Data that accurately capture the spatial structure of biodiversity are required for many paleobiological questions, from assessments of changing provinciality and the role of geographic ranges in extinction and originations, to estimates of global taxonomic or morphological diversity through time. Studies of temporal changes in diversity and global biogeographic patterns have attempted to overcome fossil sampling biases through sampling standardization protocols, but such approaches must ultimately be limited by available literature and museum collections. One approach to evaluating such limits is to compare results from the fossil record with models of past diversity patterns informed by modern relationships between diversity and climatic factors. Here we use present-day patterns for marine bivalves, combined with data on the geologic ages and distributions of extant taxa, to develop a model for Pliocene diversity patterns, which is then compared with diversity patterns retrieved from the literature as compiled by the Paleobiology Database (PaleoDB). The published Pliocene bivalve data (PaleoDB) lack the first-order spatial structure required to generate the modern biogeography within the time available (<3 Myr). Instead, the published data (raw and standardized) show global diversity maxima in the Tropical West Atlantic, followed closely by a peak in the cool-temperate East Atlantic. Either today's tropical West Pacific diversity peak, double that of any other tropical region, is a purely Pleistocene phenomenon—highly unlikely given the geologic ages of extant genera and the topology of molecular phylogenies—or the paleontological literature is such a distorted sample of tropical Pliocene diversity that current sampling standardization methods cannot compensate for existing biases. A rigorous understanding of large-scale spatial and temporal diversity patterns will require new approaches that can compensate for such strong bias, presumably by drawing more fully on our understanding of the factors that underlie the deployment of diversity today.

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.”

The temporal dimension of fossil sequences provides a critical component to the study of intraspecific dynamics and species formation. Here I report on the branching and subsequent morphological evolution of two gastropods (Melanopsis fossilis and M. vindobonensis) from the Late Miocene of the Pannonian basin in eastern and central Europe. Although morphological divergence between species is rapid, intermediates between the two species co-occur with typical individuals for approximately 1 m.y. and then disappear. The long-term persistence of intermediates followed by their ultimate disappearance is a pattern that, to my knowledge, has not been previously observed.

Distinguishing genetic from ecophenotypic influences on shell form in freshwater prosobranchs is difficult. Nevertheless, consideration of the temporal, geographic, lithologic, and paleoecologic patterns of this sequence suggests that the morphologic differences between M. fossilis and M. vindobonensis had some genetic basis. Whether these forms were initially morphs of a single species or two species with some hybridization between them is impossible to determine. In either case, the morphological changes that resulted in M. vindobonensis were rapid, but the attainment of complete isolation between M. fossilis and M. vindobonensis apparently did not occur until approximately 1 m.y. later.

Geochemical tools, including the analysis of stable isotopes from fossil mammals, are often used to infer regional climatic and environmental differences. We have further developed an oxygen isotope aridity index and used oxygen (δ18O) isotope values and carbon (δ13C) isotope values to assess regional climatic differences between the southeastern and southwestern United States during the Pleistocene. Using data collected from previously published studies, we assigned taxa to evaporation-sensitivity categories by quantifying the frequency and magnitude of aridity index values (i.e., an average taxon δ18O value minus a site specific proboscidean δ18O value). Antilocapridae, Camelidae, Equidae, and Cervidae were identified as evaporation-sensitive families, meaning that a majority of their water comes from the food they eat, thus indicating that they are more likely to capture changing climatic conditions. Bovidae, Tayassuidae, and Tapiridae were identified as less sensitive families, possibly because of increased or more variable drinking behavior. While it is difficult to tease out individual influences on δ18O values in tooth enamel, the use of an aridity index will provide a more in-depth look at relative aridity in the fossil record. Greater aridity index values in the Southwest suggest a drier climate than in the Southeast during the Pleistocene, and δ13C values suggest that diet does not determine evaporation sensitivity. The combination of more-positive δ13C values and the lack of forest indicator taxa in the Southwest suggest that landscapes were more open than in the Southeast. Inferred higher aridity in the Southwest may indicate that aridity or seasonal aridity/precipitation, not temperature or pCO2, was a greater driver of C4 abundance during the Pleistocene. Collectively, these data suggest that regional climatic and environmental interpretations can be improved by using an aridity index and a more detailed understanding of mammalian paleobiology.

Entelodonts are medium to large (perhaps 150–750 kg) Oligocene–Miocene bunodont artiodactyls with unique crania but typical artiodactyl postcrania. Functional and ecological interpretations are difficult because there is no clear modern analog to an entelodont in size, dentition, and cranial morphology. Entelodont crania combine primitive and derived features, including laterally expanded zygomatic arch/large temporal fossa (suggesting a large temporalis muscle), unreduced dental formula, long premolar row, fused mandibular symphysis, isognathy, and subcylindrical dentary condyles. Furthermore, the cranium has unique architectural and ontogenetic aspects unparalleled in extant mammals. Canines show heavy, carnivoran-like, apical wear in old individuals, suggesting regular contact with food. Conical premolars and associated diastemata dominate the tooth row. Premolars are often apically worn, in a fashion somewhat like those of carnivorans (e.g., Crocuta, Borophagus). Molars are low-cusped crushing teeth. Wide gape, indicated by the form of the coronoid process and temporal fossa, facilitated canine and premolar use, probably both in feeding and in social behavior. Jaw mechanics, tooth morphology, and tooth wear are compatible with omnivory and probable scavenging, an intriguing proposition for the huge Dinohyus hollandi.

Morphological responses of nonmammalian herbivores to external ecological drivers have not been quantified over extended timescales. Herbivorous nonavian dinosaurs are an ideal group to test for such responses, because they dominated terrestrial ecosystems for more than 155 Myr and included the largest herbivores that ever existed. The radiation of dinosaurs was punctuated by several ecologically important events, including extinctions at the Triassic/Jurassic (Tr/J) and Jurassic/Cretaceous (J/K) boundaries, the decline of cycadophytes, and the origin of angiosperms, all of which may have had profound consequences for herbivore communities. Here we present the first analysis of morphological and biomechanical disparity for sauropodomorph and ornithischian dinosaurs in order to investigate patterns of jaw shape and function through time. We find that morphological and biomechanical mandibular disparity are decoupled: mandibular shape disparity follows taxonomic diversity, with a steady increase through the Mesozoic. By contrast, biomechanical disparity builds to a peak in the Late Jurassic that corresponds to increased functional variation among sauropods. The reduction in biomechanical disparity following this peak coincides with the J/K extinction, the associated loss of sauropod and stegosaur diversity, and the decline of cycadophytes. We find no specific correspondence between biomechanical disparity and the proliferation of angiosperms. Continual ecological and functional replacement of pre-existing taxa accounts for disparity patterns through much of the Cretaceous, with the exception of several unique groups, such as psittacosaurids that are never replaced in their biomechanical or morphological profiles.

Predation is an important process in modern oceans and in the evolutionary history of marine ecosystems. Consequently, it has been hypothesized that shelled prey modified their ornamentation in response to predation. However, bivalve ornamentation has also been argued to be important in maintaining a stable life position in the sediment and in burrowing. To test whether concentric ribs were effective against drilling by carnivorous gastropods, we examined drill hole position and completeness for four Cenozoic bivalve species that differ in rib strength (Astarte radiata, A. goldfussi, Lirophora glyptocyma, and L. latilirata). The percentage of drill holes located between the ribs increases with increasing rib strength, whereas the percentage of drill holes on top of ribs decreases. This result suggests that gastropods select the drill hole site more effectively as rib strength increases, thereby saving time and energy, and that natural selection favors gastropods that select drill hole sites between ribs. Because of this greater stereotypy, the percentage of drill holes that are incomplete is generally lower in strongly ribbed species. The proportion of drill holes located on top of ribs is greater for incomplete than complete holes, implying that ribs can be effective against predators, but only when selected as the drilling location. We show that ribs are most effective against drilling predation for bivalves with moderately sized ribs, between which gastropods have difficulty siting drill holes. Concentric ribs are unlikely to have evolved as an adaptation against drilling predation because concentric ribs evolved in the Paleozoic and were already common in the Mesozoic, whereas drilling frequency increased later, in the Late Cretaceous–Paleogene. Moreover, rib strength of North American Astarte did not change through this time interval. Thus, the ribs considered here are a likely exaptation to drilling given their effectiveness at deterring drilling predation on bivalves with moderate ribs.

The statistical significance of differences in evolutionary rate between major taxonomic groups is evaluated using conventional chi-square techniques on stratigraphic range data. Romer's (1966) compilation of stratigraphic ranges of fossil mammals is used to determine whether orders differ significantly from each other in generic origination and extinction rates. The evolutionary histories of 2180 genera (primarily Cenozoic in age) are analyzed. Chi-square testing shows that significantly high or low (P ≥ 0.99) extinction or origination occurs in 15% of the testable cases. Significantly high or low evolutionary turnover in a taxon (orders in this case) we term taxotely. Significantly high turnover rate is equivalent to Simpson's tachytely and significantly low turnover is equivalent to his bradytely.

In the mammal data set, taxotely is largely attributable to the influence of South American endemics. Some of the effect is interpreted as an artifact of biases in the fossil record (or its study) and some is attributed to real biological aspects of mammalian evolution.

The Cretaceous–Paleogene (K/Pg) extinction appears to have been geographically heterogeneous for some organismal groups. Southern Hemisphere K/Pg palynological records have shown lower extinction and faster recovery than in the Northern Hemisphere, but no comparable, well-constrained Southern Hemisphere macrofloras spanning this interval had been available. Here, macrofloral turnover patterns are addressed for the first time in the Southern Hemisphere, using more than 3500 dicot leaves from the latest Cretaceous (Maastrichtian) and the earliest Paleocene (Danian) of Argentine Patagonia. A maximum ca. 90% macrofloral extinction and ca. 45% drop in rarefied species richness is estimated across the K/Pg, consistent with substantial species-level extinction and previously observed extirpation of host-specialized leaf mines. However, prior palynological and taxonomic studies indicate low turnover of higher taxa and persistence of general floral composition in the same sections. High species extinction, decreased species richness, and homogeneous Danian macrofloras across time and facies resemble patterns often observed in North America, but there are several notable differences. When compared with boundary-spanning macrofloras at similar absolute paleolatitudes (ca. 50°S or 50°N) from the Williston Basin (WB) in the Dakotas, both Maastrichtian and Danian Patagonian species richnesses are higher, extending a history of elevated South American diversity into the Maastrichtian. Despite high species turnover, our analyses also reveal continuity and expansion of leaf morphospace, including an increase in lobed and toothed species unlike the Danian WB. Thus, both Patagonian and WB K/Pg macrofloras support a significant extinction event, but they may also reflect geographically heterogeneous diversity, extinction, and recovery patterns warranting future study.

Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and sampled fossils were generated by the same underlying diversification process. A crucial advantage of this model is that it incorporates the possibility that some species may never be sampled. Here, we present an FBD model that estimates tree-wide diversification rates from stratigraphic range data when the underlying phylogeny of the fossil taxa may be unknown. The model can be applied when only occurrence data for taxonomically identified fossils are available, but still accounts for the incomplete phylogenetic structure of the data. We tested this new model using simulations and focused on how inferences are impacted by incomplete fossil recovery. We compared our approach with a phylogenetic model that does not incorporate incomplete species sampling and to three fossil-based alternatives for estimating diversification rates, including the widely implemented boundary-crosser and three-timer methods. The results of our simulations demonstrate that estimates under the FBD model are robust and more accurate than the alternative methods, particularly when fossil data are sparse, as the FBD model incorporates incomplete species sampling explicitly.

Sauropodomorpha included the largest known terrestrial vertebrates and was the first dinosaur clade to achieve a global distribution. This success is associated with their early adoption of herbivory, and sauropod gigantism has been hypothesized to be a specialization for bulk feeding and obligate high-fiber herbivory. Here, we apply a combination of biomechanical character analysis and comparative phylogenetic methods with the aim of quantifying the evolutionary mechanics of the sauropodomorph feeding apparatus. We test for the role of convergence to common feeding function and divergence toward functional optima across sauropodomorph evolution, quantify the rate of evolution for functional characters, and test for coincident evolutionary rate shifts in craniodental functional characters and body mass. Results identify a functional shift toward increased cranial robustness, increased bite force, and the onset of static occlusion at the base of the Sauropoda, consistent with a shift toward bulk feeding. Trends toward similarity in functional characters are observed in Diplodocoidea and Titanosauriformes. However, diplodocids and titanosaurs retain significant craniodental functional differences, and evidence for convergent adoption of a common “adaptive zone” between them is weak. Modeling of craniodental character and body-mass evolution demonstrates that these functional shifts were not correlated with evolutionary rate shifts. Instead, a significant correlation between body mass and characters related to bite force and cranial robustness suggests a correlated-progression evolutionary mode, with positive-feedback loops between body mass and dietary specializations fueling sauropod gigantism.

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.

Analysis of stratigraphically separated collections of Late Ordovician fossilized marine invertebrates suggests that our understanding of faunal changes through time may be enhanced by considering them in terms of a successional framework. The faunal succession in the Nicolet River Valley, St. Lawrence Lowlands, Quebec, began with the initial colonization of an offshore barren mud by two or three presumably opportunistic deposit-feeding species. Diversity, both of species and of trophic types, increased gradually, peaked, and then decreased slightly with some faunal shifts, especially in the numerical predominance of the epifaunal element. A three-fold repetition of this quiet-water succession seems in each case to have been terminated by an external physical perturbation. There also appears to be a second, separate successional sequence which became localized on a somewhat coarser-grained and perhaps less stable substratum as the paleoshoreline was approached, due to sediment filling of the basin.

Recent phylogenetic studies of Paleozoic gastropods show the classification provided by the Treatise on Invertebrate Paleontology to include numerous highly polyphyletic taxa. Here we test whether this classification reflects limits on the range of possible designs, general architectural constraints, or common functional solutions for Paleozoic gastropods. Our test evaluates whether superfamilial/subordinal level archetypes as defined by the Treatise evolved more frequently than expected among 626 Late Cambrian–Middle Devonian species. Using a previously established phylogeny and five general shell features (spire angle, exhalent current position, base angle, umbilical width, and apertural inclination) we show that there are fewer gastropod morphotypes than expected given the frequency of change in these features. This is true even after accounting for architectural constraints implied by the data. Moreover, the most common morphotypes include significantly more species and evolved significantly more times than expected. These results imply a set of architectural attractors for lower–middle Paleozoic gastropods, consistent with ecomorphological theory that particular morphotypes are best suited for particular lifestyles. Thus, the Treatise classifications likely reflect these ecomorphological patterns within subclades rather than phylogenetic patterns.

With species found throughout both marine and fresh waters, the diatom order Thalassiosirales is one of the most phylogenetically and ecologically diverse lineages of planktonic diatoms. A clear understanding of the timescale of Thalassiosirales evolution would provide novel insights into the rates and patterns of species diversification associated with major habitat shifts, as well as provide valuable context for understanding the age and evolutionary history of the model species, Cyclotella nana (= Thalassiosira pseudonana). The freshwater fossil record for Thalassiosirales is extensive, well characterized, and generally supportive of a Miocene origin for the major freshwater lineages. The marine record is, by comparison, more sparse and in many cases, unverified. The discovery of freshwater thalassiosiroids in Eocene sediments pushed the freshwater fossil record considerably further back in time, highlighting an apparent gap of some 30 million years. An alternative interpretation is that the Miocene and Eocene reports represent competing hypotheses. In the absence of additional independent and decisive fossil data, I explored the relative plausibility of these two scenarios with Bayesian relaxed molecular clock methods under a range of fossil calibration schemes. Although I found no support for the Eocene fossil dates, the two major freshwater colonization events probably occurred much earlier than previously thought—as early as the Paleocene for Cyclotella, followed by an Eocene origin for the cyclostephanoid lineage. Much of the extant freshwater diversity in both lineages traces back to the Miocene, however, giving the impression of a single Miocene origin. Efforts to infer the timescale of Thalassiosirales evolution more accurately would benefit from a systematic reevaluation of the marine fossil record and formal integration of fossil species into existing phylogenetic hypotheses.

We have recently shown how capture-recapture models can be used in conjunction with stratigraphic range data to estimate taxonomic extinction rates and taxonomic diversity. Here we present a new method that can be used to estimate taxonomic turnover (defined here as the proportion of taxa extant at time i, that originated in the interval i – 1 to i). We used these methods in conjunction with stratigraphic range data for families in five phyla of Paleozoic marine invertebrates. We estimated fossil encounter probabilities, extinction rates, diversity, and turnover and used these estimates to test hypotheses about variation among phyla and geologic series. Encounter probabilities varied among taxa and showed evidence of a decrease over time for the geologic series examined. The number of families varied substantially among the five phyla and showed some evidence of an increase over the series examined. There was no evidence of variation in extinction probabilities among the phyla. Although there was evidence of temporal variation in extinction probabilities within phyla, there was no evidence of a linear decrease in extinction probabilities over time, as has been reported by others. We did find evidence of high extinction probabilities for the two intervals that had been identified by others as periods of mass extinction. We found no evidence of variation in turnover among the five phyla. There was evidence of temporal variation in turnover, with greater turnover occurring in the older series.

The compound eyes of trilobites provide the best examples of fossilized sensory organs for which the function in life can be worked out today because the optical array of their corneal lenses preserves the geometry with which the eye originally sampled the visual world. An analysis of trilobite vision is strengthened by the use of new mathematical approaches to compound eye design. In particular, the product of the facet diameter (D) and the interommatidial angle (Δϕ) gives the value of the eye parameter, DΔϕ, which is a reliable indicator of the photic conditions in which the eye was used. In modern arthropods, DΔϕ values range from 0.3 for animals active in bright sunlight to 20 or more for nocturnal or deep-sea animals. Two major types of compound eyes existed in trilobites: schizochroal and holochroal. In our previous work with schizochroal eyes in the phacopids Phacops rana crassituberculata and Phacops rana milleri, we found that eye parameter values ranged from 10 to >150. These values of the eye parameter are much greater than in any living arthropod, implying that modern compound eye theory does not apply to schizochroal eyes. We suggested that each ommatidium of the schizochroal eye served as a miniature lens eye. If so, phacopid vision must have been unique, with multiply overlapping visual fields. In the new work of this paper, we examined holochroal compound eyes in Asaphus cornutus, Isotelus gigas, and Homotelus sp. Holochroal eyes contain far more ommatidia than do schizochroal types, reducing both facet diameter (D) and interommatidial angle (Δϕ). Thus, DΔϕ values in these species fall into the same range as in modern nocturnal compound eyes. This implies that function of the holochroal eye was similar to that of modern arthropods, and that they were used in moderate to dim intensities of light.

Euproops danae, a xiphosuran from the Mazon Creek (Braidwood) Fauna, had two sets of spines—genal and ophthalmic—extending from the posterior margin of its prosoma. In young individuals, the genal spines were longer than the ophthalmic spines. During growth, the relative length of each type of spine increased, but the rate of increase was much greater for ophthalmic spines. In order to explain these morphological and ontogenetic features, I have studied the hydrodynamic behavior of whole-animal models representing the actual morphology of E. danae, and various modifications thereof, at different body sizes. It can be argued that passive settling, while in an enrolled posture, was probably the primary defensive reaction that a swimming individual would have exhibited in response to an encounter with a potential predator. Experiments show that the array of spines on E. danae was an important control on the style of settling experienced by an enrolled individual. Models of the actual morphology settle steadily, while models with either longer or shorter prosomal spines tend to undergo lateral oscillations induced by turbulence in the wake. Steady fall would have rendered the horseshoe crab less perceptible to either the visual or lateral line systems of contemporary aquatic vertebrates, and thus a morphology capable of producing it would have been an important adaptation for reducing the risk of predation. This minimization of oscillatory movement would actually obtain for a variety of conceivable spine morphologies, but actual morphologies represent those ‘solutions’ which simultaneously optimize other aspects of spine function, such as mechanical protection. This optimum design changes during ontogeny because settling dynamics scale non-linearly with size. This work has both specific applications to the interpretation of similar structures in other arthropods and more general implications for the study of evolutionary functional morphology.

Plant-insect interactions are vital for structuring terrestrial ecosystems. It is still unclear how climate change in geological time might have shaped plant-insect interactions leading to modern ecosystems. We investigated the effect of Quaternary climate change on plant-insect interactions by observing insect herbivory on leaves of an evergreen sclerophyllous oak lineage (Quercus section Heterobalanus, HET) from a late Pliocene flora and eight living forests in southwestern China. Among the modern HET populations investigated, the damage diversity tends to be higher in warmer and wetter climates. Even though the climate of the fossil flora was warmer and wetter than modern sample sites, the damage diversity is lower in the fossil flora than in modern HET populations. Eleven out of 18 damage types in modern HET populations are observed in the fossil flora. All damage types in the fossil flora, except for one distinctive gall type, are found in modern HET populations. These results indicate that Quaternary climate change did not cause extensive extinction of insect herbivores in HET forests. The accumulation of a more diverse herbivore fauna over time supports the view of plant species as evolutionary “islands” for colonization and turnover of insect species.

We developed a new method to generate topographic maps of tooth crowns from X-ray synchrotron microtomographic data. Maps are drawn after cervix-plane orientation of tooth image stacks, without the need for a geographic information system. Classical topographic maps with contour lines are complemented by slope maps and angularity maps. Cartography allows precise comparisons of cusps morphologies, and quantification of the directions of cusp axis elongation and slope. Application of this method to muroid rodents with cricetine and murine dental patterns reveals clear-cut differences in cusps morphology that are indicative of the direction of the chewing movement, in agreement with wear facet analyses. Rodents with a murine dental pattern were derived from ancestors with a cricetine pattern, and their origin is associated with important changes in cusp morphology and organization. In order to understand such evolutionary change, our investigation is applied to a sample of extant and fossil muroid rodents that are characterized by either a murine dental plan or a cricetine one, or a dental pattern intermediate between those of cricetines and murines.