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.

Three homogeneous models of species origination and extinction are used to assess the probability that ancestor-descendant pairs are preserved in the fossil record. In the model of cladogenetic budding, a species can persist after it branches and can therefore have multiple direct descendants. In the bifurcation model, a species branches to give rise to two distinct direct descendants, itself terminating in the process. In the model of phyletic transformation, a species gives rise to a single direct descendant without branching, itself terminating in the process. Assuming homogeneous preservation, even under pessimistic assumptions regarding the completeness of the fossil record, the probability of finding fossil ancestor-descendant pairs is not negligible. Even if all species of Phanerozoic marine invertebrates in the paleontologically important taxa had the same probability of preservation, on the order of 1%-10% or more of the known fossil species would be directly ancestral to other known fossil species. However, this is likely to be an underestimate, since the probability of finding ancestor-descendant pairs is enhanced by taxonomic, temporal, and spatial heterogeneities in preservation probability. Moreover, indirect genealogical relationships substantially increase the probability of finding ancestor-descendant pairs. The model of budding, the only one in which an ancestor can persist after a branching event, predicts that half or more of extant species have ancestors that are also extant. Thus, the question of how to recognize ancestor-descendant pairs must be carefully considered.

One of the most intriguing questions in community ecology remains unanswered: Are ecological communities open assemblages with each species reacting individually to environmental change, or are they integrated units consisting of multispecies assemblages acting in concert? I address this question for marine organisms by examining the taxonomic composition and diversity of Indo-Pacific reef coral communities that have undergone repeated global change between 125 and 30 Ka (thousand years before present).

Investigation of community constancy through time relies on two critical questions: (1) Are there significant differences in taxonomic composition among communities from different times? and if not, (2) Are the observed patterns in temporal similarity significantly different from expected patterns resulting from a random sampling of the available within-habitat species pool?

Constancy in taxonomic composition and species richness of Pleistocene reef coral assemblages is maintained through a 95-k.y. interval in the raised reef terraces of the Huon Peninsula, Papua New Guinea. Fossil reef coral assemblages show limited membership in species composition despite repeated exposure to marked fluctuations in sea level (up to 120 m) and sea-surface temperatures (up to 6°). During the 95-k.y. interval, the reefs experienced nine cycles of perturbation and subsequent reassembly with similar species composition. Spatial differences in reef coral species composition were greater among the three study sites than among reefs of different ages. Thus local environmental parameters associated with riverine and terrestrial sources had a greater influence on reef coral composition than global climate and sea level changes.

The ecological dynamics of reef communities from Papua New Guinea are in marked contrast to those of Quaternary terrestrial and level bottom marine communities which appear to show unlimited community membership on both larger and smaller time scales. Differences in community assembly among ecosystems mean either that coral reefs are fundamentally different or that different ecological patterns and processes are occurring at different temporal scales.

The rate and pattern of phenotypic evolution of the endemic land-snail Mandarina chichijimana in the oceanic Bonin Islands through 40,000 years were examined by using radiocarbon-dated fossil specimens. There are drastic variations in rates and patterns of changes detected. Some characters show irregular fluctuation within a restricted range. Other characters show a rapid shift from stasis in one state to stasis in an alternative state. Because of the isolation, the limited distributions, and the presence of transitional forms, these changes are regarded as genuine evolutionary transformations within a lineage. These findings suggest that phyletic evolution is essentially irregular and punctuated.

Principal components analysis of Upper Carboniferous (Pennsylvanian) ammonoids (all 117 genera), using 21 variables to measure shell geometry, sculpture and suture complexity, shows that following a sharp decline (∼30%) in generic diversity after the mid-Carboniferous boundary, seven morphotypes persisted throughout the Pennsylvanian (ca. 30 m.y.). Six of these were polyphyletically adopted at different times, while the seventh was monopolized by the prolecanitids, a group whose evolution accelerated during the Pennsylvanian and later gave rise to Mesozoic ammonoids. Innovations in suture geometry distinguished at least 17 of 39 (44%) Pennsylvanian ammonoid families. Average suture complexity increased almost threefold; this was achieved by various methods (lobe serration, insertion of umbilical elements, prong subdivision, lobe trifurcation, and secondary bifurcation), which were recurrent and crossed morphotype boundaries. The Pennsylvanian record supports suggestions that Paleozoic ammonoids were confined to a certain suite of basic shell geometries, showing preference for a limited number of sites in the spectrum of available morphospace. However, these morphic constraints did not, with one possible exception (the prolecanitids), control the emergence of increasing sutural complexity during the Pennsylvanian, which occurred among different lineages in all seven morphotypes.

The morphologic radiation of Early Jurassic ammonites following the near extinction at the end of the Triassic is analyzed from 436 species of 156 genera that form a representative sample of morphs occurring worldwide in the first three stages of the Jurassic (Hettangian, Sinemurian, Pliensbachian: 36 subzones, 24 m.y.). Morphologic diversity is analyzed independently of taxonomy by processing 18 shape parameters using multivariate analysis and clustering techniques. The morphospace thus defined indicates that morphs fall readily into two groups made up of four and five adjacent morpho-subsets. The temporal pattern of morphospace occupation in the 36 Lower Jurassic subzones displays diversification, depletion (sometimes total), and displacement of successive parts of the morphospace, reflecting a complex history in which morphologic radiation appears to be more than a process of diffusion. The history of the morphologic evolution is tentatively related to sea-level changes and there is a suggestion that morphologic diversity increases during second-order transgressive periods.

Heterochrony, change in developmental rate and timing, is widely recognized as an agent of evolutionary change. Heterotopy, evolutionary change in spatial patterning of development, is less widely known or understood. Although Haeckel coined the term as a complement to heterochrony in 1866, few studies have detected heterotopy or even considered the possibility that it might play a role in morphological evolution. We here review the roles of heterochrony and heterotopy in evolution and discuss how they can be detected. Heterochrony is of interest in part because it can produce novelties constrained along ancestral ontogenies, and hence result in parallelism between ontogeny and phylogeny. Heterotopy can produce new morphologies along trajectories different from those that generated the forms of ancestors. We argue that the study of heterochrony has been bound to an analytical formalism that virtually precludes the recognition of heterotopy, so we provide a new framework for the construction of ontogenetic trajectories and illustrate their analysis in a phylogenetic context. The study of development of form needs tools that capture not only rates of development but the space in which the changes are manifest. The framework outlined here provides tools applicable to both. When appropriate tools are used and the necessary steps are taken, a more comprehensive interpretation of evolutionary change in development becomes possible. We suspect that there will be very few cases of change solely in developmental rate and timing or change solely in spatial patterning; most ontogenies evolve by changes of spatiotemporal pattern.

Size and shape are analyzed for Pliocene lineages of the rodent genus Stephanomys Schaub 1938. Previous phylogenetic studies were based mainly on size variation and descriptive comparisons, without any attempt to quantify shape changes. Hence, on the basis of regular size increase, Stephanomys has been considered a prime example of phyletic gradualism. In order to quantify morphological variation within the lineage, a method for analyzing complex outlines, the elliptic Fourier transform, was applied to tooth contour (upper and lower first molars). It was then possible to compare evolution in size, estimated by tooth area, as well as evolution of shape, represented by Fourier coefficients.

While size seems to change gradually through time, morphology gives a rather discontinuous evolutionary pattern for both the upper and lower molar. Such a discrepancy between the evolution of size and shape of a single structure suggests that different genetic determinisms and mechanical constraints may act on size and shape. Hence it may be misleading to infer generalized evolutionary processes from either size or shape alone.

The evolutionary origin of Morozovella angulata from its immediate ancestor, Praemurica uncinata, is preserved in Paleocene sediments from the Gulf of Mexico. This event represents the beginning of the morozovellid radiation and marks the first appearance of keeled planktonic foraminifera after the Cretaceous/Tertiary extinction. Parallel biometric and isotopic analyses were performed on size-segregated specimens from a succession of stratigraphic horizons. The biometric data reveal a temporal pattern of variation consistent with paedomorphosis. The appearance of angulose juvenile chambers in the otherwise rounded ancestral form (Praemurica uncinata) results in an allometry that becomes more pronounced upsection. At the origin of M. angulata, the juvenile morphology of the ancestor is retained throughout the entire ontogeny. Isotopic analysis of this sequence reveals the gradual acquisition of an increasingly heavy adult δ13C signal relative to that of the juvenile, while the δ18O data display no temporal or size-related trends. The temporal increase seen in the slope of the δ13C/size relationship may reflect the evolution of an increased dependency on photosymbionts.

Oxygen and carbon isotopic analyses have been conducted on Miocene to Pliocene (6.0 to 2.9 Ma) members of the gradually evolving, deep-dwelling planktonic foraminiferal clade, Globoconella, in temperate waters of the southwest Pacific, Deep Sea Drilling Project (DSDP) Site 593. In the late Miocene the clade began with Globoconella conoidea, and continued through G. conomiozea, G. sphericomiozea, and G. puncticulata to the extant form G. inflata. Isotopic analyses were performed on ancestor-descendant species within the clade to determine if isotopic differences exist between these species which would, in turn, suggest depth and/or seasonal habitat differences and perhaps segregation, as well as ecological changes in the clade. Isotopic analyses were also conducted on the relatively shallow-dwelling planktonic foraminifer Orbulina universa and the benthic form Cibicidoides wuellerstorfi to determine if any relationships exist between the evolution of Globoconella and paleoceanographic/paleoclimatic change.

Small (usually 0.1–0.15 ‰ but up to 0.3 ‰) oxygen isotopic differences exist between ancestor and descendant forms that we believe represent small (∼1°) temperature differences. These temperature differences are inferred to indicate depth and/or seasonal habitat differences and possible segregation between the species during the gradual evolution. The largest differences in oxygen isotopic values occur between ancestor and descendant forms during the most conspicuous morphological transition within the clade near the Miocene/Pliocene boundary. During this interval, the clade underwent a transformation from conical to spherical forms and there was a loss of the keel. No consistent differences were observed between ancestor and descendant carbon isotopic values.

Both morphological and ecological evolution appear to have been associated with paleoceanographic/paleoclimatic changes. Intervals marked by warming of surface-to-upper intermediate waters are associated with evolution of forms with a spherical test and inferred adaptation to cooler waters relative to ancestral forms. We propose two alternative models for the evolution of the Globoconella clade. In the first model, we assume that depth and/or seasonal segregation between ancestor and descendant forms provided a partial barrier to gene flow and that evolution resulted from genetic drift and/or differential selective pressures acting on each morphotype. In the second model, we assume that coeval members of Globoconella formed a vertical and/or seasonal morphocline in the water column and that segregation did not provide an effective barrier to gene flow. Evolution proceeded as directional selection acted on morphotypes of Globoconella inhabiting selectively advantageous positions in the water column.

It has long been suspected that trends in global marine biodiversity calibrated for the Phanerozoic may be affected by sampling problems. However, this possibility has not been evaluated definitively, and raw diversity trends are generally accepted at face value in macroevolutionary investigations. Here, we analyze a global-scale sample of fossil occurrences that allows us to determine directly the effects of sample size on the calibration of what is generally thought to be among the most significant global biodiversity increases in the history of life: the Ordovician Radiation. Utilizing a composite database that includes trilobites, brachiopods, and three classes of molluscs, we conduct rarefaction analyses to demonstrate that the diversification trajectory for the Radiation was considerably different than suggested by raw diversity time-series. Our analyses suggest that a substantial portion of the increase recognized in raw diversity depictions for the last three Ordovician epochs (the Llandeilian, Caradocian, and Ashgillian) is a consequence of increased sample size of the preserved and catalogued fossil record. We also use biometric data for a global sample of Ordovician trilobites, along with methods of measuring morphological diversity that are not biased by sample size, to show that morphological diversification in this major clade had leveled off by the Llanvirnian. The discordance between raw diversity depictions and more robust taxonomic and morphological diversity metrics suggests that sampling effects may strongly influence our perception of biodiversity trends throughout the Phanerozoic.