Each of the perspectives on the fossil record represented by contributions to this short course (and many that are not) can claim a legitimate share of the mantle of “Analytical Paleontology,” earned by combining rigor and insight to provide some unique constraint on our understanding of the history of life. Dare I claim more for phylogeny? Certainly not, if “more” suggests that phylogeny is some final synthesis, complete unto itself, sought by all, and needing no further justification. Such a posture would make phylogenetic inference an end in itself, and, although it may sometimes appear that phylogeneticists have this in mind, I will argue here that it is the service role of phylogenetic analysis that makes it important in shaping our knowledge of evolution. Interpretation of the phylogenetic relationships of the organisms we study has profound implications for virtually all of our other ways of handling data from the fossil (or Recent) record.

A consortium dominated by archaeocyaths and calcified microorganisms (calcimicrobes) constructed the first metazoan reefs during an eleven-million-year interval of the Early Cambrian. However, archaeocyaths were not the first metazoan reef dwellers; the weakly calcified organism Namacalathus, and the more heavily biomineralized organism Namapoikia, occupied microbial reef environments during the late Neoproterozoic, but they were not involved in reef construction. Throughout the late nineteenth century, and during most of the twentieth century, the biological affinities of archaeocyaths were unsettled, which caused paleobiologists to avoid including them in analyses of the Cambrian fauna. However, in the late twentieth century the discovery of living, aspiculate sponges led to a consensus among archaeocyathan workers that these fossils represent an extinct class of aspiculate, calcareous sponges. The majority of archaeocyathan-calcimicrobial reefs are relatively small, lenticular mounds, typically about a meter thick and a few meters in diameter, but the archaeocyathan-calcimicrobial consortium also constructed massive, ecologically zoned, wave-resistant, framework reefs. The Great Siberian Cambrian Reef Complex is 200-300 km wide and stretches for 1500 km across northern Siberia. A consensus has not yet been found among Cambrian reef workers concerning photosymbiosis, which is such an important aspect of the ecology of modern coralgal reefs. Two extinction events hit during the Early Cambrian, the second of which is associated with a eustatic sea-level drop. The attendant marine regression eliminated reefs, and the archaeocyathan-calcimicrobial reef community disappeared. While the disappearance of reefs at this time is perfectly understandable, it is nevertheless surprising that the metazoan-calcimicrobe reef-building consortium was not able to recover within a few million years. Approximately forty million years passed æ from the end of the Early Cambrian to the beginning of the Middle Ordovician æ before metazoans finally returned to reef-building. We present seven hypotheses to explain this metazoan-reef-free window. The testing of these hypotheses will, in part, be the challenge of the next phase of research on Early Cambrian reefs.

Taken as a whole, Devonian and Carboniferous floras represent vastly different evolutionary stages in the colonization of the Earth's surface by plants. When only Late Devonian and Mississippian floras are considered, however, all of the floral innovations that led to and characterize the increasingly sophisticated plant communities of the Carboniferous began in the Famennian. When examined carefully enough, the stratigraphical succession of floras at the Devonian/Mississippian boundary reveals a gradual decline of typical Late Devonian elements and an equally gradual increase of plant types that eventually characterize the Early Mississippian. Furthermore, significant floral changes occur throughout the Late Devonian as archaic genera, that originated in Middle Devonian or earlier, disappear and new types appear that will become important in the Mississippian. Within the Mississippian too, the earliest floras contain elements left over from the Devonian, but show the origins or expansions of groups that ultimately were of great importance in the Pennsylvanian.

There are three major groups of living arthropods: Crustacea, Chelicerata, and Uniramia. To these may be added a fourth, the extinct trilobites. Determining the relationships of these higher taxa is difficult. A variety of approaches has led to different conclusions. At one extreme is the suggestion that the interrelationships of the major arthropod groups cannot be resolved, that they are quite distinct and are more appropriately treated as separate phyla (Manton, 1977; Schram, 1978). At the other is the view that while some basic arthropod characters — the hard exoskeleton, jointed appendages etc. — might have been acquired convergently, a more parsimonious approach is to treat them as monophyletic (Patterson, 1978).

Patterns of phenotypic change documented in the fossil record offer the only direct view scientists have of evolutionary transitions arrayed over significant durations of time. What lessons should be drawn from these data, however, has proven to be rather contentious. Although we as paleontologists have made great progress in documenting the geological record of phenotypic evolution with greater thoroughness and sophistication, these successes have been limited by the use of verbal models of how phenotypes change. Descriptive terms such as “gradual” have been understood differently by different authors, and this has led to completely incompatible summary statements about the fossil record of morphological evolution. Here I argue that the solution to this ambiguity lies in insisting that different evolutionary interpretations be represented as explicit, statistical models of evolution. With such an approach, the powerful machinery of likelihood-based inference can be help resolve long-standing paleontological questions.

Here I first review this approach and some aspects of its implementation. Then, I show how this approach leads to new traction on important issues in evolutionary paleobiology, including: understanding modes of evolution and determining their relative importance, separating evolutionary mode from tempo, assessing the evidence for hypotheses of punctuated change, and detecting adaptive evolution in the fossil record.

Although taphonomic processes alter or destroy much of the preservable portion of the original community, many of these processes also imprint valuable paleoecological information about the fauna and the environment of deposition which might be employed in paleoenvironmental reconstruction (Brett and Baird, 1986; Speyer and Brett, 1986, 1988). Accordingly, taphonomic analysis of modern and ancient death assemblages has received much attention recently (Powell et al., in press; Parsons et al., 1988; Kidwell and Behrensmeyer, 1988) and a new concept, that of the taphofacies, has been developed (e.g., Speyer, 1988). Taphofacies are based on distinct suites of taphonomic characteristics, taphonomic signatures, imprinted on the shell material and on its relationship to the sedimentary fabric by mixtures of physical, biological and chemical processes, which potentially are unique for a given environment. Ideally, if unique taphonomic signatures can be identified and the formative processes understood in a wide range of modern environments, this baseline can be employed to make more accurate reconstructions of equivalent paleoenvironments.

The isotopic composition of fossil invertebrates contains a wealth of information about the physical and chemical environments of the ancient past. The exploitation of this biogeochemical archive by paleontologists began about 50 years ago with the realization that the ratios of oxygen isotopes in the shells and skeletons of marine organisms offered the potential to accurately reconstruct paleoenvironmental conditions, particularly temperature (Urey, 1947; Urey et al., 1951). With the introduction of the oxygen isotope paleotemperature methodology (Epstein et al., 1951, 1953; Epstein and Lowenstam, 1953), the field of “isotope paleontology” was born (Wefer and Berger, 1991).

Macrostratigraphy is the study and statistical analysis of sediment packages that formed continuously at a specified scale of temporal resolution and that are bound by gaps recognizable at that same scale. The temporal ranges of gap-bound packages, compiled separately for different geographic locations, permit area-weighted, survivorship-based measures of rock quantity and spatio-temporal environmental continuity to be measured. Analytical basin fill models suggest that the parameters controlling sedimentation and sequence stratigraphic architecture, such as base level and sediment supply, can be detected quantitatively by macrostratigraphy.

Macrostratigraphic analysis of the marine sedimentary rock record in the United States at a temporal resolution of ~106 years reproduces most of the well-known Sloss sequences, but it also identifies two prominent megasequences, the Paleozoic and Modern megasequences, which are separated by a Permian-Triassic discontinuity and Phanerozoic minimum in rock quantity. Many short- and long-term features of the macroevolutionary history of marine animals are reproduced by macrostratigraphy, including 1) many patterns in genus richness, 2) patterns in rates of genus extinction and, to a lesser degree, rates of origination, and 3) patterns of extinction selectivity and the shifting relative richness of Sepkoski's Paleozoic and Modern evolutionary faunas. The extent to which macrostratigraphy reproduces the macroevolutionary history of marine animals transcends what is expected by geologically-controlled sampling biases. Instead, the processes which control the spatio-temporal dynamics of shelf sedimentation, including expansions and contractions of shallow epicontinental seas, have probably exerted a consistent influence on the macroevolutionary history of marine animals. Exploring the common cause hypothesis by putting fossils back into rocks and rocks into a new quantitative framework for physical environmental change holds considerable promise for paleobiology.

What is the range of time-averaging in the terrestrial vertebrate record? How are time-averaged assemblages distributed within the terrestrial vertebrate record? What are the implications of time-averaging for vertebrate paleobiological analysis?

Not all organisms have an equal chance of entering the fossil record. Previo—us attempts to quantify this percentage suggest that for megascopic marine organisms (megafauna), ∼30% would be predicted to leave no identifiable fossils. Here, that exercise is repeated for marine macrofauna, for which ∼80% are predicted to leave no identifiable fossils. The percentage will be far higher for meiofauna, the numerically most dominant marine animals. The organisms which are often most abundant in marine sediments, such as small polychaetes and nematodes, have essentially no fossil record. Yet such organisms are ecologically important in the modern oceans, and almost certainly were in ancient environments as well, so it is useful to consider the roles they play in different ecosystems. Insight into the evolution and paleoecology of these groups can be gained by using molecular divergence estimates to infer temporal origins combined with modern distributional and ecological data. As a case study, this approach is applied to the small and soft-bodied early animal fauna living under low levels of atmospheric oxygen that likely characterized the Precambrian.

Mass extinctions shape the history of life and can be used to inform understanding of the current biodiversity crisis. In this paper, a general introduction is provided to the methods used to investigate the ecosystem effects of mass extinctions (Part I) and to explore major patterns and outstanding research questions in the field (Part II). The five largest mass extinctions of the Phanerozoic had profoundly different effects on the structure and function of ecosystems, although the causes of these differences are currently unclear. Outstanding questions and knowledge gaps are identified that need to be addressed if the fossil record is to be used as a means of informing the dynamics of future biodiversity loss and ecosystem change.

Within a family, genera are usually separated on the basis of their colonial structure. The periodic occurrence of transgeneric highly variable specific units (spectra) in the fossil record poses nomenclatural and phylogenetic problems. A detailed example among Jurassic montlivaltiids is presented in this paper involving the genera Montlivaltia, Coenotheca, Thecosmilia, Latiphyllia and Complexastrea. These spectra are related to peculiar unstable nonreefal environments and are characterized by the dominance of young stages of the colonial growth (astogeny). The arising nomenclatural difficulties are solved by way of spectral nomenclature which allows naming morphological types, as well as taxonomic units and keeping some stability within the general frame of nominal taxa. Genera correspond to grades (solitary, thamnasterioid, phaceloid, meandroid, cerioid) rather than clades and the colonial structure is a labile character. Several alternative phylogenetic hypotheses are proposed, among which, some can renew our vision of this group and emphasize that the iterative production of generic-level shapes is best explained by mean of heterochronic processes. It is suggested that testing of these hypotheses be extended to other families such as Microsolenidae, Stylophyllidae or Fungiidae.

Stalked crinoids (sea lilies) are not extinct, but are restricted to depths below 100 m and comprise over 80 living species. Over the past 20 years, a wide range of new information on the biology of stalked crinoids has been acquired from deep-sea photography and submersible studies. Taphonomic studies show that stalked crinoids can disarticulate and undergo breakage and abrasion without significant transportation, although crinoids can survive the rigors of transportation without damage if decay has not weakened connective tissues. Because stalks can remain articulated longer than crowns, the occurrence of articulated fossil crinoid stalks should not be interpreted as proof of rapid burial. Stalked crinoids are passive suspension feeders forming filtration fans oriented normal to bottom currents of low velocity. Mutable collagenous tissues comprising the ligaments of stalk, cirri, and arms are significant in providing variable stiffness that enables stalked crinoids to maintain elevation of the stalk and the filtration fan feeding posture. Regenerated arms and stalks lacking crowns suggest that stalked crinoids are subject to predation by fish in deep water, although predation pressure is likely lower than in shallow water.

Large theropod dinosaurs like tyrannosaurs were the biggest land-living predators in earth history. Because of this, there has been considerable interest in reconstructing the paleobiology of these immense carnivores (Bakker, 1986; Bakker et al., 1988; Paul, 1988; Molnar and Farlow, 1990; Farlow et al., 1991; Abler, 1992; Farlow, 1993, in press; Horner and Lessem, 1993). In the present paper we consider a topic relevant to interpretations of how tyrannosaurs used their teeth during feeding: the incidence of wear surfaces on tyrannosaur teeth.

Confocal laser scanning microscopy is a well-established optical technique allowing for three-dimensional (3-D) visualization of fluorescent specimens with a resolution close to the diffraction limit of light. Thanks to the availability of a wide range of fluorescent dyes and selective staining using antibodies, the technique is commonly used in life sciences as a powerful tool for studying different biological processes, often at the level of single molecules. However, this type of approach is often not applicable for specimens that are preserved in historical slide collections, embedded in amber, or are fossilized, and cannot be exposed to any form of selective staining or other form of destructive treatment. This usually narrows the number of microscopic techniques that can be used to study such specimens to traditional light microscopy or scanning electron microscopy. However, these techniques have their own limitations and cannot fully reveal 3-D structures within such barely accessible samples. Can confocal microscopy be of any help? The answer is positive, and it is due to the fact that many paleontological specimens exhibit a strong inherent autofluorescence that can serve as an excellent source of emitted photons for confocal microscopy visualizations either through reconstruction of the induced autoflourescent signal from the sample, or through reconstruction of the reflected signal from the sample surface. Here, we describe the workflow and methodology involved in acquiring confocal data from a sample and reprocessing the resulting image stack using the image-processing program imageJ before reconstructing the data using the open-source 3-D rendering program, Drishti. This approach opens new possibilities for using confocal microscopy in a nondestructive manner for visualizing complex paleontological material that has never previously been considered as suitable for this type of microscopic technique.

Issues of scale are becoming increasingly important to paleobiological interpretations of the fossil record. Nevertheless, a number of biological processes display scale-independent behaviors. The effects of predation on the distribution of dense populations of epifaunal, suspension-feeding ophiuroids are scale-independent, at scales ranging from the microecological to the macroevolutionary. On a microecological scale (meters to kilometers, hours to days), dense ophiuroid populations are limited in shallow-water environments by predatory fishes and crabs. On a larger, ecological scale (tens to hundreds of kilometers, decades to centuries), circumstantial evidence indicates that oceanographically driven, multidecadal cycles of predator abundance determine the abundance of ophiuroids throughout the western English Channel. On a macroevolutionary scale (millions to tens of millions of years, global spatial scale), dense, autochthonous assemblages of ophiuroids declined in conjunction with the Mesozoic diversification of modern shell-crushing predators: teleostean fishes, decapod crustaceans, and neoselachian sharks. The sporadic reappearance of dense ophiuroid populations in a late Eocene, shallow marine deposit in Antarctica suggests that predator-prey relationships were disrupted as temperatures declined in the region at that time. Scale-independence is a useful model for explaining and predicting patterns of distribution of dense ophiuroid populations in time and space.

Ostracodes are bivalved Crustacea whose fossil shells constitute the most abundant and diverse metazoan group preserved in sediment cores from deep and intermediate ocean water depths. The ecology, zoogeography, and shell chemistry of many ostracode taxa makes them useful for paleoceanographic research on topics ranging from deep ocean circulation, bottom-water temperature, ecological response to global climate change and many others. However, the application of ostracodes to the study of climate change has been hampered by a number of factors, including the misconception that they are rare or absent in deep-sea sediments and the lack of taxonomic and zoogeographic data. In recent years studies from the Atlantic, Pacific, and Arctic Oceans show that ostracodes are abundant enough for quantitative assemblage analysis and that the geochemistry of their shells can be a valuable tool for paleotemperature reconstruction. This paper presents practical guidelines for using ostracodes in investigations of climate-driven ocean variability and the ecological and evolutionary impacts of these changes.

Introducing Students to microfossils in the K-12 curriculum can be a rewarding and exciting experience for both instructor and student. Students, even those who collect fossils as a hobby, are generally unaware of microfossils. Exposure to microfossils opens up a whole new world of inquiry, and the extent to which that inquiry is developed can be adjusted to the grade-level and interest-level of the individual student.

Because of their great abundance, widespread distribution, excellent preservation potential (Foote and Sepkoski, 1999), and a tendency not to disarticulate after death, brachiopods are ideal subjects for paleoecological research involving morphometrics, population analysis, and phylogenetics. Paleoecology is a subdiscipline that demands large data sets and statistical tests, and brachiopods provide the opportunity to create such databases. I fully expect to see brachiopods play a major role in the coming years in studies on the cutting edge of paleoecology. My approach in this chapter is to provide some background and tools that hopefully will inspire many new ideas for using brachiopods in the study of paleoecology. My intent is not to convince anyone of the correctness of my ideas, but rather to encourage future research in these directions.