Long thought to be inaccessible to empirical inquiry, Earth's early biosphere has in recent decades become a central focus of evolutionary and paleobiological research. Knowledge of Precambrian ecosystems comes from three principal sources. The conventional fossil record consists of the compressed and permineralized remains of cyanobacteria, protists and other microorganisms (e.g., Knoll, 1996), complemented by stromatolites and oncolites, the accretionary trace fossils of microbial mat communities (Walter, 1976). Independent inferences about early evolution can be drawn from molecular phylogenies (Pace, 1997). The third principal source of information comprises biogeochemical signatures encrypted in the chemistry of ancient sedimentary rocks. Biomarker molecular fossils and distinctive isotopic compositions record the metabolic activities of organisms not necessarily preserved morphologically (Summons and Walter, 1990). In this paper, we review the inferences about early life and environments that can be drawn from the isotopic records of carbon and sulfur.

The exceptional preservation of plant fossils falls into two categories: whole plant preservation and anatomical detail. Whole plant preservation is controlled primarily by transport and event preservation (e.g., ash falls), whereas anatomical preservation can occur through one of several taphonomic pathways: compression-impression, silicification, coal-ball formation, pyritization, and charcoalification. This review focuses on these taphonomic pathways, highlighting important factors and controls on the exceptional preservation of plants. Special emphasis is given to data garnered from experimental and actualistic approaches.

Pollen analysis is an exercise in seeing. The ultimate goal is to see into the past, to send down a periscope and view what went on. The metaphor of the periscope is too limited, however; a video recorder from high in space with resolution in places up to 10 m is more encompassing of what is possible. The images that are retrieved can be of high or low resolution temporally, spatially, taxonomically, and numerically, and they can illustrate local to global changes in plant populations, vegetation, climate, human activity, fire frequency, and plant diseases over decades to millennia. Because each of these entities or phenomena varies spatially and temporally, records of data covering a breadth of scales in space and time are needed. To obtain the highest quality images about a specific phenomenon requires an understanding of the sensing system that accumulated the data. How does the periscope or video recorder work and what are the scaling characteristics of the images that it registers? These characteristics include breadth of coverage, sampling resolution, and sampling density in time, space, and taxonomy. Actualistic and taphonomic studies of Quaternary data covering a variety of temporal and spatial scales have helped provide this understanding, and temporal resolution is just one concern in these studies.

Symbiotic associations are a poorly studied aspect of the fossil record, owing largely to the taphonomic biases that inhibit direct observation that two organisms shared an intimate association in life. A symbiosis between an infesting animal and a skeleton-producing host can form a bioclaustration cavity that directly preserves the association and has a high preservation potential. Identification of ancient mutuals and parasites must reject the null hypothesis of commensalism by demonstrating that the symbiosis correlates with a positive or negative change in host fitness as compared to a non-symbiotic relative of the host taxon. Reviews of the Paleozoic record of marine symbionts show that the majority are hosted by colonial animals, especially corals and calcareous sponges. These hosts include structural forms that have moderate to high levels of integration and can support bioclaustrations between clonal units, mitigating the negative effects of symbionts, and perhaps facilitating the symbiosis.

The fossil record is biased toward recording long-lasting, widespread, equilibrated associations. By contrast, parasitisms that are especially negative to the host are expected to be fossilized rarely. The symbiotic associations that form bioclaustrations may also represent an endolithic adaptive strategy in response to biological antagonisms, such as predation and spatial competition. The Late Ordovician rise in symbiotic bioclaustrations joins burrows and borings as trace fossil examples of infaunalization strategies that accompany the Ordovician faunal radiation.

The study of evolution by natural selection is difficult because, by definition, it occurs under uncontrolled conditions. All biological organisms are highly complex entities and their interactions with the environment and each other are unpredictable, except in the most general terms. Countless chance events impact cumulatively on the genetic composition of a descendant lineage, resulting in substantial evolutionary change over very long periods of time. Understanding how evolution works in practice is a matter for basic science, but it is attended by unique and difficult problems.

Recent advances in crinoid functional morphology have been concentrated predominantly in two areas, one involving the study of mutable collagenous tissues (MCTs), and the other dealing with the implications of crinoids' rheophilic nature. The presence of MCTs in crinoid cirri and stalks, and their importance to the function of these structures has been demonstrated in several studies. It has been recently reported that MCTs have contractile properties (Birenheide and Motokawa, 1996); if this is corroborated, it would help resolve many fundamental problems in crinoid functional morphology. Studies of the crinoids in their natural setting have confirmed their predominantly rheophilic nature. The application of the rheophilic paradigm and the principles of physics and engineering to crinoids has provided insights into several areas of crinoid functional morphology, including: (1) mechanics of particle interception—direct interception (and not sieving) as the dominant mode of particle capture by the tube feet (no mucus net); (2) the importance of feeding posture and orientation—(a) bilateral symmetry of the feeding posture (oral side downcurrent), (b) the problems associated with maintaining such a posture under bi- or multi-directional flow (swiveling of pinnules, arms, and /or entire filters); (3) the effect of filter resistivity on fluid interception—solid filters need high ambient current velocities; and (4) the influence of nearest neighbors on fluid interception—side-by-side neighbors might be favored over upstream–downstream neighbors.

The utilization of taphonomic information to formulate biostratinomic models for modern and ancient assemblages has become a potentially powerful tool in paleoecologic analysis. The division of fossil assemblages into discrete suites of taphonomically-similar material adds an extra dimension to the interpretation of depositional setting and paleoecologic structure (Brett and Baird, 1986; Speyer and Brett, 1986, 1988; Speyer, 1987). This approach uses the hypothesis that taphonomic alteration varies in a predictable way with depositional setting. In other words, each specific environment (e.g., low-salinity muddy bay, storm-dominated clastic shelf) is characterized by a unique suite of physical, chemical and biological processes: these processes imprint a unique and predictable “taphonomic signature” on the death assemblage.

Authigenic pyrite preserves non-biomineralized tissues in the fossil record under exceptional circumstances. Diagenetic models and taphonomic experiments demonstrate that active, localized sulfate reduction in iron-rich pore waters results in a strong concentration gradient, which confines pyrite precipitation to decaying organic matter. The locus and timing of pyrite precipitation is also influenced by the original composition of the organic matter. In recent decades, new sites with three-dimensional pyritized soft tissues have been discovered, although the Hunsrück Slate (Devonian) and Beecher's Trilobite Bed (Ordovician), known since the late 1800s, remain the primary examples in terms of diversity, abundance, and quality of preservation. Sedimentological and geochemical analyses at these sites have shown that rapid burial in fine-grained, reworked sediments sets up the high iron, low organic carbon conditions necessary for soft-tissue pyritization. Soft-tissue pyritization may also occur in association with other taphonomic modes, in particular with Burgess Shale-type preservation and carbonaceous preservation in lakes, although many of these specimens are now weathered. Continued comparison among sites and between specimens with variable degrees of preservation could help clarify the limits to soft-tissue pyritization and its distribution in ancient sediments.

The exceptionally preserved fossil record of soft tissues sheds light on a wide range of evolutionary episodes from across geological history. Understanding how soft tissues become hard fossils is not a trivial process. A powerful tool in this context is experimentally derived decay data. By studying decay in a laboratory setting and on a laboratory timescale, an understanding of the processes and patterns underlying soft-tissue preservation can be achieved. The considerations and problems particular to experimental decay are explored here in terms of experimental aims, design, variables, and utility. Aims in this context can relate to either reconstruction of the processes of soft-tissue preservation, or to elucidation of the patterns of morphological transformation and data loss occurring during decay. Experimental design is discussed in terms of hypotheses and relevant variables: i.e., the subject organism being decayed (phylogeny, ontogeny, and history), the environment of decay (biological, chemical, and physical) and the outputs (how to measure decay). Variables and practical considerations are illustrated with reference to previous experiments. The principles behind application of experimentally derived decay data to the fossil record are illustrated with three case studies: the interpretation of fossil color, feasibility of fossil embryos, and phylogenetic bias in chordate preservation. A rich array of possibilities for further decay experiments exists and it is hoped that the methodologies outlined herein will provide guidance and a conceptual framework for future studies.

In the last two decades, advances in computational imaging techniques and digital visualization have created novel avenues for the study of fossil organisms. As a result, paleontology has undergone a shift from the pure study of physically preserved bones and teeth, and other hard tissues, to using virtual computer models to study specimens in greater detail, restore incomplete specimens, and perform biomechanical analyses. The rapidly increasing application of these techniques has further paved the way for the digital reconstruction of soft-tissue structures, which are rarely preserved or otherwise available in the fossil record. In this contribution, different types of digital soft-tissue reconstructions are introduced and reviewed. Provided examples include methodological approaches for the reconstruction of musculature, endocranial components (e.g., brain, inner ear, and neurovascular structures), and other soft tissues (e.g., whole-body and life reconstructions). Digital techniques provide versatile tools for the reconstruction of soft tissues, but given the nature of fossil specimens, some limitations and uncertainties remain. Nevertheless, digital reconstructions can provide new information, in particular if interpreted in a phylogenetically grounded framework. Combined with other digital analytical techniques (e.g., finite element analysis [FEA], multibody dynamics analysis [MDA], and computational fluid dynamics [CFD]), soft-tissue reconstructions can be used to elucidate the paleobiology of extinct organisms and to test competing evolutionary hypotheses.

The great bulk of the angiosperm fossil record consists of isolated fossil leaves that preserve abundant shape and venation (leaf architectural) information but are difficult to identify because they are not attached to other plant organs. Thus, poor taxonomic knowledge has tempered the tremendous potential of fossil leaves for constructing finely resolved records of biodiversity through time, extinction and recovery, past climate change and biotic response, paleoecology, and plant-animal associations. Moreover, paleoecological and paleoclimatic interpretations of fossil leaves are in great need of new approaches. Recent work is rapidly increasing the scientific value of fossil angiosperm leaves through advances in traditional paleobotanical reconstruction, phylogenetic understanding of both leaf architecture and the response of leaf shape to climate, quantitative plant ecology using measurable, correlatable leaf traits, and improved understanding of insect leaf-feeding damage. These emerging areas offer many novel opportunities to link paleoecology and neoecology. Increased collaboration across traditionally separate research areas is critical to continued success.

It is a great understatement to say that our knowledge of morphologic, stratigraphic, and paleobiogeographic variation among brachiopods has expanded enormously over the past 35 years. The number of brachiopod genera discovered and named since 1965 has more than doubled the approximately 1700 genera described in Part H of the Treatise on Invertebrate Paleontology (Williams and others, 1965). 4827 genera and subgenera named as of 1995 are listed in Doescher (1996); it is likely that over 5000 exist by now. Some are certain to be reevaluated as synonyms, but we have no reason to believe that this would apply to most new genera. This remarkable increase in raw data required a thorough reexamination of the phylogenetic relationships and higher-level classification of the group, encouraged largely by the revision of Part H of the Treatise, initiated in the late 1980s by Alwyn Williams.

The purpose of this chapter is to evoke new concepts, provide guidelines and new frontiers for future research, and demonstrate that invertebrate traces actually comprise the “backbone” of continental (as well as marine) ichnology. Invertebrate organisms that inhabit the continental, nonmarine realm include some of the most diverse and populous classes in the animal kingdom. For example, both the Insecta and Crustacea exhibit burrowing behaviors unique to subaqueous freshwater and subaerial systems. Because of the sheer biomass of burrowing pupae, larvae, juvenile, and adult stages of these organisms, invertebrates dependent on the position of the water table form the basis for ecological niche-partitioning of depositional systems within all of the continental realm. A distinction must be made here between continental and marine ichnocoenoses because they represent distinctly different styles of living. These in turn dictate different behavioral and genetic responses of the organisms that inhabit them. Burrow architectures that occur in both continental and marine ichnocoenoses can be differentiated by subtle differences in morphology that are due to convergence of the burrowing mechanisms of the respective organisms.

Diatoms, golden brown algae, are present in most aqueous environments. Within the marine environment marine diatoms occupy the photic zone and represent the lowest level of the marine food chain. Diatoms are either planktonic or benthic and possess an external siliceous skeleton or frustule, that is boxlike in structure. The size of diatom frustules ranges from less than 1 μm to more than 1,000 μm, but most frustules range in size from 10 to 100 μm. Diatoms are present in the geological record from at least the Cretaceous (Harwood and Nikolaev, this volume) and have numerous advantages for biostratigraphic correlation and paleoenvironmental reconstruction of marine sedimentary sequences. This chapter summarizes the current state of marine diatom biostratigraphy for the Cenozoic and provides examples of how marine diatoms are used in paleoenvironmental reconstructions. No attempt is made to illustrate the various diatom taxa discussed; the reader is referred to published references such as the syntheses of Fenner (1985) and Barron (1985).

Catalytic hydropyrolysis (HyPy) is a powerful analytical technique for fragmenting macromolecular organic matter, such as kerogen (insoluble sedimentary organic matter), and releasing covalently-bound molecular constituents including branched and cyclic biomarker hydrocarbons. Here we illustrate our molecular approach to paleobiology with lipid biomarker data collected from rock bitumens and kerogens hosted within sedimentary units of the Neoproterozoic Huqf Supergroup, South Oman Salt Basin, Sultanate of Oman. We emphasize that parallel analyses of free and bound biomarker pools affords more confidence that we have correctly identified syngenetic compounds. One enigmatic class of compounds that is prominent in many late Proterozoic and Cambrian sedimentary rocks and oils, including from the Huqf Supergroup, is a series of C14-C30 mid-chain methylalkanes which were originally denoted X-peaks. Despite their abundance in the Precambrian rock record, little is known about the organisms responsible for their biosynthesis. Here we propose a possible origin of X-peak methylalkanes from colorless sulfur bacteria (a very heterogeneous group of chemolithotrophic γ-proteobacteria). In modern marine settings, these bacteria are abundant mat formers wherever a sedimentary sulfide-rich horizon intersects the seafloor producing a steep geochemical redox gradient. This condition may have been met more commonly on shallow marine shelves in late Neoproterozoic basins and these benthic mats may have acted as environmental buffers consuming hydrogen sulfide. If our hypothesis is correct, proliferation of sulfide-oxidizing benthic microbial mats, commencing in the late Cryogenian in South Oman Salt Basin, implies unique and specific benthic conditions during the evolution of the earliest metazoans.

Bony fishes or osteichthyans comprise two main monophyletic groups: the actinopterygians (rayfins, including the staples of the fish market and aquarium) and sarcopterygians (lobefins, fringefins or tasselfins, including lungfishes, coelacanths, and, perhaps unexpectedly or inconveniently, all land vertebrates or tetrapods). In the broadest terms, the two groups have similar histories, each with beginnings in the late Silurian or earliest Devonian, each with a primary radiation in the late Devonian and Mississippian, a secondary radiation in the Mesozoic, and a major Tertiary radiation, and each with an extant diversity of roughly 25,000 species (Nelson, 1994, p. 2). The remainder of this course (eight topics) is devoted to sarcopterygians, so I shall give almost all my space to the other half of bony fish diversity, the actinopterygians.

The purpose of photographing fossils for study and for publication is to provide information regarding the morphology of the fossil. Typically, this morphology is expressed as topographic relief. Tonal patterns and color rarely serve to enhance the expression of morphology and may, instead, provide false information. As a result, it is desirable typically to eliminate, or reduce, the effects of variations in tonal pattern over the surface to be photographed to emphasize aspects of relief of the specimen and, therefore, actual expressions of morphology. Furthermore, uncoated specimens may be lustrous so that lighting the specimen for photography may produce undesirable highlights. A simple, and non-destructive, technique for whitening fossil specimens involves the application of ammonium chloride sublimate to the surface of the specimen (Figure 1). This coating is non-destructive, produces a uniform, nonlustrous white surface that enhances detail, and can be readily removed without damage to the specimen.

New morphometric methods for distinguishing morphologically similar species of Recent colonial scleractinian corals involve the analysis of three dimensional landmarks digitized on calical surfaces. Variables suitable for multivariate statistical analysis are derived from the landmark data by applying various geometrical techniques, including Bookstein size and shape coordinates and generalized resistant fitting. Cluster analyses of these variables and study of the relative positions of replicates from the same colony on the resulting dendrograms are used to recognize clusters of colonies representing morphospecies. Comparisons with the results of genetic analyses on the same specimens suggest that these morphospecies correspond closely with biological species.

Although slightly less effective, similar analyses of two dimensional landmark data collected on thin sections of the same specimens also distinguish species, and suggest that biological species can be approximated in the fossil record. Multivariate statistical analyses show that variables derived from two dimensional landmarks can be used to trace the stratigraphic ranges of these fossil species. The appropriate method for tracing ranges depends of the evenness of sampling in different geologic horizons. Preliminary comparisons of observed stratigraphic ranges determined by this approach with those determined by cladistic analysis suggest that overall patterns in evolutionary rates through geologic time are the same for both approaches. Thus, nontraditional morphologic characters determined by subsequent examination of morphometrically-defined species have potential for providing sufficient resolution for phylogenetic analysis.

The fossil record of plants principally results from individuals, variously sampled from one or more communities, that generally are associated with a depositional site. The processes responsible for the transfer of plant parts from the biosphere to the lithosphere may be biotic (e.g. physiological, animal herbivory, etc.) or abiotic (e.g. traumatic loss by wind and/or water; Krassilov, 1975) in nature. The factors ultimately responsible for the preservation of these plant parts are sedimentological and geochemical. The goals of the subdiscipline of Taphonomy, the study of processes of preservation and how they affect information in the fossil record (Behrensmeyer and Kidwell, 1985), are to understand fossilization through necrology, biostratinomy, and diagenesis (Figure 1). The purpose of this chapter is to provide an overview of taphonomic factors responsible for the generation and preservation of plant macrodetritus. It is not meant to be an exhaustive dissertation or definitive discussion on phytotaphonomy.

Mesozoic soil ecosystems are intriguing because they are the products of many unique factors and events in geologic history. One of the most notable events that likely shaped Mesozoic soil ecosystems was the Permo-Triassic extinction. At that time, estimates of 20% of plant species, 50% of tetrapod genera, roughly 60% of insect families, and approximately 91 to 97% of shallow marine life became extinct (e.g., Padian and Clemens, 1985; Raup, 1986; Niklas et al., 1980; Wing and Sues, 1992; Labandeira and Sepkoski, 1993; and references therein). Over the span of the next 180 million years the supercontinent Pangea disassembled and the continents moved toward the configuration we see today (Scotese and Golonka, 1992); the Pangean mega-monsoonal climate pattern deteriorated into more zonal climates through to the Cretaceous (e.g., Parrish et al., 1982; Dubiel et al., 1991; Parrish, 1993); sea-level rose and flooded continental interiors, reaching its second greatest maximum since the Ordovician (e.g., Haq et al., 1987, 1988); and several major evolutionary episodes occurred, including the evolution and diversification of the angiosperms, mammals, birds, and many of the neopteran insects (Lillegraven et al., 1979; Carpenter and Burham, 1985; Friis et al., 1987; Wing and Sues, 1992; Labandeira and Sepkoski, 1993).