The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.

Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics).

The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa.

Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.

A theoretical approach to the analysis of historical factors (Raup 1972) in evolutionary morphology is presented which addresses transformational hypotheses about structural systems. This (structural) approach to testing historical hypotheses about phylogenetic constraints on form and function and structural and functional versatility involves (1) the reconstruction of nested sets of structural features in monophyletic taxa, (2) the use of general or emergent organizational properties of structural and functional systems (as opposed to uniquely derived morphological features), and (3) the comparative examination of the consequences for structural and functional diversity of these general features in related monophyletic taxa.

Three examples of emergent organizational properties are considered: structural complexity, repetition of parts, and the decoupling of primitively constrained systems. Two classes of hypotheses about the evolution of design are proposed. Transformational hypotheses concern historical pathways of change in form as a consequence of general organizational features which are primitive for a lineage. Relational hypotheses involve correlations between structure-function networks primitive for a clade and morphological diversity both between and within terminal taxa. To the extent that transformational and relational hypotheses about form are corroborated, they provide evidence of underlying regularity in the transformation of organic design that may be a consequence of the hierarchical organization of structural and functional patterns in organisms.

Precise estimates of past temperatures are critical for understanding the evolution of organisms and the physical biosphere, and data from continental areas are an indispensable complement to the marine record of stable isotopes. Climate is considered to be a primary selective force on leaf morphology, and two widely used methods exist for estimating past mean annual temperatures from assemblages of fossil leaves. The first approach, Leaf Margin Analysis, is univariate, based on the positive correlation in modern forests between mean annual temperature and the proportion of species in a flora with untoothed leaf margins. The second approach, known as the Climate-Leaf Analysis Multivariate Program, is based on a modern data set that is multivariate. I argue here that the simpler, univariate approach will give paleotemperature estimates at least as precise as the multivariate method because (1) the temperature signal in the multivariate data set is dominated by the leaf-margin character; (2) the additional characters add minimal statistical precision and in practical use do not appear to improve the quality of the estimate; (3) the predictor samples in the univariate data set contain at least twice as many species as those in the multivariate data set; and (4) the presence of numerous sites in the multivariate data set that are both dry and extremely cold depresses temperature estimates for moist and nonfrigid paleofloras by about 2°C, unless the dry and cold sites are excluded from the predictor set.

New data from Western Hemisphere forests are used to test the univariate and multivariate methods and to compare observed vs. predicted error distributions for temperature estimates as a function of species richness. Leaf Margin Analysis provides excellent estimates of mean annual temperature for nine floral samples. Estimated temperatures given by 16 floral subsamples are very close both to actual temperatures and to the estimates from the samples. Temperature estimates based on the multivariate data set for four of the subsamples were generally less accurate than the estimates from Leaf Margin Analysis. Leaf-margin data from 45 transect collections demonstrate that sampling of low-diversity floras at extremely local scales can result in biased leaf-margin percentages because species abundance patterns are uneven. For climate analysis, both modern and fossil floras should be sampled over an area sufficient to minimize this bias and to maximize recovered species richness within a given climate.

The beginnings of biospheric evolution had far-reaching biogeochemical consequences for the related evolutions of atmosphere, hydrosphere, and lithosphere. Feedback to the sedimentary record from these several simultaneously interacting aspects of crustal evolution provides the evidence from which historical biogeology is reconstructed. The interpretation of that evidence, however, is beset with pitfalls. Both biogenicity and a primary origin need to be demonstrated, or confidence limits established for each supposed morphological and biochemical fossil. Relevance to biospheric or related evolutions must be critically evaluated for every geochemical and sedimentological anomaly.

Indirect evidence suggests primitive, oxygen-generating autotrophy by ∼ 3.8 × 109 years ago (3.8 Gyr or gigayears), while free O2 first began to accumulate only ∼ 2 Gyr ago. Various reduced substances in the atmosphere and in solution functioned as oxygen sinks, keeping photolytic and biogenic O2 at levels tolerable by primitive anaerobic and microaerophilic procaryotes.

The oldest demonstrably biogenic and certainly primary microstructures are procaryotes from ∼ or > 2 Gyr old strata around Lake Superior. Improved biologic O2 mediation, continued carbon segregation, and filling of O2 sinks initiated atmospheric O2 buildup, leading to an ozone screen ∼ or < 2 Gyr ago. Consequences were essential termination of banded iron formation, onset of red beds, and O2 shielding of anaerobic intracellular processes, heralding the eucaryotic cell.

Probable eucaryotes appear in ∼ 1.3 Gyr old rocks in California as large unicells and large-diameter, branched, septate filaments. Likely consequences of eucaryotic evolution were increased atmospheric O2, increased carbonate and sulfate ion, and the rise of sexuality. Meiosis had definitely evolved > 0.7 Gyr ago and probably > 1.3 Gyr ago, perhaps simultaneously with the mitosing cell. Whatever the timing, it completed the evolution of the eucaryotic heredity mechanism and foreshadowed (given sufficient free O2) the differentiation of tissues, organs, and advanced forms of life—with all their potential for biogeochemical feedback to sedimentary, diagenetic, and metallogenic processes. The first Metazoa appeared ∼ 0.7 Gyr ago. Being dependent on simple diffusion for O2, they lacked exoskeletons. The latter appeared, perhaps 0.6 Gyr ago, when increasing O2 levels favored the emergence of more advanced respiratory systems.

Observed stratigraphic ranges almost always underestimate true longevities. Strauss and Sadler (1987, 1989) provide a method for calculating confidence intervals on the endpoints of local stratigraphic ranges. Their method can also be applied to composite sections; confidence intervals may be placed on times of origin and extinction for entire species or lineages. Confidence interval sizes depend only on the length of the stratigraphic range and the number of fossil horizons. The technique's most important assumptions are that fossil horizons are distributed randomly and that collecting intensity has been uniform over the stratigraphic range. These assumptions are more difficult to test and less likely to be fulfilled for composite sections than for local sections.

Confidence intervals give useful baseline estimates of the incompleteness of the fossil record, even if the underlying assumptions cannot be tested. Confidence intervals, which can be very large, should be calculated when the fossil record is used to assess absolute rates of molecular or morphological evolution, especially for poorly preserved groups. Confidence intervals have other functions: to determine how rich the fossil record has to be before radiometric dating errors become the dominant source of error in estimated times of origin or extinction; to predict future fossil finds; to predict which species with fossil records should be extant; and to assess phylogenetic hypotheses and taxonomic assignments.

The biomass of marine consumers increased during the Phanerozoic. This is indicated by the increase in both fleshiness and average size of individuals of dominant organisms, coupled with the conservative estimate that dominant organisms in the Cenozoic are at least as abundant as those in the Paleozoic. As faunal dominants replaced one another during the Phanerozoic the general level of metabolic activity increased due to both increase in basal metabolism and increase in more energetic modes of life. This demonstrates that the expenditure of energy by marine consumers has increased with time as well. There is a time lag in the expansion of more energetic life habits from environmental settings known to have high food supply into regions expected to have lower rates of food supply (e.g., bivalves into offshore carbonate environments or deep burrowing deposit feeders into the full range of shelf environments), and a time lag in diversification of energetic modes of life (e.g., predation or deep burrowing deposit feeding) for long intervals after they first appeared. This suggests that the supply of food increased across the whole spectrum of marine habitats during the Phanerozoic. The great diversification of specialized predators especially suggests that biomass increase took place all the way down the food chain to the level of primary production. The development of plant life on land and the impact of land vegetation on stimulating productivity in coastal marine settings, coupled with the transfer of organic material and nutrients from coastal regions to the open ocean, and the increase through time in diversity and abundance of oceanic phytoplankton all point to increased productivity in the oceans through the Phanerozoic.

Owls are important consumers of small vertebrates, and because they regurgitate pellets rich in bone, they may be important potential contributors of the concentrated remains of small vertebrates to the fossil record. Owls of three sizes, the large great horned owl (Bubo virginianus), the medium-sized barn owl (Tyto alba), and the small screech owl (Otus asio), were fed a common diet of mice. The bony contents of the pellets were analyzed to determine the amount of bone loss by digestion, bone completeness, and sites of bone breakage. For all three species, only about half the number of bones ingested were recovered in the pellets. Mandibles and femora were most abundant, and pelves and scapulae were the least abundant. Screech owls broke 80% of the cranial and limb elements, barn owls only 30%. Skulls fared poorly in great horned and screech owl pellets, while barn owls returned 80% of the skulls intact, with only the caudal portion of the cranium damaged; barn owls also returned articulated strings of vertebrae and complete paws. These results provide a baseline for the recognition of owls as agents of accumulation of small bones in the fossil record and suggest that the actions of ancient predators may be revealed by species-specific patterns of bone destruction of an assemblage of fossil prey species.

The distribution of numbers of species and the median number of species from 386 selected fossil communities are tabulated for high stress, variable nearshore, and open marine environments during the Lower, Middle, and Upper Paleozoic, the Mesozoic and the Cenozoic. The number of species always increases from high stress to variable nearshore to open marine environments. Within-habitat variation in number of species is small for long intervals of the Phanerozoic. The median number of species in communities from high stress environments remains fixed at about 8 from the Cambrian to the Pleistocene. In open marine environments, the median is near 30 for the Middle and Upper Paleozoic and almost the same for the Mesozoic. Increases of 50% in median number of species between the Lower and Middle Paleozoic and 2 times between the Mesozoic and Cenozoic occur in open marine environments with parallel, but less pronounced, increases in variable nearshore environments. Conditions controlling overall within-habitat species richness changed at those times. These changes do not correlate directly with evolution of new major taxa, change in physical conditions, predation, space availability or oxygen supply. They may be related to changes in resource availability influenced by factors such as the developing terrestrial flora, to lag-time inherent in the evolutionary process of diversification, or to as yet undetermined factors. Although provinciality determines total species richness for the biosphere, the within-habitat data suggest that the number of marine invertebrate species in the world has increased since the Middle Paleozoic, contrary to Raup's (1976b) contention, but possibly only by about 4 times, not the order of magnitude or more suggested by Valentine (1970).

Calibrating levels of time resolution that are accessible in the fossil record is important in understanding what evolutionary phenomena can be profitably studied using fossils. A model for attritional bone assemblage formation in fluvial deposits, based on observations of taphonomic processes in modern environments, provides order-of-magnitude estimates for time intervals represented in single unit, ‘contemporaneous' vertebrate samples. In order to form units with adequate material for analysis of morphological variation or paleoecological associations, it appears that bones must be spatially concentrated or stratigraphically condensed by sedimentary processes or biological agencies. In many cases this means that significant periods of time will be represented by single unit assemblages. According to predictions from modern environments, carcasses contributed through normal attrition can accumulate in the soil to ‘fossiliferous' densities over time intervals of 102–104 yrs. Attritional channel assemblages include bones from three sources: floodplain land surfaces, floodplain deposits, and the active channel, and represent time intervals on the order of 102–104 yrs. Given additional limitations on the composition of the fossil sample imposed by circumstances of preservation, outcrop availability and collecting strategy, attritional fluvial assemblages probably can be resolved only to 103 years even under the best conditions. Time intervals represented by fossils are not necessarily the same as those represented by sedimentary events in fluvial systems because bones can continue to accumulate and may be concentrated during times of erosion or non-deposition. Fluvial vertebrate assemblages of comparable taphonomic history can be used to document evolutionary changes over periods longer than their finest level of time resolution. While they may not be applicable to questions of punctuated or gradual transitions over shorter time scales, the longer-term patterns should have their own evolutionary significance.

Living crocodilians and limbed lepidosaurs have a large caudofemoralis longus muscle passing from tail to femur. Anatomical and electromyographic data support the conclusion that the caudofemoralis is the principal femoral retractor and thus serves as the primary propulsive muscle of the hind limb. Osteological evidence of both origin and insertion indicates that a substantial caudofemoralis longus was present in archosaurs primitively and was retained in the clades Dinosauria and Theropoda. Derived theropods (e.g., ornithomimids, deinonychosaurs, Archaeopteryx and birds) exhibit features that indicate a reduction in caudofemoral musculature, including fewer caudal vertebrae, diminished caudal transverse processes, distal specialization of the tail, and loss of the fourth trochanter. This trend culminates in ornithurine birds, which have greatly reduced tails and either have a minute caudofemoralis longus or lack the muscle entirely.

As derived theropod dinosaurs, birds represent the best living model for reconstructing extinct nonavian theropods. Bipedal, digitigrade locomotion on fully erect limbs is an avian feature inherited from theropod ancestors. However, the primitive saurian mechanisms of balancing the body (with a large tail) and retracting the limb (with the caudofemoralis longus) were abandoned in the course of avian evolution. This strongly suggests that details of the orientation (subhorizontal femur) and movement (primarily knee flexion) of the hind limb in extant birds are more properly viewed as derived, uniquely avian conditions, rather than as retentions of an ancestral dinosaurian pattern. Although many characters often associated with extant birds appeared much earlier in theropod evolution, reconstructing the locomotion of all theropods as completely birdlike ignores a wealth of differences that characterize birds.

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy.

Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased. (3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

Two major ichnotypes of sauropod trackways have been described: “narrow-gauge,” in which both manus and pes prints approach or intersect the trackway midline, and “wide-gauge,” in which these prints are well apart from the midline. This gauge disparity could be the result of differences in behavior, body size, or morphology between the respective trackmakers. However, the biomechanics of locomotion in large terrestrial vertebrates suggest that sauropods were probably restricted in locomotor behavior, and the lack of systematic size differences between footprint gauges argues against body-size-related influences. We argue that skeletal morphology is responsible for gauge differences and integrate data from locomotor biomechanics and systematics with the track record to predict the hindlimb morphology of wide-gauge trackmakers. Broader foot stances in large, graviportal animals entail predictable mechanical consequences and hindlimb modifications. These could include outwardly angled femora, offset knee condyles, and a more eccentric femoral midshaft cross-section. A survey of sauropod hindlimb morphology reveals that these features are synapomorphies of titanosaurs, suggesting that they were the makers of wide-gauge trackways. The temporal and geographic distribution of titanosaurs is consistent with this hypothesis because wide-gauge trackways predominate during the Cretaceous and are found worldwide. Additional appendicular synapomorphies of titanosaurs are interpreted in light of identifying these animals as wide-gauge trackmakers. We suggest that titanosaurs may have used a bipedal stance more frequently than did other sauropods. These correlations between ichnology, biomechanics, and systematics imply that titanosaurs were unique among sauropods in having a more varied repertoire of locomotor habits.

Benthic ecologists have successfully applied rarefaction techniques to the problem of compensating for the effect of sample size on apparent species diversity (= species richness). The same method can be used in studies of diversity at higher taxonomic levels (families and orders) in the fossil record where samples represent world-wide distributions of species or genera over long periods of geologic time.

Application of rarefaction to several large samples of post-Paleozoic echinoids (totaling 7,911 species) confirms the utility of the method. Rarefaction shows that the observed increase in the number of echinoid families since the Paleozoic is real in the sense that it cannot be explained solely by the increase in numbers of preserved species. There has been no statistically significant increase in the number of families since mid-Cretaceous, however. At the order level, echinoid diversity may have been nearly constant since late Triassic or early Jurassic.

Two methods are discussed for assessing the contributions of subgroups to the morphological disparity of the larger group containing them. (1) Given an ordination of points representing specimens or species in morphological space, morphological disparity of the entire group is measured as the average squared distance of points from the centroid. The contribution that a subgroup makes to morphological disparity is measured as the average squared distance of its points from the overall centroid (not the subgroup centroid), weighted by the subgroup sample size relative to the total group sample size. Thus, morphological disparity of a group can be additively partitioned into the disparity components of its subgroups, and the relative contributions of these subgroups can be assessed quantitatively. (2) An alternative approach is to compare morphological disparity of a group to the disparity it would have if a certain subgroup were omitted. If the resulting disparity differs substantially from the original disparity, then the subgroup in question is considered to have a significant effect on morphological disparity. Because some subgroups are very centralized in morphological space, omitting them can cause an increase in morphological disparity when disparity is measured as the average dissimilarity among species. In general, relatively large subgroups that are located peripherally in morphospace make the greatest contributions to morphological disparity, and failure to sample smaller groups often has little effect on disparity estimates. The two methods are applied to morphological disparity in trilobites, partitioned at different levels in the taxonomic hierarchy. Results of the two methods are intuitively reasonable and largely in agreement, and point to the predominance of Early Cambrian olenelloids, Cambro-Ordovician Libristoma, Ordovician Asaphina and Cheirurina, Siluro-Devonian Phacopida and Phacopina, and Devonian Proetida.

In a nonhierarchical world, where selection on organisms regulated all nonrandom evolutionary change, the traditional equation of selection (a cause of sorting) with sorting itself (differential birth and death among varying organisms within a population) would rarely lead to error, even though the phenomena are logically distinct (for sorting is a simple description of differential “success,” and selection a causal process). But in a hierarchical world, with entities acting as evolutionary individuals (genes, organisms, and species among them) at several levels of ascending inclusion, sorting among entities at one level has a great range of potential causes. Direct selection upon entities themselves is but one possibility among many. This paper discusses why hierarchy demands that sorting and selection be disentangled. It then presents and illustrates an expanded taxonomy of sorting for a hierarchical world. For each of three levels (genes, organisms, and species), we show how sorting can arise from selection at the focal level itself, and as a consequence either of downward causation from processes acting on individuals at higher levels or upward causation from lower levels. We then discuss how hierarchy might illuminate a range of evolutionary questions based on both the logical structure of hierarchy and the historical pathways of its construction—for hierarchy is a property of nature, not only a conceptual scheme for organization.

A review of the processes required for exceptional preservation of soft-bodied fossils demonstrates that anoxia does not significantly inhibit decay and emphasizes the importance of early diagenetic mineralization. Early diagenesis is the principal factor amongst the complex processes leading to soft-part preservation. The development of a particular preservational mineral is controlled by rate of burial, amount of organic detritus, and salinity. A new causative classification of soft-bodied fossil biotas is presented based upon fossil mineralogy and mineral paragenesis.

Rarefaction is a method for comparing community diversities that has consistently been abused by paleoecologists: here its assumptions are clarified and advice given on its application. Rarefaction should be restricted to comparison of collections from communities that are taxonomically similar and from similar habitats: the collections should have been obtained by using standardised procedures. The rarefaction curve is a graph of the estimated species richness of sub-samples drawn from a collection, plotted against the size of sub-sample: it is a deterministic transform of the collection's species-abundance distribution. Although rarefaction curves can be compared statistically, it may be more efficient to compare the species-abundance distributions directly. Both types of comparison are discussed in detail.

Hierarchy is a central phenomenon of life. Yet it does not feature as such in traditional biological theory. The genealogical hierarchy is a nested organization of entities at ascending levels. There are phenomena common to all levels: (1) Entities such as genomic constituents, organisms, demes, and species are individuals. (2) They have aggregate characters (statistics of characters of subparts), but also emergent characters (arising from organization among subparts). Character variation changes by (3) introduction of novelty and (4) sorting by differential birth and death. Causation of introduction and sorting of variation at each level may be (5) upward from lower levels, (6) downward from higher levels, or (7) lodged at the focal level. The term “selection” applies to only one of the possible processes which cause sorting at a focal level. Neo-Darwinian explanations are too narrow, both in the levels (of genotypes and phenotypes) and in the directive process (selection) which are stressed. The acknowledgment of additional, hierarchical phenomena does not usually extend beyond lip service. We urge that interlevel causation should feature centrally in explanatory hypotheses of evolution. For instance, a ready explanation for divergence in populations is “selection of random mutants.” But upward causation from genome dynamics (or downward causation from the hierarchical organism) to the directed introduction of mutants may be more important in a given case. Similarly, a long-term trend is traditionally explained as additive evolution in populations. But sorting among species may be the cardinal factor, and the cause may not be species selection but upward causation from lower levels. A general theory of biology is a theory of hierarchical levels—how they arise and interact. This is a preliminary contribution mainly to the latter question.

Taphonomy established itself in paleontology primarily as a subdiscipline of paleoecology, but it has evolved into a much broader study of the ways in which preservation affects the fossil record. The past decade has seen a change in emphasis from descriptive taphonomic studies of fossil assemblages to more experimental, process-oriented investigations of necrolysis, stratification, and diagenesis of organic remains in modern environments. These actualistic studies are increasing the sophistication of taphonomic analysis in the fossil record by sharpening the diagnosis of bias in paleontological data and by providing a baseline for quantitative modeling of preservational patterns. The analysis of bias is also expanding into the evaluation of temporal resolution in the fossil record (sample acuity, stratigraphic completeness), and taphonomic research is thus contributing to broad-scale problems in evolution, biogeography, and biostratigraphy. In addition, taphonomic studies are providing new insights into paleoenvironmental reconstruction and into the direct paleobiological significance of post mortem processes such as the behavior of scavengers and the role of dead hardparts in structuring benthic communities. One of taphonomy's most promising new frontiers is comparative analysis applied to different taxonomic groups within assemblages and across environments, tectonic settings, and climatic regimes. All of this currently active research is contributing to a better understanding of the fossil record as the result of a dynamic, evolving, integrated system of biological and sedimentological processes that have both limited and enhanced knowledge of Earth history.