Nature's discontinuities occur both in the hierarchical structuring of genealogical individuals and in the distinct processes operating at different scales of time, here called tiers. Conventional evolutionary theory denies this structuring and attempts to render the larger scales as simple extrapolation from (or reduction to) the familiar and immediate—the struggle among organisms at ecological moments (conventional individuals at the first tier). I propose that we consider distinct processes at three separable tiers of time: ecological moments, normal geological time (trends during millions of years), and periodic mass extinctions.

I designate as “the paradox of the first tier” our failure to find progress in life's history, when conventional theory (first tier processes acting on organisms) expects it as a consequence of competition under Darwin's metaphor of the wedge. I suggest a resolution of the paradox: whatever accumulates at the first tier is sufficiently reversed, undone, or overriden by processes of the higher tiers. In particular, punctuated equilibrium at the second tier produces trends for suites of reasons unrelated to the adaptive benefits of organisms (conventional progress). Mass extinction at the third tier, a recurring process now recognized as more frequent, more rapid, more intense, and more different than we had imagined, works by different rules and may undo whatever the lower tiers had accumulated.

For some higher taxa, species can be identified in the fossil record with a high degree of reliability. The great geological durations of species indicate that phyletic evolution is normally so slow that little change occurs within a lineage during 105–107 generations. Failure to recognize sibling species in the fossil record has no bearing on this conclusion because they embody virtually no morphological change. Although slowness is the rule, we have no more precise assessment of morphological rates of phyletic evolution for any major taxon. Morphological data that have been assembled to assess rates of phyletic evolution have been meager, unrepresentative, and predominantly reflective of nothing more than body size. Net selection pressures within long segments of phylogeny—even ones that embrace large amounts of evolution—are infinitesimal and seemingly unsustainable against random fluctuations. This suggests that natural selection operates in a highly episodic fashion.

Rates of adaptive radiation and extinction at the species level can be estimated for many taxa and, from them, rates of speciation in adaptive radiation. Species selection should universally tend to increase rate of speciation and decrease rate of extinction, yet these rates are positively correlated in the animal world, apparently because they are linked by common controls: both rate of speciation and rate of extinction seem to increase with level of stereotypical behavior and to decrease with dispersal ability. Only a few “supertaxa” have been able to combine high rates of speciation with moderate rates of extinction.

Morphological continuity in the fossil record is the principal evidence favoring evolution as a historical explanation for the diversity of life. Continuity is usually discussed on scales broader than the species level. Patterns of morphological variation characteristic of living species are useful in recognizing species on time planes in the fossil record, but the fossil record is rarely complete enough temporally or geographically to preserve more than a fraction of species living in a given interval. Transitions between known species are even rarer. Where transitions are preserved, new species appear to arise through anagenesis (transformation of an ancestral stock producing a modified descendant) and through cladogenesis (subdivision of an ancestral lineage where one or more descendants differ from the ancestral stock). Evolutionary species are often necessarily bounded arbitrarily in the dimension of time.

Orthogenesis and punctuated equilibrium lie at opposite poles in a spectrum of speciation modes. Orthogenesis, highly constrained anagenesis, is probably rare. Cladogenesis appears to differ little from anagenesis once ancestral stocks are segregated. Limited evidence suggests that morphological differentiation during cladogenesis postdates genetic isolation. Hence punctuated equilibrium may be rare as well. Patterns of gradual change over time indicate that morphological evolution is reasonably viewed as continuous within and between species. Rates of evolution vary greatly (continuity does not require constancy). Rate distributions are truncated and biased by limits of stratigraphic completeness and time resolution: moderate to high rates of morphological evolution and species turnover are rarely recorded by fossils. Species durations are poorly characterized, but they appear to be so variable that there is no suggestion of periodicity. Species longevity is unpredictable. The episodic nature of faunal turnover suggests that extrinsic environmental factors rather than intrinsic homeostatic factors govern evolution at the species level.

The evolutionary pattern of speciation and extinction in any biologic group may be described by a variety of mathematical models. These models provide a framework for describing the history of taxonomic diversity (clade shape) and other aspects of larger evolutionary patterns. The simplest model assumes time homogeneity: that is, speciation and extinction probabilities are constant through time and within taxonomic groups. In some cases the homogeneous model provides a good fit to real world paleontological data, but in other cases the model serves only as a null hypothesis that must be rejected before more complex models can be applied. In cases where the homogeneous model does not fit the data, time-inhomogeneous models can be formulated that specify change, regular or episodic, in speciation and extinction probabilities. An appendix provides a list of the most useful equations based on the homogeneous model.

Problems of taphonomy and sampling adequacy hinder direct evolutionary interpretations of pattern in the Precambrian paleontological record; however, molecular studies of microbial phylogeny and comparative physiological and ecological investigations of living microorganisms can be combined with geological research to establish patterns of early evolution. The Late Proterozoic record of planktonic algae resembles those of Phanerozoic plants, animals, and microplankton in its patterns of diversification and turnover, as well as in the importance of major extinction events in shaping the course of evolution. Late Proterozoic eukaryotes thus appear to be discussable in terms of the macroevolutionary issues that have become central to Phanerozoic paleobiology. In contrast, evolutionary patterns in Precambrian prokaryotes appear to be different from those of plants and animals, a possible consequence of their differing systems of genetic organization and recombination.

Systematics, ostensibly the “old” paleontology, actually plays a central and crucial role in modern paleobiology. We argue that a revised ontology has recently clarified the nature of species and has expressly added monophyletic groups to the roster of spatiotemporally bounded entities—“individuals”—that are now seen as participants in the evolutionary process. Systematics is the study of species and monophyletic taxa, and fossils alone provide the data on the temporal boundedness of such taxa.

Cladistics (phylogenetic systematics) is explicitly geared to the recognition of monophyletic taxa. We review aspects of the core problem of character analysis in systematics, particularly addressing the still contended issue of the seemingly competitive claims of three methodologies: out-group comparison, comparative ontogeny, and the “paleontological method.” We find that these methods overlap in their basic assumptions to a significant extent, yet each retains a characteristic and distinctive flavor. They are not all “the same,” nor are they always “complementary”—and no one method is superior to the others in all circumstances.

Far from being the Victorian symbol of a moribund science, systematics lies at the very heart of modern paleobiological research, providing the central data for paleobiology's truly unique contribution, both real and potential, to evolutionary biology in general.

In the past decade paleobiologists have applied the techniques of both ecological and historical biogeography, although vicariance/cladistic approaches have as yet had minimal impact. The traditional focus of paleobiogeographic study has been the province, a statistical entity defined by clusters of range endpoints of individual taxa. The study of such provinces has been useful in inferring past continental positions (although ambiguities remain that must be resolved using independent geological criteria) and in understanding the role of past global geographies in regulating biotic diversity through changes in the numbers and extent of provinces. This approach can be complemented by the treatment of geographic ranges of taxa as irreducible or emergent traits with far-reaching evolutionary effects upward and downward within a genealogical hierarchy. Temperature tolerances in benthic marine organisms appear to be by-products of selection for enzyme structures imparting favorable activity levels within the normal temperature range rather than direct products of selection for resistance to temperature extremes. Thus geographic range endpoints, which are also influenced by dispersal capability and the resulting scale of gene flow among disjunct populations, are not direct products of selection. However, the magnitudes of geographic ranges of species and clades behave as emergent properties and significantly influence taxonomic survivorship during background and mass extinctions in ways that are not extrapolations of effects at lower hierarchical levels. Biogeography shapes macroevolutionary patterns of origination and extinction during times of normal, background extinction and mass extinction. Preferential extinction among regions or among endemic rather than widespread clades can result in strong biases in the nature of the survivors of mass extinctions, with taxa being lost not because of selection against attributes of individual organisms but because of higher-order patterns of geographic selectivity.

In the past decade, evolutionary paleoecology has shifted away from corroborative research of the “me-too-ecology” type toward its proper domain—the evolutionary consequences of ecological properties, roles, and strategies at the individual, population, community, and species levels. The science of evolutionary paleoecology tests for linkage between a species' ecology and its macroevolutionary history. Do the ecological characters of species within clades influence differential rate dynamics, particularly rates of faunal turnover and diversification? Intellectual coequality, once hampered by the misunderstanding that the role of paleoecology is to find examples of past ecology imperfectly entombed in the fossil record, is strengthened by the increasing number of evolutionary ecologists who have called for explicit paleontological contributions to resolve theoretical issues. The fossil record provides a necessary perspective to an understanding of process.

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.

Many questions have emerged recently regarding the importance and methodology of analysis of adaptation. Divergent views reflect both problems of definition and more substantive issues of interpretation. Defining the state of adaptation in terms of its contribution to current fitness, rather than origin by natural selection, is essential if natural selection is to be considered an explanation of adaptation. The context dependency and relativity of fitness apply also to adaptation. Design criteria are essential components of adaptation, but only to the extent that they are subsumed as elements of the causal interactions determining relative reproductive potential. The local, relational, contingent character of adaptation supports only limited reference to improvement. Most long-term patterns of change can be better described as diffusion within a structured design-space than as progressive improvement of design. The analysis of adaptation is part of a broader inquiry into the processes and constraints that control form and the history of changing form. It offers one perspective on how organisms operate on ecological time scales and how their configurations might be maintained or transformed over evolutionary time. Hypotheses concerning adaptation are sometimes tested by reference to predictions concerning the central tendency or trend of some aspect of an anatomical-behavioral system. These can be interpreted with minimal reference to assumptions of optimality if the analysis is viewed in terms of Bayesian inference. However, an alternative and frequently preferable approach to testing relies on limit-oriented predictions. Analysis of adaptation can be visualized as inferring the pattern and nature of interactions comprising the causal plexus that determines fitness. A comprehensive understanding of form and form-change requires that this be integrated with the perspective offered by studies of development, genetics, phylogenetic history, and external perturbations acting on the system.