Since the early 1990s, methods for the acquisition of three-dimensional (3-D) data and computer-assisted techniques for the visualization of such data have grown increasingly popular among biologists, paleontologists, and paleoanthropologists. However, thus far no standardized repository for complex virtual models based on 3-D digital data of specimens has emerged, whereas the need for researchers to provide access to 3-D models of specimens as well as the pressure imposed on authors by scientific journals to make original 3-D morphological data publicly available have increased. MorphoMuseuM (M3) aims to fill this gap. M3 is both a peer-reviewed scientific journal (M3 Journal) and a virtual specimen repository (M3 Repository). All scientific articles and their associated 3-D models deposited in M3 go through a formal review process. Each published model is given a DOI and a unique identifier code, which should be cited by researchers using this model in their scientific publications. In this paper, we describe the place of M3 among other online repositories for 3-D data, and explain how the growing community of biologists working with 3-D data can benefit from using M3.

Frequent and repeated climate fluctuations of the late Quaternary serve as a “natural experiment” for the response of species to environmental change. Analysis of the FAUNMAP database documents individualistic shifts in the geographic distributions for late Quaternary mammals. However, because the individualistic response is not necessarily random and because many species share similar niche parameters, it is possible that some species appear to form coherent groups of core species. In reality their dispersals are individualistic with regard to rate and timing. The individualistic response of mammals, as well as that of other organisms, has created late Quaternary communities without modern analogues. This concept has profound implications for the design of biological reserves and for land use management with respect to future global climate change. However, the relevance of non-analogue mammal communities has been challenged by Alroy (1999), who claims that non-analogue associations were not common in the Quaternary and that they appeared to occur in both the Pleistocene and Holocene. Reexamination of his analysis shows that he employed a different definition for non-analogue faunas and that his methods of analyses created artificially low counts of non-analogue communities and consequently an underestimate of their importance.

Seasonal temperature variation at any location is most strongly regulated by the annual cycle of solar insolation, which is controlled by latitude and orbital parameters; other factors are continentality, albedo feedbacks, stratification and advection, and water depth. Seasonal minima, maxima, and range vary with change in mean annual temperature (MAT) across latitudes; seasonal variation in ocean-water temperature is highest in the mid-latitudes. Seasonal temperature range at depth is likely to be less than that at the sea surface. The chemistry of accretionary biogenic carbonate can preserve a record of seasonal temperature variation experienced by an organism over some portion of its ontogeny. Sampling early parts of ontogenies will yield a more complete temperature record because growth is faster (so temporal resolution is higher) and more likely to be continuous throughout the year. Biases due to preferential season of growth can be recognized by characteristic patterns of isotope data when plotted versus distance along the ontogenetic trajectory. Multiple years are needed to reliably characterize seasonal temperature range and inter-annual variability for a stratigraphic horizon in a given region; single-shell studies are less useful in this regard unless they contain very long records. Data from multiple time intervals or regions using the same taxon, sampled the same way, and from the same facies can establish meaningful trends in average temperature and seasonal range. Deep-time studies exploring seasonal temperature extremes and ranges can be coupled with proxies for mean annual temperature to offer a more complete understanding of changing climate conditions through time.

The shell chemistry of ostracodes is a useful indicator of past environmental conditions especially when the chemistry data are considered along with other proxy data. The complexities involved with the chemical and isotopic changes accompanying hydrologic change, solute evolution, and the autoecology of ostracodes all point to the need to exercise caution when interpreting shell chemistry. Nevertheless, the stable-isotope values and cation ratios (e.g., Mg/Ca, Sr/Ca) as well as the species assemblage of ostracodes can provide powerful tools for the reconstruction of paleoclimate and paleohydrology. In particular, the changes in Mg/Ca and Sr/Ca of well-calcified ostracodes shells record the qualitative changes in solute composition, and when the dissolved Mg/Ca remains relatively constant, the Mg/Ca in the ostracode shell is proportional to water temperature.

Fossils and the science of paleontology provide a charismatic gateway to integrate STEM teaching and learning. With the new Next Generation Science Standards (NGSS), as well as the exponentially increasing use of three-dimensional (3-D) printing and scanning technology, it is a particularly opportune time to integrate a wider variety of fossils and paleontology into K–12 curricula. We describe a curricular prototype that integrates all four components of STEM (Science, Technology, Engineering, Math) into authentic research using dentitions of the Neogene giant shark Megalodon (Carcharocles megalodon Agassiz, 1843). This prototype has been implemented in two middle and two high schools in California and Florida. Consistent with prior evidence-based research, student engagement increases when they have hands-on experiences with fossils, particularly with a charismatic species such as Megalodon. Access to museum specimens helps students understand big ideas in ‘Deep Time.’ In addition to engaging students in authentic STEM practices and scaffolding development of content knowledge, paleontology is an integrative science that connects and informs socially relevant topics, including long-term (macro-) evolution and climate change. The application of 3-D printing and scanning to develop curricula using fossils has immense potential in K–12 schools in the U.S.

The Cretaceous record of the diatoms presented here outlines our understanding of their early morphological development. Recent documentation of well preserved Lower Cretaceous (Aptian/Albian) diatom assemblages provides a window into the early history of the diatoms and serves as a base for comparing their subsequent morphological changes. A brief review of diatom biology and morphology is provided to introduce this paper and that of Barron and Baldauf (this volume). Additional background information on the diatoms can be found in the works of Schrader and Schuette (1981), Tappan (1980), Bach and Burkhardt (1984), Barron (1985a, 1993), Fenner (1985), Ricard (1987), Bradbury (1988), Round et al. (1990), and Picket-Heaps et al. (1990).

Synapsids include modern mammals and their fossil ancestors, the non-mammalian synapsids, or ‘mammal-like reptiles' of old classifications. The synapsid fossil record extends from the Late Carboniferous to the present, a span of nearly 300 million years. However, it can be broken into two distinct phases of diversification, separated by about 150 million years. The first phase extends from the Late Carboniferous to the mid-Triassic, includes the first large land predators on Earth, and is almost entirely non-mammalian. The second phase begins about 65 million years ago after the demise of the dinosaurs, includes only mammals, and extends to the present. In this overview of synapsid predators, we emphasize terrestrial species of large size, and their adaptations for killing and feeding, rather than locomotion. Despite fundamental differences in jaw mechanics and tooth morphology, there are significant parallels in the non-mammalian and mammalian radiations of synapsid predators. Both groups evolve sabertooth forms more than once, and both evolve short-snouted, powerful biting forms. In addition, both the Late Carboniferous—Triassic and Cenozoic phases are characterized by repeated patterns of clade replacement, in which one or a few clades evolve large size and seem to dominate the carnivore guild for several million years, but then decline and are replaced by new taxa. Moreover, within both ancient and Cenozoic predator clades, there are parallel trends over time toward increased body size and hypercarnivory that likely result from a combination of interspecific competition and energetic constraints.

Morphometric techniques for the analysis of shape change in organisms have experienced a noteworthy development in the last decade. But despite the significant contributions that ostracodologists made to the field, their use in standard ostracode research is far from common. This contribution stresses the usefulness of morphometric methods to describe ostracode valve outlines and to summarize shape changes cued by environmental factors. Focus is on nonmarine ostracodes which are generally poorly ornamented so that their carapaces offer few landmarks for characterization of morphological change. Out of several alternatives three techniques for shape analysis are applied here: the B-splines method for approximative description of ostracode contours, Elliptic Fourier Analysis (EFA) and a Generalized (Resistant Fit) Procrustes Analysis. B-splines method is presented here for the first time within a biological framework and both its mathematical basis and practical usage are discussed. Additionally a computer program, Morphomatica, developed for performing B-splines analyses of ostracod outlines is briefly documented.

Three case studies exemplify here how morphometric analysis might help either to detect environmental influences in ostracode shape or to show how morphological diversity of ostracode valve reflects environmental change. First, morphological variability within a clonal lineage of Heterocypris barbara (Gauthier and Brehm) is shown to be related to environmental variables (mainly temperature) when raised under controlled conditions in the lab. Second, carapace variability at the population level is explored in a widely distributed species (Limnocythere inopinata Baird) sampled from distant localities. Morphometric analyses illustrate how such variability is not related to geographic distance but to environmental conditions. Finally, patterns of temporal change in morphological diversity of a widely distributed ostracode group, the Candoninae, are elucidated by using the B-splines method combined with multivariate statistical analysis.

It is concluded that morphometric methods deserve to be included in the methodological toolbox of practicing ostracodologists as they can provide useful information in ecological and paleoecological research.

The Precambrian-Cambrian transition saw the burgeoning of diverse skeletal organisms (“small shelly fossils”), represented in the fossil record by spicules, tubes, tests, conchs, shells, and a variety of sclerites and ossicles. Whereas calcareous biomineralization as such may have been facilitated by changes in ocean chemistry at this time, the utilization of biominerals in mineralized skeletons is a different process. The massive appearance of skeletons is most likely an epiphenomenon of the general radiation of body plans and tissues. The “choice” of biominerals (mainly calcium carbonates, calcium phosphates, and silica) may reflect the environmental conditions under which the particular skeleton first evolved.

The amber fossil record provides a distinctive, 320-million-year-old taphonomic mode documenting gymnosperm, and later, angiosperm, resin-producing taxa. Resins and their subfossil (copal) and fossilized (amber) equivalents are categorized into five classes of terpenoid, phenols, and other compounds, attributed to extant family-level taxa. Copious resin accumulations commencing during the early Cretaceous are explained by two hypotheses: 1) abundant resin production as a byproduct of plant secondary metabolism, and 2) induced and constitutive host defenses for warding off insect pest and pathogen attack through profuse resin production. Forestry research and fossil wood-boring damage support a causal relationship between resin production and pest attack. Five stages characterize taphonomic conversion of resin to amber: 1) Resin flows initially caused by biotic or abiotic plant-host trauma, then resin flowage results from sap pressure, resin viscosity, solar radiation, and fluctuating temperature; 2) entrapment of live and dead organisms, resulting in 3) entombment of organisms; then 4) movement of resin clumps to 5) a deposition site. This fivefold diagenetic process of amberization results in resin→copal→amber transformation from internal biological and chemical processes and external geological forces. Four phases characterize the amber record: a late Paleozoic Phase 1 begins resin production by cordaites and medullosans. A pre-mid-Cretaceous Mesozoic Phase 2 provides increased but still sparse accumulations of gymnosperm amber. Phase 3 begins in the mid-early Cretaceous with prolific amber accumulation likely caused by biotic effects of an associated fauna of sawflies, beetles, and pathogens. Resiniferous angiosperms emerge sporadically during the late Cretaceous, but promote Phase 4 through their Cenozoic expansion. Throughout Phases 3 and 4, the amber record of trophic interactions involves parasites, parasitoids, and perhaps transmission of diseases, such as malaria. Other recorded interactions are herbivory, predation, pollination, phoresy, and mimicry. In addition to litter, amber also captures microhabitats of wood and bark, large sporocarps, dung, carrion, phytotelmata, and resin substrates. These microhabitats are differentially represented; the primary taphonomic bias is size, and then the sedentary vs. wandering life habits of organisms. Organismic abundance from lekking, ant-refuse heaps, and pest outbreaks additionally contribute to bias. Various techniques are used to image and analyze amber, allowing assessment of: 1) ancient proteins; 2) phylogenetic reconstruction; 3) macroevolutionary patterns; and 4) paleobiogeographic distributions. Three major benefits result from study of amber fossil material, in contrast to three different benefits of compression-impression fossils.

Three properties of predation make this form of consumption an important agency of evolution: universality (all species have predators), high frequency (encounters of prey with predators test both parties often), and imperfection (many predatory attacks fail, enabling antipredatory selection to take place). On long time scales, predators have two principal effects: they influence their victims' phenotypes, and prey species that are highly vulnerable to all phases of predatory attacks are evolutionarily restricted to environments where predators are rarely encountered. Although predator and prey can affect each other's behavior and morphology on timescales commensurate with individual lifespans, predators have the evolutionary upper hand over the long run, especially in the expression of sensory capacities, locomotor performance, and the application of force. Only in passive defenses (armor, toxicity, large body size) does escalation favor the prey. In a review of methods for inferring predation in the geological past, I argue against the use of whole assemblages, which combine species of contrasting adaptive type, Instead, I strongly favor species-level and clade-level approaches (including examples of clade replacement) in which comparisons among places and among time intervals are made within the same adaptive types and the same physical environments. The available evidence, much of which comes from studies of shell drilling and shell breakage, points to temporal increases in both predator power and prey defenses. Escalation between species and their enemies, including predators, has proceeded episodically against a backdrop of generally increasing productivity and increasing top-down evolutionary control by high-energy predators during the Phanerozoic, the consumer age.

Perhaps the most conspicuous of associations between insects and plants is pollination. Pollinating insects are typically the first and most obvious of interactions between insects and plants when one encounters a montane meadow or a tropical woodland. The complex ecological structure of insect pollinators and their host plants is a central focus within the ever-expanding discipline of plant-insect interactions. The relationships between plants and insects have provided the empirical documentation of many case-studies that have resulted in the formulation of biological principles and construction of theoretical models, such as the role of foraging strategy on optimal plant-resource use, the advantages of specialized versus generalized host preferences as viable feeding strategies, and whether “pollination syndromes” are meaningful descriptions that relate flower type to insect mouthpart structure and behavior (Roubik, 1989; Ollerton, 1996; Waser et al., 1996; Johnson and Steiner, 2000). Much of the recent extensive discussion of plant-insect associations has centered on understanding the origin, maintenance, and evolutionary change in plant/pollinator associations at ecological time scales and increasingly at longer-term macroevolutionary time intervals (Armbruster, 1992; Pellmyr and Leebens-Mack, 1999). Such classical plant-insect association studies—cycads and cycad weevils, figs and fig wasps, and yuccas and yucca moths—were explored at modern time scales and currently are being examined through a long-term geologic component that involves colonization models based on cladogenetic events of plant and insect associates, buttressed by the fossil record (Farrell, 1998; Pellmyr and Leebens-Mack, 1999; A. Herre, pers. comm.). In addition to tracing modern pollination to the earlier Cenozoic and later Mesozoic, there is a resurgence in understanding the evolutionary history of earlier palynivore taxa (spore, prepollen and pollen consumers), which led toward pollination as a mutualism (Scott et al., 1992).

X-ray computed tomography (CT) provides a nondestructive means of studying the inside and outside of objects. It allows accurate visualization and measurement of internal features, that are otherwise impossible to obtain nondestructively, and is a lasting digital record that can be made available to future researchers, museums, and the general public. Here, an overview of CT scanning methodologies and protocol is provided, as well as some recent examples of how this technology is allowing paleontologists to make new inroads into understanding the ecology, evolution, and development of both extant and extinct organisms. Lastly, some frontiers and outstanding questions in the acquisition, processing, and storage of digital 3-D morphological data are highlighted.

During the Cretaceous and Paleogene, the Indian subcontinent was isolated as it migrated north from the east coast of Africa to collide with Asia. As it passed over the Reunion hotspot in the late Maastrichtian–early Danian, a series of lava flows extruded, known as the Deccan Traps. Also during this interval, there was a major mass-extinction event at the Cretaceous–Paleogene boundary, punctuated by a meteorite impact at Chicxulub, Mexico. What were the biological implications of these changes in paleogeography and the extensive volcanism in terms of biodiversity, evolution, and biogeography? By combining chronostratigraphic, paleosol, and paleobotanical data, an understanding of how the ecosystems and climates changed and the relative contributions of the Chicxulub impact, Deccan Traps volcanism, and paleogeographic isolation can be gained. Understanding relative ages of paleobotanical localities is crucial to determining floristic changes, and is challenging because different methods (e.g., magnetostratigraphy, radiometric dating, vertebrate and microfossil biostratigraphy) sometimes give conflicting answers, or have not been done for paleobotanical localities. Climatic data can be obtained quantitatively by studying paleosol geochemistry, as well as qualitatively by examining functional traits and nearest living relatives of fossil plants. An additional challenge is revising macrofossil data, which includes some confidently identified taxa and others with uncertain affinities. This is important for understanding ecosystem composition both spatially and temporally, as well as the biogeographic implications of an isolated India.

Stylophora and Homoiostelea are the largest classes of the subphylum Homalozoa. They have also been placed in the Calcichordata but that position is herein rejected. Stylophorans are divided into two orders the Cornuta and Ankyroida: cornutes have asymmetrical thecae, aulacophores with stylocones and cover plates over the food groove that open widely; ankyroids have essentially bilaterally symmetrical thecae, aulacophores with styloids and in most the cover plates do not open widely. Epispires, cothurnopores, and lamellipores in cornutes are respiratory structures not atypical of early echinoderms and are only superficially similar to chordate gill slits. The superior and inferior faces of cornute and ankyroid thecae and the aulacophores are homologous. There is no evidence that ‘mitrates’ (most ankyroids) are inverted or their aulacophores(calcichordate tail) have been lost and re-evolved.

Homoiosteles are superficially similar to stylophorans: the column or stele resembles the aulacophore and the theca in younger genera develope distinct marginal and somatic plate patterns. The earliest homoiosteles are attached by a holdfast, at least in juvenile stages, and this fixation may have imprinted some morphological features on steles of vagile genera. Earliest homoiosteles share significant characters with coeval species of the eocrinoid Gogia and it serves as outgroup.

Cladograms for Stylophora and Homoiostelea were generated by NONA, a phylogenetic program for personal computers.

Functional analysis through computer modeling can inform on how extinct organisms moved and fed, allowing us to test long-standing paleobiological hypotheses. Many such studies are based on digital models derived from computed tomography or surface scanning, but these methods are not appropriate for all fossils. Here, we show that box modeling—3-D modeling of complex shapes based on simple objects—can be used to reconstruct the morphology of various fossil specimens. Moreover, the results of computational functional analyses utilizing such models are very similar to those for models derived from tomographic or surface-based techniques. Box modeling is more broadly applicable than alternative methods for digitizing specimens; hence, there is great potential for this approach in paleontological functional analysis. Possible applications include large-scale comparative studies, analyses of hypothetical morphologies, and virtually restoring incomplete/distorted specimens.

The Synapsida is the mammal-like ramus of the Amniota, the sister group of the Sauropsida (or Reptilia of Gauthier et al., 1988). Synapsids are characterized by the possession of a lateral temporal fenestra (Fig. 1A), among other features (see Gauthier, this volume). Of all the great transitions between major structural grades within vertebrates, the transition from basal amniotes to basal mammals is represented by the most complete and continuous fossil record, extending from the Middle Pennsylvanian to the Late Triassic and spanning some 75 to 100 million years. Structural evolution of particular functional systems has been well investigated, notably the feeding mechanism (Barghusen, 1968; Crompton, 1972; Crompton and Parker, 1978; Crompton and Hylander, 1986) and the middle ear (Hopson, 1966; Allin, 1975, 1986; Allin and Hopson, 1992), and these studies have demonstrated the gradual nature of these major adaptive modifications.

Leaf physiognomy (size and shape) in fossils is commonly used to reconstruct terrestrial paleoclimate. Physiognomic leaf-climate methods are underpinned mostly by the covariation between toothed margins and mean annual temperature (MAT) and between leaf size and mean annual precipitation. Digital leaf physiognomy, a multivariate method based largely on variables that are functionally linked to climate and that can be measured by computer algorithm, minimizes many of the deficiencies present in other approaches. Nevertheless, the relationships between MAT and many physiognomic variables, especially tooth-related variables, are confounded by leaf thickness, leaf habit (deciduous vs. evergreen), and phylogenetic history. Until these factors are properly accounted for, a minimum error in MAT of ±4 ° for digital leaf physiognomy and ±5 ° for other methods should be assumed.

Among the most intriguing and significant aspects of the marine stratigraphic record are patterns of temporal change in fossil assemblages and paleocommunities. Understanding the stratigraphic patterns and the correct temporal scale of such faunal change is crucial to interpreting the underlying processes involved. Inattention to the temporal scale at which paleontological data are collected, and at which faunal change is observed, often results in the use of entirely inappropriate explanatory models. In many cases modern ecological theories have been misapplied to the fossil record because problems of scale were not adequately considered. The term “community” itself has been applied to such a wide range of fossil accumulations that it has ceased to have any consistent paleoecologic meaning (see discussion in Järvinen et al.,1986). For this reason, we prefer to use the term “assemblage” for time-averaged accumulations of fossils, and restrict “community” to only those organisms which actually lived together in the same space and time (i.e., a biocoenosis). Therefore, faunal assemblages, even when untransported, are the preserved amalgamated record of many successive communities within which short-term (10 – 100 years) changes may or may not be resolvable. Recurrent, compositionally similar assemblages, believed to have occupied generally similar benthic environments, are then grouped into biofacies which can be seen to intergrade and migrate through time.