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.

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.

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.

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.

This paper assesses the reliability with which fossil reefs record the diversity and community structure of adjacent Recent reefs. The diversity and taxonomic composition of Holocene raised fossil reefs was compared with those of modern reef coral life and death assemblages in adjacent moderate and low-energy shallow reef habitats of Madang Lagoon, Papua New Guinea. Species richness per sample area and Shannon-Wiener diversity (H′) were highest in the fossil reefs, intermediate in the life assemblages, and lowest in the death assemblages. The taxonomic composition of the fossil reefs was most similar to the combination of the life and death assemblages from the modern reefs adjacent to the two fossil reefs. Depth zonation was recorded accurately in the fossil reefs. The Madang fossil reefs represent time-averaged composites of the combined life and death assemblages as they existed at the time the reef was uplifted.

Because fossil reefs include overlapping cohorts from the life and death assemblages, lagoonal facies of fossil reefs are dominated by the dominant sediment-producing taxa, which are not necessarily the most abundant in the life assemblage. Rare or slow-growing taxa accumulate more slowly than the encasing sediments and are underrepresented in fossil reef lagoons. Time-averaging dilutes the contribution of rare taxa, rather than concentrating their contribution. Consequently, fidelity indices developed for mollusks in sediments yield low values in coral reef death and fossil assemblages. Branching corals dominate lagoonal facies of fossil reefs because they are abundant, they grow and produce sediment rapidly, and most of the sediment they produce is not exported.

Fossil reefs distinguished kilometer-scale variations in community structure more clearly than did the modern life assemblages. This difference implies that fossil reefs may provide a better long-term record of community structure than modern reefs. This difference also suggests that modern kilometer-scale variation in coral reef community structure may have been reduced by anthropogenic degradation, even in the relatively unimpacted reefs of Madang Lagoon. Holocene and Pleistocene fossil reefs provide a time-integrated historical record of community composition and may be used as long-term benchmarks for comparison with modern, degraded, nearshore reefs. Comparisons between fossil reefs and degraded modern reefs display gross changes in community structure more effectively than they demonstrate local extinction of rare taxa.

Recently, there has been much interest in detecting and measuring patterns of change in disparity. Although most studies have used one or two measures of disparity to quantify and characterize the occupation of morphospace, multiple measures may be necessary to fully detect changes in patterns of morphospace occupation. Also, the ability to detect morphological trends and occupation patterns within morphospace depends on using the appropriate measure(s) of disparity. In this study, seven measures were used to determine and characterize sensitivity to sample size of the data, number of morphological characters, percentage of missing data, and changes in morphospace occupation pattern. These consist of five distance measures—sum of univariate variances, total range, mean distance, principal coordinate analysis volume, average pairwise dissimilarity—and two non-distance measures—participation ratio and number of unique pairwise character combinations. Evaluation of each measure with respect to sensitivity to sample size, number of morphological characters, and percentage of missing data was accomplished by using both simulated and Ordovician crinoid data. For simulated data, each measure of disparity was evaluated for its response to changes of morphospace occupation pattern, and with respect to simulated random and nonrandom extinction events. Changes in disparity were also measured within the Crinoidea across the Permian extinction event.

Although all measures vary in sensitivity with respect to species sample size, number of morphological characters, and percentage of missing data, the non-distance measures overall produce the lowest estimates of variance (in bootstrap analyses). The non-distance measures appear to be relatively insensitive to changes in morphospace occupation pattern. All measures, except average pairwise dissimilarity, detect changes in occupation pattern in simulated nonrandom extinction events, but all measures, except number of unique pairwise character combinations and principal coordinate analysis volume, are relatively insensitive to changes in pattern in simulated random extinction events. The distance measures report similar changes in disparity over the Permian extinction event, whereas the non-distance measures differ. This study suggests that each measure of disparity is designed for different purposes, and that by using a combination of techniques a clearer picture of disparity should emerge.

An example of actual shell growth in the pentameride brachiopod Lycophoria nucella (Dalman) reveals that the axis-computing morphometric technique (Aldridge 1998; Van Osselaer and Grosjean 2000) produces hypothetical ideal logarithmic spirals that fail to morphometrically characterize the biological realities determined by the actual geometry of the shells to which the axis-computing technique is applied. In contrast, the actual-outline morphometric technique (McGhee 1980) links the measurement coordinate system directly to the ontogeny of the animal under analysis, and it yields morphometric parameterizations of geometric aspects of the shell of direct biological significance to the animal (the presence or absence of ontogenetic alterations in shell convexity, rates of change of shell convexity in the case of anisometric growth, and the nature of anisometric changes in shell convexity—i.e., whether the shell becomes increasingly more convex with growth, or whether the shell becomes increasingly flatter with growth).

Co-ossified pygal and caudal vertebrae in Late Cretaceous mosasaurs from the southeast Netherlands, northeast Belgium, and North America are compared with lumbar and caudal vertebrae from fossil and extant whales. Both infectious spondylitis and idiopathic vertebral hyperostosis afflicted these marine tetrapods. The causes of the infectious disease and of the idiopathic disease are similar in the compared life forms. The location of idiopathic hyperostosis along the vertebral column implicates axial locomotion in mosasaurs, as in whales.

In computational studies of the body mass and surface area of vertebrates, it is customary to assume that body cross-sections are approximately elliptical. However, a review of actual vertebrate cross-sections establishes that this assumption is not usually met. A new cross-sectional model using superellipses is therefore introduced, together with a scheme that allows estimates to be given with ranges. Tests of the new method, using geometrical shapes, miniature vertebrate models, and actual animals, show that the method has a high accuracy in body mass estimation. A new computer program to perform the computation is introduced. The application of the method to some Mesozoic marine reptiles suggests that the tuna-shaped ichthyosaur Stenopterygius probably had body masses comparable to those of average cetaceans of the same body length.

The estimation and interpretation of temporal patterns in origination and extinction rates is a major goal of paleobiology. However, the possibility of coincident variation in the quality and completeness of the fossil record makes the identification of such patterns particularly difficult. Previously, Nichols and Pollock (1983) proposed that capture-mark-recapture (CMR) models be adapted to address this problem. These models can be used to estimate both sampling and turnover rates, reducing the risk of confounding the two quantities. Since that time, theoretical advances have made possible the application of these tools to a much broader range of problems. This paper reviews those advances likely to be of greatest relevance in paleobiological studies. They include (1) joint estimation of per-taxon origination and extinction rates, (2) modeling sampling or turnover rates as explicit functions of causal variables, (3) ranking of alternative models according to their fit to the data, and (4) estimation of parameter values using multiple models. These are illustrated by application to an Ordovician database of benthic marine genera from key higher taxa. Robustness of these methods to violation of assumptions likely to be suspect in paleobiological studies further suggests that these models can make an important contribution to the quantitative study of macroevolutionary dynamics.

The Ordovician Radiation exhibited a global transition in dominance from the Cambrian evolutionary fauna (e.g., trilobites), to the Paleozoic and Modern faunas (e.g., articulate brachiopods and bivalve molluscs). Although its causes have yet to be determined definitively, the transition coincided with increased global tectonism. Erosion of source areas uplifted during orogenic activity increased the siliciclastic richness of marine substrates in many venues, and it has been hypothesized previously that higher taxa with affinities for siliciclastics diversified in association with these environmental changes, whereas higher taxa not exhibiting such affinities either failed to radiate or declined in diversity. Here, we provide an initial test of this substrate affinity hypothesis by evaluating the Ordovician affinities of trilobites and articulate brachiopods.

Our analyses—at the class level for both trilobites and articulate brachiopods, and at the order level for orthid and strophomenid brachiopods—were based on the affinities of constituent genera for siliciclastic, carbonate, and mixed siliciclastic/carbonate settings. Individual genus affinities are calculated with a database of genus occurrences encompassing nine Ordovician paleocontinents. Using these values, we developed a standardized relative affinity (SRA) metric to compare the propensities of higher taxa, and to assess changes in relative affinities of individual higher taxa from series to series.

A simple comparison of trilobites and articulate brachiopods for the Ordovician in aggregate does not appear to support the substrate affinity hypothesis: articulate brachiopods, which contributed increasingly to overall diversity through the period, exhibit an overall affinity for carbonates and an aversion to siliciclastics. However, a rather different view emerges when we consider the affinity trajectories of higher taxa through the period: articulate brachiopods exhibit a growing affinity for siliciclastics and a declining affinity for carbonates, whereas the opposite is the case among trilobites. Among constituent articulate brachiopod orders, the affinity trajectories of orthids and strophomenids mirror that of the class. Thus, the increasing dominance of articulate brachiopods in the Middle and Late Ordovician may have been linked to the affinity for siliciclastics of a diversifying subset of the group, but further investigation will be required to verify this claim.

During the Ordovician Radiation, domination of benthic marine communities shifted away from trilobites, toward articulate brachiopods, and, to a lesser degree, toward bivalves and gastropods. In this paper, we identify the patterns in origination and extinction probabilities that gave rise to these transitions. Using methods adapted from capture-mark-recapture (CMR) population studies, we estimate origination, extinction, and sampling probabilities jointly to avoid confounding patterns in turnover rates with temporal variation in the quality of the fossil record. Not surprisingly, higher extinction probabilities in trilobites relative to articulate brachiopods, bivalves, and gastropods were partly responsible for relative decreases in trilobite diversity. However, articulate brachiopods also had higher origination probabilities than trilobites, indicating that relative increases in articulate brachiopod diversity would have occurred even in the absence of between-class differences in extinction probabilities. This contrasts with inferences based on earlier Phanerozoic-scale, long-term averages of turnover probabilities, and it indicates that a major cause of this faunal transition has been overlooked.