Paleoecological and paleoenvironmental studies have a rich tradition of actualistic work on Recent biotas and environments. Ever since Lyell (and before) geologists have examined present–day sedimentary environments and faunas in an effort to interpret the environments and life of the past. After all, if the present is not the key to the past, it is at least a key to the past. However, there is no similarly long tradition of studying the Recent in an effort to gain insight into issues of the temporal resolution of fossil assemblages.

The history of investigations of planktonic foraminifera leading to their current, wide applications in biostratigraphic correlation of Mesozoic and Cenozoic marine sediments can be traced to the discovery by Owen (1867) of the floating habit of certain foraminifera, later confirmed by Brady (1884), and the recognition by Murray and Renard (1891) that their shells constitute a major portion of deep-sea sediments over large regions of the seafloor. The utilitarian value of planktonic foraminifera in paleoecological analysis is also widely accepted today. Fortunately for students of paleoecology, many species of planktonic foraminifera are still extant and live in large numbers in all oceanic regions. Their areal, vertical and seasonal occurrences have been resolved to such a degree that a global synthesis of their distribution patterns is now available (e.g. Bradshaw, 1959; Belyaeva, 1964; Be and Tolderlund, 1971).

In the first Paleontological Society short course dealing with functional morphology of extinct brachiopod taxa, Grant (1981, p. 127) emphasized analogy with living species in reconstruction of life habits, but then cited many pitfalls of taxonomic uniformitarianism. The present is hardly the key as to how brachiopod shells functioned in the past, given the plethora of morphologic structures that have vanished since the Paleozoic diversity climax of articulates. Although direct observations (Table 1), such as clasping spines encircling a blastoid columnal (Grant, 1963), or biomechanical tests (e.g., Thayer, 1975a) and flume experiments (e.g., LaBarbera, 1978) on living articulate brachiopods, enable convincing assertion of a morphologic structure's function, indirect methodologies (Savazzi, 1999)(Table 1) have supplanted mere analogies with living brachiopods. Indirect methodologies (Savazzi, 1999, p. 6) reconstruct and infer the function of skeletal structures from theoretical (morphospace) and actual scaled models of extinct taxa, hydrodynamic and biomechanical tests on empty shells, commensal associations with fossilized epibionts, clinal variations in structures over paleogeographic and paleobathymetric gradients, and post-mortem, post-burial orientational evidence. The common denominator of indirect methodologies is that inferences are made on dead shells usually, but not always, from extinct taxa. Although such inferences of skeletal function of extinct taxa vary in the rigor by which they are deduced, indirect methodologies have been increasingly refined over the last 20 years (Table 1).

The term dysaerobic was first coined by Rhoads and Morse (1971) to define conditions in which oxygen levels ranged between 1.0 and 0.1 mL of oxygen/litre of water. Such low oxygen tensions were thought to exclude all but soft-bodied invertebrates with the absence of shelly fossils being one of the diagnostic features of the dysaerobic zone. Subsequent observations of recent dysaerobic environments has revealed that shelly invertebrates can survive in oxygen values as low as 0.3 mL/L (e.g. Savrda, Bottjer and Gorsline, 1984). Consequently the dysaerobic zone is now used in the more qualitative sense to denote conditions in which oxygen levels are sufficiently low to cause a notable change in the fauna (Kammer and others, 1986; Wignall and Myers, 1988). Faunal abundance and diversity is reduced under low oxygen conditions compared to more normally oxygenated (aerobic) biofacies.

This article discusses past greenhouse climates with an emphasis on recent progress in the comparison of models and data in the Eocene. These past climates—about 10° warmer than modern—provide valuable lessons in the climate dynamics of a world with higher-than-modern greenhouse-gas concentrations, reduced temperature gradients, and a lack of polar ice. Some key points that emerge from this analysis are: 1) Past greenhouse climates are characterized by warmer-than-modern global mean temperatures and winter season warmth, as well as strong polar amplification of warming that generates weak meridional temperature gradients. 2) A trade-off exists between heat transport in a warmer world and a world with smaller temperature gradients; a range exists in which a warmer world with weak temperature gradients can transport as much heat as a cooler world with stronger gradients. 3) These features can be reproduced in models if global mean and tropical temperatures are allowed to increase significantly over modern values. 4) Local radiative-convective feedbacks play an important role, perhaps dominating over transport, or acting in conjunction with transport to maintain relatively warm, weak temperature gradient climates. 5) Past greenhouse climates appear to have many of the modern modes of variability from orbital to interannual. 6) Modeling efforts are most useful when done independently of proxy data; model output can then be compared with proxies to evaluate potential weaknesses in the model. 7) Model-data mismatch might be due to incorrect boundary or initial conditions or resolution, or to missing or incomplete representation of relevant physics. 8) Refinements and new developments in proxies for temperature and other variables offer much potential for discriminating among the next generation of modeled scenarios, thereby allowing a better understanding of the conditions under which greenhouse climates exist.

Virtually all paleontologic and historical geologic interpretations require information on the time resolution of individual samples. For relatively broad segments of the record such as facies tracts and entire basins, a variety of approaches can be used to determine the relative and absolute duration of a “sample”. For finer subdivisions, however, such as individual beds and assemblages that are within the error-bars of radiometric dates or within the span of a biostratigraphic zone, estimating elapsed time per unit becomes far more difficult. Assessing time at this scale is important, however, because this is the usual sampling interval for autecologic, synecologic, morphometric, and species-level biostratigraphic and evolutionary studies.

The transition to the diverse and complex biosphere of the Ediacaran and early Paleozoic is the culmination of a complex history of tectonic, climate, and geochemical development. Although much of this rise occurred in the middle and late intervals of the Neoproterozoic Era (1000–541 million years ago [Ma]), the foundation for many of these developments was laid much earlier, during the latest Mesoproterozic Stenian Period (1200–1000 Ma) and early Neoproterozoic Tonian Period (1000–720 Ma). Concurrent with the development of complex ecosystems, changes in the composition, configuration, and tectonic interaction between continental plates have been proposed as major shapers of both climate and biogeochemical cycling, but there is little support in the geologic record for overriding tectonic controls. Biogeochemical evidence, however, suggests that an expansion of marine oxygen concentrations may have stabilized nutrient cycles and created more stable environmental conditions under which complex, eukaryotic life could gain a foothold and flourish. The interaction of tectonic, biogeochemical, and climate processes, as described in this paper, resulted in the establishment of habitable environments that fostered the Ediacaran and early Phanerozoic radiations of animal life and the emergence of complex, modern-style ecosystems.

Although the majority of publications on extant nonmarine ostracode species in North America are concerned with lacustrine settings, many species that are potentially valuable as indicators of water quality changes live in non-lacustrine settings. Ostracode distributions in 157 springs, wetlands and streams in the United States are examined here in order to assess 1) species richness, 2) association with physical and chemical parameters of their habitats and 3) the presence of potentially useful biomonitors and environmental sentinels. The 157 non-lacustrine sites are a subset of a large database (North American Non-marine Ostracode Database: NANODe version 1) consisting of 611 mostly lacustrine sites with ostracode species, presence-absence data, hydrochemistry and climate data (Forester et al., in review). Of the 89 species represented in NANODe version 1, 51 species are found in springs, 59 species are found in wetlands and only 15 species are found in streams. Many species are found in at least two of these habitats and some in all three. Principal Components Analysis of these 157 sites indicates that 71% of the variance is explained by salinity (total ionic concentration), alkalinity and temperature, a result consistent with previously published analyses of natural water. Cluster analysis shows that spring species are most strongly tied to temperature, whereas wetlands and streams are most strongly tied to ionic composition. Three species are found to be potentially valuable biomonitors: Cavernocypris wardi in springs, Fabaeformiscandona rawsoni in wetlands and Physocypria globula in streams.

Ichnotaxonomy is a formal, hierarchical classification system for trace fossils (=ichnofossils, the fossilized results of behavior). It includes a binomial nomenclature similar to the zoological taxonomic hierarchy applied to organisms. A common observation from non-ichnologists is that a formal system of classification and nomenclature for footprints, burrows, and other holes in the ground seems a bit excessive. Surely a burrow by any other name is still a burrow? However, ichnology has a real need of formal classification and names. There is a great diversity of both trace fossils and of processes that affect their form. Understanding and making use of this diversity requires an effective and generally agreed upon means of classification and nomenclature. To show that this is the case, one must understand both the principles of classification and how they are applied to trace fossils.

Food webs represent trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for the consideration of paleocommunity food webs. The fossil record presents challenges in this regard, but the problem can be approached with combinatoric analysis and network theory. This paper is an introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores a probabilistic and numerical approach.

How Earth and organisms interacted in the past is one of the largest questions in paleobiology. Observed histories of organisms and Earth environments need to be linked under a set of uniformitarian assumptions to address this question. Functional morphology, which studies how organismal body parts interact with their physical environments, is an important tool in establishing the link. Being uniformitarian or ergodic, functional morphology is most robust when directly incorporating physical (or mechanical) principles into hypotheses and their tests. Such ‘physical functional morphology’ may not be always possible, but the number of examples is slowly increasing. Once a series of robust functional inferences are made, it may be possible to study its correlation or correspondence with the historical record of environmental proxies. This framework was applied to the Mesozoic marine reptiles Ichthyopterygia, which is known for the evolution of fish-shaped body profiles in the derived clade Parvipelvia. A suite of evidence suggests that parvipelvians had advanced cruising ability and dark-adapted vision that were lacking in the more basal forms, which they replaced during the major marine transgression between the latest Anisian (Middle Triassic) and the middle Norian (Late Triassic). The ability to forage in broader expanses of and deeper water may have enabled parvipelvians to survive when shallow water environments became reduced during the major regression phase, but much more study is needed to test such an inference.

Brachiopods within the subphyla Linguliformea Williams et al., 1996 and Craniiformea Popov et al., 1993 comprise most, but not all, of the taxa previously grouped together in the Class Inarticulata Huxley, as defined in the first edition of the brachiopod volume of the Treatise on Invertebrate Paleontology (Rowell, 1965). The phylogeny and classification of the inarticulated organophosphatic-shelled linguliforms (typified by the modern lingulides; Fig. 1) and the inarticulated and partly articulated organocarbonate-shelled craniiforms (typified by the modern craniides; Fig. 1) have been debated during the last decade, in connection with attempts to analyze the phylogeny of the entire phylum (for summaries see Holmer et al., 1995; Carlson, 1995; Williams et al., 1996, 2000a). Much of the discussion has been centered around the conflicting results of phylogenetic analyses, either based exclusively on the anatomy and morphology of the Recent taxa (e.g., Popov et al., 1993; Carlson, 1991, 1995), or including also the more numerous, mainly Cambro-Ordovician, fossil taxa (e.g., Carlson, 1991; Holmer et al., 1995; Williams et al., 1996, 2000a). The cladistic analyses have either tended to support the monophyly of the Class Inarticulata (e.g., Carlson, 1991, 1995), or indicated that this group is paraphyletic (e.g., Popov et al., 1993, Holmer et al., 1995; Fig. 1). The resulting cladograms in the comprehensive studies of fossil and modern taxa by Williams et al. (1996, 2000a), which were the basis for the classification adopted in the latest edition of the brachiopod volume of the Treatise on Invertebrate Paleontology, largely support a monophyletic Subphylum Linguliformea; however, the phylogenetic position of the Craniiformea remains uncertain, although it may represent a monophyletic group (Fig. 1). Recent molecular phylogenies have given some support to a monophyletic Linguliformea, but also more surprisingly have indicated that the phoronids might form a clade (formally recognized as the Subphylum Phoroniformea Cohen 2000) within the Brachiopoda, possibly together with the inarticulated modern forms (Cohen and Gawthrop, 1996, 1997; Cohen, 2000).

One of the most important and challenging aspects of stratigraphy is the interpretation of the temporal scope of sedimentary units (Schindel, 1980, 1982; Sadler, 1981; Brandt Velbel, 1984). The problem arises at the scale of individual beds and of stratigraphic intervals up to many meters thick. Does a particular bed or interval-represent hours, days, years, centuries, or millennia? Resolution of this question is critical for determination of rates of sedimentation and biotic processes, and in assessing the reliability of the sample for paleoecological or evolutionary analysis. In the absence of a reliable framework of absolute radiometric dates the question can only be answered by indirect inference. Biostratigraphic zonation is a critical first step. But zonation is typically too coarse to resolve temporal scales less than 106 years and many zones are not firmly anchored to absolute dates. It is also important to keep separate the issue of temporal duration represented by fossils (as bioclasts) within a given stratum and that of the deposition of the sedimentary unit itself. There are many instances of thin graded beds full of fossils, which would be characterized unambiguously by sedimentologists as deposits of a single event of sedimentation, but in which the fossils may differ in age by thousands or even millions of years. Examples include many condensed, lag deposits of bones and conodonts (Baird and Brett, 1991), and condensed ammonoid beds containing fossils of several ammonite zones (Fürsich, 1971). Sedimentologic criteria provide one avenue of approach to this issue but commonly fall short of unambiguous answers.

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.

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.

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.

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.

Exceptional biotas—those in which the non-biomineralized tissues of organisms are preserved—are an important record of the evolutionary biology of the late Neoproterozoic—early Phanerozoic interval. Most of these biotas exhibit one of four modes of preservation: preservation of either 1) internal and external detail (Doushantuo-type preservation) or, 2) external cuticles (Orsten-type preservation) in calcium phosphate; 3) coating in pyrite films and infills (Beecher's Bed-type preservation); and 4) preservation of organic remains (Burgess Shale-type preservation). The global environmental and temporal distribution of each mode of preservation is reasonably well constrained, but not why these taphonomic windows existed when they did. The late Neoproterozoic – early Phanerozoic interval is characterized by complex, interlinked, physical, geochemical and biological changes to the Earth's biosphere and geosphere. The changing ecology of marine environments (from matground to mixgrounds: the ‘Agronomic Revolution’) occurred via an intermediate phase of stiffened, but not microbially bound sediments that extended the interval over which exceptional preservation occurred. Prolonged eustatic sea-level rise across flat-lying continental platforms ensured environments conducive to exceptional preservation were developed and, critically, sustained over large contiguous areas. During this, regolith on continental surfaces was recycled, providing an integral source of sediment and ions relevant to mineral authigenesis. Superimposed on these broad-scale changes are specific drivers that controlled the duration of individual taphonomic windows; elucidating these requires a better understanding of the environmental context and diagenetic history of fossiliferous successions at the intra-basinal scale.

Microbes and the sedimentary record of their activity, microbialites, have existed since the Archaean. During the Neoproterozoic-Cambrian interval, there is a marked shift in the fossil record of microbialites with the widespread proliferation of thrombolites (clotted microbialites) and the appearance and proliferation of dendrolites (microbialites composed of dendritic clusters) alongside stromatolites (laminated microbialites). Calcimicrobes also diversified during this interval. The end of this resurgence coincided with the increase in invertebrate taxa at the end of the Early Ordovician. The ìMicrobialite Resurgenceî has long been recognized but the importance of the Neoporoterozoic microbialite record for deciphering trends of this interval has not been so widely realized. It is critical to note that some of the oldest skeletal invertebrates and calcimicrobes are found in Neoproterozoic microbial reefs. Also, microbe-invertebrate synecology and invertebrate abundance trends during this interval suggests that a simple model that keys the resurgence tied in to a lack of competition from reef-building sponges and corals may not be valid. Current re-evaluation of the environmental conditions, principally the fluctuations in the geochemical conditions of the global oceans and atmosphere, will likely shed new light on understanding the Neoproterozoic-Cambrian microbialite record.