It is difficult to assign the animal-like body fossils of the late Neoproterozoic to crown metazoan phyla. Many Neoproterozoic fossils appear to share an architectural theme, which was characterized by Seilacher (1984, 1989) as modular; he noted that the modules, named pneus, could be arranged in a series of distinctive geometries to produce many of the Neoproterozoic fossil morphologies. The assemblages of pneus formed “quilted” constructions. Seilacher further suggested that these fossils might represent a multicellular clade that evolved independently of Metazoa–in effect, that they represented a kingdom of their own, which he named the Vendozoa. In later contributions, Seilacher (1992) renamed putatively quilted forms as the Vendobionta, and Buss and Seilacher (1994) considered Vendobionta to be a possible sister to Eumetazoa. The affinities suggested for vendobionts by various workers form a long list, ranging from protistans through fungi to several animal groups. Many vendobionts appear to be at the tissue grade of construction, and in this respect resemble cnidarians, to which they are most often compared. Neoproterozoic fossil assemblages also contain numbers of forms that are unlikely to be vendobionts, including a variety of “medusoids,” tentaculate fossils such as Hiemolora and Ediacaria (see Fedonkin 1992) that somewhat resemble sea anemones and may well be stem anthozoans. Additionally, numbers of Neoproterozoic forms have been suggested to be bilaterians, most notably the sluglike Kimberella (Fedonkin and Waggoner 1997). The contents and morphological limits of Vendobionta, and of some other higher taxa proposed for Neoproterozoic forms, are uncertain.

The record of fossil mammals from the Shungura Formation, lower Omo Valley of southern Ethiopia, represents one of the largest and most carefully controlled samples for deciphering the responses of land faunas to global-scale climatic change. We use the abundant and continuous fossil record of the family Bovidae to analyze the effects of a late Pliocene climatic shift toward increased aridity in Africa beginning at 2.8 Ma and intensifying at about 2.4 Ma. A database consisting of 4233 specimen-based records collected under well-defined procedures is used to define patterns through time in bovid abundances while also controlling for taphonomic and other potential biases. Univariate and multidimensional (correspondence analysis) methods are used to study changes in bovid abundances through time. Our results indicate that bovids experienced an increase in species richness and a rapid episode of change in taxonomic abundances at 2.8 ± 0.1 Ma (between Members B and C), and that this shift was followed by gradual and prolonged changes in abundance between 2.8 and 2.0 Ma (between Member C and upper Member G). An analysis of skeletal-element abundances through the Shungura sequence shows that only moderate changes in taphonomic conditions occurred between 3.0 and 2.1 Ma, when the lower Omo Valley was dominated by a large, meandering river, but that significant changes in the mode of preservation accompanied the onset of lacustrine depositional environments at 2.1 Ma (between lower and upper Member G). A juxtaposition of taxonomic with taphonomic patterns shows that the shift in taxonomic abundances at 2.8 Ma occurred in the absence of significant changes in taphonomic conditions. The main changes in bovid relative abundances and diversity appear to have been driven by broad environmental and climatic changes in Africa. As environmental indicators, bovids show a transition in the Omo at about 2.8 Ma from closed and wet environments in Member B to closed but dry environments in Member C. This drying trend intensified in Members D, E, and F, between about 2.5 and 2.3 Ma. In lower Member G, between 2.3 and 2.1 Ma, there was an increase in bovid abundance and diversity, which may be a result of greater environmental heterogeneity. The pattern of environmental change depicted by Shungura bovids is consistent with independently derived evidence of Omo paleoenvironments (from paleosols, paleoflora, and micromammals), and with regional and global evidence of climatic changes, especially acute between 2.8 and 2.3 Ma, that caused the initiation of glacial cycles in the north and drier climate in the tropics of Africa. Even though the Omo bovids showed distinct responses to large-scale climatic and environmental change, the Omo bovid community also had important attributes of long-term stability: two species, Aepyceros shungurae and Tragelaphus nakuae, dominated the community for nearly one million years. This study highlights the importance of carefully controlled collection procedures of fossil vertebrates and provides an important demonstration of the potential complexity in mode and rate of responses of land faunas to climatic change.

The reconstruction of phylogenies using cladistic methods is a powerful and well-established tool for evolutionary biologists and paleobiologists. Indeed, the construction of rigorous phylogenetic hypotheses has become widely accepted as an essential first step in the analysis of historical patterns for both extant and extinct organisms. In the past few years, there has arisen a healthy and constructive debate as to the exact methods that will lead to the most accurate tree (for example whether statistical inference or stratigraphic information has any part to play in phylogenetic reconstruction). Although important, this debate has tended to focus on the problems of tree construction and divert attention away from the applications of tree-based research. The construction of a phylogeny is, after all, only a first step, and phylogenetic trees provide the starting point from which to address a wide range of interesting biological and geological topics.

When transitional fossils blur previously clear boundaries between major groups, drawing that line can be problematic. While the need to rigorously define formal taxon names is widely acknowledged (e.g., de Queiroz and Gauthier 1992; Cantino et al. 1997), the need for similar precision in the scientific use of vernacular terms is not widely appreciated. The lack of accepted usages for common names has engendered endless arguments about when a fish becomes (also?) a tetrapod (e.g., Clack 1997), when a dinosaur becomes (also?) a bird (e.g., Padian and Chiappe 1998), and when a mammal-like reptile becomes (also?) a mammal (e.g., Rowe and Gauthier 1992). Recent descriptions of fossil snakes with well-developed hindlimbs have raised similar questions about where to draw the line between lizards and snakes and initiated a lively debate over the origin of snakes. However, lack of a precise definition of the vernacular term “snake,” as well as lack of a consensus on what constitutes a higher taxon's “origins,” has seriously hindered discussion of “snake origins.” Here, precise definitions of both terms are proposed and justified and their paleobiological implications discussed. The origin of higher taxa remains one of the most intriguing macroevolutionary problems, but scientists risk arguing at cross-purposes unless they agree on the exact boundaries of vernacular groups, and the exact meaning of the term “origin.”

Many features of global diversity compilations have proven robust to continued sampling and taxonomic revision. Inherent biases in the stratigraphic record may nevertheless substantially affect estimates of global taxonomic diversity. Here we focus on short-term (epoch-level) changes in apparent diversity. We use a simple estimate of the amount of marine sedimentary rock available for sampling: the number of formations in the stratigraphic Lexicon of the United States Geological Survey. We find this to be positively correlated with two independent estimates of rock availability: global outcrop area derived from the Paleogeographic Atlas Project (University of Chicago) database, and percent continental flooding. Epoch-to-epoch changes in the number of formations are positively correlated with changes in sampled Phanerozoic marine diversity at the genus level. We agree with previous workers in finding evidence of a diversity-area effect that is substantially weaker than the effect of the amount of preserved sedimentary rock. Once the mutual correlation among change in formation numbers, in diversity, and in area flooded is taken into consideration, there is relatively little residual correlation between change in diversity and in the extent of continental flooding. These results suggest that much of the observed short-term variation in marine diversity may be an artifact of variation in the amount of rock available for study. Preliminary results suggest the same possibility for terrestrial data.

Like the comparison between change in number of formations and change in sampled diversity, which addresses short-term variation in apparent diversity, the comparison between absolute values of these quantities, which relates to longer-term patterns, also shows a positive correlation. Moreover, there is no clear temporal trend in the residuals of the regression of sampled diversity on number of formations. This raises the possibility that taxonomic diversity may not have increased substantially since the early Paleozoic. Because of limitations in our data, however, this question must remain open.

Sideritic “coprolites” from the late Miocene of southwest Washington, the Upper Cretaceous of Saskatchewan and Madagascar, and the Permian of China have often been claimed to be pseudofossils. They are here interpreted as intestinal casts (cololites) prefossilized by bacterial activity and later transformed into siderite with no traces of original food particles left. All occurrences are found within fluvial overbank deposits that carry no other vertebrate remains. Their absence could be due to aquifer roll-fronts that destroyed phosphatic bones and teeth but favored siderite precipitation.

One of the most extensively studied aspects of phylogenetic tree shape is balance, which is the extent to which nodes divide a tree into clades of equal size. Several authors have stressed the importance of tree balance for understanding patterns of evolution. It has been remarked that paleontological studies commonly produce very unbalanced trees (also called pectinate cladograms or “Hennigian combs”). This claim is tested here by comparing the balance of 50 paleontological trees and 50 neontological trees, all taken from the recent literature. Each tree was reanalyzed from the published data matrix to ensure its accuracy. The results confirm that paleontological trees tend to be more imbalanced than neontological trees.

That paleontological trees are more imbalanced has been represented as a shortcoming of fossil data sets, but here it is argued that this is the expected result. Even under a simple Markovian model in which all speciations and extinctions occur randomly and with equal probability in all parts of the tree, trees based on taxa from a single time period (e.g., the present day) are generally more balanced than trees based on all taxa that ever existed within the clade. Computer simulation is used to calculate the expected balance and standard deviation of trees for up to 40 terminal taxa over the entire history of a model clade. The balance is measured using Colless's index, Ic, and the expected balance conforms well with published paleontological trees. The study underlines the difficulty of applying neontological tree statistics in paleontology.

An intriguing phenomenon in the study of evolutionary rates of morphological change measured from fossil lineages has been the dependence of these rates on the inverse of the measurement interval. This effect has been reported across wide ranges of species as well as within single lineages, and has been interpreted as representing a smooth extension of evolutionary rate from generational timescales to paleontological timescales, suggesting that macroevolution may be simply microevolution extended over longer intervals. There has been some debate about whether this inverse dependence is a real feature of evolutionary change, or a mathematical or psychological artifact associated with the interpretation of data.

Our analysis indicates that the strong inverse dependence of rate on interval is an artifact produced by the phenomenon of spurious self-correlation. Spurious self-correlation can appear in any calculation when a ratio is plotted against its denominator, as is done in plotting rate versus interval, and when these two quantities are not well correlated with one another. We demonstrate that the effect of spurious self-correlation appears in seven published data sets of evolutionary rate that range from taxonomically broad compendia to studies of single families. The effect obscures the underlying information about the dependence of evolutionary change on interval that is present in the data sets. In five of the seven data sets examined there is no significant correlation between the extent of evolutionary change and elapsed time. Where such a correlation does exist, the inverse dependence of rate on interval length is weakened. We describe the role played by taxonomic, dynamic, and character inhomogeneity in producing the lack of correlation of change with interval in each of these data sets. This lack of correlation of change with interval, and the accompanying inverse correlation of rate with interval, most likely arises from discontinuous modes of evolutionary change in which a distinct long-term dynamic dominates net change over geological time spans. It is poorly explained by the extrapolationary microevolutionary models that have been said to account for this phenomenon.

Apparent variation in rates of origination and extinction reflects the true temporal pattern of taxonomic rates as well as the distorting effects of incomplete and variable preservation, effects that are themselves exacerbated by true variation in taxonomic rates. Here I present an approach that can undo these distortions and thus permit estimates of true taxonomic rates, while providing estimates of preservation in the process. Standard survivorship probabilities are modified to incorporate variable taxonomic rates and rates of fossil recovery. Time series of these rates are explored by numerical optimization until the set of rates that best explains the observed data is found. If internal occurrences within stratigraphic ranges are available, or if temporal patterns of fossil recovery can otherwise be assumed, these constraints can be exploited, but they are by no means necessary. In its most general form, the approach requires no data other than first and last appearances. When tested against simulated data, the method is able to recover temporal patterns in rates of origination, extinction, and preservation. With empirical data, it yields estimates of preservation rate that agree with those obtained independently by tabulating internal occurrences within stratigraphic ranges. Moreover, when empirical occurrence data are artificially degraded, the method detects the resulting gaps in sampling and corrects taxonomic rates. Preliminary application to data on Paleozoic marine animals suggests that some features of the apparent record, such as the forward smearing of true origination events and the backward smearing of true extinction events, can be detected and corrected. Other features, such as the end-Ordovician extinction, may be fairly accurate at face value.

The incorporation of the random walk model into stratophenetic analysis marked a turning point by presenting a potential null model for microevolutionary patterns. Random walks are derived from a family of statistical fractals, and their statistics can be reconstructed using appropriate techniques. This paper lays the foundation for the explicit and uniform description of evolutionary mode in stratophenetic series using random walk null models and the information contained within incompletely preserved time series.

The method relies upon the iterative analysis of subseries of an original stratophenetic series by measuring the presence of deviations from statistical randomness as the lineage evolves. This measure, and its probability of significance (evaluated using a randomization test), forms the dimensions of a descriptive space for microevolutionary modes. Each stratophenetic series can then be viewed as a journey through this space. Computer simulation of various evolutionary modes demonstrates that different modes, for example stasis and gradualism, have differing trajectories and occupy different regions of the microevolutionary space. The method is applied to two published foraminiferal stratophenetic series, the Mio-Pliocene Globorotalia plesiotumida-tumida punctuated transition and an anagenetic trend in the Late Cretaceous Contusotruncana fornicata-contusa lineage. An anagenetic trend is strongly supported in the latter example, whereas transformation of the Globorotalia species seems to result from the fluctuating effectiveness of constraining processes.

Analyses of limb joint morphology in nonmammalian therapsid “mammal-like reptiles” have suggested that among many lineages, individual animals were capable of shifting between sprawling and upright hindlimb postures, much like modern crocodilians. The ability to use multiple limb postures thus might have been ancestral to the generally more upright posture that evolved during the transition from “mammal-like reptiles” to mammals. Here I derive a biomechanical model to test this hypothesis through calculations of expected posture-related changes in femoral stress for therapsid taxa using different limb postures. The model incorporates morphological data from fossil specimens and experimental data from force platform experiments on iguanas and alligators.

Experimental data suggest that the evolutionary transition from sprawling to nonsprawling posture was accompanied by a change in the predominant loading regime of the limb bones, from torsion to bending. Changes in the cross-sectional morphology of the hindlimb bones between sphenacodontid “pelycosaurs” and gorgonopsid therapsids are consistent with the hypothesis that bending loads increased in importance early in therapsid evolution; thus, bending stresses are an appropriate model for the maximal loads experienced by the limb bones of theriodont therapsids. Results from the model used to estimate stresses in these taxa do not refute the use of both sprawling and more upright stance among basal theriodont therapsids. Thus, the hypothesis that the use of multiple postures was ancestral to the more upright posture typical of most mammals is biomechanically plausible. Model calculations also indicate that the axial rotation of the femur typical in sprawling locomotion can reduce peak bending stresses. Therefore, as experimental data from alligators and iguanas suggest, the evolution of nonsprawling limb posture and kinematics in therapsids might have been accompanied by increased limb bone bending stress.

Evidence for species range shifts in response to climatic change is common in the Pleistocene and earlier fossil record. However, little work has been done to model how such shifts in species range limits would change compositions of species assemblages over different spatial scales. Here I present a simple model that explores the role of biogeography in constraining changes in the compositions of species assemblages under the null hypothesis of random range shifts. The model predicts that localities where most species are far away from the edges of their ranges (e.g., localities at the center of a biogeographic province) would show relatively stable diversity patterns even during episodes of climatic change. Only localities with many range endpoints (such as those near the edges of biogeographic provinces) would show large fluctuations in species composition (and richness) in response to changes in the ambient climatic conditions. I test the predictions of the model using (1) simulations and (2) the Pleistocene bivalve fauna of California. The simulations as well as the empirical data from the Pleistocene terraces are consistent with the model predictions. These results show that attempts to quantify temporal trends in local and regional diversity and assemblage compositions need to take biogeographic structure into account.

Heterochrony is considered to be an important and ubiquitous mechanism of evolutionary change. Three components are necessary to describe heterochrony: phylogenetic relationships, size and shape change, and timing of developmental events. Patterns and processes of heterochrony are all too often invoked before all three components have been investigated. Phylogenetic hypotheses affect the interpretation of heterochrony in three ways: rooting of a clade, topology of a clade, and character polarity. To study these effects we examined the distribution of shell microstructure, lophophore support structures, and body size in four different phylogenetic hypotheses of thecideide brachiopods (Triassic to Recent), a group of minute, cryptic, benthic marine invertebrates.

Thecideides are consistently monophyletic in experiments using terebratulide, strophomenate, and spire-bearing outgroups together and separately, varying ingroup membership, and experimentally withholding certain character complexes. Thecideide monophyly is also supported by bootstrap analysis. Hypotheses of heterochrony in thecideide origins and evolution are therefore not merely artifacts of classification and can be pursued further. Using either strophomenate or spire-bearing outgroups, Triassic Thecospira is the most primitive thecideide. Trees constructed using terebratulide outgroups are rooted instead at Eudesella, a taxon derived in every other phylogenetic reconstruction, and the Triassic thecideides occupy derived rather than primitive positions.

Our phylogenetic results support the traditional interpretation of the reduction or loss of the secondary fibrous shell layer as a paedomorphic pattern, whereas the evolution of lophophore support structures suggests a peramorphic pattern. Reduction in thecideide adult body size is gradual, phylogenetically, and results in an overall paedomorphic pattern. Heterochrony in these three character suites may play a role in the subsequent evolution of the clade, but apparently not in the origin of the clade, as is commonly thought. Heterotopy, rather than—or in addition to—heterochrony, may account for both the origin and evolution of the lophophore support structures and in the reduction and loss of the secondary shell layer. These phylogenetic hypotheses suggest that heterochrony can result from a complex mosaic of processes and provide specific, testable predictions about the processes responsible for producing the patterns, whether heterochronic or not. Categorizing an entire clade (such as thecideides), rather than individual characters, as globally paedomorphic may allow interesting peramorphic patterns in individual characters to be overlooked.

Phylogenies provide a rich source of information that should be exploited in designing quantitative hypothesis tests in paleobiological contexts. Viewing such data analysis problems through the prism of phylogenetically structured comparisons can help add realism and depth to paleobiological data-analysis strategies. Two examples of the importance of adopting a phylogenetic perspective are discussed. In the first example, a phylogenetic-comparative approach is used to test correlations between ecological, morphological, and biological characteristics of planktonic foraminifera. Results suggest that the presence of spines and photosynthetic symbionts in Neogene-Recent species are not adaptations to living in shallow-intermediate planktonic depth habitats. In the second, a phylogenetic-comparative approach is used to reveal the presence of morphological correlations with locomotor function in a mammalian carnivore data set. Paleontologists can play an active role in improving comparative data analyses by (1) helping to develop improved phylogenies, especially those that provide better estimates of branch lengths, and (2) helping to resolve a number of outstanding issues surround the question of ancestral character-state specification.

The ontogeny of arthropod exoskeletons is punctuated by short periods of growth following each molt, separated by longer stages of unchanging morphology called instars. The recognition of instar clusters in size distributions has been important in understanding the growth and evolution of fossil arthropods. Generally, these clusters have been identified by inspection, but this approach has been criticized for its subjectivity. In this paper, we describe a statistical framework for evaluating hypotheses of clustering based on maximum likelihood analysis of mixture models. The approach assumes that individuals are normally distributed within instars; thus an arthropod size distribution can be considered a mixture of normal distributions. This methodology provides an objective framework to compare various plausible hypotheses of grouping, including the possibility that there is no significant grouping at all.

We apply this method to evaluate clustering in two trilobite species, Ampyxina bellatula and Piochaspis sellata. Both of these data sets show statistically significant evidence of clustering, a phenomenon rarely documented for holaspid-stage trilobites. After consideration of alternative causes of clustering, we argue that the observed groupings are best explained as instar groups. In these two species, growth increments between molts were similar throughout the observed portion of ontogeny, although subtle yet significant variation can be seen within the ontogeny of Ampyxina bellatula.

Histologic studies of embryonic and perinatal longbones of living birds, non-avian dinosaurs, and other reptiles show a strong phylogenetic signal in the distribution of tissues and patterns of vascularization in both the shafts and the bone ends. The embryonic bones of basal archosaurs and other reptiles have thin-walled cortices and large marrow cavities that are sometimes subdivided by erosion rooms in early stages of growth. The cortices of basal reptiles are poorly vascularized, and osteocyte lacunae are common but randomly organized. Additionally, there is no evidence of fibrolamellar tissue organization around the vascular spaces. Compared with turtles, basal archosaurs show an increase in vascularization, better organized osteocytes, and some fibrolamellar tissue organization. In dinosaurs, including birds, vascularization is greater than in basal archosaurs, as is cortical thickness, and the osteocyte lacunae are more abundant and less randomly organized. Fibrolamellar tissues are evident around vascular canals and form organized primary osteons in older perinates and juveniles.

Metaphyseal (“epiphyseal”) morphology varies with the acquisition of new features in derived groups. The cartilage cone, persistent through the Reptilia (crown-group reptiles, including birds), is completely calcified in ornithischian dinosaurs before it is eroded by marrow processes; cartilage canals, absent in basal archosaurs, are present in Dinosauria; a thickened calcified hypertrophy zone in Dinosauria indicates an acceleration of longitudinal bone growth.

Variations in this set of histological synapomorphies overlap between birds and non-avian dinosaurs. In birds, these variations are strongly correlated with life-history strategies. This overlap, plus independent evidence from nesting sites, reinforces the hypothesis that variations in bone growth strategies in Mesozoic dinosaurs reflect different life-history strategies, including nesting behavior of neonates and parental care.

Using museum and literature data, we characterize faunal turnover in bivalves and brachiopods of the North American Midcontinent over approximately 12.5 Myr spanning the Pennsylvanian/Permian boundary. The two groups experienced indistinguishable rates of background faunal turnover but differed in the type and timing of elevated turnover episodes. Bivalves underwent an episode of elevated first appearance in the Missourian Series whereas brachiopods underwent an episode of elevated disappearance in the Wolfcampian Series. In neither group does turnover history strongly correlate to long-term changes in basinal lithofacies, which reflect evolution of regional climate. Comparison with other time intervals and basins suggests that magnitude and frequency of turnover episodes during the late Paleozoic was intermediate between the more episodic early Paleozoic and less episodic Mesozoic.

The association between mass extinction in the marine realm and eustatic sea-level change in the Mesozoic is well documented, but perplexing, because it seems implausible that sea-level change could actually cause a major extinction. However, large-scale cycles of sea-level change can and do alter the ratio of shallow to deep marine continental-shelf deposits preserved in the rock record both regionally and globally. This taphonomic megabias alone could be driving patterns of first and last occurrence and standing diversity because diversity and preservation potential both change predictably with water depth. We show that the Cenomanian/Turonian faunal event in western Europe has all the predicted signatures expected if taphonomic megabias was the cause. Grade taxa terminating in pseudoextinction and Lazarus taxa are predominantly found in the onshore facies that disappear for extended periods from the rock record. Before other mass extinctions are taken at face value, a much more careful analysis of biases in the rock record needs to be carried out, and faunal disappearances need to be analyzed within a phylogenetic framework.