Oxygen isotope paleotemperature studies of the Mesozoic and Paleozoic are based mainly on conodonts, belemnite guards, and brachiopod shells—material resistant to diagenesis and generally precipitated in oxygen isotope equilibrium with ambient water. The greatest obstacle to accurate oxygen isotope paleothermometry in deep time is uncertainty in the oxygen isotopic composition of the ambient seawater. The second greatest obstacle is fossil diagenesis. Useful application of the oxygen isotope method to brachiopod shells requires extreme care in sample screening and analyses, and is best done with scanning-electron microscopy, and petrographic and cathodoluminescence microscopy, and trace-element analysis. Correct interpretation of oxygen isotope data is greatly aided by thorough understanding of the paleolatitude, paleoecology, and depositional environment of the samples. The oxygen isotope record for the Triassic, based on brachiopod shells, is too sparse to show any distinct isotopic features. Jurassic and Early Cretaceous δ18O records, based on belemnites, show a Toarcian (Jurassic) decline (warming), a Callovian-Oxfordian acme, and an Early Cretaceous increase (cooling) to a Valanginian-Hauterivian maximum, followed by a decline (warming) to a middle Barremian minimum. Deep-time applications to oxygen isotope thermometry provide evidence for cooling and glaciation in the Ordovician, Carboniferous, and Permian. The δ18O values from Silurian and Devonian brachiopod shells and conodonts average lower than those of the remaining Phanerozoic because of the absence of continental glaciers and possibly higher temperatures (~37°?), although slightly lower (≤2%o) seawater δ18O cannot be ruled out. The hypothesis of high temperatures in the early Paleozoic implies a relatively constant hydrospheric δ18O, which is supported by clumped isotope paleotemperatures. However, more research is needed to develop methods for evaluating clumped isotope reordering in fossils. Ongoing and future research in oxygen isotope and clumped isotope thermometry hold the promise of resolving deep-time temperatures, seawater δ18O, and salinity with heretofore unavailable accuracy (±2°, ±0.4%o, and ±2 psu), providing the environmental setting for the evolution of metazoan life on Earth.

Predatory theropod dinosaurs can usually be identified as such by features of their jaws, teeth, and postcrania, but different clades of these reptiles differed in their adaptations for prey handling. Inferences about theropod diets and hunting behavior based on functional morphology are sometimes supported by evidence from taphonomic associations with likely prey species, bite marks, gut contents, coprolites, and trackways. Very large theropods like Tyrannosaurus are unlikely to have been pure hunters or scavengers, and probably ate whatever meat they could easily obtain, dead or alive. Theropods were not the only dinosaur hunters, though; other kinds of large reptiles undoubtedly fed on dinosaurs as well The taxonomic composition of dinosaurian predator-prey complexes varies as a function of time and geography, but an ecologically remarkable feature of dinosaurian faunas, as compared with terrestrial mammalian faunas, is the very large size commonly attained by both herbivorous and carnivorous dinosaurs. The K/T extinction event(s) did not end dinosaurian predation, because carnivorous birds remained prominent predators throughout the Cenozoic Era.

In this chapter we discuss methods for analyzing continuous traits, with an emphasis on those approaches that rely on explicit statistical models of evolution and incorporate genealogical information (ancestor–descendant or phylogenetic relationships). After discussing the roles of models and genealogy in evolutionary inference, we summarize the properties of commonly used models including random walks (Brownian motion), directional evolution, and stasis. These models can be used to devise null-hypothesis tests about evolutionary patterns, but it is often better to fit and compare models equally using information criteria and related approaches. We apply these methods to a published data set of dental measurements in a sequence of ancestor–descendant populations in the early primate Cantius, with the particular goal of determining the best-supported mode of evolutionary change in this lineage. We also assess a series of questions about the evolution of femoral dimensions in several clades of dinosaurs, including testing for a trend of increasing body size (Cope's Rule), testing for correlations among characters, and reconstructing ancestral states. Finally, we list briefly some additional models, approaches, and issues that arise in genealogically informed analyses of phenotypic evolution.

Like most classifications of molluscan shell microstructure published during the past 25 years (e.g., MacClintock, 1967; Kobayashi, 1964, 1971; Taylor, Kennedy and Hall, 1969, 1973; Grégoire, 1972a), the present one is based largely on Bøggild's (1930) monographic work, redefined from a modern perspective of combined light and scanning electron microscopy. However, this is the first attempt to integrate shell microstructure terminology for mollusks with that employed by students of bryozoan and brachiopod shell microstructure (e.g., Williams, 1968a,b, 1970, 1973; Williams and Wright, 1970; Armstrong 1968, 1969; Sandberg, 1971, 1977; Brunton, 1972; MacKinnon, 1974, 1977; MacKinnon and Williams, 1974; Iwata, 1981, 1982). An integration of nomenclatorial schemes is desirable for purposes of interphylum comparison, and is presently needed because there is considerable overlap and inconsistency in the application of microstructural terminology even within single molluscan classes. The present synthesis of shell microstructure nomenclature is possible primarily because of the extensive data base of invertebrate shell mineralogy, microstructure and especially ultrastructure published in more than 300 references in the past 15 years. To these data, the authors have contributed original information of shell mineralogy and microstructure for scores of Recent and fossil mollusks, brachiopods and bryozoans, with a clear emphasis on bivalved mollusks. Many inadequately described microstructure terms have been reanalyzed during the course of this study, either by examining species cited in the literature, or by using closely related species. Perhaps because they are better studied, but probably for other reasons as well, the diversity of molluscan shell microstructures is considerably greater than that of brachiopods and bryozoans combined (Carter, 1979). Consequently, most of the present nomenclature is based on mollusks, and only three of the major microstructural arrangements described in this guide (crossed bladed, semi-nacreous and semi-foliated) were known first in brachiopods or bryozoans and later recognized in molluscs.

Virtual paleontology is the study of fossils through three-dimensional digital visualizations; it represents a powerful and well-established set of tools for the analysis and dissemination of fossil data. Techniques are divisible into tomographic (i.e., slice-based) and surface-based types. Tomography has a long predigital history, but the recent explosion of virtual paleontology has resulted primarily from developments in X-ray computed tomography (CT), and of surface-based technologies (e.g., laser scanning). Destructive tomographic methods include forms of physical-optical tomography (e.g., serial grinding); these are powerful but problematic techniques. Focused Ion Beam (FIB) tomography is a modern alternative for microfossils; it is also destructive but is capable of extremely high resolutions. Nondestructive tomographic methods include the many forms of CT, which are the most widely used data-capture techniques at present, but are not universally applicable. Where CT is inappropriate, other nondestructive technologies (e.g., neutron tomography, magnetic resonance imaging, optical tomography) can prove suitable. Surface-based methods provide portable and convenient data capture for surface topography and texture, and might be appropriate when internal morphology is not of interest; technologies include laser scanning, photogrammetry, and mechanical digitization. Reconstruction methods that produce visualizations from raw data are many and various; selection of an appropriate workflow will depend on many factors, but is an important consideration that should be addressed prior to any study. The vast majority of three-dimensional fossils can now be studied using some form of virtual paleontology, and barriers to broader adaptation are being eroded. Technical issues regarding data sharing remain problematic. Technological developments continue; those promising tomographic recovery of compositional data are of particular relevance to paleontology.

Clumped isotopes geochemistry measures the thermodynamic preference of two heavy, rare, isotopes to bind with each other. This preference is temperature dependent, and is more pronounced at low temperatures. Carbonate clumped isotope values are independent of the carbonate δ13C and δ18O, making them independent of the carbon or oxygen composition of the solution from which the carbonate precipitated. At equilibrium, it is therefore a direct proxy for the temperature in which the carbonate mineral formed. In most cases, carbonate clumped isotopes record the temperature of carbonate formation, irrespective of the mineral form (calcite, aragonite, or bioapatite) or the organism making it. The carbonate formation temperatures obtained from carbonate clumped isotope analysis can be used in conjunction with the δ18O of the same carbonate, to constrain the oxygen isotope composition of the water from which the carbonate has precipitated. There are, however, cases of deviation from thermodynamic equilibrium, where both clumped and oxygen isotopes are offset from the expected values. Such carbonates must be characterized and calibrated separately. For deep-time applications, special care must be paid to the preservation of the original signal, in particular with respect to diagenetic alteration associated with atomic scale diffusion that may be undetectable by common tests for diagenesis.

Photosymbiosis has been an important process in the evolution of ancient reef systems and in reef success today. Modern reefs and many of those in the geologic past inhabited nutrient-depleted settings. The complete collapse of some ancient reef ecosystems may be attributed to the breakdown of the ecologic and physiologic relationships between symbiont and host. Many algal groups developed symbioses with calcifying metazoans and protists and live with them, but the most common of these today are dinoflagellates in the genus Symbiodinium, sometimes called zooxanthellae. This photosymbiotic relationship conferred important metabolic advantages to both partners, allowing exploitation of tropical, shallow-water oligotrophic settings. In addition to improved metabolism, a by-product was rapid calcification which increased the growth of reefs and provided advantages to the hosts through larger and stronger skeletal support. Strong evolutionary pressures exerted by the symbiont-host relationship created bonds and favored longevity and adaptive novelty. Photosynthesis accounts for the remarkable reef growth and carbonate sedimentation in the tropics. Photosymbiosis gave reef organisms an adaptive edge to develop new life strategies that could not be developed by organisms which did not foster this relationship. Many living calcified organisms harbor many different photosymbionts and likely a variety of ancient calcified organisms did too (foraminifera, calcified sponges, corals, brachiopods and bivalve mollusks). Symbiodinium now a dominant symbiont apparently appeared in the Eocene and so was probably not utilized by earlier reef organisms, although the fossil record of dinoflagellates most closely related to Symbiodinium extends back to the Triassic. Today Symbiodinium inhabits a wide variety of unrelated host organisms from protists to mollusks. While the identity of more ancient photosymbionts is unclear, indirect evidence suggests photosymbiotic ecosystems existed as far back as the Proterozoic and possibly even earlier.

Assessment of photosymbiosis in ancient reef ecosystems requires recognition of specific characteristics possessed by the calcifying reef organisms. Since the symbionts do not fossilize, the presence of photosymbiosis in fossils is a working hypothesis based on modern symbioses and best confirmed by a set of specific morphologic adaptations and isotopic analyses. Important among these is the thin tissue syndrome—the modification to achieve the “solar panel” effect. Large size and unusual or complex morphology also may indicate photosymbiosis. In the case of colonial organisms such as corals, high levels of corallite integration, where corallites are modified for increasing cooperation, may assist because most colonial photosymbiotic organisms today, such as corals, are exclusively photosymbiotic.

Analysis of organisms and reefs through geologic time permits assessment of the strength of photosymbiosis as a driving force. Reef ecosystems revealing the strongest assessment for photosymbiosis are those of the mid-Paleozoic (Late Ordovician to Devonian), late Paleozoic, early Mesozoic and Neogene. The Early Cambrian archaeocyathan (sponge) reefs indicate photosymbiosis but perhaps with different ancient symbionts such as cyanobacteria, also contained in some modern sponges. Reef ecosystems of the late Paleozoic and early part of the Jurassic indicate the presence of some photosymbiosis. The extinction of many photosymbiotic reef ecosystems during critical intervals of mass extinctions may have been driven by the failure of the symbiosis or demise of the symbionts. Reef gaps in the geologic record reflect the absence of photosymbiosis. The present-day reef crisis involves disturbance of photosymbiosis, and study of future reef declines will benefit by application of data from the fossil record.

A broad array of the highly variable morphological characters available in Ostracoda were used (1) to construct a new tabular key to the families of the subclass Myodocopa (and to differentiate the Myodocopa from the Podocopa), and (2) to explore the evolution of bioluminescence in the myodocopid family Cypridinidae. Results of a cladistic analysis of the Cypridinidae strongly support a single origin of bioluminescence within the family; a single clade contains at least 64 species known to luminesce (not all described). Furthermore, within that large clade, complex bioluminescent mating displays were confined by the analysis to a single clade of exclusively Caribbean cypridinids, though that result was unresolved by bootstrap analysis.

Chemically different bioluminescence occurs convergently in two ostracode groups; it is produced within carapace glands of certain Halocypridina, but it is produced and extruded from the upper lips of many cypridinid Myodocopida and serves as an antipredatory behavior in both groups. Additionally at least 60 cypridinid species also produce spectacular and complex species-specific male mating displays nightly in the Caribbean Sea. The cladistic analysis using 58 morphological characters of 44 taxonomic units (24 described genera of Cypridinidae, 11 individual species assigned to the genus Vargula, six groups of bioluminescent signalling Caribbean species (many undescribed), the Cylindroleberididae, and the Philomedidae) was performed using PAUP with the parsimony criterion. Twenty-five of the characters were previously underutilized characters of the complex upper lip and large male copulatory limbs discovered through dissection and SEM. These proved especially valuable, but characters of all other limbs were also included.

The Cypridinidae was confirmed as a monophyletic taxon with several well-supported subclades in addition to the large bioluminescent one. Skogsbergia, which apparently uses an antennular fan of iridescent blue filaments in courtship (Parker, 1997) belongs to a clade with five other cypridinid genera, including the four that have a similar fan. The genus Vargula was determined to be a polyphyletic assemblage. New genera will be established for former Vargula species including: “V.” tubulata, “V.” hilgendorfii, “V.” tsujii and all bioluminescent signaling species. Similar problems may exist for other large cypridinid genera, and clearer resolution of generic definitions might possibly reveal more significant patterns of geographic distribution within the family.

Most characters of the carapace were found to be too convergent to be useful. Though carapace characters are diagnostic for some ostracode taxa, most should not be used by themselves to identify ostracodes with certainty. General aspects of reproduction are also reviewed.

Echinoderms underwent a major two-part radiation that produced all of the major groups found in the fossil record between the Early Cambrian and the Middle Ordovician. A small initial radiation in the Early and Middle Cambrian produced about nine classes containing low-diversity members of the Cambrian Evolutionary Fauna. These were characterized by primitive morphology, simple ambulacral feeding structures, and the early development of a multiplated stalk or stem for attachment to skeletal fragments on a soft substrate. Several groups became extinct at the end of the Middle Cambrian, leaving the Late Cambrian as a gap of very low diversity in the fossil record of echinoderms with only four classes preserved and very few occurrences of complete specimens, mostly associated with early hardgrounds. The survivors from this interval re-expanded in the Early Ordovician and were joined by many newly evolved groups to produce a much larger radiation of more advanced, diverse, and successful echinoderms representing the Paleozoic Evolutionary Fauna on both hard and soft substrates. At least 17 classes were present by the Middle Ordovician, the all-time high point for echinoderm class diversity, and nearly all of the major ways-of-life (except for deep infaunal burrowing) had been developed. With the rise to dominance of crinoids, many less successful or archaic groups did not survive the Middle Ordovician, and echinoderm class diversity dropped further because of the mass extinction at the end of the Ordovician. This weeding-out process of other less-successful echinoderm groups continued throughout the rest of the Paleozoic, and only five classes of echinoderms have survived to the Recent from this early Paleozoic radiation.

Since their inception in 1978, the annual short courses sponsored by the Paleontological Society have aimed to broaden and to enhance the professional education of paleontologists, including students new to the field. The 1993 short course continues in that tradition, but differs from many previous courses in focussing not on a taxonomic group but on a broader aspect of the fossil record, namely the time resolution of fossil assemblages. This seemed an especially good topic for a short course because questions of absolute and relative time – how old? how fast? how synchronously? – pervade paleontology and historical geology in general.

Arms races between predators and prey may be driven by two related processes—escalation and coevolution. Escalation is enemy-driven evolution. In this top-down view of an arms race, the role of prey (with the exception of dangerous prey) is downplayed. In coevolution, two or more species change reciprocally in response to one another; prey are thought to drive the evolution of their predator, and vice versa. In the fossil record, the two processes are most reliably distinguished when the predator-prey system is viewed within the context of the other species that may influence the interaction, thus allowing for a relative ranking of the importance of selective agents. Detailed documentation of the natural history of living predator-prey systems is recommended in order to distinguish the processes in some fossil systems. A geographic view of species interactions and the processes driving their evolution may lead to a more diverse array of testable hypotheses on how predator-prey systems evolve and what constraints interactions impose on the evolution of organisms. Scale is important in evaluating the role of escalation and coevolution in the evolution of species interactions. If short-term reciprocal adaptation (via phenotypic plasticity or selection mosaics among populations) between predator and prey is a common process, then prey are likely to exert some selective pressure over their predators over the short term (on ecological time scales), but in the long run predators may still exert primary “top-down” control in directing evolution. On the scale of evolutionary time, predators of large effect likely control the overall directionality of evolution due to the inequalities of predator and prey in control of resources.

Body mass is a key parameter for understanding the physiology, biomechanics, and ecology of an organism. Within paleontology, body mass is a fundamental prerequisite for many studies considering body-size evolution, survivorship patterns, and the occurrence of dwarfism and gigantism. The conventional method for estimating fossil body mass relies on allometric scaling relationships derived from skeletal metrics of extant taxa, but the recent application of three-dimensional imaging techniques to paleontology (e.g., surface laser scanning, computed tomography, and photogrammetry) has allowed for the rapid digitization of fossil specimens. Volumetric body-mass estimation methods based on whole articulated skeletons are therefore becoming increasingly popular. Volume-based approaches offer several advantages, including the ability to reconstruct body-mass distribution around the body, and their relative insensitivity to particularly robust or gracile elements, i.e., the so-called ‘one bone effect.’ Yet their application to the fossil record will always be limited by the paucity of well-preserved specimens. Furthermore, uncertainties with regards to skeletal articulation, body density, and soft-tissue distribution must be acknowledged and their effects quantified. Future work should focus on extant taxa to improve our understanding of body composition and increase confidence in volumetric model input parameters.

Ostracodes are ecologically diverse at the present day, inhabiting marine, nonmarine and (semi)terrestrial environments. Modern benthic faunas are dominated by Podocopa (marine and nonmarine Podocopida, marine Platycopida, and extremely rare marine Palaeocopida), while the Myodocopa (Myodocopida and Halocyprida) are diverse in the marine pelagic realm, as well as having many nektobenthic taxa. Their excellent fossil record facilitates reconstructions of their phylogenetic relationships and ecological adaptations throughout their Phanerozoic history. The earliest known ostracodes are of Ordovician age, when representatives of the extant orders Podocopida, Platycopida and Palaeocopida were already present, together with (possible) early Myodocopa and extinct orders such as the Leperditicopida. Cambrian bivalved arthropods such as bradoriids and phosphatocopids are no longer regarded as Ostracoda.

Ordovician ostracodes were predominantly marine meiobenthos, diversifying into depth-related assemblages dominated by palaeocopids. The beginnings of podocopan radiations in marginal marine environments (brackish and hypersaline waters) are seen in the Silurian, as is an ecological shift of nektobenthic myodocopans to form the first pelagic ostracode faunas. Of the diverse marine Paleozoic palaeocopids, only a single lineage, the puncioids, survived beyond the Permian and today live interstitially in high-energy shallow marine environments. Post-Paleozoic marine benthic ostracode faunas are dominated by cytheroidean podocopids which gave rise to several radiations in the Mesozoic and Cenozoic. The healdiid metacopines (podocopans), of Devonian origins, enjoyed a marine radiation in the Triassic and Early Jurassic and then became extinct. Marine platycopids were also significant components of Mesozoic marine faunas and are relatively diverse in warm, shallow carbonate environments today.

Suggestions that the first freshwater ostracodes were Devonian leperditicopids are controversial; undoubted nonmarine / freshwater radiations developed during the Early Carboniferous, including darwinuloidean and carbonitoidean podocopids and possibly some platycopids, together with cytheroidean podocopids (limnocytherids) in the Late Carboniferous. Of these only the darwinuloideans and limnocytherids survived the end-Permian extinctions and are still found in modern nonmarine waters; however, the dominant freshwater ostracodes today are the cypridoidean podocopids, whose radiation began in the Triassic and attained explosive proportions in the Late Jurassic - Early Cretaceous (although there are controversial suggestions of Paleozoic origins for this group). In addition to the limnocytherids there have been several other, separate invasions of nonmarine waters by cytheroidean podocopids, notably the cytherideids and the commensal entocytherids. Radiations in damp terrestrial environments have been initiated by both marine and nonmarine groups, but such invasions lack a recognized fossil record; (semi)terrestrial cypridoideans and darwinuloideans may represent Late Mesozoic radiations, while the Terrestricytheroidea, with marine affinities, may be much older, possibly Late Paleozoic in origin.

Application of planktonic foraminifera to micropaleontological, paleoceanographic and paleoclimatic research has enjoyed more than 150 years of activity. During the first century, foraminifera were used primarily for biostratigraphic analysis. Although fossil shells were recognized from beach sands and deep sea sediments as early as 1826 (d'Orbigny, 1826; Parker and Jones, 1865), it wasn't until Owen (1867) and the scientific results of the Challenger expedition (Brady, 1884) that the planktonic life habitat of these marine protozoans was clearly established. By the early 20th century, researchers were studying the biology of planktonic foraminifera at the cellular level (Rhumbler, 1901; Le Calvez, 1936), and linking their distributional patterns to regions of the ocean surface (Lohmann, 1920; Schott, 1935).

New information and discussions regarding Mesozoic diatoms presented over the last decade advanced our knowledge of their origin and early history. The oldest confirmed centric diatom fossils are presented here from the earliest Cretaceous, and araphid and raphid pennate diatoms now date from the Late Cretaceous; all from terrestrial sediments. Molecular sequencing helped clarify relationships between diatom lineages, and verify the position of diatoms within the heterokontophytes. Molecular clock approaches estimate a diatom origin near ~135 Ma, but not before 240 Ma. Biomarkers in marine sediments are able to trace a diatom presence back to the mid-Cretaceous, even when siliceous fossils are absent. Seasonal growth and encystment cycles in Late Cretaceous planktonic marine diatoms are now well documented. A biostratigraphic framework for the Late Cretaceous Arctic will aid regional and global biostratigraphic correlations. The systematic position of many new taxonomic groups is now included within a more natural classification scheme that better reflects phylogenetic relationships evident in molecular data and affirmed by biostratigraphic micropaleontology. Discussions regarding the impact of diatoms on several global systems are maturing, as more information becomes available. Four stages in diatom evolution are proposed to explain the history of radiation, extinction, and expansion into new environments and habitats during the Mesozoic.

Carnivory is the consumption of one animal by another animal; among invertebrates in terrestrial and freshwater ecosystems this type of feeding can take three forms: predation, parasitoidism, and parasitism. Differences among these three functional modes involve (i) whether the duration of feeding on the prey item is quick or there is an accommodation, coevolutionary or otherwise, between the carnivore and the host prey; (ii) whether the prey or host is killed; (iii) whether single or multiple prey or host items are consumed during the carnivore's lifespan, and (iv) the relative sizes of the carnivore and its prey or host. Uniformitarian and nonuniformitarian evidence directly relating to the history of carnivory can be found in exceptionally preserved deposits from the mid-Paleozoic to the Recent, but such evidence is relatively rare because carnivores are the least represented trophic group in ecosystems. Six types of paleobiological data provide evidence for carnivory: taxonomic affiliation, fossil structural and functional attributes, organismic damage, gut contents, coprolites, and indications of mechanisms for predator avoidance.

Only 12 invertebrate phyla have become carnivorous in the continental realm. Six are lophotrochozoans (Acanthocephala, Rotifera, Platyhelminthes, Nemertinea, Mollusca, and Annelida) and six are ecdysozoans (Nematoda, Nematomorpha, Tardigrada, Onychophora, Pentastoma, and Arthropoda). Most of these groups have poor continental fossil records, but the two most diverse—nematodes and arthropods—have comparatively good representation. The record of arthropods documents (i) the presence of predators among primary producers, herbivores, and decomposers in early terrestrial ecosystems; (ii) the addition later in the fossil record of the more accommodationist strategies of parasitoids and parasites interacting with animal hosts; (iii) the occurrence of simpler food-web structures in terrestrial ecosystems prior to parasitoid and parasite diversification; and (iv) a role for mass extinction in the degradation of food-web structure that ultimately affected carnivory. Future research should explore how different modes of carnivory have brought about changes in ecosystem structure through time. Despite numerous caveats and uncertainties, trace fossils left by predators on skeletons of their prey remain one of the most promising research directions in paleoecology and evolutionary paleobiology.

The Cryptogamic, or spore-producing, plants of today are composed of three nonvascular, bryophyte groups (mosses, liverworts, and hornworts) and several vascular groups (ferns, club mosses, and horsetails). All of these plants produce abundant spores, which serve as propagules for dispersing and, to some extent, preserving plants through periods of ecological stress. Plant spores are typically formed as the end products of meiosis (reduction division) from a dividing sporocyte, or spore mother cell (smc). Because of this, they typically occur in groups of four, with each individual spore bearing a characteristic trilete, or Y-shaped mark on its common contact surface. Spore walls, composed of an inert, heterogeneous polymer called sporopollenin, are extremely resistant to the chemical vicissitudes of the terrestrial environment. This property of typical plant spores ultimately allows them to be quite abundant in fine grained clastic rocks. Although fossilized spores represent only a small part of the once-living plant, in many cases, they represent an important component of the plant fossil record, especially when the preservation of macroscopic tissues is lacking.

We rely on observations of occurrences of fossils to infer the rates and timings of origination and extinction of taxa. These estimates can then be used to shed light on questions such as whether extinction and origination rates have been higher or lower at different times in earth history or in different geographical regions, etc. and to investigate the possible underlying causes of varying rates. An inherent problem in inference using occurrence data is one of incompleteness of sampling. Even if a taxon is present at a given time and place, we are guaranteed to detect or sample it less than 100% of the time we search in a random outcrop or sediment sample that should contain it, either because it was not preserved, it was preserved but then eroded, or because we simply did not find it. Capture-mark-recapture (CMR) methods rely on replicate sampling to allow for the simultaneous estimation of sampling probability and the parameters of interest (e.g. extinction, origination, occupancy, diversity). Here, we introduce the philosophy of CMR approaches especially as applicable to paleontological data and questions. The use of CMR is in its infancy in paleobiological applications, but the handful of studies that have used it demonstrate its utility and generality. We discuss why the use of CMR has not matched its development in other fields, such as in population ecology, as well as the importance of modelling the sampling process and estimating sampling probabilities. In addition, we suggest some potential avenues for the development of CMR applications in paleobiology.

This paper addresses the taphonomic processes responsible for fossil preservation in calcium phosphate, or phosphatization. Aside from silicification and rarer examples of carbonaceous compression, phosphatization is the only taphonomic mode claimed to preserve putative subcellular structures. Because this fossilization window can record such valuable information, a comprehensive understanding of its patterns of occurrence and the geochemical processes involved in the replication of soft tissues are critical endeavors. Fossil phosphatization was most abundant during the latest Neoproterozoic through the early Paleozoic, coinciding with the decline of non-pelletal phosphorite deposits. Its temporal abundance during this timeframe makes it a particularly valuable window for the study of early animal evolution. Several occurrences of phosphatization from the Ediacaran through the Permian Period, including Doushantuo-type preservation of embryo-like fossils and acritarchs, phosphatized gut tracts within Burgess Shale-type carbonaceous compressions, Orsten-type preservation of meiofaunas, and other cases from the later Paleozoic are reviewed. In addition, a comprehensive description of the geochemical controls of calcium phosphate precipitation from seawater is provided, with a focus on the rates of phosphate nucleation and growth, favorable nucleation substrates, and properties of substrate tissue and pore-fluid chemistry. It is hoped that the paleontological and geochemical summaries provided here offer a practical and valuable guide to the Neoproterozoic–Paleozoic phosphatization window.