of larger species. However, to our knowledge the relative importance of within- and among-lineage processes in driving overall trends in body size has never been compared quantitatively. In this study, we use a global, specimen-level database of foraminifera to study size evolution from the Late Permian through Late Triassic. We explicitly decompose size evolution into within- and among-genus components. We find that size reduction following the end-Permian mass extinction was driven more by size reduction within surviving species and genera than by the selective extinction of larger taxa. Similarly, we find that increase in mean size across taxa during Early Triassic biotic recovery was a product primarily of size increase within survivors and the extinction of unusually small taxa, rather than the origination of new, larger taxa. During background intervals we find no strong or consistent tendency for extinction, origination, or within-lineage change to move the overall size distribution toward larger or smaller sizes. Thus, size stasis during background intervals appears to result from small and inconsistent effects of within- and among-lineage processes rather than from large but offsetting effects of within- and among-taxon components. These observations are compatible with existing data for other taxa and extinction events, implying that mass extinctions do not influence size evolution by simply selecting against larger organisms. Instead, they appear to create conditions favorable to smaller organisms.

Bipedalism evolved more than twice among archosaurs, and it is a characteristic of basal dinosaurs and a prerequisite for avian flight. Nevertheless, the reasons for the evolution of bipedalism among archosaurs have barely been investigated. Comparative analysis using phylogenetically independent contrasts showed a significant correlation between bipedality (relative length of forelimb) and cursoriality (relative length of metatarsal III) among Triassic archosaurs. This result indicates that, among Triassic archosaurs, bipeds could run faster than quadrupeds. Bipedalism is probably an adaptation for cursoriality among archosaurs, which may explain why bipedalism evolved convergently in the crocodilian and bird lineages. This result also indicates that the means of acquiring cursoriality may differ between archosaurs and mammals.

Fossil specimens can be recovered easily only from exposed localities, so rock exposure area should represent a better proxy for rock availability than the frequently used outcrop (i.e., map) area. Data collected via remote sensing and GIS show that map area does not consistently correlate with exposure area in different regions. Proportional rock exposure is not geographically consistent and is influenced by a number of variables that are independent of outcrop area, including proximity to the coast, elevation, bedrock age, land use and lithology. These variables appear to be non-independent in their influence on rock exposure, and are not consistent in their effects across continents. The inconsistency in the correlation between outcrop and exposure area, and the variability in the influence of different factors on rock exposure, suggests that using outcrop area as a sampling proxy is poorly supported. The weaknesses in using outcrop area as a sampling proxy, highlighted by the lack of correlation with exposure area, suggest that a single accurate global sampling proxy may never be attained and it is premature to assume that paleodiversity curves can be corrected using such proxies. It is therefore preferable to work on a regional scale, comparing regional fossil collection data with a number of proxies representing all aspects of sampling. The lack of correlation between outcrop and exposure area suggests that the covariance detected between outcrop area and paleodiversity might be better explained by a common-cause model, and that geological megabiases may not have had as profound an effect on paleodiversity curves as previously thought.

We studied the morphological diversity of gastropod shell forms from the viewpoint of theoretical morphology, emphasizing the relationships of shell form to postural stability and the available space for soft body, which we assessed in terms of the moment of force and soft-tissue ratio calculations, respectively. The results of computer simulations suggest a functional trade-off between postural stability and available space for soft body: a compact shell possessing a low spire and small umbilicus exhibits high postural stability, whereas a less overlapped shell form with a high spire and large umbilicus makes available space for soft body. A functional morphospace analysis using theoretical models reveals that outward and downward inclination of the aperture moderates the functional trade-off between these parameter values and permits compatibility between stable posture and efficient shell construction. The hypothetical optimum that realizes this compatibility is consistent with the observed range of forms estimated from 359 extant gastropod species. The biometric results also suggest that land snails are more highly constrained than marine species in achieving a balance between postural stability and available space for soft body.

We investigate whether musculoskeletal anatomy and three-dimensional (3-D) body proportions were modified during the evolution of large (>6000 kg) body size in Allosauroidea (Dinosauria: Theropoda). Three adaptations for maintaining locomotor performance at large body size, related to muscle leverage, mass, and body proportions, are tested and all are unsupported in this analysis. Predictions from 3-D musculoskeletal models of medium-sized (Allosaurus) and large-bodied (Acrocanthosaurus) allosauroids suggest that muscle leverage scaled close to isometry, well below the positive allometry required to compensate for declining muscle cross-sectional area with increasing body size. Regression analyses on a larger allosauroid data set finds slight positive allometry in the moment arms of major hip extensors, but isometry is included within confidence limits. Contrary to other recent studies of large-bodied theropod clades, we found no compelling evidence for significant positive allometry in muscle mass between exemplar medium- and large-bodied allosauroids. Indeed, despite the uncertainty in quantitative soft tissue reconstruction, we find strong evidence for negative allometry in the caudofemoralis longus muscle, the single largest hip extensor in non-avian theropods. Finally, we found significant inter-study variability in center-of-mass predictions for allosauroids, but overall observe that consistently proportioned soft tissue reconstructions produced similar predictions across the group, providing no support for a caudal shift in the center of mass in larger taxa that might otherwise reduce demands on hip extensor muscles during stance. Our data set provides further quantitative support to studies that argue for a significant decline in locomotor performance with increasing body size in non-avian theropods. However, although key pelvic limb synapomorphies of derived allosauroids (e.g., dorsomedially inclined femoral head) evolved at intermediate body sizes, they may nonetheless have improved mass support.

Recovery of marine biodiversity following the Permo-Triassic extinction is thought to have been delayed relative to other mass extinctions. Terrestrial vertebrate biodiversity is said to have taken as much as 15 Myr longer to recover than the marine. The present study tests, at the scale of an individual fossil community, whether a disparity in biodiversity existed in the American Southwest, between the Moenkopi Formation, containing an early Middle Triassic (Anisian) terrestrial tetrapod fauna, and the Chinle Formation, containing a successor Late Triassic (Norian) tetrapod fauna. Taking Chinle faunal biodiversity to represent full biotic recovery, comparison of taxonomic and guild diversity of faunas from similar depositional and taphonomic environments in these two formations allowed us to assess the possibility of incipient terrestrial recovery of biodiversity in the Anisian.

Comparisons were made between the Holbrook Member fauna of the Moenkopi, a unit best characterized as a low-sinuosity medium- to coarse-grained fluvial deposit, and each of four Chinle stratigraphic units, representing fluvial settings from sandy low-sinuosity to muddy high-sinuosity. Three metrics were applied: generic and familial taxonomic diversity and guild diversity; these were compared by rarefaction. Simpson and Shannon diversity metrics augmented the analysis. Units of extraordinary preservation in the Chinle—the so-called blue layers—were removed from the analysis. In all tests the biodiversity of the Holbrook Member fauna is within the variation seen in Chinle faunas.

If the results of our study represent global conditions, they suggest that by at least early Anisian time (∼6 Myr after the P/T extinction) biodiversity had reached levels comparable to those seen in the Late Triassic. This potentially brings the terrestrial vertebrate recovery in line with the 4–8 Myr it took for recovery in the marine realm.

The deep-sea microfossil record is characterized by an extraordinarily high density and abundance of fossil specimens, and by a very high degree of spatial and temporal continuity of sedimentation. This record provides a unique opportunity to study evolution at the species level for entire clades of organisms. Compilations of deep-sea microfossil species occurrences are, however, affected by reworking of material, age model errors, and taxonomic uncertainties, all of which combine to displace a small fraction of the recorded occurrence data both forward and backwards in time, extending total stratigraphic ranges for taxa. These data outliers introduce substantial errors into both biostratigraphic and evolutionary analyses of species occurrences over time. We propose a simple method—Pacman—to identify and remove outliers from such data, and to identify problematic samples or sections from which the outlier data have derived. The method consists of, for a large group of species, compiling species occurrences by time and marking as outliers calibrated fractions of the youngest and oldest occurrence data for each species. A subset of biostratigraphic marker species whose ranges have been previously documented is used to calibrate the fraction of occurrences to mark as outliers. These outlier occurrences are compiled for samples, and profiles of outlier frequency are made from the sections used to compile the data; the profiles can then identify samples and sections with problematic data caused, for example, by taxonomic errors, incorrect age models, or reworking of sediment. These samples/sections can then be targeted for re-study.

The clade Archosauria contains two very different sister groups in terms of diversity (number of species) and disparity (phenotypic variation): Crurotarsi (taxa more closely related to crocodiles than to birds) and Ornithodira (pterosaurs and dinosaurs including birds). The extant species of Crurotarsi may constitute a biased sample of past biodiversity regarding growth patterns and metabolic rates. Bone histological characters can be conserved over hundreds of millions of years in the fossil record and potentially contain information about individual age at death, age at sexual maturity, bone growth rates, and basal metabolic rates of extinct vertebrates. Using a sample of extant amniotes, we have constructed a paleobiological model to estimate bone growth rate from bone histological traits. Cross-validation tests show that this model is reliable. We then used it to estimate bone growth rates in a sample of extinct archosaurs including Crurotarsi and Ornithodira. After testing for phylogenetic signal, optimization of femoral growth rates through squared change parsimony onto a time-calibrated tree of amniotes shows two divergent evolutionary trends: whereas bone growth rates increase from the last common ancestor of Ornithodira to extant birds, they decrease from the last common ancestor of Crurotarsi to extant crocodiles. However, we conclude, on the basis of recent evidence for unidirectional airflow in the lungs of alligators, that crocodiles may have retained the capacity of growing at high rates.

Northern Appalachian Basin deposits and associated fossils have served as exemplars for ecological-evolutionary investigations, and as the reference interval for the concept of coordinated stasis. Here, we examine faunal and environmental changes within the uppermost Hamilton and lowermost Genesee Groups of the late Middle Devonian succession of New York State. Dramatic diversity loss, faunal migrations, and ecological restructuring recognized in these strata have been used previously to define the end of the Hamilton ecological-evolutionary subunit, and, furthermore, these strata and corresponding faunal changes represent the type region for the global Taghanic Biocrisis. We present and analyze a new, high-resolution data set of post-Taghanic Genesee fossil assemblages, in which we recognize 11 biofacies corresponding to an onshore-offshore (depth) gradient. The Genesee Fauna shows an unexpectedly high taxonomic similarity to nearshore biofacies of the pre-Taghanic Hamilton Fauna, related to the persistence of siliciclastic-dominated nearshore settings through the Taghanic Biocrisis, whereas the onset of anoxic/dysoxic conditions typified offshore portions of the environmental gradient. The “Nearshore Refugium Model” of Erwin offers a possible explanation for the persistence of taxa through the biocrisis in nearshore settings. This constriction was followed by subsequent expansion of these residual taxa to offshore environments in relatively similar associations, as increased Acadian orogenic activity and resultant delta progradation increased habitable space offshore by decreasing the extent of deeper-water, oxygen-poor settings. Although taxonomic similarity was high between the Hamilton and Genesee Faunas, biofacies structure differed primarily because of tectonically driven physical transformations to the basin and associated biotic turnover. Nevertheless, the combination of high taxonomic persistence of Hamilton nearshore taxa and the introduction of relatively few new taxa in the Genesee Fauna resulted in a taxonomic holdover that was much higher than observed in the original formulation of coordinated stasis.

There is growing evidence that changes in deep-sea benthic ecosystems are modulated by climate changes, but most evidence to date comes from the North Atlantic Ocean. Here we analyze new ostracod and published foraminiferal records for the last 250,000 years on Shatsky Rise in the North Pacific Ocean. Using linear models, we evaluate statistically the ability of environmental drivers (temperature, productivity, and seasonality of productivity) to predict changes in faunal diversity, abundance, and composition. These microfossil data show glacial-interglacial shifts in overall abundances and species diversities that are low during glacial intervals and high during interglacials. These patterns replicate those previously documented in the North Atlantic Ocean, suggesting that the climatic forcing of the deep-sea ecosystem is widespread, and possibly global in nature. However, these results also reveal differences with prior studies that probably reflect the isolated nature of Shatsky Rise as a remote oceanic plateau. Ostracod assemblages on Shatsky Rise are highly endemic but of low diversity, consistent with the limited dispersal potential of these animals. Benthic foraminifera, by contrast, have much greater dispersal ability and their assemblages at Shatsky Rise show diversities typical for deep-sea faunas in other regions.

Statistical analyses also reveal ostracod-foraminferal differences in relationships between environmental drivers and biotic change. Rarefied diversity is best explained as a hump-shaped function of surface productivity in ostracods, but as having a weak and positive relationship with temperature in foraminifera. Abundance shows a positive relationship with both productivity and seasonality of productivity in foraminifera, and a hump-shaped relationship with productivity in ostracods. Finally, species composition in ostracods is influenced by both temperature and productivity, but only a temperature effect is evident in foraminifera. Though complex in detail, the global-scale link between deep-sea ecosystems and Quaternary climate changes underscores the importance of the interaction between the physical and biological components of paleoceanographical research for better understanding the history of the biosphere.