Taxonomic diversity and morphological disparity are different measures of biodiversity that together can describe large-scale evolutionary patterns. Diversity measures are often corrected by extending lineages back in time or adding additional taxa necessitated by a phylogeny, but disparity analyses focus on observed taxa only. This is problematic because some morphologies required by phylogeny are not included, some of which may help fill poorly sampled time bins. Moreover the taxic nature of disparity analyses makes it difficult to compare disparity measures with phylogenetically corrected diversity or morphological evolutionary rate curves. We present a general method for using phylogeny to correct measures of disparity, by including reconstructed ancestors in the disparity analysis. We apply this method to discrete character data sets focusing on Triassic archosaurs, Cenozoic carnivoramorph mammals, and Cretaceous-Cenozoic euarchontogliran mammals. Phylogenetic corrections do not simply mirror the taxic disparity patterns, but affect the three analyses in heterogeneous ways. Adding reconstructed ancestors can inflate morphospace, and the amount and direction of expansion differs depending on the taxonomic group in question. In some cases phylogenetic corrections give a temporal disparity curve indistinguishable from the taxic trend, but in other cases disparity is elevated in earlier time intervals relative to later bins, due to the extension of unsampled morphologies further back in time. The phylogenetic disparity curve for archosaurs differs little from the taxic curve, supporting a previously documented pattern of decoupled disparity and rates of morphological change in dinosaurs and their early contemporaries. Although phylogenetic corrections should not be used blindly, they are helpful when studying clades with major unsampled gaps in their fossil records.

C4 grasses form the foundation of warm-climate grasslands and savannas and provide important food crops such as corn, but their Neogene rise to dominance is still not fully understood. Carbon isotope ratios of tooth enamel, soil carbonate, carbonate cements, and plant lipids indicate a late Miocene-Pliocene (8–2 Ma) transition from C3 vegetation to dominantly C4 grasses at many sites around the world. However, these isotopic proxies cannot identify whether the C4 grasses replaced woody vegetation (trees and shrubs) or C3 grasses. Here we propose a method for reconstructing the carbon isotope ratio of Neogene grasses using the carbon isotope ratio of organic matter trapped in plant silica bodies (phytoliths). Although a wide range of plants produce phytoliths, we hypothesize that in grass-dominated ecosystems the majority of phytoliths will be derived from grasses, and will yield a grass carbon isotope signature. Phytolith extracts can be contaminated by non-phytolith silica (e.g., volcanic ash). To test the feasibility of the method given these potential problems, we examined sample purity (phytolith versus non-phytolith silica), abundance of grass versus non-grass phytoliths, and carbon isotope ratios of phytolith extracts from late Miocene-Pliocene paleosols of the central Great Plains. Isotope results from the purest samples are compared with phytolith assemblage analysis of these same extracts. The dual record spans the interval of focus (ca. 12–2 Ma), allowing us, for the first time, to investigate how isotopic shifts correlate with floral change.

We found that many samples contained high abundances of non-biogenic silica; therefore, only a small subset of “pure” samples (>50% of phytoliths by volume) with good preservation were considered to provide reliable carbon isotope ratios. All phytolith assemblages contained high proportions (on average 85%) of grass phytoliths, supporting our hypothesis for grass-dominated communities. Therefore, the carbon isotope ratio of pure, well-preserved samples that are dominated by grass biosilica is considered a reliable measure of the proportion of C3 and C4 grasses in the Neogene.

The carbon isotope ratios of the pure fossil phytolith samples indicate a transition from predominantly C3 grasses to mixed C3-C4 grasses by 5.5 Ma and then a shift to more than 80% C4 grasses by 3–2 Ma. With the exception of the Pliocene sample, these isotopic data are broadly concordant with phytolith assemblages that show a general increase in C4 grasses in the late Miocene. However, phytolith assemblage analysis indicates lower relative abundance of C4 grasses in overall vegetation than do the carbon isotopes from the same phytolith assemblages. The discrepancy may relate to either (1) incomplete identification of (C4) PACMAD phytoliths, (2) higher production of non-diagnostic phytoliths in C4 grasses compared to C3 grasses, or (3) biases in the isotope record toward grasses rather than overall vegetation. The impact of potential incomplete characterization of (C4) PACMAD phytoliths on assemblage estimates of proportion of C4, though important, cannot reconcile discrepancies between the methods. We explore hypothesis (2) by analyzing a previously published data set of silica content in grasses and a small data set of modern grass leaf assemblage composition using analysis of variance, independent contrasts, and sign tests. These tests suggest that C4 grasses do not have more silica than C3 grasses; there is also no difference with regard to production of non-diagnostic phytoliths. Thus, it is most likely that the discrepancy between phytolith assemblages and isotope ratios is a consequence of hypothesis (3), that the isotope signature is influenced by the contribution of non-diagnostic grass phytoliths, whereas the assemblage composition is not. Assemblage-based estimates of % C4 within grasses, rather than overall vegetation, are in considerably better agreement with the isotope-based estimates. These results support the idea that, in grass-dominated assemblages, the phytolith carbon isotope method predominantly records shifts in dominant photosynthetic pathways among grasses, whereas phytolith assemblage analysis detects changes in overall vegetation. Carbon isotope ratios of fossil phytoliths in conjunction with phytolith assemblage analysis suggest that the late Neogene expansion of C4 grasses was largely at the expense of C3 grasses rather than C3 shrubs/trees. Stable isotopic analysis of phytoliths can therefore provide unique information about grass community changes during the Neogene, as well as help test how grass phytolith morphology relates to photosynthetic pathway.

The rapid ecological expansion of grasses with C4 photosynthesis at the end of the Neogene (8–2 Ma) is well documented in the fossil record of stable carbon isotopes. As one of the most profound vegetation changes to occur in recent geologic time, it paved the way for modern tropical grassland ecosystems. Changes in CO2 levels, seasonality, aridity, herbivory, and fire regime have all been suggested as potential triggers for this broadly synchronous change, long after the evolutionary origin of the C4 pathway in grasses. To date, these hypotheses have suffered from a lack of direct evidence for floral composition and structure during this important transition. This study aimed to remedy the problem by providing the first direct, relatively continuous record of vegetation change for the Great Plains of North America for the critical interval (ca. 12–2 Ma) using plant silica (phytolith) assemblages.

Phytoliths were extracted from late Miocene-Pliocene paleosols in Nebraska and Kansas. Quantitative phytolith analysis of the 14 best-preserved assemblages indicates that habitats varied substantially in openness during the middle to late Miocene but became more uniformly open, corresponding to relatively open grassland or savanna, during the late Miocene and early Pliocene. Phytolith data also point to a marked increase of grass short cells typical of chloridoid and other potentially C4 grasses of the PACMAD clade between 8 and 5 Ma; these data suggest that the proportion of these grasses reached up to ∼50–60% of grasses, resulting in mixed C3-C4 and highly heterogeneous grassland communities by 5.5 Ma. This scenario is consistent with interpretations of isotopic records from paleosol carbonates and ungulate tooth enamel. The rise in abundance of chloridoids, which were present in the central Great Plains since the early Miocene, demonstrates that the “globally” observed lag between C4 grass evolution/taxonomic diversification and ecological expansion occurred at the regional scale. These patterns of vegetation alteration imply that environmental change during the late Miocene-Pliocene played a major role in the C3-C4 shift in the Great Plains. Specifically, the importance of chloridoids as well as a decline in the relative abundance of forest indicator taxa, including palms, point to climatic drying as a key trigger for C4 dominance.

Extinctions are caused by environmental and ecological change but are recognized and measured in the fossil record by the disappearance of clades or lineages. If the ecological preferences of lineages or taxa are weakly congruent with their phylogenetic relationships, even large ecological perturbations are unlikely to drive major clades extinct because the factors that eliminate some species are unlikely to affect close relatives with different ecological preferences. In contrast, if phylogenetic relatedness and ecological preferences are congruent, then ecological perturbations can more easily cause extinctions of large clades. In order to quantify this effect, we used a computer model to simulate the diversification and extinction of clades based on ecological criteria. By varying the parameters of the model, we explored (1) the relationship between the extinction probability for a clade of a given size (number of terminals) and the overall intensity of extinction (the proportion of the terminals that go extinct), and (2) the congruence between ecological traits of the terminals and their phylogenetic relationships. Data from two extinctions (planktonic foraminifera at the Eocene/Oligocene boundary and vascular land plants at the Middle/Late Pennsylvanian boundary) show phylogenetic clustering of both ecological traits and extinction probability and demonstrate the interaction of these factors. The disappearance of large clades is observed in the fossil record, but our model suggests that it is very improbable without both high overall extinction intensities and high congruence between ecology and phylogeny.

We use Fourier analysis and related techniques to investigate the question of periodicities in fossil biodiversity. These techniques are able to identify cycles superimposed on the long-term trends of the Phanerozoic. We review prior results and analyze data previously reduced and published. Joint time-series analysis of various reductions of the Sepkoski Data, Paleobiology Database, and Fossil Record 2 indicate the same periodicity in biodiversity of marine animals at 62 Myr. We have not found this periodicity in the terrestrial fossil record. We have found that the signal strength decreases with time because of the accumulation of apparently “resistant” long-lived genera. The existence of a 62-Myr periodicity despite very different treatment of systematic error, particularly sampling-strength biases, in all three major databases strongly argues for its reality in the fossil record.

We describe statistical methods to formulate and validate statements about survival rates given a small number of individuals. These methods allow one to estimate the age-specific survival rate and assess its uncertainty, to assess whether the survival rates during some age range differ from the survival rates during another age range, and to assess whether the survivorship curve has a particular shape. We illustrate these methods by applying them to a sample of 22 Albertosaurus sarcophagus individuals. We show that this sample is too small to provide any confidence in the claim that this species had a “convex” survivorship curve arising from age-specific survival rates that decreased monotonically with age. However, we show that a sample of 50 to 100 individuals has reasonable statistical power to support such a claim. There is evidence for the much weaker claim that average survival rates for ages 2 to 15 were higher than survival rates for later ages. Finally, we describe one way to account for size-dependent fossilization rates and show that a plausible positively-size-dependent fossilization rate results in a substantially non-convex survivorship curve for A. sarcophagus.

The floral community along South Africa's southwest coast today is dominated by shrubby strandveld, renosterveld, and coastal fynbos vegetation. The grass family (Poaceae), represented primarily by C3 taxa, is scarce by comparison. Nevertheless, grass has a long history along this coast, as indicated by the presence of ∼5-million-year-old C3 grass pollen and phytoliths in sediments at the fossil locality of Langebaanweg E Quarry. Because the pollen and phytoliths of other plant families, including fynbos, have also been found, it has been difficult to determine whether grass was scarce or abundant in this environment. In order to shed light on this issue, I analyzed the dental mesowear of the E Quarry bovids. Results indicate that only one (Simatherium demissum) of seven analyzed species was a grazer. These compare well with the results of a microwear texture analysis, which indicate that none of the seven analyzed species were obligate grazers. These two studies point strongly toward a heavily wooded environment and not one that was dominated by grass. Although a conventional dental microwear analysis did identify three out of seven E Quarry bovid species as grazers (Bed3aN Damalacra, Kobus subdolus, and S. demissum), only S. demissum probably actually was a grazer. I suggest that the grazer signal exhibited by the other two bovid samples indicate that these species were taking advantage of a spike in grass abundance, probably during the winter growth season.

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.

Diversity dynamics of the Permian–Triassic land plants in South China are studied by analyzing paleobotanical data. Our results indicate that the total diversity of land-plant megafossil genera and species across the Permian/Triassic boundary (PTB) of South China underwent a progressive decline from the early Late Permian (Wuchiapingian) to the Early-Middle Triassic. In contrast, the diversity of land-plant microfossil genera exhibited only a small fluctuation across the PTB of South China, showing an increase at the PTB. Overall, land plants across the PTB of South China show a greater stability in diversity dynamics than marine faunas. The highest extinction rate (90.91%) and the lowest origination rate (18.18%) of land-plant megafossil genera occurred at the early Early Triassic (Induan), but the temporal duration of the higher genus extinction rates (>60%) in land plants was about 23.4 Myr, from the Wuchiapingian to the early Middle Triassic (Anisian), which is longer than that of the coeval marine faunas (3–11 Myr). Moreover, the change of genus turnover rates in land-plant megafossils steadily fluctuated from the late Early Permian to the Late Triassic. More stable diversity and turnover rate as well as longer extinction duration suggest that land plants near the PTB of South China may have been involved in a gradual floral reorganization and evolutionary replacement rather than a mass extinction like those in the coeval marine faunas.