Issues of directionality in the history of life can be framed in terms of six major evolutionary steps, or megatrajectories (cf. Maynard Smith and Szathmáry 1995): (1) evolution from the origin of life to the last common ancestor of extant organisms, (2) the metabolic diversification of bacteria and archaea, (3) evolution of eukaryotic cells, (4) multicellularity, (5) the invasion of the land and (6) technological intelligence. Within each megatrajectory, overall diversification conforms to a pattern of increasing variance bounded by a right wall as well as one on the left. However, the expanding envelope of forms and physiologies also reflects—at least in part—directional evolution within clades. Each megatrajectory has introduced fundamentally new evolutionary entities that garner resources in new ways, resulting in an unambiguously directional pattern of increasing ecological complexity marked by expanding ecospace utilization. The sequential addition of megatrajectories adheres to logical rules of ecosystem function, providing a blueprint for evolution that may have been followed to varying degrees wherever life has arisen.

The study of evolution has increasingly incorporated considerations of history, scale, and hierarchy, in terms of both the origin of variation and the sorting of that variation. Although the macroevolutionary exploration of developmental genetics has just begun, considerable progress has been made in understanding the origin of evolutionary novelty in terms of the potential for coordinated morphological change and the potential for imposing uneven probabilities on different evolutionary directions. Global or whole-organism heterochrony, local heterochrony (affecting single structures, regions, or organ systems) and heterotopies (changes in the location of developmental events), and epigenetic mechanisms (which help to integrate the developing parts of an organism into a functional whole) together contribute to profound nonlinearities between genetic and morphologic change, by permitting the generation and accommodation of evolutionary novelties without pervasive, coordinated genetic changes; the limits of these developmental processes are poorly understood, however. The discordance across hierarchical levels in the production of evolutionary novelties through time, and among latitudes and environments, is an intriguing paleontological pattern whose explanation is controversial, in part because separating effects of genetics and ecology has proven difficult. At finer scales, species in the fossil record tend to be static over geologic time, although this stasis—to which there are gradualistic exceptions—generally appears to be underlain by extensive, nondirectional change rather than absolute invariance. Only a few studies have met the necessary protocols for the analysis of evolutionary tempo and mode at the species level, and so the distribution of evolutionary patterns among clades, environments, and modes of life remains poorly understood. Sorting among taxa is widely accepted in principle as an evolutionary mechanism, but detailed analyses are scarce; if geographic range or population density can be treated as traits above the organismic level, then the paleontological and macroecological literature abounds in potential raw material for such analyses. Even if taxon sorting operates on traits that are not emergent at the species level, the differential speciation and extinction rates can shape large-scale evolutionary patterns in ways that are not simple extrapolations from short-term evolution at the organismal level. Changes in origination and extinction rates can evidently be mediated by interactions with other clades, although such interactions need to be studied in a geographically explicit fashion before the relative roles of biotic and physical factors can be assessed. Incumbency effects are important at many scales, with the most dramatic manifestation being the postextinction diversifications that follow the removal of incumbents. However, mass extinctions are evolutionarily important not only for the removal of dominant taxa, which can occur according to rules that differ from those operating during times of lower extinction intensity, but also for the dramatic diversifications that follow upon the removal or depletion of incumbents. Mass extinctions do not entirely reset the evolutionary clock, so survivors can exhibit unbroken evolutionary continuity, trends that suffer setbacks but then resume, or failure to participate in the recovery.

The emergence of Phanerozoic global diversity as a central theme of investigation has resulted from a confluence of factors, including the assembly by several researchers of global taxonomic databases; the advent of computers, which permitted construction and analysis of global Phanerozoic diversity trajectories; and the recognition that Phanerozoic diversity trends are important bellwethers of the evolutionary processes that cause biotic transitions. Despite the enormous progress in the measurement and interpretation of Phanerozoic diversity over the past quarter century, much of which has been reported in Paleobiology, these studies have collectively generated at least as many new questions as they have answered—arguably the mark of an area of inquiry that continues to be vital. In this essay, I discuss several outstanding issues in the investigation of Phanerozoic diversity, ranging from the viability of literature-derived databases for investigating global diversity trends, to the biological significance of the myriad biotic transitions that have taken place throughout the Phanerozoic.

Mathematical modeling of cladogenesis and fossil preservation is used to explore the expected behavior of commonly used measures of taxonomic diversity and taxonomic rates with respect to interval length, quality of preservation, position of interval in a stratigraphic succession, and taxonomic rates themselves. Particular attention is focused on the independent estimation of origination and extinction rates. Modeling supports intuitive and empirical arguments that single-interval taxa, being especially sensitive to variation in preservation and interval length, produce many undesirable distortions of the fossil record. It may generally be preferable to base diversity and rate measures on estimated numbers of taxa extant at single points in time rather than to adjust conventional interval-based measures by discarding single-interval taxa.

A combination of modeling and empirical analysis of fossil genera supports two major trends in marine animal evolution. (1) The Phanerozoic decline in taxonomic rates is unlikely to be an artifact of secular improvement in the quality of the fossil record, a point that has been argued before on different grounds. (2) The post-Paleozoic rise in diversity may be exaggerated by the essentially complete knowledge of the living fauna, but this bias is not the principal cause of the pattern. The pattern may partly reflect a secular increase in preservation nevertheless.

Apparent temporal variation in taxonomic rates can be produced artificially by variation in preservation rate. Some empirical arguments suggest, however, that much of the short-term variation in taxonomic rates observed in the fossil record is real. (1) For marine animals as a whole, the quality of the fossil record of a higher taxon is not a good predictor of its apparent variability in taxonomic rates. (2) For a sample data set covering a cross-section of higher taxa in the Ordovician, most of the apparent variation in origination and extinction rates is not statistically attributable to independently measured variation in preservation rates. (3) Previous work has shown that standardized sampling to remove effects of variable preservation and sampling yields abundant temporal variation in estimated taxonomic rates. While modeling suggests which rate measures are likely to be most accurate in principle, the question of how best to capture true variation in taxonomic rates remains open.

Taphonomy plays diverse roles in paleobiology. These include assessing sample quality relevant to ecologic, biogeographic, and evolutionary questions, diagnosing the roles of various taphonomic agents, processes and circumstances in generating the sedimentary and fossil records, and reconstructing the dynamics of organic recycling over time as a part of Earth history. Major advances over the past 15 years have occurred in understanding (1) the controls on preservation, especially the ecology and biogeochemistry of soft-tissue preservation, and the dominance of biological versus physical agents in the destruction of remains from all major taxonomic groups (plants, invertebrates, vertebrates); (2) scales of spatial and temporal resolution, particularly the relatively minor role of out-of-habitat transport contrasted with the major effects of time-averaging; (3) quantitative compositional fidelity; that is, the degree to which different types of assemblages reflect the species composition and abundance of source faunas and floras; and (4) large-scale variations through time in preservational regimes (megabiases), caused by the evolution of new bodyplans and behavioral capabilities, and by broad-scale changes in climate, tectonics, and geochemistry of Earth surface systems. Paleobiological questions regarding major trends in biodiversity, major extinctions and recoveries, timing of cladogenesis and rates of evolution, and the role of environmental forcing in evolution all entail issues appropriate for taphonomic analysis, and a wide range of strategies are being developed to minimize the impact of sample incompleteness and bias. These include taphonomically robust metrics of paleontologic patterns, gap analysis, equalizing samples via rarefaction, inferences about preservation probability, isotaphonomic comparisons, taphonomic control taxa, and modeling of artificial fossil assemblages based on modern analogues. All of this work is yielding a more quantitative assessment of both the positive and negative aspects of paleobiological samples. Comparisons and syntheses of patterns across major groups and over a wider range of temporal and spatial scales present a challenging and exciting agenda for taphonomy in the coming decades.

As paleobiology continues to address an ever broader array of questions, it becomes increasingly important to interpret confidently the meaning of the pattern of fossil occurrences as found in outcrop. To this end, sequence stratigraphy is an important tool for paleobiologists because it predicts the distribution of unconformities, facies changes, and changes in sedimentation rate, all factors known from numerous previous studies to affect the quality of the fossil record. Computer simulations now make it possible not only to model sequence architecture within sedimentary basins, but also to model the occurrence of fossils within those basins. These models generate predictions regarding the stratigraphic distribution of first and last occurrences, changes in species abundance, changes in species morphology, and the distribution of gaps in fossil ranges. Although confirmation of some of these predictions has been found in field studies, the extent to which these predictions describe the fossil record in general is still unknown. If the predicted patterns of fossil occurrences are found to be widespread, it will suggest that a relatively simple model of fossil occurrences in outcrops could become a new tool for solving a wide array of paleobiologic and biostratigraphic problems. With such models, paleobiologists and biostratigraphers will be able to use model data to test the accuracy of newly developed methods of analysis.

The preservation of compounds of biological origin (nucleic acids, proteins, carbohydrates, lipids, and resistant biopolymers) in terrigenous fossils and the chemical and structural changes that they undergo during fossilization are discussed over three critical stratigraphic levels or “time slices.” The youngest of these is the archeological record (e.g., <10 k.y. b.p.), when organic matter from living organisms undergoes the preliminary stages of fossilization (certain classes of biomolecule are selectively preserved while others undergo rapid degradation). The second time slice is the Tertiary. Well-preserved fossils of this age retain diagenetically modified biomarkers and biopolymers for which a product–precursor relationship with the original biological materials can still be identified. The final time slice is the Carboniferous. Organic material of this age has generally undergone such extensive diagenetic degradation that only the most resistant biopolymers remain and these have undergone substantial modification. Trends through time in the taphonomy and utility of ancient biomolecules in terrigenous fossils affect their potential for studies that involve chemosystematic and environmental data.

The environmental and biotic history of the late Quaternary represents a critical junction between ecology, global change studies, and pre-Quaternary paleobiology. Late Quaternary records indicate the modes and mechanisms of environmental variation and biotic responses at timescales of 10¹–10⁴ years. Climatic changes of the late Quaternary have occurred continuously across a wide range of temporal scales, with the magnitude of change generally increasing with time span. Responses of terrestrial plant populations have ranged from tolerance in situ to moderate shifts in habitat to migration and/or extinction, depending on magnitudes and rates of environmental change. Species assemblages have been disaggregated and recombined, forming a changing array of vegetation patterns on the landscape. These patterns of change are characteristic of terrestrial plants and animals but may not be representative of all other life-forms or habitats. Complexity of response, particularly extent of species recombination, depends in part on the nature of the underlying environmental gradients and how they change through time. Environmental gradients in certain habitats may change in relatively simple fashion, allowing long-term persistence of species associations and spatial patterns. Consideration of late Quaternary climatic changes indicates that both the rate and magnitude of climatic changes anticipated for the coming century are unprecedented, presenting unique challenges to the biota of the planet.

The excellent fossil record of the past few million years, combined with the overwhelming similarity of the biota to extant species, provides an outstanding opportunity for understanding paleoecological and macroevolutionary patterns and processes within a rigorous biological framework. Unfortunately, this potential has not been fully exploited because of lack of well-sampled time series and adequate statistical analysis. Nevertheless, four basic patterns appear to be of general significance. First, a major pulse of extinction occurred 1–2 m.y. ago in many ocean basins, more or less coincident with the intensification of glaciation in the Northern Hemisphere. Rates of origination also increased greatly but were more variable in magnitude and timing. The fine-scale correlation of these evolutionary events with changes in climate is poorly understood. Similar events probably occurred on land but have not been tested adequately. Second, rates of origination and extinction in the oceans waned after the pulse of extinction, especially during the past 1 m.y. Thus, most marine species originated long before the Pleistocene under very different environmental circumstances, suggesting that they are “exapted” rather than adapted to their present ecological circumstances. The same may be true for many terrestrial groups, but not for the mammals or fresh-water fishes that have continued to undergo speciation throughout the Pleistocene. Third, community membership of late Pleistocene coral reef communities was more stable than expected by chance. These are the only paleoecological data adequate to test hypotheses of community stability, so that we do not know whether community structure involving other taxa or environments typically reflects more than the collective behavior of individual species distributions. Regardless, the strong evidence for nearly universal exaptation of ecological characteristics argues strongly against ideas of coevolution of species in communities. Finally, ecological communities were profoundly altered by human activities long before modern ecological studies began. Holocene paleontological, archeological, and historical data constitute the only ecological baseline for “pristine” ecological communities before significant human disturbance. Holocene records should be much more extensively used as a baseline for Recent ecological studies and for conservation and management.

Pelagic (open-ocean) species have enormous population sizes and broad, even global, distributions. These characteristics should damp rates of speciation in allopatric and vicariant evolutionary models since dispersal should swamp diverging populations and prevent divergence. Yet the fossil record suggests that rates of evolutionary turnover in pelagic organisms are often quite rapid, comparable to rates observed in much more highly fragmented terrestrial and shallow-marine environments. Furthermore, genetic and ecological studies increasingly suggest that species diversity is considerably higher in the pelagic realm than inferred from many morphological taxonomies.

Zoogeographic evidence suggests that ranges of many pelagic groups are much more limited by their ability to maintain viable populations than by any inability to disperse past tectonic and hydrographic barriers to population exchange. Freely dispersing pelagic taxa resemble airborne spores or wind-dispersed seeds that can drift almost anywhere but complete the entire life cycle only in favorable habitats. It seems likely that vicariant and allopatric models for speciation are far less important in pelagic evolution than sympatric or parapatric speciation in which dispersal is not limiting. Nevertheless, speciation can be quite rapid and involve cladogenesis even in cases where morphological data suggest gradual species transitions. Indeed, recent paleoecological and molecular studies increasingly suggest that classic examples of “phyletic gradualism” involve multiple, cryptic speciation events.

Paleoceanographic and climatic change seem to influence rates of turnover by modifying surface water masses and environmental gradients between them to create new habitats rather than by preventing dispersal. Changes in the vertical structure and seasonality of water masses may be particularly important since these can lead to changes in the depth and timing of reproduction. Long-distance dispersal may actually promote evolution by regularly carrying variants of a species across major oceanic fronts and exposing them to very different selection pressures than occur in their home range. High dispersal in pelagic taxa also implies that extinction should be difficult to achieve except though global perturbations that prevent populations from reestablishing themselves following local extinction. High rates of extinction in some pelagic groups suggests either that global perturbations are common, or that the species are much more narrowly adapted than we would infer from current taxonomies.

We compare refined data sets for Atlantic benthic foraminiferal oxygen isotope ratios and for North American mammalian diversity, faunal turnover, and body mass distributions. Each data set spans the late Paleocene through Pleistocene and has temporal resolution of 1.0 m.y.; the mammal data are restricted to western North America. We use the isotope data to compute five separate time series: oxygen isotope ratios at the midpoint of each 1.0-m.y. bin; changes in these ratios across bins; absolute values of these changes (= isotopic volatility); standard deviations of multiple isotope measurements within each bin; and standard deviations that have been detrended and corrected for serial correlation. For the mammals, we compute 12 different variables: standing diversity at the start of each bin; per-lineage origination and extinction rates; total turnover; net diversification; the absolute value of net diversification (= diversification volatility); change in proportional representation of major orders, as measured by a simple index and by a G-statistic; and the mean, standard deviation, skewness, and kurtosis of body mass. Simple and liberal statistical analyses fail to show any consistent relationship between any two isotope and mammalian time series, other than some unavoidable correlations between a few untransformed, highly autocorrelated time series like the raw isotope and mean body mass curves. Standard methods of detrending and differencing remove these correlations. Some of the major climate shifts indicated by oxygen isotope records do correspond to major ecological and evolutionary transitions in the mammalian biota, but the nature of these correspondences is unpredictable, and several other such transitions occur at times of relatively little global climate change. We conclude that given currently available climate records, we cannot show that the impact of climate change on the broad patterns of mammalian evolution involves linear forcings; instead, we see only the relatively unpredictable effects of a few major events. Over the scale of the whole Cenozoic, intrinsic, biotic factors like logistic diversity dynamics and within-lineage evolutionary trends seem to be far more important.

Attempts to model form-function relationships for fossil plants rely on the facts that the physiological and structural requirements for plant growth, survival, and reproductive success are remarkably similar for the majority of extant and extinct species regardless of phyletic affiliation and that most of these requirements can be quantified by means of comparatively simple mathematical expressions drawn directly from the physical and engineering sciences. Owing in part to the advent and rapid expansion of computer technologies, the number of fossil plant form-function models has burgeoned in the last two decades and encompasses every level of biological organization ranging from molecular self-assembly to ecological and evolutionary dynamics. This recent and expansive interest in modeling fossil plant form-function relationships is discussed in the context of the general philosophy of modeling past biological systems and how the reliability of models can be examined (i.e., direct experimental manipulation or observation of the system being modeled). This philosophy is illustrated and methods of validating models are critiqued in terms of four models drawn from the author's work (the quantification of wind-induced stem bending stresses, wind pollination efficiency of early Paleozoic ovulate reproductive structures, population dynamics and species extinction in monotypic and “mixed” communities, and the adaptive radiation of early vascular land plants). The assumptions and logical (mathematical) consequences (predictions) of each model are broadly outlined, and, in each case, the model is shown to be overly simplistic despite its ability to predict the general or particular behavior or operation of the system modeled. Nonetheless, these four models, which illustrate some of pros and cons of modeling fossil form-function relationships, are argued to be pedagogically useful because, like all models, they expose the internal logical consistency of our basic assumptions about how organic form and function interrelate.

Functional analysis of fossils is and should remain a key component of paleobiological research. Despite recently expressed doubts, conceptual and methodological developments over the past 25 years indicate that robust and testable claims about function can be produced. Functional statements can be made in at least three different hierarchical contexts, corresponding to the degree of structural information available, the position in the phylogenetic hierarchy, and the degree of anatomical specificity. The paradigm approach, which dominated thinking about function in the 1960s and 1970s, has been supplanted with a methodology based on biomechanics. Paleobiomechanics does not assume optimality in organismal design, but determines whether structures were capable of carrying out a given function. The paradigm approach can best be viewed as a way of generating, rather than testing, functional hypotheses. Hypotheses about function can also be developed and supported by well-corroborated phylogenetic arguments. Additional functional evidence can be derived from studies of trace fossils and of taphonomy. New computer techniques, including “Artificial Life” studies, have the potential for producing far more detailed ideas about function and mode of life than have been previously possible. Functional analysis remains the basis for studies of the history of adaptation. It is also an essential component of many paleoecological and paleoenvironmental studies.

The origin of evolutionary novelty involves changes across the biological hierarchy: from genes and cells to whole organisms and ecosystems. Understanding the mechanisms behind the establishment of new designs involves integrating scientific disciplines that use different data and, often, different means of testing hypotheses. Discoveries from both paleontology and developmental genetics have shed new light on the origin of morphological novelties. The genes that play a major role in establishing the primary axes of the body and appendages, and that regulate the expression of the genes that are responsible for initiating the making of structures such as eyes, or hearts, are highly conserved between phyla. This implies that it is not new genes, per se, that underlie much of morphological innovation, but that it is changes in when and where these and other genes are expressed that constitute the underlying mechanistic basis of morphological innovation. Gene duplication is also a source of developmental innovation, but it is possible that it is not the increased number of genes (and their subsequent divergence) that is most important in the evolution of new morphologies; rather it may be the duplication of their regulatory regions that provides the raw material for morphological novelty. Bridging the gap between microevolution and macroevolution will involve understanding the mechanisms behind the production of morphological variation. It appears that relatively few genetic changes may be responsible for most of the observed phenotypic differences between species, at least in some instances. In addition, advances in our understanding of the mechanistic basis of animal development offer the opportunity to deepen our insight into the nature of the Cambrian explosion. With the advent of whole-genome sequencing, we should see accelerated progress in understanding the relationship between the genotype, phenotype, and environment: post-genomics paleontology promises to be most exciting.

Tree-based paleobiological studies use inferred phylogenies as models to test hypotheses about macroevolution and the quality of the fossil record. Such studies raise two concerns. The first is how model trees might bias results. The second is testing hypotheses about parameters that affect tree inference.

Bias introduced by model trees is explored for tree-based assessments of the quality of the fossil record. Several nuisance parameters affect tree-based metrics, including consistency of sampling probability, rates of speciation/extinction, patterns of speciation, applied taxonomic philosophy, and assumed taxonomy. The first two factors affect probabilistic assessments of sampling, but also can be tested and accommodated in sophisticated probability tests. However, the final three parameters (and the assumption of a correct phylogeny) do not affect probabilistic assessments.

Often paleobiologists wish to test hypotheses such as rates of character change or rates of preservation. Assumptions about such parameters are necessary in simple phylogenetic methods, even if the assumptions are that rates are homogeneous or that sampling is irrelevant. Likelihood tests that evaluate phylogenies in light of stratigraphic data and/or alternative hypotheses of character evolution can reduce assumptions about unknowns by testing numerous unknowns simultaneously. Such tests have received numerous criticisms, largely based in philosophy. However, such criticisms are based on incorrect depictions of the logical structures of parsimony and likelihood, misunderstandings about when arguments are probabilistic (as opposed to Boolean), overly restrictive concepts of when data can test a hypothesis, and simply incorrect definitions of some terms.

Likelihood methods can test multiparameter hypotheses about phylogeny and character evolution (i.e., rates, independence, etc.). The best hypothesis positing a single rate of independent character change (with no variation among character states) is determined for each topology. Hypotheses about rate variation among characters or across phylogeny, character independence, and different patterns of state evolution then are examined until one finds the simplest (i.e., fewest varying parameters) hypothesis that cannot be rejected given knowledge of a more complicated hypothesis. This is repeated for alternative topologies. An example is presented using hyaenids. Two trees are contrasted, one of which requires the minimum necessary steps and the other of which requires at least seven additional steps. Given either tree, likelihood rejects fewer than three general rates of character change and also rejects the hypothesis of independence among the characters. However, hypotheses of changes in rates across the tree do not add substantially to the tree likelihood. The likelihoods of the trees given stratigraphic data also are determined. Both morphologic and stratigraphic data suggest that the multiparameter hypothesis including the parsimony tree is significantly less likely than the multiparameter hypothesis including a different tree.