Flowering plants are a classic example of a group arising late in Earth history and yet achieving very high diversity, abundance, and ecological and morphological variety in a great array of environments and climatic conditions on all continents. Thus, the success of flowering plants raises basic questions about how new lineages become inserted into existing terrestrial ecosystems. To what degree did flowering plants replace older lineages competitively, and to what extent did their expansion depend on large-scale environmental disruption or extinction of older groups? Is the higher taxonomic diversity of flowering plants a consequence of higher rates of speciation, lower rates of extinction, or both? Have flowering plants expanded the total area and range of habitats occupied by terrestrial vegetation? What were the effects of the diversification and spread of flowering plants on the structure of habitats and the types of resources available to terrestrial heterotrophs?

Empty molluscan shells retain paleoecological and taphonomic information that may be temporally complex (e.g., successive layers of encrusting organisms) to less complex (e.g., drill holes produced by predatory gastropods at one point in time). Yet, at all levels of complexity, unraveling the ancient “transcripts” requires not only a hopeful paleontologist but also knowledge of the various temporal roles molluscan shells play in community structure.

Upland floras (Chaloner, 1958), clastic substrate inhabitors (Dimichele et al., 1985), extrabasinal floras (Pfefferkorn, 1980), dryland floras (Havlena, 1960), seamforming Flöznahe and more distant Flözfremde (Daber, 1959; Havlena, 1961) mesophilous and xerophilous floras (Havlena, 1971), Callipteris-Walchia assemblage (Gothan and Gimm, 1930; Gothan and Remy, 1957), Megalopteris-Cordaites assemblage (Cross, 1977; Leary, 1981; Read and Mamay, 1964), Gigantopteris flora and Callipteris flora (Read and Mamay, 1964), early Permian floras (White, 1934), roof nodule floras (Stopes and Watson, 1907), the Mesophytic flora (Frederiksen, 1972), and “Permian” aspect (Elias, 1936a,b), are some of the terms that have been devised in recognition of the observation that many Late Paleozoic plant communities did not form coal swamp peats and their vegetational composition changed in response to global tectonism. The peat swamps clearly changed floral composition through time (Phillips, et al., 1974; Phillips, 1981; Dapples and Hopkins, 1969), but can be reasonably easily characterized, because “coal” swamp plants were commonly deposited in situ, or very near their sites of growth.

Techniques and field observations that detect “spatial variation” and “temporal dynamics” in fossil deposits have become important research programs in paleosynecology. These studies attempt to delineate aggregates and sequences of fossils at varied scales that appear to result from processes encompassing larger areas and greater time spans than the processes familiar to neoecologists. Description and modeling of patterns and processes at these scales would be significant contributions to historical biology, but little attention has been given to the ontology of “natural” multispecies units discernable in fossil data sets at varied spatio-temporal scales of resolution. Do patterns at any of these nested levels of variation – patches within shell beds, shell beds within biofacies, and so on – represent the elusive original community of organisms?

Isotopic studies of vertebrate material have a short history, while isotopic analyses of invertebrates originated in the 1940's. Interestingly, the driving force behind Harold Urey's desire to derive a carbonate paleotemperature scale in the 1940's and 1950's was the hope that it would solve the mystery of dinosaur extinction by demonstrating temperature changes at the K/T boundary. The most useful and commonly investigated stable isotopes for paleobiologic studies of vertebrates are carbon, nitrogen and oxygen. Oxygen is available from the inorganic bone or tooth apatite phase. Carbon is most often derived from tooth enamel carbonate or organic collagen, and nitrogen is derived from collagen. Each of these stable isotopes provides information on different aspects of an animal's biology and when combined, provide powerful analyses for ecological and evolutionary reconstructions. In the 1970's, much work was done describing the carbon and nitrogen variations in plants. This period was followed in the late 1970's and early 1980's by research on these isotopic variables in mammals (e.g., DeNiro and Epstein, 1978, 1981; Vogel, 1978; Van der Merwe, N.J., 1982). The utility of these isotopes for dietary recognition led to their extensive investigation in archeological studies. Not until the mid to late 1980's and 1990's have these isotopes been utilized in both the inorganic component of teeth and bones as well as the organic component of bones in Pleistocene and older paleobiologic studies. The 1980's also saw the emergence of research on the oxygen isotopic variations in mammals. However, the focus of isotopic studies on vertebrates was not for paleobiologic purposes, but rather, for attempts to derive paleohydrologic or paleoclimatic information from them (e.g., Longinelli, 1984; Luz et al., 1984).

The oxygen isotope method is probably the most widely used proxy of paleotemperature determination in the fossil record. The relationship as first proposed by Urey (1947) suggests that the ratio of 18O to 16O in the calcitic shells of fossils is proportional to temperature. This was subsequently confirmed by empirical studies (Epstein et al, 1951, Emiliani, 1954; 1955). However, Shackleton (1967), suggested on the basis of co-variance of benthonic and planktonic foraminifera, that the δ18O composition of seawater varied only as a function of glacial ice growth and decay. However, more recent studies have shown that there is still a residual temperature component in the δ18O variability of deep waters.

A systematic classification generally reflects accurately the state of knowledge of a group. As information concerning the group increases, both similarities and differences become more apparent. New characters then may be utilized to develop a more complex classification, that better serves to indicate presumed relationships. Assuming that organisms have evolved through time, the more detailed classification may also prove more valuable to the biostratigrapher.

Foraminiferida are an order of rhizopod protozoans characterized by the presence of granuloreticulopods and a test. Together with the Order Athalamida, they are the only Rhizopoda with anastomozing pseudopodia that contain granules (Fig. 1). The difference between the Athalamida and Foraminiferida is arbitrary because some foraminifera are known to leave their tests and move about, later returning to them (Marszalek, 1969), and some Athalamida attach foreign particles to the cell surface.

Generating and testing hypotheses is an integral part of any science, and some of the most stimulating paleobiological hypotheses of the past few decades relate to the ecological properties of fossils or fossil assemblages. Here, we outline recent methods for framing paleoecological questions that should facilitate the further quantitative evaluation of paleoecological hypotheses. First, we describe theoretical ecospaces, which are frameworks for classifying the ecologic properties of individuals or species based on multiple characters. We discuss the utility of theoretical ecospace in understanding evolutionary constraints and biodiversification, among other topics. Second, we discuss the reconstruction of high-resolution paleoecological gradients using ecological ordination techniques. Ordination can help uncover the paleoenvironmental factors that controlled fossil assemblage composition, track these factors through time, and evaluate the environmental and ecological context of major biotic changes. As an example, we present a new gradient analysis of the Yorktown Formation (Pliocene) of Virginia in which substrate and disturbance controlled molluscan assemblage composition. As a further example, we ordinate samples of mid-Paleozoic and late Cenozoic marine fossil assemblages based on their ecological content (as determined using a theoretical ecospace) to test whether the same environmental and ecological factors controlled the distribution of ecological lifestyles in both time intervals, despite the many differences between them. Although depth-related variation is evident in both data sets, the Cenozoic samples show stronger evidence of environmental control on ecologic content within depth zones. In contrast, Paleozoic gradients are consistent with a more random component in assemblage content. These analyses are quite preliminary, however, and should be verified with more extensive data.

In recent decades, research on ostracodes has grown dramatically. While many aspects of the group have been investigated, this review focuses on the paleoenvironmental applications of ostracodes from marine and nonmarine environments. It is argued that while ostracodes have great potential as paleoenvironmental tools, much of that potential has not yet been fully realized because of our imperfect understanding of ostracode biology, taxonomy, systematics and ecology. Future developments will be sure to result from additional studies in these areas, and will also be effected by exchange of ideas with scientists working on related proxies. However, the flow of ideas should not be one-way; workers in other disciplines can also learn from the study of ostracodes.

Mapping geographic ranges of species and higher taxa using Geographic Information Systems (GIS) produces quantitative data on spatial and temporal changes in geographic ranges. The primary advantage of GIS analysis is that it has the capacity to utilize large amounts of occurrence data of species to produce quantitatively constrained geographic range reconstructions that are amenable to statistical analysis. The basic steps in GIS range reconstruction are database assembly (including taxonomic, geographic, and stratigraphic information for each specimen), mapping of localities of species on modern continental configuration, rotation of occurrence data of species onto paleocontinental reconstructions, and reconstructions of geographic ranges. GIS analysis of ranges of species has been used to assess faunal dynamics of the Late Devonian Biodiversity Crisis, and three case studies are presented here. In these case studies, GIS-derived ranges of species are used to assess the relationship of biogeography with sea level, speciation and extinction rates, mass extinction survival, speciation mode, and invasive history of taxa. These case studies represent a subset of the potential for GIS analyses to examine paleontological patterns and contribute to improving understanding of the interaction between paleobiogeography, paleoecology, and evolution in the fossil record.

Macroecology is a rapidly growing sub-discipline within ecology that is concerned with characterizing statistical patterns of species' abundance, distribution and diversity at spatial and temporal scales typically ignored by traditional ecology. Both macroecology and paleoecology are concerned with answering similar questions (e.g., understanding the factors that influence geographic ranges, or the way that species assemble into communities). As such, macroecological methods easily lend themselves to many paleoecological questions. Moreover, it is possible to estimate the variables of interest to macroecologists (e.g., body size, geographic range size, abundance, diversity) using fossil data. Here we describe the measurement and estimation of the variables used in macroecological studies and potential biases introduced by using fossil data. Next we describe the methods used to analyze macroecological patterns and briefly discuss the current understanding of these patterns. This chapter is by no means an exhaustive review of macroecology and its methods. Instead, it is an introduction to macroecology that we hope will spur innovation in the application of macroecology to the study of the fossil record.

The fossilization potential of organic molecules is extremely variable. Some organic compounds which are very common in living organisms are extremely rare in the fossil record, and are only preserved under exceptional conditions. For example DNA, despite its abundance in living organisms, is apparently only rarely preserved in recognizable form as fossils, primarily because it is concentrated in vulnerable soft-tissues, and the molecule itself is highly reactive and therefore easily broken down. In contrast the recognizable remains of molecules such as proteins, lipids and certain pigments are extremely abundant in the fossil record, to the extent that a group of fossilized molecules derived from bacterial cell walls is present in quantities which exceed that of the total organic carbon in the present day biosphere. Such preservation reflects the inherent relative stability of the molecular structure, or at least the relative stability of the building blocks of which it is constructed. Even simple biological molecules tend to be constructed from smaller molecular subunits, and their long-term stability, and ultimately their fossilization potential, depends both on the strength of the bonding between these smaller modular building blocks as well as on the durability of the building blocks themselves if they become dissociated during or after fossilization. As would be expected from their geological record, the constituent nucleic acids of DNA are much less stable than the amino acids which make up proteins.

Taphocoenoses can be powerful indicators of ancient environments, even in depositional settings in which rates of sedimentation are low and tidal currents are strong.

The rich subtropical mollusc fauna of the northern Gulf of California exhibits a distinct zonation across an extensive tidal flat at Bahia la Choya (Sonora, Mexico). The distribution of live faunas is largely controlled by substrate, energy level, availability of food, and period of submergence. Despite strong tidal currents and the effects of time-averaging, the distribution of taphocoenoses closely reflects the distribution of the live communities. Indeed, the zonation of individual species is often reflected in the distribution of their shelly remains.

The outer flat, middle flat, inner flat, tidal channel, and salt marsh subenvironments within the tidal flat complex can be defined by the taxonomic composition, trophic/life habit groups and taphonomic attributes of their taphocoenoses. Gastropods dominate on hard and firm substrates (rocky flats, channel and marsh) while bivalves prevail on sandy substrates. Herbivores are most common on rocky and shelly substrates; detritus feeders occur on the firm substrates of the inner flat and marsh; suspension-feeders predominate in sandy and rocky bottoms. Shell abrasion, encrustation and boring decrease landward.

We tested an integrated approach to paleoenvironmental analysis by examining a Pleistocene shell bed from Bahia la Choya. Taxonomic, ecologic and taphonomic criteria suggest deposition by a storm event in a very shallow subtidal to lowest intertidal environment.

Changes in nutrient cycles and energy fluxes (i.e., ecosystem dynamics) likely drove numerous trends and disruptions in the history of life. Advances in geochemistry offer great insights into paleoecosystem function, as does an understanding of the biogeochemical roles played by ancient organisms. A theoretical ecospace that describes the chemical exchanges between organisms and their environments is presented. Previous descriptions of ecospace principally described spatial and physical aspects of ecology; the new ecospace description broadens the concept to encompass a wider range of ecological processes that control abundance and diversity of fossil organisms. Organisms require materials from the environment for generating energy and building tissues, and these factors are broken down, ultimately specifying particular substances acquired from the environment. Different organisms require specific substances in different amounts depending on factors such as physiology, environmental conditions, etc.; thus, physiological ecospace describes an organism's sensitivity to ecosystem/earth system perturbations and trends. Several examples relating to organisms' requirements for skeletal minerals are reviewed, and a new analysis of extinction selectivity related to ocean acidification is presented. Selective extinction of heavily calcified metazoa is demonstrated to have occurred at least eight times during the Phanerozoic, including the early Cambrian, Frasnian (Late Devonian), and Aptian (Early Cretaceous). Multidimensional structure of ecospace occupation (e.g., correlations among ecological traits) strongly controls the effects of an extinction such that the same kill mechanism applied at different times will affect the ecological composition of the biosphere in a variety of ways.

If taxonomic richness or ecological diversity defines evolutionary success, then the gastropods must be placed among the most successful clades of all time. Today, the gastropods are the most speciose class of fossilizable marine invertebrates. They have a rich fossil record extending nearly to the base of the Phanerozoic, documenting an almost uninterrupted taxonomic and ecological diversification (Figure 1). Yet the snails have been often overlooked as a focus of evolutionary or paleoecological study. Classic evolutionary studies of gastropods, for example Fisher et al.'s (1964) study of Athleta or Gould's (1969) work on Poecilozonites, indicate no inherent deficiencies in the taxon and suggest a simple lack of attention. The purpose of this paper is to summarize some of the major features of the history of gastropod evolution, to review problems in the analysis of fossil gastropods, and to reiterate some long-standing questions about the evolution and relationships of ancient snails. The goal is not only to provide a useful guide for non-specialists facing the prospect of lecturing on the beasts, but also to direct prospective students to problems perhaps worthy of their future research effort.

Acetate peels are replicas of etched surfaces embedded in sheets of cellulose acetate. These replicas are usually so detailed that the fine structure of shells and various sedimentary rocks can be easily studied under a light microscope. Because these peels can be quickly and easily produced, the procedure is now commonly used in most geologic laboratories.