‘Virtual paleontology’ entails the use of computational methods to assist in the three-dimensional (3-D) visualization and analysis of fossils, and has emerged as a powerful approach for research on the history of life. Three-dimensional imaging techniques allow poorly understood or previously unknown anatomies of fossil plants, invertebrates, and vertebrates, as well as microfossils and trace fossils, to be described in much greater detail than formerly possible, and are applicable to a wide range of preservation types and specimen sizes (Table 1). These methods include non-destructive high-resolution scanning technologies such as conventional X-ray micro-tomography and synchrotron-based X-ray tomography. In addition, form and function can be rigorously investigated through quantitative analysis of computer models, for example finite-element analysis.

Cranial endocasts, infillings of the skeletal void that once contained the brain and associated soft tissues, represent detailed anatomical structures that have long been the focus of paleontological investigation. We applied computed tomographics (CTs) in order to generate endocast models for the Paleozoic actinopterygian fishes Mimipiscis and Kentuckia, which serve as key representatives of anatomically primitive, early ray fins in analyses of early vertebrate relationships. The resultant endocranial models generally corroborate existing accounts of endocranial anatomy in these genera, drawn from descriptions of the inner face of the brain cavity. However, the endocasts also provide new anatomical details, the most significant of which are the presence in Mimipiscis of widely divergent olfactory tracts, small optic lobes, and anterior and posterior semicircular canals that extend dorsal to the roof of the endocranial chamber. By contrast, Kentuckia possesses a single, straight olfactory tract, wide optic lobes, and anterior and posterior semicircular canals that do not reach the dorsal surface of the endocast. In each of these features, Kentuckia resembles stratigraphically younger actinopterygians such as Lawrenciella and Kansasiella, whereas Mimipiscis more closely resembles sarcopterygians and other outgroups. This character distribution provides further support for earlier phylogenetic interpretations of these genera.

The Pliocene fossil porpoise SDSNH 65276 has extremely elongate mandibular morphology, unlike that of any marine amniote, and is superficially most similar to the living bird species known as skimmers (Rynchops sp.). Endocasts of the pterygoid sinuses and endocranial cavity were digitally segmented from high-resolution X-ray CT scans of the specimen to explore internal anatomy of functionally and phylogenetically important anatomical features of this specimen and odontocetes in general. The sinuses are similar in volume and shape to extant porpoise species, but the dorsal extension of the preorbital lobes are particularly elongate as in the harbor porpoise (Phocoena phocoena). The cranial endocast also shows similarities with extant porpoises, but has much deeper interhemispheric fissures, which are filled by ossified meninges, particularly a deep falx cerebri and shallower tentorium cerebelli. Ossifications of these parts of the meninges may reflect faster angular accelerations of the head, deeper diving ability, or both. Penetrations of the endocranial cavity for cranial nerves and blood vessels are like those of extant porpoises. The internal skull morphology of this unique delphinoid sheds additional light both on its phylogenetic affinities and novel odontocete adaptations.

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.

Studies of the development of organisms can reveal crucial information on homology of structures. Developmental data are not peculiar to living organisms, and they are routinely preserved in the mineralized tissues that comprise the vertebrate skeleton, allowing us to obtain direct insight into the developmental evolution of this most formative of vertebrate innovations. The pattern of developmental processes is recorded in fossils as successive stages inferred from the gross morphology of multiple specimens and, more reliably and routinely, through the ontogenetic stages of development seen in the skeletal histology of individuals. Traditional techniques are destructive and restricted to a 2-D plane with the third dimension inferred. Effective non-invasive methods of visualizing paleohistology to reconstruct developmental stages of the skeleton are necessary.

In a brief survey of paleohistological techniques we discuss the pros and cons of these methods. The use of tomographic methods to reconstruct development of organs is exemplified by the study of the placoderm dentition. Testing evidence for the presence of teeth in placoderms, the first jawed vertebrates, we compare the methods that have been used. These include inferring development from morphology, and using serial sectioning, microCT or synchrotron X-ray tomographic microscopy (SRXTM), to reconstruct growth stages and directions of growth. The ensuing developmental interpretations are biased by the methods and degree of inference. The most direct and reliable method is using SRXTM data to trace sclerochronology. The resulting developmental data can be used to resolve homology and test hypotheses on the origin of evolutionary novelties.

The application of synchrotron radiation X-ray tomographic microscopy (SRXTM) to the study of mesofossils of Cretaceous age has created new possibilities for the three-dimensional visualization and analysis of the external and internal structure of critical plant fossil material. SRXTM provides cellular and subcellular resolution of comparable or higher quality to that obtained from permineralized material using thin sections or the peel technique. SRXTM also has the advantage of being non-destructive and results in the rapid acquisition of large quantities of data in digital form. SRXTM thus refocuses the effort of the investigator from physical preparation to the digital post-processing of X-ray tomographic data, which allows great flexibility in the reconstruction, visualization, and analysis of the internal and external structure of fossil material in multiple planes and in two or three dimensions. A review of recent applications in paleobotany demonstrates that SRXTM will dramatically expand the level of information available for diverse fossil plants. Future refinement of SRXTM approaches that further increases resolution and eases digital post-processing, will transform the study of mesofossils and create new possibilities for advancing paleobotanical knowledge. We illustrate these points using a variety of Cretaceous mesofossils, highlighting in particular those cases where SRXTM has been essential for resolving critical structural details that have enhanced systematic understanding and improved phylogenetic interpretations.

A fossil plant of Eocene age from Antarctica was studied using X-ray and neutron tomography to reveal the three-dimensional plant structures encased within carbonate nodules. The fossil was identified as a branch and leaves of an araucarian conifer, which grew on the volcanic highlands of the Antarctic Peninsula region approximately 50 million yr ago. Both X-ray and neutron imaging techniques successfully exposed the full three-dimensional structure of the fossil without destroying the original specimen, revealing that most of the fossil was present as voids in the concretion and little organic matter was present. However, neutron tomography was found to produce images with superior quality and detail.

A new method of analyzing the internal shell morphology (including the complete brachidium of internal molds) of articulated brachiopod shells through the use of serial sections and digital three-dimensional reconstruction is presented. The method introduced is essential for the study of internal shell structures such as brachidia, or cardinalia, if computed tomography (CT) is not suitable or if a CT scanner is not available. A new species of Athyris from Givetian beds of Northwest Africa was selected to exemplify this method. To compare this species with figured serial sections in the literature, two-dimensional drawings of grinding surfaces are provided. Athyris africana n. sp. is only preserved as internal molds of articulated specimens. The new species is included in the evolutionary lineage of the group around Athyris concentrica. The faunal assemblage of A. africana n. sp. shows affinities to Western European and North American brachiopod faunas.

Fenestrate microbialites from the 2521±3 Ma Gamohaan Formation, South Africa, are composed of calcite with traces of kerogen that represent the remains of ancient microbial mats. To delineate the 3-D geometry of these microbialites, specimens were serial-sectioned; sequential slices were polished in 120 μm increments and scanned to yield an image stack, which was rendered into a virtual model of the microbialites. The resulting virtual representation allowed for visualization and characterization of microbial growth geometries that were not visible from 2-D surfaces. Several new insights into the structure of microbialites emerged from characterizing their 3-D structure including the recognition of two new features, linear structures and tubular structures. The long, thin nature of these structures makes them difficult to identify in two dimensions. However, in three dimensions, they can be traced as thin ropes of fossilized microbial communities emerging from more typical microbial mat structures. Overall, these results demonstrate a new set of microbial features in the Gamohaan Formation that were only characterized by reconstructing the full geometry of the microbialites in three dimensions.

Virtual paleontology unites a variety of computational techniques and methods for the visualization and analysis of fossils. Due to their great potential and increasing availability, these methods have become immensely popular in the last decade. However, communicating the wealth of digital information and results produced by the various techniques is still exacerbated by traditional methods of publication. Transferring and processing three-dimensional information, such as interactive models or animations, into scientific publications still poses a challenge. Here, we present different methods and applications to communicate digital data in academia, outreach and education. Three-dimensional PDFs, QR codes, anaglyph stereo imaging, and rapid prototyping—methods routinely used in the engineering, entertainment, or medical industries—are outlined and evaluated for their potential in science publishing and public engagement. Although limitations remain, these are simple, mostly cost-effective, and powerful tools to create novel and innovative resources for education, public engagement, or outreach.

This paper serves two roles. First, it acts as an introduction to Blender, an open-source computer graphics program, which can be of utility to paleontologists. To lessen the software's otherwise steep learning curve, a step-by-step guide to create an idealized reconstruction of a fossil in the form of a three-dimensional model in Blender, or to use the software to render results from ‘virtual paleontology' techniques, is provided as an online supplemental data file. Second, here we demonstrate the use of Blender with a case study on the extinct trigonotarbid arachnids. We report the limb articulations of members of the Devonian genus Palaeocharinus on the basis of exceptionally preserved fossils from the Rhynie Cherts of Scotland. We use these newly reported articulations to create a Blender model, and draw comparisons with the gait of extant arachnids to produce as accurate a representation of the trigonotarbid flexing its limbs and walking as possible, presented in additional online supplemental data files. Knowledge of the limb articulations of trigonotarbid arachnids also allows us to discuss their functional morphology: trigonotarbids' limbs and gait were likely comparable to extant cursorial spiders, but lacked some innovations seen in more derived arachnids.

The analysis of trace fossils usually is performed qualitatively, which makes comparing trace fossils from different units less objective than quantitative approaches. Quantifying the shape of trace fossils enables scientists to compare trace fossils described by different people with greater precision and accuracy. This paper describes several methods for quantifying invertebrate trace fossils, including morphology dependent methods (motility index, mesh size, topology, tortuosity, branching angle, and the number of cell sides) and morphology independent methods (fractal analysis, burrow area shape, and occupied space percentage (OSP)). These tools were performed on a select group of graphoglyptid trace fossils, highlighting the benefits and flaws of each analytical approach. Combined together, these methods allow for more objective comparisons between different trace fossils.

Finite element analysis (FEA) is a powerful quantitative tool that models mechanical performance in virtual reconstructions of complex structures, such as animal skeletons. The unique potential of FEA to elucidate the function, performance, and ecological roles of extinct taxa is an alluring prospect to paleontologists, and the technique has gained significant attention over recent years. However, as with all modeling approaches, FE models are highly sensitive to the information that is used to construct them. Given the imperfect quality of the fossil record, paleontologists are unlikely to ever know precisely which numbers to feed into their models, and it is therefore imperative that we understand how variation in FEA inputs directly affects FEA results. This is achieved through sensitivity and validation studies, which assess how inputs influence outputs, and compare these outputs to experimental data obtained from extant species. Although these studies are restricted largely to primates at present, they highlight both the power and the limitations of FEA. Reassuringly, FE models seem capable of reliably reproducing patterns of stresses and strains even with limited input data, but the magnitudes of these outputs are often in error. Paleontologists are therefore cautioned not to over-interpret their results. Crucially, validations show that without knowledge of skeletal material properties, which are unknowable from fossilized tissues, absolute performance values such as breaking stresses cannot be accurately determined. The true power of paleontological FEA therefore lies in the ability to manipulate virtual representations of morphology, to make relative comparisons between models, and to quantitatively assess how evolutionary changes of shape result in functional adaptations.

Ocean Drilling Program (ODP) Holes 980 B and C, Feni Drift at the eastern slope of the Rockall Plateau, eastern North Atlantic, were examined for late Quaternary deep-sea ostracode taxonomy. Nineteen genera and 32 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images. One new species Cytheropteron paramassoni n. sp. is described and one new name Eucytherura zehali is proposed for Eucytherura hazeli Yasuhara et al., 2009. This study provides updated taxonomic information for deep-sea ostracode genera and species from the eastern North Atlantic, which is an important baseline for application of deep-sea ostracodes to paleoceanographical reconstructions and paleoecological studies in this region.

Cretaceous non-marine deposits are widespread in China and have been studied comprehensively. The Songliao Basin in northeast China is thought to be well suited for investigation of Cretaceous biostratigraphy. However, despite much research having been conducted in the basin, little is known about its Late Cretaceous biostratigraphy and paleoenvironment. Here, we establish a high-resolution biostratigraphy of the Late Cretaceous based on ostracods from borehole SK1(n) in the Songliao Basin, northeast China. As part of the present study, 45 species assigned to 20 genera have been recovered, with one new species (Ilyocypris bisulcata n. sp.) and five ostracod assemblages: the Cypridea gunsulinensis–Mongolocypris magna assemblage, which is marked by the first occurrence (F.O.) of Ilyocyprimorpha with nodes and spines; the Ilyocyprimorpha–Limnocypridea sunliaonensis–Periacanthella assemblage, which ranges from the F.O. of Ilyocyprimorpha with nodes and spines to the F.O. of Strumosia sp.; the Strumosia inandita assemblage from the F.O. of Strumosia sp. to the lower occurrence (L.O.) of Strumosia inandita; the Talicypridea amoena–Metacypris kaitunensis–Ziziphocypris simakovi assemblage from the F.O. of Mongolocypris apiculata (Cea) and Talicypridea amoena to the F.O. of Ilyocypris sp.; and the Ilyocypris assemblage from the F.O. of Ilyocypris sp. to the L.O. of Ilyocypris bisulcata n. sp.

Moreover, the zonal fossil Ilyocypris bisulcata n. sp. of Zone 5 is here described for the first time from the upper Mingshui Formation, and Paleocene charophyte genera including Neochara and Grovesicahra have been found to coexist with the Zone 5 fauna. The age of the Ilyocypris Assemblage is assigned to the latest Maastrichtian to the earliest Danian.

The non-marine Lower Cretaceous ostracod genus Kegelina new genus (Cypridoidea, Cyprideidae) is known from South America (Bahia state, eastern Brazil), West Africa (Gabon and ‘Congo'), and North America (Montana, Idaho and Wyoming, U.S.A.). It comprises five species: Kegelina anomala (Peck, 1941) new combination, Kegelina armata (Krömmelbein, 1962) new combination, Kegelina bisculpturata (Wicher, 1959) new combination, Kegelina depressa (Moura, 1972) new combination, and Kegelina kegeli (Wicher, 1959) new combination, all of which having formerly been described as representatives of Cypridea Bosquet, 1852. The closer relationships of Kegelina new genus among the Cyprideidae Martin, 1940 are discussed. Other potential species of Kegelina n. gen. are presumed to occur in northeastern China and Europe but remain to be examined.

A new species in the extant genus, Hydrotrupes Sharp, H. prometheus n. sp., (Coleoptera, Dytiscidae) is described from Baltic amber (Eocene) based on examination of a single female specimen. This description represents one of a limited number of diving beetle taxa described from fossiliferous amber and is currently the oldest known fossil assigned to Agabinae. Based on this specimen Hydrotrupes is at least 40 million years old. The occurrence of Hydrotrupes during the Eocene suggests that the current disjunct distribution of living Hydrotrupes species occurring in western North America and eastern China is a relict of former widespread distribution in the northern continents. Considering the age of this fossil and its similarity to living members of the genus Hydrotrupes, the conservation of morphology in this lineage of diving beetles is notable. Key morphological characters of the new species are illustrated, and the significance of this discovery for understanding Agabinae evolution and the biogeography of this previously hypothesized trans-Beringian lineage is discussed.

A new species of boreopterid pterosaur from the new fossil locality, Heichengzi, Beipiao, western Liaoning, China allows a reassessment of the Boreopteridae. In this new analysis, three species, Boreopterus cuiae, Boreopterus giganticus n. sp., and Zhenyuanopterus longirostris, are included within the Boreopteridae united by the autopomorphic occurrence of two main tooth morphologies, an equal length of the tibia and femur, and weak feet. Other taxa previously placed within the Boreopteridae are not in a monophyletic group with the former three species. Boreopterus has fewer teeth and a shorter tooth row than that in Zhenyuanopterus. This new Boreopterus species has a large size, a piriform orbit, an extensively fenestrated lacrimal, and a posteriorly directed lacrimal process, that differs from Boreopterus cuiae.