The commonly observed fact that the principal biologic groups appear early in an adaptive radiation is shown to be an artifact of the geometry of the evolutionary tree. For marine invertebrates of the Phanerozoic, total diversity and species turnover rates combine to make early origins of major groups inevitable. This is demonstrated through an analysis of the theoretical probability distribution of divergence time (time to most recent common ancestor) in comparison with observed distributions. Whereas the fact of early origins does not require ecological explanations, the interpretation of the morphologic distinctness of major groups when they first appear remains an ecological problem.

Preservation in the fossil record is never perfect in the sense that we cannot sample all individuals of a given population in time and space. Incomplete detection (i.e., preservation and modern-day sampling of fossils) often affects estimates of other paleobiological parameters of interest, such as occupancy and turnover. Here, I simultaneously model the occupancy and detection probability of taxa, teasing apart the zeros in data that reflect true absences and those that imply non-detection of taxa that were actually present in the space and time of interest. Occupancy modeling, an approach first developed in population ecology, can easily incorporate covariates of interest, such as sampling effort and habitat variables. I use a data set of brachiopod taxa from the Paleozoic to illustrate the utility of this approach for paleontological questions. I demonstrate a range of models, including those that allow colonization between time intervals and those that incorporate facies as site covariates. I also suggest how future data collection can be improved so that process- and sampling-oriented approaches such as occupancy modeling can be applied with ease to paleobiological settings to answer important paleoecological and evolutionary questions.

The shovel-tusked gomphotheres are normally portrayed scooping up water plants with their shovellike mandibular tusks. This portrayal is based on speculation about the possible functions of the lower tusks and misinterpretation of mandibular-tusk wear patterns that goes back to the 1920s and 1930s. In addition, most literature concerning shovel-tusker feeding behavior ignores the possibility that the upper tusks may have had a role in feeding, as they do in modern African elephants. Because wear patterns on tusks provide direct evidence as to how tusks were used during feeding, I examined and interpreted patterns on the lower and upper tusks of shovel-tusked gomphotheres on the basis of theoretical models of tusk wear to determine how the tusks were used in feeding.

This examination led to the following conclusions. (1) The genus Amebelodon was characterized by feeding opportunism, gathering food with both its lower and upper tusks in a variety of ways. (2) There is evidence for similar flexibility within the genus Serbelodon. (3) Wear patterns on mandibular tusks of Platybelodon grangeri and Torynobelodon barnumbrowni indicate that these taxa did not practice mandibular shoveling but used these tusks to cut tough vegetation in a specialized fashion. (4) The flaplike trunks (probosces) generally attributed to shovel-tusked gomphotheres in restorations are shown almost certainly to be erroneous; morphological and functional evidence suggests that these animals had trunks similar to those of modern elephants. (5) Strong tusk sexual dimorphism is unknown in the shovel-tusked gomphotheres except for Platybelodon and should not be found in any taxa that relied on their tusks for procuring food. New restorations of both Amebelodon and Platybelodon are provided that are more consistent with the actual evidence bearing on their feeding behavior.

Eocene lake beds of Horsefly, British Columbia, are preserved in varves, or discrete yearly layers representing seasonal changes in the lake. These varves allow study of temporal variation and rates of change in morphological and ecological characters on a very short time scale. One of the most sensitive indicators of the paleoenvironmental conditions on the floor of the lake may be the taphonomic condition of the fishes, which vary between perfectly articulated and completely disarticulated skeletons. Patterns of disarticulation correspond to those produced by scavengers. The taphonomy supports the hypothesis that the lake was warm monomictic, circulating in the winter, at which time scavengers could gain access to the bottom of the lake. Larger-scale environmental events (on the order of hundreds of years) are suggested by the fact that the proportion of well-preserved specimens reached two peaks within the seven centuries of deposition, one peak during the second century and another during the fifth and sixth centuries. These results clearly demonstrate two principles: that taphonomy can be a sensitive indicator of paleoenvironmental conditions, and that temporal averaging can affect the taphonomic properties of this fossil site, and presumably of others with equal or lower time resolution.

Phanerozoic trends in shell and life habit traits linked to postmortem durability were evaluated for the most common fossil brachiopod, gastropod, and bivalve genera in order to test for changes in taphonomic bias. Using the Paleobiology Database, we tabulated occurrence frequencies of genera for 48 intervals of ∼11 Myr duration. The most frequently occurring genera, cumulatively representing 40% of occurrences in each time bin, were scored for intrinsic durability on the basis of shell size, reinforcement (ribs, folds, and spines), life habit, and mineralogy.

Shell durability is positively correlated with the number of genera in a time bin, but durability traits exhibit different temporal patterns across higher taxa, with notable offsets in the timing of changes in these traits. We find no evidence for temporal decreases in durability that would indicate taphonomic bias at the Phanerozoic scale among commonly occurring genera. Also, all three groups show a remarkable stability in mean shell size through the Phanerozoic, an unlikely pattern if strong size-filtering taphonomic megabiases were affecting the fossil record of shelly faunas. Moreover, small shell sizes are attained in the early Paleozoic in brachiopods and in the latest Paleozoic in gastropods but are steady in bivalves; unreinforced shells are common to all groups across the entire Phanerozoic; organophosphatic and aragonitic shells dominate only the oldest and youngest time bins; and microstructures having high organic content are most common in the oldest time bins.

In most cases, the timing of changes in durability-related traits is inconsistent with a late Mesozoic Marine Revolution. The post-Paleozoic increase in mean gastropod reinforcement occurs in the early Triassic, suggesting either an earlier appearance and expansion of durophagous predators or other drivers. Increases in shell durability hypothesized to be the result of increased predation in the late Mesozoic are not evident in the common genera examined here. Infaunal life habit does increase in the late Mesozoic, but it does not become more common than levels already attained during the Paleozoic, and only among bivalves does the elevated late Mesozoic level persist through the Holocene.

These temporal patterns suggest control on the occurrence of durability-related traits by individual evolutionary histories rather than taphonomic megabiases. Our findings do not mean taphonomic biases are absent from the fossil record, but rather that their effects apparently have had little net effect on the relative occurrence of shell traits generally thought to confer higher preservation potential over long time scales.

Vertebrate microfossil bonebeds (VMBs)—localized concentrations of small resilient vertebrate hard parts—are commonly studied to recover otherwise rarely found small-bodied taxa, and to document relative taxonomic abundance and species richness in ancient vertebrate communities. Analyses of taphonomic comparability among VMBs have often found significant differences in size and shape distributions, and thus considered them to be non-isotaphonomic. Such outcomes of “strict” statistical tests of isotaphonomy suggest discouraging limits on the potential for broad, comparative paleoecological reconstruction using VMBs. Yet it is not surprising that sensitive statistical tests highlight variations among VMB sites, especially given the general lack of clarity with regard to the definition of “strict” isotaphonomic comparability. We rigorously sampled and compared six VMB localities representing two distinct paleoenvironments (channel and pond/lake) of the Upper Cretaceous Judith River Formation to evaluate biases related to sampling strategies and depositional context. Few defining distinctions in bioclast size and shape are evident in surface collections, and most site-to-site comparisons of sieved collections are indistinguishable (p≤0.003). These results provide a strong case for taphonomic equivalence among the majority of Judith River VMBs, and bode well for future studies of paleoecology, particularly in relation to investigations of faunal membership and community structure in Late Cretaceous wetland ecosystems. The taphonomic comparability of pond/lake and channel-hosted VMBs in the Judith River Formation is also consistent with a formative model that contends that channel-hosted VMBs were reworked from pre-existing pond/lake assemblages, and thus share taphonomic history.

Body mass is estimated for extinct species of Sigmodon. These data are then used in appropriate equations derived among Recent mammals to estimate a suite of physiological and ecological variables which are followed through almost 4 ma of cotton rat history. A statistical trend towards large size is documented. Despite large swings in population size and other parameters, hypothetical values of population metabolism remain virtually constant, suggesting negligible population energetic benefit to size change in either direction. Studies of extant cotton rats and unrelated taxa sharing the same adaptive zone suggest that there is now, and has been in the past, negligible thermoregulatory advantage to modification of cotton rat body mass. Large size appears to be associated in Sigmodon with heightened aggression to the point that two species, particularly if of dichotomous size, cannot coexist in the same microhabitat. At least with regard to cotton rats, this conclusion represents a challenge to the comfortable hypotheses of coevolution and character displacement. The overall trend toward large size during Pleistocene time is considered then as the interplay of selection acting to favor large size in areas of sympatry and stochastic processes originating cotton rat populations of different body size. Because morphology and ecological strategies are stable within the cotton rat adaptive zone for millions of years, it is suggested that mammalian speciation events that result in exploitation of a new adaptive zone are uncommon and occasionally cross higher taxonomic categories. These events are defined as first-order speciation events, in contrast to second-order events that occur in clades within the same adaptive zone.

Recent data from mollusks suggest that mode of larval development may have important consequences for rates of speciation and extinction of marine organisms. The present study examines two methods that may be used to infer mode of development in the tests of fossil and Recent echinoids: genital pore size and crystallographic patterns of apical plates. Extant species with known modes of development were examined, and the following hypotheses were tested. 1) Species that produce large eggs and have nonfeeding larval development have larger genital pores than species that produce small eggs and have feeding larval development. 2) Orientations of crystallographic axes (c-axes) of genital and ocular plates differ in species with differing modes of development and can be used to infer mode of development. Genital pore size was found to be strongly dependent on body size within a species. For some taxa, pairwise interspecific comparisons of the relationships between genital pore size and body size support the hypothesis of larger genital pores for species with nonfeeding larval development. However, in multiple comparisons of linear regressions, species with nonfeeding larval development always overlapped other species with feeding larval development. An examination of the allometry of genital pore growth showed some species with nonfeeding larval development differed from those with feeding larval development; other species with differing modes of development could not be distinguished on the basis of allometric growth parameters. Orientations of c-axes of genital plates were found to be accurate indicators of mode of development, but orientations of c-axes of ocular plates were not. Among regular echinoids, 71 of 72 species supported the hypothesis that orientation of c-axes of genital plates is indicative of mode of development. Among 19 spatangoid echinoids studied, orientations of c-axes of genital plates generally allowed separation of species with differing modes of development. This method cannot be used to infer modes of development in taxa with reduced numbers of genital plates such as some spatangoids, some cassiduloids, and all clypeasteroids. Taxonomic differences in c-axis orientations require that inferences be made from comparisons between species within families.

Marine shelf lagoon deposits of Middle Ordovician age in Tennessee contain the record of repeated ecological successions which began on soft, azoic, terrigenous muds and progressed to a complex bryozoan-brachiopod community. The stages of succession formed a skeletal limestone bed. The process led to an interbedded shale-limestone stratigraphic sequence. The pioneer was the brachiopod Strophomena basilica which paved the soft mud with accumulated shells. Encrusting bryozoans colonized this shell pavement and were followed by ramose bryozoans. The final stages of succession included bryozoans, gastropods, pelecypods, and pelmatozoans but were dominated by the brachiopod Rostricellula rostrata.

Measurements of total length, width, length to growth lines (Strophomena only), and thickness (Rostricellula only) were used to generate growth-rate, and survivorship curves for these two species. Strophomena shows low juvenile mortality, a moderate, linear growth-rate, and increased mortality in later ages. Rostricellula shows relatively higher juvenile mortality, a rapid non-linear growth rate, and nearly constant mortality. These attributes are contrary to expectations derived from theory, but can be understood in the light of autecological factors for each species. Adaptation to soft substrata was the primary factor controlling population dynamics in Strophomena, and crowding was the main factor in Rostricellula.

The Tulip Beds locality on Mount Stephen (Yoho National Park, British Columbia) yields one of the most abundant and diverse (~10,000 specimens in 110 taxa) Burgess Shale fossil assemblages in the Canadian Rockies. Detailed semi quantitative and quantitative analyses of this assemblage suggest strong similarities with the Walcott Quarry on Fossil Ridge. Both assemblages are dominated by epibenthic, sessile, and suspension feeding taxa, mostly represented by arthropods and sponges and have comparable diversity patterns, despite sharing only about half the genera. However, the Tulip Beds has a higher relative abundance of suspension feeders and taxa of unknown affinity compared to the Walcott Quarry. These biotic variations are probably largely attributable to ecological and evolutionary differences between the two temporally distinct communities that adapted to similar, but not identical, environmental settings. For instance, the Tulip Beds is farther away from the Cathedral Escarpment than the Walcott Quarry. The Tulip Beds and Walcott Quarry assemblages are more similar to each other than either one is to the assemblages of the Chengjiang biota, although the relative diversity of major taxonomic groups and ecological patterns are similar in all assemblages. The conserved diversity patterns and ecological structures among sites suggest that the ecological composition of Cambrian Burgess Shale-type communities was relatively stable across wide geographic and temporal scales.

Macroevolutionary and macroecological studies must account for biases in the fossil record, especially when questions concern the relative abundance and diversity of taxa that differ in preservation and sampling potential. Using Cenozoic marine mollusks from a temperate setting (New Zealand), we find that much of the long-term temporal variation in gastropod versus bivalve occurrences is correlated with the stage-level sampling probabilities of aragonitic versus calcitic taxa. Average sampling probabilities are higher for calcitic species, but this contrast is time-varying in a predictable way, being concentrated in stages with widespread carbonate deposition.

To understand these results fully, we link them with analyses at the level of individual point occurrences. Doing so reveals that aragonite bias is effectively absent in terrigenous clastic sediments. In limestones, by contrast, calcitic species have at least twice the odds of sampling as aragonitic species. This result is most pronounced during times of widespread carbonate deposition, where the difference in the per-collection odds of sampling species is a factor of eight. During carbonate-rich intervals, calcitic taxa also have higher odds of sampling in clastics. At first glance this result may suggest simple preservational bias against aragonite. However, comparing relative odds of aragonitic versus calcitic sampling with absolute sampling rates shows that the positive calcite bias during carbonate-rich times reflects higher than average occurrence rates for calcitic taxa (rather than lower rates for aragonitic taxa) and that the negative aragonite bias in limestones reflects lower than average occurrence rates for aragonitic taxa (rather than higher rates for calcitic taxa).

Our results therefore indicate a time-varying interplay of two main factors: (1) taphonomic loss of aragonitic species in carbonate sediments, with no substantial bias in terrigenous clastics; and (2) an ecological preference of calcitic taxa for environments characteristic of periods with pervasive carbonate deposition, irrespective of lithology per se.

For well over 50 years, the telome theory of Walter Zimmermann has been extremely influential in interpreting the evolutionary history of land plant architecture. Using the “telome/mesome” distinction, and the concept of universal “elementary processes” underlying the change in form in all plants, the theory was an ambitious synthesis based on the proposition that evolutionary change might be understood by a simple set of developmental or evolutionary rules. However, a major problem resides in deciding exactly how assertions of change are to span both developmental and evolutionary domains simultaneously, and, we argue, the theory critically fails testability as a scientific theory. Thus, despite continued popularity for the descriptive terms derived from the theory in evolutionary studies of early land plants, time has come to replace it with a more explicit, testable approach. Presented here is an attempt to clarify perhaps the most important issue raised by the telome theory—whether simple changes in basic developmental processes suffice to describe much of early land plant evolution. Considering the morphology of Silurian–Devonian fossil members, it is hypothesized that early land plants possessed a common set of developmental processes centered on primary growth of shoot apical meristems. Among these were (1) the capacity to monitor and act upon internal physiological status here modeled as “apex strength,” (2) a mechanism for allocation of apex strength in a context-dependent way at each point of branching, (3) a rule for context-dependent apex angle for branches, (4) a largely invariant phyllotaxis unrelated to physiological status, and (5) a simple switch for terminating primary growth, based in part on genetics. Implemented as a set of developmental rules within a simple L-system model, these aspects of primary development in plants determine a sizable range of resultant morphologies, some of which are highly reminiscent of the early fossils. Thus, some support is found, perhaps, for Zimmermann's intuition. However, traditional concepts of growth patterns in plants, including the contrast between epidogenesis and apoxogenesis, require updating. In our reformulation, developmental processes, stated as rules of developmental dynamics, together constitute what we term the plant's developmental state. Using a hypothetico-deductive format, one may hypothesize intrinsic (or genetic) developmental processes that play out as realized developmental activity in specific spatial/temporal contexts, as modified by multiple context factors. The resultant plant morphology is highly dependent on multiple and simultaneous pathway ontogenetic trajectories. Within a likely set of developmental rules reasonably inferred from plant development, some of Zimmermann's elementary processes are perhaps recognizable whereas others are not. Progressively “overtopped” morphologies are easily produced by modifying intrinsic branch allocation. However, even so, the other developmental rules have a profound effect on final architectures. Planate architectures and circination vernation, often treated as special cases by plant morphologists, are perhaps better understood in terms of recurrent or iterative developmental relationships. Much analytic work remains before a completely specified system of rules will emerge. A well-articulated relationship between ontogeny and phylogeny remains fundamentally important in assessing evolutionary change. Fossil and living plants make it abundantly clear that current evolutionary concepts involving modification of a single ontogenetic trajectory from ancestor to descendant need to be greatly expanded into consideration of the entire logical geometry of causation in development. A mechanism for testing is also required that need not wait for complete elucidation at the molecular level. The relative simplicity of plant development, combined with an outstanding fossil record of early members, offers unique opportunities along these lines.

Recent studies have provided detailed insight into life cycles of early amphibians. These ontogenies were diverse and their evolution involved numerous kinds of change, which can now be addressed by comparison of ontogenetic trajectories. The plesiomorphic trajectory included (1) an early period in which a larval, aquatic predator was established, (2) an intermediate period in which the axial skeleton was strengthened, and (3) a final period during which the jaw joint, braincase, and limbs were ossified, producing an adult capable of terrestrial locomotion if completed. Heterochrony, among other factors, enabled the fine-tuning of the ontogenetic formation of ecologically important features (feeding, respiration, locomotion). Most common was a simple truncation of the trajectory that produced aquatic taxa of various kinds, while changes in the ontogenetic sequence often had a deeper impact on morphology. The most fundamental changes were accompanied by multiple heterochronies, resulting in the condensation or unpacking (stretch-out) of developmental events: metamorphosis evolved by an ever closer packing, whereas a novel larval feeding mechanism was established by a pull-apart of numerous critical events.

Colonies of Late Paleozoic lyre-shaped fenestrate bryozoans began growth on rigid substrates which were on the sea floor. After production of a basal disc, a fenestrate network developed in the shape of an erect bowed fan. The fenestrate fan was initially concave on the apertural side, but the curvature reversed a few millimeters above the base. Colonies were then separated along or just above the basal disc, and rested directly on the sea floor. The zooecial apertures were directed upward. The lateral margin of the fan grew to form the supporting struts of the soon-to-be lyre-shaped colony. An open vault formed below the upwardly bowed fan.

Lyre-shaped colonies are interpreted to have lain on the sea floor so that each had the proximal end on the upcurrent side. Feeding zooids were on the upper surface and pulled water through their expanded tentacles. The filtered water passed through the fenestrules, into the vault, and out the open end of the vault, which was on the downcurrent side.

Extinction in the fossil record is most often measured by the percentage of taxa (species, genera, families, etc.) that go extinct in a certain time interval. This is a measure of taxonomic loss, but previous work has indicated that taxonomic loss may be decoupled from the ecological effects of an extinction. To understand the role extinction plays in ecological change, extinction should also be measured in terms of loss of functional diversity. This study tests whether ecological changes increase correspondingly with taxonomic changes during the Late Ordovician M4/M5 extinction, the Ordovician/Silurian mass extinction, and the Late Devonian mass extinction. All three extinctions are evaluated with regional data sets from the eastern United States. Ecological effects are measured by classifying organisms into ecological lifestyles, which are groups based on ecological function rather than evolutionary history. The taxonomic and ecological effects of each extinction are evaluated with additive diversity partitioning, detrended correspondence analysis, and relative abundance distributions. Although the largest taxonomic changes occur in the Ordovician/Silurian extinction, the largest ecological changes occur in the Late Devonian extinction. These results suggest that the ecological consequences of extinction need to be considered in addition to the taxonomic effects of extinction.

Large-scale trends in planktonic foraminiferal diversity have so far been based on utilization of synoptic biostratigraphic range charts. Although this approach ensures the taxonomic consistency and quality of the data being used, it takes no formal account of any sampling biases that might exist in the fossil record. We demonstrate that the occurrence data of planktonic foraminifera, as recorded in the primary literature, are strongly biased by sampling. We do this by demonstrating that raw diversity curves derived from the land-based and deep-sea records are strikingly different, but that they each correlate with the intensity of sampling in their respective environments, and thus are ultimately controlled by the structure of the geological record in each setting. Because sampling of the Mesozoic record is best in our land record whereas sampling of the Cenozoic is best in our deep-sea record, we combine the two to generate the best-supported estimates of species and genus diversity over time from these data. We correct for sampling bias using shareholder quorum subsampling and a modeling approach. The data are then transformed to generate a range-through plot of species richness that is compared with two earlier estimates of the diversity history where comparable species-in-bin data can be recovered. No robust statistical correlation is found among the three estimates. Although differences in amplitude are to be expected, differences in the actual shape of the curve are surprising. We conclude that these differences stem from the nature of the data themselves, namely the taxonomic scheme adopted and the taxonomic coverage used.

Diversity and faunal turnover of North American land mammals are calibrated against the magnetic polarity time scale for million-year intervals for the latest Eocene through late Oligocene. A major, gradual Late Eocene decline in diversity, caused mostly by an extended period of extinction of archaic forms, seems to be related to the worldwide crisis known as the “Terminal Eocene Event.” Along with other evidence of gradual changes in deep-sea microfossils, this evidence argues against a catastrophic explanation for late Eocene extinctions.

Faunal stability characterized the rest of the Oligocene except for a wave of extinctions in the mid-Oligocene (Chadronian-Orellan boundary, about 32.4 ma). This mid-Oligocene event is sudden and severe, occurring in less than 200,000 yr, based on estimates from sedimentation rates calibrated from magnetic polarity interval boundaries. The mid-Oligocene event is found in many paleoclimatic records, but not in all of them. It may be related to the completion of the Circum-Antarctic Current and to increased mid-Oligocene glaciation.

Study of the assemblage of encrusting organisms on co-occurring disarticulated valves of the bivalves Crassostrea virginica and Mercenaria mercenaria in Bogue Sound, North Carolina, indicates that there is little or no substrate specificity among the encrusting organisms but that the shape of the shells has an important influence on how extensively members of each higher taxon collectively inhabit the shells. Encrusting bryozoans, a dense low mat composed of many species from diverse phyla, and a unicellular film cover most of the area of both exterior and interior surfaces. The encrusting bryozoans most extensively cover both surfaces of C. virginica but are in second place behind the multispecies mat on exterior surfaces of M. mercenaria and behind the unicellular film on its interior surfaces. These differences are inferred to result from different physical stability of valves of the two bivalve species, which exhibit different frequencies of circumrotatory growth.

Degradation of the assemblage by sodium hypochlorite, to simulate loss of organic matter during fossilization, results in the complete loss of encrusting sponges, erect hydrozoans, erect bryozoans, and ascidians. Loss of these taxa results in overexposure and more apparently uniform distribution of skeletal taxa with respect to their surface representation in living assemblages and also in complete loss of the higher tiers present in the living assemblage. However, indications of the original structural organization of the living assemblage is indicated by preservation of the most abundant taxa in the lower tiers and by the retention in the reduced treated assemblage of the patterns of distribution that characterized the living assemblage.

Dental measurements are commonly used in the diagnosis of fossil elephant species, yet elephant teeth develop slowly, within a highly dynamic context that enhances opportunities for physical deformation (or its subtler manifestation, quantitative phenotypic variation). This paper examines intraspecific variation in elephant teeth and compares it with variability in other mammals (83 species in 7 orders). I conclude that (1) male elephants tend to have slightly larger cheek teeth than females, though the difference is not marked; (2) of the full complement of six cheek teeth per jaw quadrant, no single tooth consistently varies less than the others (so on this basis, for taxonomic decisions no tooth is preferable to the customarily used M3 = tooth VI); (3) single-population samples vary less than more inclusive, geographically heterogeneous samples of elephant teeth; (4) although differential wear and eruption are important sources of variation in dental measurements, complete elephant teeth are consistently more variable in length and width than the cheek teeth of other mammals; (5) variability in dental dimensions of recognized fossil species of elephants is in general not grossly inconsistent with variability noted in modern elephants, but there are some exceptions. With the information and guidelines presented here, consideration of variability, and assessment of the statistical power permitted by available samples, can enhance confidence and precision in the delimitation of species and provide a firmer basis for macroevolutionary inferences.