The Synapsida is the mammal-like ramus of the Amniota, the sister group of the Sauropsida (or Reptilia of Gauthier et al., 1988). Synapsids are characterized by the possession of a lateral temporal fenestra (Fig. 1A), among other features (see Gauthier, this volume). Of all the great transitions between major structural grades within vertebrates, the transition from basal amniotes to basal mammals is represented by the most complete and continuous fossil record, extending from the Middle Pennsylvanian to the Late Triassic and spanning some 75 to 100 million years. Structural evolution of particular functional systems has been well investigated, notably the feeding mechanism (Barghusen, 1968; Crompton, 1972; Crompton and Parker, 1978; Crompton and Hylander, 1986) and the middle ear (Hopson, 1966; Allin, 1975, 1986; Allin and Hopson, 1992), and these studies have demonstrated the gradual nature of these major adaptive modifications.

In the past few decades, we have come a long way in making paleobiology more rigorous. We have accumulated an impressive array of quantitative techniques – statistical and otherwise – and these are in use with the full range of paleobiological problems. Also striking is the way the added rigor of our science has spilled over into non-quantitative judgments and interpretations. No longer is the Just-So Story allowed to stand unchallenged. Rather, we respond to these bald assertions and ad hoc theories with: “Can you prove it?” or “Can this be tested?”

Among the most intriguing and significant aspects of the marine stratigraphic record are patterns of temporal change in fossil assemblages and paleocommunities. Understanding the stratigraphic patterns and the correct temporal scale of such faunal change is crucial to interpreting the underlying processes involved. Inattention to the temporal scale at which paleontological data are collected, and at which faunal change is observed, often results in the use of entirely inappropriate explanatory models. In many cases modern ecological theories have been misapplied to the fossil record because problems of scale were not adequately considered. The term “community” itself has been applied to such a wide range of fossil accumulations that it has ceased to have any consistent paleoecologic meaning (see discussion in Järvinen et al.,1986). For this reason, we prefer to use the term “assemblage” for time-averaged accumulations of fossils, and restrict “community” to only those organisms which actually lived together in the same space and time (i.e., a biocoenosis). Therefore, faunal assemblages, even when untransported, are the preserved amalgamated record of many successive communities within which short-term (10 – 100 years) changes may or may not be resolvable. Recurrent, compositionally similar assemblages, believed to have occupied generally similar benthic environments, are then grouped into biofacies which can be seen to intergrade and migrate through time.

This chapter reviews major types of statistical resampling approaches used in paleontology. They are an increasingly popular alternative to the classic parametric approach because they can approximate behaviors of parameters that are not understood theoretically. The primary goal of most resampling methods is an empirical approximation of a sampling distribution of a statistic of interest, whether simple (mean or standard error) or more complicated (median, kurtosis, or eigenvalue). This chapter focuses on the conceptual and practical aspects of resampling methods that a user is likely to face when designing them, rather than the relevant mathematical derivations and intricate details of the statistical theory. The chapter reviews the concept of sampling distributions, outlines a generalized methodology for designing resampling methods, summarizes major types of resampling strategies, highlights some commonly used resampling protocols, and addresses various practical decisions involved in designing algorithm details. A particular emphasis has been placed here on bootstrapping, a resampling strategy used extensively in quantitative paleontological analyses, but other resampling techniques are also reviewed in detail. In addition, ad hoc and literature-based case examples are provided to illustrate virtues, limitations, and potential pitfalls of resampling methods.

Silicification is the replacement of original skeletal material accomplished through the concurrent dissolution of calcium carbonate and precipitation of silica. The processes is aided by the nucleation of silica to organic matter which surrounds the mineral crystallites within the shell. Factors that control silicification are those that influence the dissolution/precipitation process: shell mineralogy, shell ultrastructure (and, therefore, surface area), the amount and location of organic matter, and the character of the enclosing matrix. Silicification, like all types of fossilization, can produce taphonomic biases: it is far more common in Paleozoic than younger deposits, is more likely to occur in organisms with low-magnesium calcite shells, in carbonate sediments, and in environments with elevated dissolved silica.

One of the many contributions paleontology makes to our understanding of the biosphere and its evolution is a direct temporal record of biotic events. However, assuming fossils have been correctly identified and accurately dated, stratigraphic ranges underestimate true temporal ranges: observed first occurrences are too young, and observed last occurrences are too old. Here I introduce the techniques developed for placing confidence intervals on the end-points of stratigraphic ranges. I begin with the analysis of single taxa in local sections – with the simplest of assumptions – random fossilization. This is followed by a discussion of the methods developed to handle the fact that the recovery of fossils is often non-random in space and time. After discussion of how confidence intervals can be used to test for simultaneous origination and extinctions, I conclude with an example application of confidence intervals to unravel the relative importance of background extinction, environmental change and mass extinction of ammonite species at the end of the Cretaceous in western Tethys.

High-precision geochronological techniques have improved in the past decade to the point where volcanic ash beds interstratified with fossil-bearing rocks can be dated to a precision of 0.1% or better. The integration of high-precision U-Pb zircon geochronology with bio/chemo-stratigraphic data brings about new opportunities and challenges toward constructing a fully calibrated time scale for the geologic record, which is necessary for a thorough understanding of the distribution of time and life in Earth history. Successful implementation of geochronology as an integral tool for the paleontologist relies on a basic knowledge of its technical aspects, as well as an ability to properly evaluate and compare geochronologic results from different methods. This paper summarizes the methodology and new improvements in U-Pb zircon geochronology by isotope dilution thermal ionization mass spectrometry, specifically focused on its application to the stratigraphic record.

A study of the anatomy and morphology of a fossil skeleton indicates the overall size, posture, and form of the animal. Even various functional aspects of the skeleton such as preferred mode of locomotion and chewing mechanisms can be deduced from such studies. But the desire to understand dinosaurs as dynamic, once-living animals and not merely as taxonomic entities arranged in phylogenetic schemes, goes beyond this. In 1842, Sir Richard Owen not only presented dinosaurs taxonomically but he also initiated the quest to understand the biology of these animals. In recent decades, the study of dinosaur paleobiology has blossomed, and has provided a crucial link between studies of morphology (structures) and that of function and physiology.

“Bioerosion” was coined by Neumann (1966) as an abbreviation of “biologic erosion”, and describes every form of biologic penetration into hard substrates, i.e., lithic (including skeletal) and woody. An extremely wide range of organisms causes bioerosion (see Bromley, 1970; Warme, 1970, 1975; Ekdale et al., 1984, p. 108–139). The work of these organisms produces trace fossils at all scales, from microscopic to gigantic. Minute scars etched by brachiopod pedicles have a paleoecologic story to tell; at another scale, cliff sapping by communities of boring bivalves and rasping limpets can cause major geographic changes. For example, the work of pholad bivalves played a leading role in the separation of England from the European continent; and had the great armada, sent against England by Philip II of Spain in 1588, not been annihilated by wood-boring shipworms (bivalves), the language of this short-course would have been Spanish.

Plants provide unmatched opportunities to evaluate long debated evolutionary patterns in terms of the detailed biology of the fossil organisms. Leaves serve here as an example of how those advantages can be exploited. Over the history of vascular plants, three important transitions in leaf evolution—the origin of laminate leaves, the progressive loss of seed plant morphological diversity, and the evolution of more angiosperm-like leaves—also represent major shifts in leaf development and physiology. These transitions often occurred in parallel in different lineages, such as the evolution of marginal growth in each of at least four independent origins of laminate leaves during the Devonian and Carboniferous. Each also entailed dramatic reorganizations of leaf hydraulics. For example, the length of the finest distributary vein order varies from up to tens of centimeters down to hundreds of microns in successive groups of dominant seed plants. Angiosperms impose an additional trend upon these patterns with the evolution of their uniquely high vein densities. Vein density strongly influences and can provide a proxy for other physiological characteristics, such as assimilation and transpiration rates. The large increase in transpiration capacity accompanying the evolution of angiosperm leaf traits may even play an important role in feeding precipitation and thereby altering local climate.

Mathematical models of fluid flow thorough plant stems permit quantitative assessment of plant ecology using anatomy alone, allowing extinct and extant plants to be measured against one another. Through this process, a series of patterns and observations about plant ecology and evolution can be made. First, many plants evolved high rates of water transport through the evolution of a diverse suite of anatomical adaptations over the last four hundred million years. Second, adaptations to increase hydraulic supply to leaves tend to precede, in evolutionary time, adaptations to increase the safety margin of plant water transport. Third, anatomical breakthroughs in water transport function tend to occur in step with ecological breakthroughs, including the appearance of leaves during the Devonian, the evolution of high leaf areas in early seed plants during the Carboniferous, and the early radiation of flowering plants during the Cretaceous. Quantitative assessment of plant function not only opens up the plant fossil record to ecological comparison, but also provides data that can be used to model fluxes and dynamics of past ecosystems that are rooted in individual plant anatomy.

Comatulid crinoids, or featherstars, are the dominant group of living crinoids and occur in a wide range of modern marine environments from the intertidal zone to the abyss. This chapter outlines current understanding of comatulid classification, distribution, feeding ecology, diets, predation, and taphonomy. A detailed introduction to morphological features, terms and associated symbology is given together with a discussion of practical aspects of working with specimens and the difficulties associated with species identifications. An artificial key to the families of comatulids is included.

The general theme of this chapter is the relationships between trace fossils and benthic oxygen availability in marine environments. Discussion is organized into three sections, which correspond to related yet distinct approaches to the analysis of ichnofossil/oxygen relationships.

Vegetation affects feedbacks in Earth's hydrologic system, but is constrained by physiological adaptations. In extant ecosystems, the mechanisms controlling plant water used can be measured experimentally; for extinct plants in the recent geological past, water use can be inferred from nearest living relatives, assuming minimal evolutionary change. In deep time, where no close living relatives exist, fossil material provides the only information for inferring plant water use. However, mechanistic models for extinct plant water use must be built on first principles and tested on extant plants. Plants serve as a conduit for water movement from the soil to the atmosphere, constrained by tissue-level construction and gross architecture. No single feature, such as stomata or veins, encompasses enough of the complexity underpinning water-use physiology to serve as the basis of a model of functional water use in all (or perhaps any) extinct plants. Rather, a “functional whole plant” model must be used. To understand the interplay between plant and atmosphere, water use in relation to environmental conditions is investigated in an extinct plant, the seed fern Medullosa ((Division Pteridospermatophyta), by reviewing methods for reconstructing physiological variables such as leaf and stem hydraulic capacity, photosynthetic rate, transpiration rate, stomatal conductance, and albedo. Medullosans had the potential for extremely high photosynthetic and assimilation rates, water transport, stomatal conductance, and transpiration—rates comparable to later angiosperms. When these high growth and gas exchange rates of medullosans are combined with the unique atmospheric gas composition of the late Paleozoic atmosphere, complex vegetation-environmental feedbacks are expected despite their basal phylogenetic position relative to post-Paleozoic seed plants.

Ecometrics is the quantitative study of functional traits at the community level, and the environmental sorting of those traits at regional and continental scales. Functional traits are properties of organisms that have a direct physical or physiological relationship to an underlying quality of the environment, which in turn has indirect links to broader environmental factors such as temperature, precipitation, elevation, atmospheric composition, or sea level. When the same environmental factor affects the performance of many taxa, ecometric sorting is the result. Ecometric patterns in trait distributions across space and through time are therefore a product of biogeographic sorting, evolution, and extinction driven by changes in Earth systems. We review concepts associated with ecometrics, with examples that illustrate how trait-based approaches differ from taxon-based methods, how ecometrics can be used to study Earth-life transitions in the fossil record, and how ecometrics can be used to compare Earth-life transitions that differ in temporal or geographic scale. This paper focuses on the climatic and biome changes of the Great Plains of North America during the Miocene, when grasslands came to be the dominant vegetation type, and of the Anthropocene of the American Midwest, which saw extensive landscape changes in the nineteenth century.

Microbial communities adjust the chemical structure of their cell membranes in response to environmental temperature. This enables the development of lipid-based paleothermometers such as the glycerol dialkyl glycerol tetraether (GDGT) proxies described here. Surface-sediment calibrations establish a strong empirical relationship between the relative distribution of GDGTs and temperature. GDGT proxies can be used in marine, lacustrine, and paleosol sequences as long as the organic material is not thermally mature. Thus far, GDGT proxies have been applied to sediments dating back to the middle Jurassic. Many of the key uncertainties of these proxies are related to our emerging understanding of archaeal (and for the branched GDGTs, bacterial) ecology.

Since the late Paleozoic, insects and arachnids have diversified in the terrestrial world so spectacularly that they have become unquestionably the most diverse group of organisms to ever inhabit the planet. In fact, this 300 million year interval may appropriately be referred to as the age of arthropods. What is the origin and history of terrestrial arthropods? How is arthropod diversity maintained on land? In this rhetorical context we will discuss (1) the degree to which terrestriality is found in arthropods, (2) the physiological barriers to terrestrialization that arthropod clades confronted, (3) the historical record of arthropod diversity on land based on paleobiological, comparative physiological and zoogeographical evidence, and (4) some tentative answers to the “why” of terrestrial arthropod success. We are providing a geochronologic scope to terrestriality that includes not only the early history of terrestrial arthropods, but also the subsequent expansion of arthropods into major terrestrial habitats.

Stromatolite shapes, sizes, and spacings are products of microbial processes and interactions with topography, sedimentation, and flow. Laboratory experiments and studies of modern microbial mats and sediments can help reconstruct processes that shaped some typical stromatolite forms and some atypical microbially influenced sediments from Neoproterozoic cap carbonates. Studies of modern, cohesive microbial mats indicate that microbialaminite facies in the lower Rasthof Formation (Cryogenian) formed in the presence of very low flow and were not deformed by strong waves or currents. Giant wave ripples, corrugated stromatolites, and tube-hosting stromatolites in basal Ediacaran cap carbonates record interactions between microbes, flow, and evolving bedforms. Preferential cementation in and close to the giant ripple crests is attributed to interactions between flow and local topography. These interactions pumped alkaline porewaters into ripple crests and helped nucleate elongated stromatolites. The similar textures of giant wave ripples and elongated, corrugated, and tube-hosting stromatolites suggest growth in the presence of organic-rich, rounded particles and microbial mats, and in flow regimes that permitted mat growth. These hypotheses can be tested by experiments and models that investigate lithification and the macroscopic morphology of microbial mats as a function of the flow regime, preexisting topography, redox-stratification in sediments, and delivery of organic-rich particles. The widespread microbially influenced textures in Cryogenian microbialaminites and basal Ediacaran cap dolostones record a strong reliance of carbonate deposition on the presence of organic nuclei, supporting carbonate accumulation rates comparable to those in modern reefs. Therefore, the unusual macroscopic morphologies of microbially influenced facies in Neoproterozoic cap carbonates may not reflect oceans that were greatly oversaturated with respect to carbonate minerals.

Many Paleontologists share the opinion of McGhee (1996), who wrote “Prior to the Devonian, there was no terrestrial ecosystem to speak of. Some primitive plants precariously establishing a beachhead in protected coastal areas was about it. The interiors of the continents of the planet Earth were as barren as the rocky landscapes of Mars.” Thus, it was with trepidation that I reported paleosols containing trace fossils of early land animals in the late Ordovician, Juniata Formation, of Pennsylvania (Retallack and Feakes, 1987; Retallack, 1992a, 1992b, 1993). My late colleague, Jane Gray, engendered considerable debate by reporting Ordovician and Early Silurian spores like those of liverworts (Gray and Boucot, 1977; Gray, 1985). This spore, trace fossil and paleosol evidence for life on land in the Ordovician has remained controversial (Buatois et al., 1998; Shear, 1998), but evidence for Ordovician life on land has continued to accumulate. Especially important was discovery of myriapod trackways from mid-Ordovician (Llandeilian-Caradocian) Borrowdale Volcanics of the Lake District, England (Johnson et al., 1994). Abundant arthropod burrows and tracks, and a single body fossil of an euthycarcinoid in the fluvial-eolian Tumblagooda Sandstone of Western Australia (White 1990; McNamara and Trewin, 1993; Trewin and McNamara, 1995) are now thought to be late Ordovician in age (Iaksy et al., 1998). An enigmatic assemblage of arthropods and plants from a mid-Ordovician paleokarst in Tennessee (Caster and Brooks, 1956) is now thought to have been lacustrine (Gray, 1988a). The fossil record of Ordovician land plants also has improved with the discovery of possible megafossil mosses (Snigirevskaya et al. 1992), and possible late Ordovician trilete spores (Nøhr-Hansen and Koppelhus, 1998; Richardson 1988; Strother, 1991; Strother et al., 1996). But the most abundant evidence for Ordovician life on land remains fossil soils, now exploited by increasingly thorough and sophisticated studies (Retallack, 1985, 1992a, 1992b, 1993; Feakes et al., 1989; Driese and Foreman 1991, 1992a, 1992b; Driese et al., 1992, 1997; Mora et al., 1991, 1996; Mora and Driese, 1993; Yapp and Poths, 1992, 1994, 1996; Yapp, 1993, 1996). Mounting evidence from fossils and paleosols now presents an increasingly detailed view of Ordovician ecosystems on land.

From the beginning of the Late Ordovician (Sandbian: 460.9myr) through end Devonian (Famennian: 359.2myr), coral-stromatoporoid sponge reefs formed a remarkable, evolving ecosystem that dominated sediment production on tropical carbonate platforms in a calcitic ocean. This was a time of maximal and unparalleled reef development in the Phanerozoic, with reef tracts vastly exceeding in size and biodiversity of those in the Holocene (e.g., the Great Barrier Reef). Within this circum-equatorial niche, the calcitic tabulate and rugose corals, and the aragonitic (or high Mg calcite) stromatoporoid sponges, were the primary Middle Paleozoic reef frame builders. These were supplemented ecologically and skeletally by now extinct groups of calcitic bryozoans, crinoids, brachiopods, and red algae, alongside aragonitic green algae, and enigmatic CaCO3 precipitating and binding calcimicrobes. This 100 myr long Middle Paleozoic reef consortium thrived under SST averages of 30°+, to latitudes as high as 45°–55°, under high atmospheric CO2 conditions of 6000+ ppm, and sealevels 150–200 m higher than today. This reef ecosystem was disrupted by several relatively short duration south polar glacial episodes, centered around northern Gondwana, defining the O/S boundary Mass Extinction Events (MEEs). Nearly all coral and stromatoporoid families survived this MEE: there were losses at the genus level. Reef-building stopped nearly everywhere, and during the ‘recovery’ interval, solitary rugose corals initially prevailed, and stromatoporoids were small. Full global re-establishment of the reef ecosystem, and biodiversity, took another 3–4 million years (not until the late Aeronian, Early Silurian). This was followed by a remarkable reef expansion in the Middle Silurian (Wenlock), then by declines in the latest Silurian (Ludlow-Pridoli), and earliest Devonian (Lochkovian) possibly due to sealevel lowstands, tectonic plate re-assembly, and ocean current re-direction. Maximal Phanerozoic reef success was during the Emsian-Givetian, when some 15 barrier reef tracts more than 1100 km long flourished in tropical shallow seas. Reef-building coral diversity exceeded 200 genera, and the calcifying stromatoporoids evolved 60+ genera, especially in the ‘Old World’ faunal province (Euramerica, Cathaysia, northern Australia). Near the end of the Middle Devonian (mid- to late Givetian), the primary reef dwellers declined sharply in diversity, marked generally by sealevel lowstand, followed in the Frasnian (Late Devonian) by shrinking latitudes for carbonate platforms, and reduced reef accommodation space. Sharp cooling, with the arrival of a global Icehouse climate, and aragonitic oceans, led to the second largest Phanerozoic Mass extinction around the Frasnian/Famennian boundary, with reef builder and reef inhabitant losses exceeding those of the O/S MEE. The global absence of coral-sponge reefs persisted for nearly all of the 16 myr long Famennian, as total CaCO3 production fell some 60–90%, as aragonitic oceans took over. Only small and scattered Famennian coral-stromatoporoid patch reefs are known, with the last of these in the late Famennian (Strunian), punctuated by total disappearance of the whole keystone reef-building order. Famennian and Strunian corals belonged to Carboniferous families. During the Famennian, calcimicrobes, the first calcifying foraminiferans, and select ‘lithistid’ calcareous sponges dominated a highly stressed reef ecosystem, lacking barrier reef tracts. Biodiversity and reef construction were decoupled under global climatic stress during the succeeding icehouse Late Paleozoic.