Evolutionary change during the interval in which a fossil sample accumulates will inflate the variance of that sample relative to the population-level standing variation. If this effect is widespread and severe, paleontological samples will not provide reliable estimates of population variation. Although the few published studies conducted to test this possibility have found similar levels of variation in samples differing greatly in temporal acuity, the paucity of case studies prevents assessing the generality of this pattern. In this paper, two independent, literature-based approaches are used to greatly expand the data available to address this issue. The first approach compares morphometric variability in Quaternary mammal samples with samples from related modern populations. The second approach artificially lumps separate samples from evolving lineages and calculates the variance effects of this analytical time-averaging. Both approaches yield consistent results indicating that variance observed in time-averaged samples is typically only slightly inflated (approximately 5%) relative to population-level values. This finding suggests that rates of evolution are typically slow when scaled to within-population variation, providing support for relative stasis as the dominant mode of within-lineage evolution. An important practical consequence of these findings is that time-averaged fossil samples generally show trait variances and covariances that are similar to population-level parameters, which has been an important but implicit assumption in many paleontological studies of phenotypic variation.

Although the causes of mass extinctions have been studied in detail, recoveries have received little attention until recently. In this study, I examine the influence of extinction versus recovery intervals on ecological patterns across the end-Cretaceous (K/T) event in veneroid bivalves. Systematic and stratigraphic data were collected for 140 subgenera of veneroids, ranging from the Late Cretaceous through Oligocene of North America and Europe. Morphological data were collected for 1236 specimens representing 101 subgenera. Extinction selectivity and differential recovery were assessed with respect to morphology, and by extension, burrowing ecology in these bivalves. Eighty-one percent of veneroid subgenera went extinct at the K/T and diversity did not return to preextinction levels until 12 million years later. Despite the severity of the K/T extinction, I found little evidence of morphological or ecological selectivity. The K/T recovery, in contrast, was strongly biased toward taxa with deep pallial sinuses (i.e., toward deeper burrowers). For veneroids, the morphological and ecological effects of the K/T event are not tied to the extinction itself, but to the recovery that followed. The K/T recovery initiated a trend toward deeper burrowing that helped to establish veneroids as one of the most abundant and successful groups of modern marine bivalves.

In post-Cambrian time, five events—the end-Ordovician, end-Frasnian in the Late Devonian, end-Permian, end-Triassic, and end-Cretaceous—are commonly grouped as the “big five” global intervals of mass extinction. Plotted by magnitude, extinction intensities for all Phanerozoic substages show a continuous distribution, with the five traditionally recognized mass extinctions located in the upper tail. Plotted by time, however, proportional extinctions clearly divide the Phanerozoic Eon into six stratigraphically coherent intervals of alternating high and low extinction intensity. These stratigraphic neighborhoods provide a temporal context for evaluating the intensity of extinction during the “big five” events. Compared with other stages and substages in the same neighborhood, only the end-Ordovician, end-Permian, and end-Cretaceous extinction intensities appear as outliers. Moreover, when origination and extinction are considered together, only these three of the “big five” events appear to have been generated exclusively by elevated extinction. Low origination contributed more than high extinction to the marked loss of diversity in the late Frasnian and at the end of the Triassic. Therefore, whereas the “big five” events are clearly times when diversity suffered mass depletion, only those at the end of the Ordovician, Permian, and Cretaceous periods unequivocally qualify as globally distinct mass extinctions. Each of the three has a unique pattern of extinction, and the diversity dynamics of these events differ, as well, from the other two major diversity depletions. As mass depletions of diversity have no common effect, common causation seems unlikely.

The relative proportions of Sepkoski's Cambrian, Paleozoic, and Modern evolutionary faunas in Cambrian–Ordovician benthic marine assemblages from mixed carbonate-shale and shale lithofacies deposited below normal wave base (herein, deep subtidal) in North America are strongly positively correlated with global relative genus richness in Sepkoski's global compendium. The correlation between local and global faunal proportions is robust regardless of how proportions are calculated, including when local proportions are based on number of specimens. Like the global pattern, the transition between the Cambrian and Paleozoic evolutionary faunas appears to occur gradually, in that Lower Arenigian (Ibexian) deep subtidal assemblages contain approximately equal proportions of Cambrian and Paleozoic faunal elements. In agreement with previous work, an onshore-offshore differentiation of faunas is evident both within Ordovician deep subtidal communities and across a larger environmental gradient.

Within the deep subtidal assemblages studied here, the Paleozoic fauna tends to have a greater proportion of individuals for a given proportion of genera than the Cambrian fauna, although both tend to accrue genera at similar rates with increasing relative abundance. The Modern evolutionary fauna appears to accrue genera more rapidly with increasing local relative abundance. The extent to which these differences reflect ecological factors such as biomass, metabolic requirements or larval recruitment patterns, taxonomic practices stemming from variable morphospace saturation, or taphonomy-related counting biases remains unclear, but it suggests the possibility that Sepkoski's evolutionary faunas may share ecological characteristics that influence both local relative abundance and global rates of taxonomic evolution.

Ecological polarities are theoretical roles of organisms, reflected in evolved behaviors and characters. Ecological polarity includes what has been called life history strategies, functional types, habitat templates, and r and K selection. Three common ecological polarities emphasize reproduction, agonistic behavior, and withstanding harsh conditions. Such organisms can be called breeders, competitors, and tolerators, respectively. Polarities of ecospace can be envisaged graphically as apices of a triangular diagram within which each species occupies a particular region. Quantitative studies of ecological polarities rely on proxy measurements of specific morphological features, such as the proportional functional area of canines (for competitors), molars (for tolerators), and incisors (for breeders) among mammals. Such proxy measures of morphospace or chemospace are traditionally judged successful by the degree to which they reveal adaptive differences between species. This approach to approximating ecological polarity is here applied to modern soils, plants, snails, and mammals, as well as to comparable fossils of the Clarno and John Day Formations (Eocene and Oligocene) of central Oregon. An advantage of this approach is that adaptive similarities can be tested quantitatively, as shown here for Oligocene oaks and maples, rather than assuming that extinct species were comparable to related living plants. Paleosols that supported fossil creatures provide useful supporting evidence of past selection pressures for ecologically significant adaptations. Degree of hardship can also be quantified from paleosol features. For example, fossil snails had narrower apertures in paleosols of drier climates as revealed by their shallower calcic horizons, and leaves of extinct relatives of Meliosma and Oreomunnea were sclerophyllous in paleosols showing evidence of waterlogging, nutrient-deficiency, and metal toxicity. Evolutionary trends of ecological specialization revealed by this approach include molarization (interpreted as evolution toward the tolerator pole) in ungulates. Adaptive breakthroughs that initiated evolutionary radiations also can be reassessed by using these approximations of ecospace, for example, the convergent evolution by bears of degree of caninization previously evolved in an extinct creodont (Hemipsalodon). Ecological polarities provide new concepts and metrics for ordering morphological, chemical, and ecological characters of fossil and modern organisms, and for reassessing evolutionary trends.

The compactness profile of femoral cross-sections and body size of 105 specimens of 46 species of lissamphibians was studied to assess the effect of lifestyle (aquatic, amphibious, or terrestrial). Several tests that incorporate phylogenetic information (permutational multiple linear regression incorporating phylogenetic distances, logistic regression using phylogenetic weighting, concentrated-changes tests) show that the return to a fully aquatic lifestyle is associated with an increase in the compactness of the femur and an increase in body size. However, amphibious taxa cannot be distinguished from terrestrial ones solely on the basis of size or compactness. Body size and compactness profile parameters of the femur exhibit a phylogenetic signal (i.e., closely related taxa tend to be more similar to each other than to distantly related taxa).

Mathematical equations obtained from our data by using logistic regression with phylogenetic weighting are used to infer the lifestyle of four early stegocephalians. The results are generally congruent with prevailing paleontological interpretations, which suggests that this method could be applied to infer the lifestyle of early taxa whose lifestyle is poorly understood.

The phylogenetic relationships of fossil and extant members of the primate superfamily Hominoidea are reassessed by using both conventional (morphological) cladistic and stratocladistic (incorporating morphological and temporal data) techniques. The cladistic analysis recovers four most parsimonious cladograms that distinguish postcranially primitive (“archaic”) and derived (“modern”) hominoid clades in the earliest Miocene of East Africa and supports distinct hominine and pongine clades. However, the relationships among the pongines and hominine clades and other Eurasian hominoids remain ambiguous and there is weak support (Bremer decay indices, reduced consensus, and bootstrap proportions) for several other parts of the proposed phylogeny.

An examination of the partitioning of homoplasy across the two major hominoid clades recovered in the cladistic analysis indicates that the majority of the observed homoplasy resides in the postcranially derived clade. An examination of the partitioning of homoplasy across anatomical regions indicates that dental characters display a significantly higher level of homoplasy than postcranial characters. A rarefaction analysis demonstrates that the higher homoplasy associated with the dental characters is not the result of sampling biases, indicating that postcranial skeletal characters are likely the more reliable phylogenetic indicators in the hominoids.

The branching order of the most parsimonious cladograms shows better than average congruence with the observed ordering of first appearances in the fossil record, implying that the hominoid fossil record is surprisingly good. As with morphologic parsimony debt, most of the stratigraphic parsimony debt in these cladograms is associated with the “modern” hominoid clade. A stratocladistic analysis of the data recovers a single most parsimonious phylogenetic tree with a different cladistic topology from the morphological cladogram. The most striking difference is the elimination of the postcranially primitive clade of hominoids in the early Miocene in favor of a pectinate succession of taxa. The relative position of the late-appearing taxon Oreopithecus is also altered in the stratocladistic hypothesis. Topological differences between the cladistic and stratocladistic hypotheses highlight two intervals of significant discord between the morphological and temporal data—the early Miocene of eastern Africa and the late Miocene of Eurasia. The first discrepancy is likely the result of poor preservation and morphological homoplasy in Morotopithecus, as the fossil record in the early Miocene of eastern Africa for the ingroup is rather good. The second discrepancy is likely the result of the unusual preservation conditions associated with the late Miocene hominoid Oreopithecus.

The quantification of disparity is an important aspect of recent macroevolutionary studies, and it is usually motivated by theoretical considerations about the pace of innovation and the filling of morphospace. In practice, varying protocols of data collection and analysis have rendered comparisons among studies difficult. The basic question remains, How sensitive is any given disparity signal to different aspects of sampling and data analysis? Here we explore this issue in the context of the radiation of the echinoid order Spatangoida during the Cretaceous. We compare patterns at the genus and species levels, with time subdivision into subepochs and into stages, and with morphological sampling based on landmarks, traditional morphometrics, and discrete characters. In terms of temporal scale, similarity of disparity pattern accrues despite a change in temporal resolution, and a general deceleration in morphological diversification is apparent. Different morphometric methods also produce similar signals. Both the landmark analysis and the discrete character analysis suggest relatively high early disparity, whereas the analysis based on traditional morphometrics records a much lower value. This difference appears to reflect primarily the measurement of different aspects of overall morphology. Disparity patterns are similar at both the genus and species levels. Moreover, inclusion or exclusion of the sister order Holasteroida and the stem group Disasteroida in the sampled morphospace did not affect proportional changes in spatangoid disparity. Similar results were found for spatangoid subclades vis-à-vis spatangoids as a whole. The relative robustness of these patterns implies that the choice of temporal scale, morphometric scheme, and taxonomic level may not affect broad trends in disparity and the representation of large-scale morphospace structure.

The study of ancient biodiversity trends is confounded by biases of the paleontologic record, but standardizing sampling intensity among time intervals can ameliorate sample-size biases. We show that several existing standardization methods are intimately linked to the spatial components of diversity (alpha, the within-assemblage diversity; and beta, the between-assemblage diversity). The subsampling curves generated by these methods can also be generated by various manipulations of alpha and beta, so that one can predict the responses of the methods to specific changes in alpha or beta diversity. The responses of the subsampling methods to changes in total diversity depend on whether measured alpha or measured beta diversity changed. Like biodiversity, sampling consists of a within-sample component (the number of specimens collected per locality) and a between-sample component (the number of localities). Several subsampling methods (rarefaction, OW, O²W) attempt to standardize sampling effort at both levels, although they use no direct information on the former. Instead, they alter sampling intensity at the beta level to compensate for perceived biases at the alpha level. We show that alpha and beta diversity are not so easily interchangeable and that the accuracy of the subsampling methods depends critically on the spatial characteristics of diversity in a data set. Current methods are calibrated only to the abundance-richness characteristics of individual collections, but the amount of beta diversity and the degree to which the rareness/commonness of taxa correlates among samples also strongly affect the accuracy of the subsampling methods. We offer new calibrations based on empirical data sets that account for these factors. Our findings do not support Alroy et al.'s (2001) tentative claim that the taxonomic radiation in the Cenozoic marine realm is an artifact of biased sampling intensity. Their diversity curves that most strongly contradict Sepkoski's traditional Phanerozoic curve are based on a method that overcorrects for local sample-size biases, whereas the remaining curves are either consistent with the traditional curve or ambiguous because of the limited temporal and taxonomic coverage of the analysis. Other factors may bias Sepkoski's curve, but there is insufficient evidence to claim that variations in sampling intensity are the major determinant of its long-term trajectory.