In this paper, we present detailed quantitative studies of evolutionary changes over all or part of the stratigraphic ranges of five fossil radiolarian species from Pacific deep-sea sediment cores. Each of these species shows some variation of a distinctive evolutionary pattern: increase in size of measured morphologic characters, preceded and/or followed by an interval during which little or no significant change occurred.

One of the species studied (Eucyrtidium matuyamai) was allopatrically differentiated from another (Eucyrtidium calvertense). The others (Calocycletta caepa, Pterocanium prismatium and Pseudocubus vema) underwent phyletic change within a single lineage. Those species undergoing phyletic change towards larger size maintained almost constant variability of shell size over long periods of time, including periods of both rapid and extremely slow evolution. This constancy of variability suggests that diminution of selection against larger size may have acted as a stimulus to size increase. In contrast, E. calvertense decreased in variability during evolution towards smaller shell size. We believe this decrease may be interpreted as the result of two factors: (1) strong selection against larger size apparently exerted on this species by its direct descendant, E. matuyamai, during the neosympatric phase of speciation and (2) continuation of previous selection against very much smaller size.

The pattern observed in nature has often served as a compelling motivation for seeking the underlying processes which are assumed to control the pattern. Spatial and temporal patterns of species diversity are the most commonly observed and described from the study of recent and paleocommunities. These patterns include those found within a local or discrete region such as succession and changes along an environmental gradient and interregional or global patterns such as latitudinal diversity gradients and comparisons of the deep-sea and the continental shelf faunas. Many hypotheses have been advanced to explain these patterns in terms of differences in the biology of species adapted to different or changing environments. However, a more simple explanation is possible: that these patterns do not result from any specific biologic processes.

We examine this possibility and show that succession can result from probabilistic immigration and local extinction of species, diversity gradients can result from probabilistic disturbance in naturally patchy environments, and that latitudinal gradients can be simply a function of the shape of the earth. As long as such diversity patterns can be explained independent of any specific biologic processes, they offer no test of the importance of these processes, either ecologically or evolutionarily.

The turnover-pulse hypothesis (TPH) makes explicit predictions concerning the potential responses of species to climate change, which is considered to be a major cause of faunal turnover (extinction, speciation, and migration). Previous studies have tested the TPH primarily by examining temporal correlations between turnover pulses and climatic events. It is rarely possible to dissect such correlations and observe turnover as it is occurring or to predict how different lineages will respond to climate change. Thus, whether climate change drives faunal turnover in the manner predicted by the TPH remains unclear. In this study, we test the underlying mechanics of the TPH using well-dated Quaternary ungulate records from southern Africa's Cape Floristic Region (CFR). Changes in sea level, vegetation, and topographic barriers across glacial-interglacial transitions in southern Africa caused shifts in habitat size and configuration, allowing us to generate specific predictions concerning the responses of ungulates characterized by different feeding habits and habitat preferences. Examples from the CFR show how climatically forced vegetation change and allopatry can drive turnover resulting from extinction and migration. Evidence for speciation is lacking, suggesting either that climate change does not cause speciation in these circumstances or that the evolutionary outcome of turnover is contingent on the nature and rate of climate change. Migrations and extinctions are observed in the CFR fossil record over geologically short time intervals, on the order of Milankovitch-scale climate oscillations. We propose that such climate oscillations could drive a steady and moderate level of faunal turnover over 104-year time scales, which would not be resolved in paleontological records spanning 105 years and longer. A turnover pulse, which is a marked increase in turnover relative to previous and subsequent time periods, requires additional, temporally constrained climatic forcing or other processes that could accelerate evolutionary change, perhaps mediated through biotic interactions.

The traces of macroboring organisms are known throughout the Phanerozoic, with diversification and exploitation of the macroboring niche paralleling variations in the development of skeletal metazoa. The oldest macroboring biota is an abundant yet low diversity fauna in hardgrounds and reefs of Lower Cambrian age. Following the extinction of archaeocyathids at the end of the Lower Cambrian (and thus the demise of skeletal reefs until the Middle Ordovician), boring organisms appear to be restricted to submarine hardgrounds. With the development of skeletal reefs in the Middle Ordovician the macroboring fauna shows a rapid speciation and a dramatic increase in diversity. This same pattern occurs again in the Devonian. This record appears to represent refuge of the fauna in low stress, hardground environments when skeletal reefs were not present and radiation in the high stress environment of the reef when large skeletal metazoa were abundant and diverse.

The Cretaceous–Tertiary (K–T) extinction reduced the gamma diversity of molluscs on the U.S. Gulf Coast from over 500 species in the late Maastrichtian to a little over 100 species in the early Danian. Gamma (total) diversity increased in a series of steps that generally tracked temperature, to a high of around 400 species in the late Middle Eocene, at which time diversity declined in the Late Eocene–Oligocene extinctions. The molluscan radiation occurred in at least two distinct phases: 1) an Initial Radiation Phase in which certain families underwent unusually high speciation, apparently filling ecological niches vacated by the extinction, followed by extinction of many of the species in these families in the late Danian; and, 2) a Secondary Radiation Phase where gamma diversity gradually increased and new genera gradually appeared. The fact that the gamma diversity of molluscs did not reach pre-extinction levels before the next extinction in the Late Eocene suggests that molluscan faunas may spend much of their evolutionary time recovering from these extinctions.

Growth processes and patterns set functional limits on the adaptive range of organisms that have evolved a particular “Bauplan.” The design of the elastic ligament has played a large part in determining the scope of the evolutionary radiation of the Arcoida. Tensional lamellar and compressional fibrous materials of this ligament, which appear to be similar in their elastic properties to those of other bivalves, are not segregated in positions where they could best perform their different mechanical functions. The growth of this unspecialized ligament exhibits strong positive allometry, with respect to shell size, in many fossil and living arcoids. A simple mechanical model shows that this allometry is essential if the strength of the ligament is to keep up with the weight of the animal, during ontogeny. Inherent disadvantages of the allometry include increasing dorsal breakage of the ligament itself, interference with the function of the hinge teeth and reduction of the closing moment exerted by the adductor muscles. Direct measurements of living arcoids show that allometric growth just maintains a linear relationship between ligament strength and animal volume. Major differences in ligament strength are related to shell growth patterns and substantially different environmental adaptations. Ligament strength is highly variable within individual populations; between populations, it is correlated with shell thickness and local environmental conditions. Most arcoids are adapted for shallow-burrowing or epifaunal modes of life in physically unstable environments, where they are frequently disturbed. The large, muscular foot enables these mobile animals to regain suitable living positions after such disturbances. The weak ligament has limited the potential specialization of the arcoids for either deeper burrowing or permanent epibyssal attachment, also requiring the retention of the foot in epifaunal forms. This ligament has made diverse adaptations possible, while preventing extreme specialization, except in isolated taxa. As such, it is largely responsible for the evolutionary reversals documented by Stanley (1972). This is konstrukionsmorphologie No. 46.

The three dimensional structure of vegetation is an important component of ecosystems, yet it is difficult to reconstruct from the fossil record. Forests or woodlands prevailed at mid-latitudes in North America during the early Eocene but tree spacing and canopy structure are uncertain. Here we use stable carbon isotope values (δ13C) in early Eocene mammalian faunas to infer canopy structure. We compare δ13C values in two diverse fossil assemblages from the central Bighorn Basin to values predicted for mammals in a variety of open and closed habitats, based on modern floras and faunas. We conclude that these early Eocene faunas occupied an open canopy forest. We also use carbon and oxygen isotopes to infer diet and microhabitat. Three higher level taxa have significantly different mean δ13C values, and values are negatively correlated with body mass. The pattern suggests diets high in leaves for larger mammals, and fruit or other non-foliar plant organs for small ones. A preference in the larger mammals for wetter habitats with high water availability to plants may also have contributed to the pattern.

Terrestrial mass extinctions have been attributed to a wide range of causes. Some of them are external to Earth, such as bolide impacts (as widely discussed for the K/T boundary) and radiation events. Among radiation events, there are possible large solar flares, nearby supernovae, gamma-ray bursts (GRBs), and others. These have variable intensity, duration, and probability of occurrence, although some generalizations are possible in understanding their effects (Ejzak et al. 2007). Here we focus on gamma-ray bursts (Thorsett 1995; Scalo and Wheeler 2002), a proposed causal agent for the end-Ordovician extinction. These are the most remote and infrequent of events, but by virtue of their power, a threat approximately competitive with, for example, that of nearby supernovae. A GRB of the most powerful type (Woosley and Bloom 2006) is thought to result from a supernova at the end of stellar evolution for very massive stars with high rotational speed. Much of their energy is channeled into beams, or jets, which include very high energy electromagnetic energy, i.e., gamma-rays and X-rays. It is a testament to the power of these events, far across the observable universe, that they were first detected in the 1969–1970 results from monitoring satellites designed to detect nuclear explosions on Earth's surface. It was not until the 1990s, when the distance to the events became known, that their power became apparent. Several such events occur every day in the observable universe. Other kinds of events are also potentially damaging, such as so-called short bursts and solar flares, but rate information is only now beginning to clarify how much threat is likely from such sources.

The thoughts and writings of Stephen Jay Gould have had an enormous impact on the shaping of macroevolutionary theory. The notion of punctuated equilibria (Eldredge and Gould 1972) remained prominent throughout his work. It also unleashed a storm of debate in paleontology and evolutionary theory. A second theme that recurs throughout Gould's opus is heterochrony (evolution by changes in the rates and timing of ontogenetic events, sensu Gould 1977a). His analyses of these two subjects have inspired many of us to explore further and add to them. My contribution discusses their expansion to encompass large numbers of lineages through long time, and the relationship of punctuated equilibria and heterochrony to physical environmental change, and to each other.

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

Analysis of a global elevation database to measure changes in shallow-marine habitat area as a function of sea level reveals an unexpectedly complicated relationship. In contrast to prevailing views, sea level rise does not consistently generate an increase in shelf area, nor does sea level fall consistently reduce shelf area. Different depth-defined habitats on the same margin will experience different changes in area for the same sea level change, and different margins will likewise experience different changes in area for the same sea level change. Simple forward models incorporating a species-area relationship suggest that the diversity response to sea level change will be largely idiosyncratic. The change in habitat area is highly dependent on the starting position of sea level, the amount and direction of sea level change, and the habitat and region in question. Such an idiosyncratic relationship between diversity and sea level reconciles the widespread evidence from the fossil record for a link between diversity and sea level change with the lack of quantitative support for such a relationship throughout the Phanerozoic.

A new hypothesis concerning the evolutionary origin of pentameral symmetry in echinoderms is presented. The BA-A-BA pattern of Lovén's law in echinoids and the 2-1-2 symmetry of the edrioasteroid Stromatocystites appear to be morphogenetically related, and this pattern appears to be locked into development. This pattern may have originated from a unirayed 0-1-0, —A—, ancestor. I propose that a duplication of the uniray occurred and resulted in the addition of a pair of rays that followed Bateson's rules of symmetry to form a three-rayed 0-1-2, —A-BA, construction. This change occurred on the side that corresponds to the left side of the organism. This event made the individual asymmetric with respect to its anterior-posterior axis. Therefore I propose that morphogenetic regulation of bilaterality of the organism then led to homeotic expression of a mirror-image pair of rays on the opposite side. These two morphogenetic steps achieved the 2-1-2, BA-A-BA pattern. “Appendage status” of rays is assumed necessary to invoke the Batesonian mirror-image duplications of the model.

Three robust morphological characters emerge from the “rays-as-appendages” model: (1) 2-1-2, BAo-A-BA, organization; (2) “locked-in” pentamerism; and (3) a 2-3 pattern of right and left rays. Results based on ray homology research are presented for echinoids, asteroids, ophiuroids, edrioasteroids, ophiocistioids, and holothurians. I speculate that helicoplacoids may have 0-1-2 triradiate construction, and that solutes may have 0-1-0 uniray construction. The model has limits; it does not explain 1-1, or 2-1, or 2-2 or 1-1-1 organization of ambulacra.

A new turnover rate metric is introduced that combines simplicity and precision. Like the related three-timer and gap-filler equations, it involves first identifying a cohort of taxa sampled in the time interval preceding the one of interest (call the intervals i0 and i1). Taxa sampled in i0 and i1 are two-timers (t2); those sampled in i0 and i2 but not i1 are part-timers (p); and taxa sampled only in either i1, i2, or i3 are newly notated here as either s1, s2, or s3. The gap-filler extinction proportion can be reformulated as (s1−s3)/(t2+p). The method proposed here is to substitute s3 with the second-highest of the three counts when the expected ordering s1≥s2≥s3 is violated. In simulation, this new estimator yields values that are highly correlated with those produced by the gap-filler equation but more precise. In particular, it rarely produces highly negative values even when sample sizes are quite small. It is mildly upwards biased when sampling is extremely poor and turnover rates are extremely low, but it is otherwise highly accurate. Examples of Phanerozoic extinction rates for four major marine invertebrate groups are given to illustrate the method’s improved precision. Based on the results, the procedure is recommended for general use.

Most studies of extinction selectivity have focused on mass extinctions. Here we analyze the patterns of susceptibility to extinction during the late Pliocene and Pleistocene of California in the family Pectinidae. The Pectinidae declined in diversity from a high of 32 species in the late Pliocene to the current level of 11 species living in the California region, indicating that the composition of the living fauna has been shaped primarily by extinction in the last several million years. Extinction appears to have occurred in one large pulse, but because of uneven sampling we were unable to resolve the timing further and have analyzed the patterns of extinction treating the late Pliocene through middle Pleistocene as a single period of elevated extinction. Extinctions were not random with regard to taxonomic relationships. Species-level extinctions were higher in more speciose genera, but these genera were buffered against genus-level extinctions. This resulted in a disproportionately large number of monospecific genera in the living fauna. In addition, extinctions were not random with regard to body size, with large species preferentially surviving. This selectivity pattern is evident only when clade membership is taken into account; when analyzed across the entire family, no pattern of size selectivity was apparent. Our results suggest that (1) patterns of extinction selectivity at the genus level may be a poor proxy for species-level patterns, and (2) whole-fauna analyses may not uncover strong selectivity within lineages.

Analysis of the evolution of the Globorotalia (Fohsella) lineage of planktic foraminifera suggests that reproductive ecology and shell shape have evolved independently in this group. The silhouette of fohsellid shells displays a nearly unbroken anagenetic trend, yet isotopic data show that the fohsellids changed their depth of reproduction during the anagenetic evolution of their skeletons. Remarkably, there are no correlations between anagenesis in skeletal shape and the establishment of reproductive isolation. Apparently, anagenesis masks at least one speciation event that is apparent only in the isotopic evidence for a change in reproductive ecology. Although anagenetic trends have been widely cited as evidence for gradual speciation in planktic foraminifera and other microfossil groups, our data suggest that they should not always be considered to record either the tempo or mode of speciation.

Speciation was apparently uncoupled from morphological evolution in fohsellids because these evolutionary phenomena occurred in different phases of ontogeny. Gradual morphological changes were associated with the main phase of shell growth of both the ancestor and descendant species in the near-surface ocean. Reproductive isolation occurred when ancestral and descendant populations became established at different depths near the end of the life cycle. Morphological evolution may also be uncoupled from reproductive isolation in other organisms that experience very different selection pressures over the duration of their ontogenies, such as parasites with many hosts, species with multiple phases of metamorphosis, and organisms that broadcast their gametes.

A preliminary report is presented documenting the evolution of the Globorotalia crassaformis (Galloway and Wissler) lineage from the Early Pliocene G. cibaoensis (Bermudez) in Hydraulic Piston Core 72/516 on the Rio Grande Rise (western South Atlantic). A new technique, eigenshape analysis, is used to describe the gross changes in morphology, and the use of “Raupian” analysis of expansion rates, angular displacement, position relative to coiling axis, and translation rates of chambers is suggested as a useful vehicle for inferring the geometric causes of observed evolutionary changes. These changes include size increase, decrease in the number of chambers per whorl, inflation, reduction of relative height of aperture, and increase in the peripheral angle. The sequence is judged to be an example of phyletic gradualism.

The recurring debate over the causes of the massive extinctions of such groups as the dinosaurs, ammonites, and calcareous nannoplankton, and the crash of the distinctive Aquilapollenites pollen province, used by biostratigraphers to mark the close of the Cretaceous, has been considerably enlivened with the resurgence of hypotheses suggesting catastrophic events. The impact of an asteroid, explosion of a supernova, sudden changes in oceanic circulation and composition, or atmospheric perturbations, to mention a few, have been put forward as malefactors. But, just how sound is the evidence of a biotic catastrophe?

Short-term fluctuations in the diversification rate of Paleozoic marine animal genera are more strongly correlated with extinction-rate variation than with origination-rate variation. Diversity dynamics are strikingly different in the Mesozoic and Cenozoic, when variation in origination is more important than extinction. Data on the lithologic context of taxonomic occurrences in the Paleobiology Database are used to assess the substrate affinities of Paleozoic genera. The greater role of extinction-rate variation in the Paleozoic is found to characterize genera with an affinity for carbonate substrates but not those that prefer terrigenous clastic substrates. It is therefore plausible that the Paleozoic to post-Paleozoic shift in diversity dynamics is underlain in part by the secular decline in the relative areal extent of carbonate environments, and the concomitant decline in the relative diversity of carbonate-versus clastic-loving taxa.

The fossil record is incomplete in the sense that taxa for which there are no preserved finds are unrepresented. Because the probability that there is at least one preserved find is greater for long-lived taxa, failure to account for this effect will bias estimation of mean taxonomic duration. This paper describes maximum likelihood estimation of mean taxonomic duration, fossil preservation rate, and completeness of the local fossil record under a model in which duration has an exponential distribution and the locations of preserved finds follow a Poisson process. The estimates under this model have simple closed forms. It is also straightforward to construct confidence regions for the model parameters. The method is applied to data on 110 trilobite species from the Upper Cambrian—Lower Ordovician in Oklahoma.

Phytogeographic analysis of three Early Carboniferous intervals (Tournaisian–early Visean, Visean, and late Visean–early Namurian A) indicates a high level of phytogeographic differentiation in the beginning of the Early Carboniferous that decreases toward the end of this period. Climatic amelioration (warmer or wetter conditions) in the north middle and high latitudes, caused by the collision of Laurussia and Gondwana at the end of the Early Carboniferous, may be responsible for this decrease in phytogeographic provinciality. Toward the end of the Early Carboniferous, a large number of equatorial genera expand their ranges northward, and the average generic diversity of assemblages in the north high latitudes (Siberia) also rises. Both support the hypothesis of climatic amelioration. Northward migration of equatorial forms and the appearance of new genera endemic to Siberia both contributed to the rise in Siberian diversity. Although this trend is not statistically significant, additional evidence of diversity increase in northern high latitudes tied to climatic amelioration comes from the northernmost limit of diverse (≥ 10 genera) assemblages, which rises from 20°N at the beginning to 55°N at the end of the Early Carboniferous. Global plant diversity assessed at the generic level remained constant during the Early Carboniferous. The increase in Siberian diversity was offset by a decrease in equatorial diversity, perhaps due to the loss of pronounced latitudinal climatic gradients between north-middle and equatorial latitudes.