The discovery in recent years of several well preserved and partially articulated skeletons of Tyrannosaurus rex has provided the impetus for a study of sexual dimorphism in dinosaurs. The fifteen significant specimens of Tyrannosaurus rex discovered to date may be divided into “robust” and “gracile” morphotypes. Examinations of extant crocodiles and birds show a link between musculature of sexual organs and sexual dimorphism of osteoskeletons. Analogous differences in articulated dinosaur remains point to a method of determining the gender of individual dinosaur skeletons and the presence of an intromittent organ in at least some species. For theropods, and particularly for Tyrannosaurus rex, the larger and more robust individuals are almost certainly female.

The first two ranks above the species level in the traditional Linnean hierarchy — the genus and family — are species based: genera have been erected to unify groups of morphologically similar, closely related species and families have been erected to group genera recognized as closely related because of the shared morphologic characteristics of their species. Diversity patterns of traditional genera and families thus appear congruent with those of species in (a) the Recent (e. g., latitudinal gradients in many groups), (b) compilations of all marine taxa for the entire Phanerozoic (including the stage level), (c) comparisons through time within individual taxa (e. g., Foraminifera, Rugosa, Conodonta), and (d) simulation studies. Genera and families often have a more robust fossil record of diversity than species, especially for poorly sampled groups (e. g., echinoids), because of the range-through record of these polytypic taxa. Simulation studies indicate that paraphyly among traditionally defined taxa is not a fatal problem for diversity studies; in fact, when degradation of the quality of the fossil record is modelled, both diversity and rates of origination and extinction are better represented by including paraphyletic taxa than by restricting data to monophyletic clades. This result underscores the utility of traditional rank-based analyses of the history of diversity.

In contrast, the three higher ranks of the Linnean hierarchy — orders, classes and phyla — are defined and recognized by key character complexes assumed to be rooted deep in the developmental program and, therefore, considered to be of special significance. These taxa are unified on the basis of body plan and function, not species morphology. Even if paraphyletic, recognition of such taxa is useful because they represent different functional complexes that reflect biological organization and major evolutionary innovations, often with different ecological capacities. Phanerozoic diversity patterns of orders, classes and phyla are not congruent with those of lower taxa; the higher groups each increased rapidly in the early Paleozoic, during the explosive diversification of body plans in the Cambrian, and then remained stable or declined slightly after the Ordovician. The diversity history of orders superficially resembles that of lower taxa, but this is a result only of ordinal turnover among the Echinodermata coupled with ordinal radiation in the Chordata; it is not a highly damped signal derived from the diversity of species, genera, or families. Despite the stability of numbers among post-Ordovician Linnean higher taxa, the diversity of lower taxa within many of these Bauplan groups fluctuated widely, and these diversity patterns signal embedded ecologic information, such as differences in flexibility in filling or utilizing ecospace.

Phylogenetic analysis is vital for understanding the origins and genealogical structure of higher taxa. Only in such fashion can convergence and its implications for ecological constraints and/or opportunities be understood. But blind insistence on the use of monophyletic classifications in all studies would obscure some of the important information contained in traditional taxonomic groupings. The developmental modifications that characterize Linnean higher taxa (and traditionally separate them from their paraphyletic ancestral taxa) provide keys to understanding the role of shifting ecology in macroevolutionary success.

Most of what we know about ecology inevitably comes from Late Quaternary ecosystems, particularly those of the past few decades. 20th Century ecosystems are the only ones for which we have direct observational and experimental studies. We can obtain detailed records of ecological dynamics at decade- to century-scales over the past few centuries using historical, permanent-plot, demographic, and paleoecological techniques, but only for a select few ecosystems. Radiocarbon-dated fossil assemblages provide records of ecological changes over the past 25,000 years. Because 14C-dating allows independent dating of the assemblages with precision of 50–500 years, detailed spatiotemporal patterns of change can be outlined, but these are limited to certain kinds of organisms and to regions with a high density of fossil sites. When we go beyond the radiocarbon barrier 30–40,000 years ago, the density of datable terrestrial assemblages decreases sharply, and our views of past ecosystems become murkier.

Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas. The second is the development of a powerful method for producing area cladograms from complex data, especially cases of reticulated area relationships, without loss of information. That method, called Phylogenetic Analysis for Comparing trees (PACT), is described herein. The third element is the replacement of the model of maximum vicariance with the model called the Taxon Pulse hypothesis. PACT analysis of Hominoidea, Hyaenidae, and Proboscidea beginning in the Miocene, reveals that all three groups share a general episode of species formation in Africa in the early Miocene, followed by “out of Africa” expansion into Europe, Asia and North America, a second general episode of species formation in Asia in the mid-Miocene, followed by “out of Asia” expansion into Africa, Europe and North America. Finally, there were two additional “out of Africa” events during the late Miocene and into the Pliocene, the last one setting the stage for the emergence and spread of Homo. In addition to these shared episodes of vicariance and dispersal, each group exhibits clade-specific within-area and peripheral isolates speciation events. The complex history of dispersal and speciation over large areas exhibited by hominoids is part of a more general history of biotic diversification by taxon pulses.

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

Species origination and extinction events far outnumber radioisotopically dated events in the ancient stratigraphic record. In order to calibrate rapid rates of Mesozoic and Paleozoic change and to estimate the ages of paleobiologic events it would be ideal to have multiple dated events in single stratigraphic sections. This condition is rarely realized and the practical alternative is to build composite sections that combine information from many different locations. The compositing process takes advantage of all available evidence of relative age to produce high resolution time lines; i.e. ordered sequences of individual events whose average spacing is much finer than the duration of biostratigraphic zones and can approach the uncertainty intervals of the highest precision radioisotopic dates. Dated events are included in the compositing process from the outset. As a result the sequencing procedure is more efficient and the dated events find their optimal positions in the time line independent of any biostratigraphic zonal schemes. The sequencing procedures follow simple logical rules that may be learned from tiny data sets. When usefully large numbers of events are involved, however, the sequencing must be undertaken by computer and there is seldom a unique solution that best fits the field data. The range of positions in sequence that an event may occupy across the full set of equally best-fit solutions is a measure of the resolving power of the event. As new high-precision dates and detailed range charts continue to become available, the quality of the time lines will improve and they will become increasingly viable alternatives to zonal time scales in the older parts of the Phanerozoic.

G. Udny Yule (1924) was perhaps the first to examine the subject of rates of taxonomic evolution mathematically, but George Gaylord Simpson was the first to examine the subject from within the confines of the so-called Modern Synthesis of Biology (Simpson, 1944). In that sense, therefore, Simpson's can be regarded as the first modern study of rates of taxonomic evolution. Although he is almost universally regarded as the catalyst behind the current interest in taxonomic evolutionary rates, it is a remarkable fact that Simpson's aims were almost entirely different from those of current workers. In a very important sense, Simpson's taxonomic rates of evolution were not taxonomic at all, but were morphological, or even more to the point, genetic.

I'll begin with the obvious question, how many people saw the movie “Jurassic Park”? How many people believed it? In the movie, “Jurassic Park”, there were basically two stars. Tyrannosaurus rex was one of them and the Velociraptors (or Deinonychus, or whatever they happened to be) were the others. What you might also know is that I was an advisor on the movie. All I was able to do was basically tell them when the dinosaurs were walking right and tell Laura Dern how to pronounce her words.

Any time the dinosaurs were going to do something, any time Steven Spielberg wanted to have the dinosaurs do something in the movie, he would ask me if I thought they could do that. If I said yes or no, he would take that as an answer. But if I said maybe, he would just do whatever he wanted. That's fiction.

The crystallographic orientations of echinoderm skeletal elements can supplement standard morphological comparisons in the exploration of echinoderm evolution. At a coarse scale, many echinoderms share a crystallographic pattern in which c axes radiate away from the axis of pentaradial symmetry. Within this common pattern, however, c axes of different taxa can differ dramatically in their degree of variability, angles of inclination, and relationships to the external morphology of skeletal elements. Crystallographic data reflect a variety of taxon-specific influences and therefore reveal different information in different taxa. In echinoids, orientations of c axes in coronal plates correlate well with high-level taxonomic groupings, while c axes of apical plates record modes of larval development. In blastoids, c axes of radial plates have a structural interpretation, with the c axis oriented parallel to the orientation of the surface of the radial plate during its initial growth stages. In crinoids, c axes do not correlate with taxonomic group, plate morphology, or developmental sequence, but instead correlate with relative positions of skeletal elements on the calyx. Although their full potential has yet to be explored, the varied crystallographic patterns in echinoderms have been used to clarify skeletal structure, characterize developmental anomalies, and infer homologies of skeletal plates both within specimens and between groups. A axes are less constrained in their orientations than c axes and offer less promise of revealing novel paleobiological information.

Computers excel at applying simple, logical rules to prodigious amounts of information. Such is the nature of biochronology. Range charts of first- and last-occurrences of fossil species must be combined from many locations to compensate for local incompleteness of the fossil record. Enlarging the geographic scope adds the complications of faunal migration and provinciality – for which the remedy is yet more information. Expert biostratigraphers have managed to divide Phanerozoic time into hundreds of biozones by limiting the amount of information they consider. A set of biozones specifies the sequence of only a fraction of available species, typically from a single clade in a particular province across a limited time interval. Once the human expertise applied to this task is rendered into logical algorithms, computers can extend the exercise to huge data sets of otherwise unmanageable scope.

Two factors make this computer-assisted sequencing of first- and last-appearance events easy to understand and implement: the biostratigraphers' ground rules are straightforward and the computations, although tediously repetitive, proceed by simply analogy rather than esoteric mathematics. Two other factors force the outcome to be a set of time lines that fit the field data equally well: there is rarely enough information to identify a unique best-fit solution and there is more than one set of expert ground-rules for measuring the fitness of paleobiologic time-lines. A set of equally well-fit time lines serves as an appropriate statement of uncertainty in the order of events. Mapping the local ranges back into a best-fit composite range can reveal biogeographic and taxonomic complications; quality control and interpretation advance together.

Atmospheric dust constitutes particles <100 μm, or deposits thereof (continental or marine); dust includes ‘loess,’ defined as continental aeolian silt (4–62.5 μm). Dust is well-known from Earth's near-time (mostly Quaternary) record, and recognized as a high-fidelity archive of climate, but remains under-recognized for deep time. Attributes such as thickness, grain size, magnetism, pedogenesis, and provenance of dust form valuable indicators of paleoclimate to constrain models of atmospheric dustiness. Additionally, dust acts as an agent of climate change via both direct and indirect effects on radiative forcing, and on productivity, and thus the biosphere and carbon cycling. Dust from the late Paleozoic of western equatorial Pangea reflects ultimate derivation from orogens (ancestral Rocky Mountains, Central Pangean Mountains), whereas dust from southwestern Pangea (Bolivia) reflects both proximal volcanism and crustal material. Records of dust conducive to cyclostratigraphic analysis, such as data on dust inputs from carbonate sections, or magnetism in paleo-loess, reveal dust cyclicity at Milankovitch timescales, but resolution is compromised if records are too brief, or irregular in interval or magnitude of the attribute being measured. Climate modeling enables identification of the primary regions of dust sourcing in deep time, and impacts of dust on radiative balance and biogeochemistry. Deep-time modeling remains preliminary, but is achievable, and indicates principal dust sources in the Pangean subtropics, with sources increasing during colder climates. Carbon cycle modeling suggests that glacial-phase dust increases stimulated extreme productivity, potentially increasing algal activity and perturbing ecosystem compositions of the late Paleozoic.

Serial sectioning (also referred to as serial grinding) is used to investigate the internal structures of three-dimensional (rock or fossil). In this process series of sections are ground or cut in sequence through a specimen to reveal its internal structures. The specimen is ground down against an abrasive surface (e.g., abrasive powder on a sheet of steel or a rotating diamond wheel on a lathe) or cut with a saw blade. The details of each section can be recorded by drawing or photography. A permanent record of each surface can be made by taking acetate peels and mounting them in glass slides (Wilson and Palmer, this volume, Chapter 13). Serial section information can be digitized and reconstructed in three-dimensions using computer techniques (Chapman, this volume, Chapter 15).

The understanding of diatom evolution has progressed greatly over the last two decades. Existing data sets have been reanalyzed, new data sets have been generated, and new tools have been employed. Hindering progress is the seemingly endless number of diatom species remaining to be described and relative small number of investigators active in the field. This problem is further confounded by the dramatic reorganization of generic level classification in the group. Despite these problems, many conclusions can be made about prior hypotheses concerning the group's development. Most notably, the origin of the diatoms can be bracketed between the Late Triassic and Early Jurassic using fossil record and molecular clock estimates. This combination of techniques has also provided consensus and clarification to the origin and duration of specific lineages enhancing our understanding of the group's diversification, early ecology, and evolutionary relationships.

Brachiopods are one of the few phyla to have lived in the world's oceans for the last 550 million years, since early Cambrian times. For much of that time they were the dominant shelled form in marine aquatic environments. Throughout all of this time their physiological structure has remained unchanged, and for some extant species their external anatomy is remarkably similar to early Cambrian forms (e.g., some inarticulated lingulids and some articulated rhynchonellides). They perform all of the basic physiological functions common to the vast majority of marine ectotherms, namely feeding, growth, reproduction, and metabolic and excretory processes. Their bodies are enclosed by two unequal shells, which are oriented dorsally and ventrally, as opposed to the lateral, equal shells in bivalve molluscs. The ventral valve in articulated species has a characteristic opening for the pedicle to pass through. In some articulated brachiopods the shells are traversed by many extensions of the mantle tissue called caeca (e.g., in Waltonia inconspicua, or Terebratulina retusa), while in others the shells form a continuous solid integument (e.g., rhynchonellides such as Notosaria nigricans). The former are the punctate brachiopods and the latter are impunctate species.

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

Diatoms are golden brown algae (class Bacillariophyceae) whose cellular contents are enclosed between two valves or shells of silica. They are classified into groups with radial symmetry (centric diatoms) and axial symmetry (pennate diatoms). The latter are subdivided as raphid and araphid diatoms according to the presence or absence of raphes (slit-like structures) that allow diatoms to move along firm surfaces. Many centric and some araphid diatoms are planktonic, maintained by turbulence in the limnetic region of a lake, whereas raphid diatoms live on the lake bottom or are attached to objects in the illuminated zone.

Carbon isotopes in Neogene-age fossil teeth and paleosol carbonates are commonly interpreted in the context of past distributions of C3 and C4 vegetation. These two plant types have very different distributions in relation to climate and ecology, and provide a robust basis for reconstructing terrestrial paleoclimates and paleoenvironments during the Neogene. Carbon isotopes in pre-Neogene fossil teeth are usually interpreted in the context of changes in the δ13C value of atmospheric CO2, and variable climate-dependent carbon-isotope discrimination in C3 plants. Carbon isotopes in pre-Neogene soil carbonates can be used to estimate past levels of atmospheric CO2. Oxygen isotopes in fossil teeth and paleosol carbonates primarily are influenced by the oxygen isotopic compositions of ancient rainfall and surface waters. The oxygen isotopic composition of rainfall is has a complex, but tractable, relationship with climate, and variably relates to temperature, elevation, precipitation amount, and other factors. Mammal species that rely on moisture in dietary plant tissues to satisfy their water requirements (rather than surface drinking water) may have oxygen isotopic compositions that track aridity. Thus, oxygen isotopes of fossil mammals can place broad constraints on paleoaridity. Carbonate clumped isotope thermometry allows for reconstruction of soil temperatures at the time of pedogenic carbonate mineralization. The method is unique because it is the only thermodynamically based isotopic paleothermometer that does not require assumptions about the isotopic composition of the fluid in which the archive mineral formed. Soil temperature reflects a complex interplay of air temperature, solar radiative heating, latent heat effects, soil thermal diffusivity, and seasonal variations of these parameters. Because plants and most animals live in and/or near the soil, soil temperature is an important aspect of terrestrial (paleo)climate.

The terrestrial vertebrate fossil record provides a window into the past evolution of taxa, communities, and ecosystems. It can also be used to reconstruct ancient environments, climates, and landscapes. Vertebrate fossils can document the evolution of humans and their interactions with fauna and environments. However, before the maximum potential of this record can be realized, it is essential to know the extent of temporal resolution, or time-averaging, represented by fossil samples.

It is now possible to reconstruct what happened when the chordates and echinoderms first split from each other. This involves a three-way comparison among: 1) the solute Coleicarpus, which is probably a stem-group dexiothete; 2) the Cincta, which seem to be the least crownward known echinoderms; and 3) the solute Castericystis, which is a stem-group chordate, probably the least crownward known. Counter-torsion of the tail, by which the effects of dexiothetism were nullified in the tail, took place in two phases, firstly in the fore tail and later in the hind tail. Echinoderms and chordates are descended from ancestors that were attached to, or lay on, the sea floor and were therefore much more liable to attack from above than beneath. This probably explains why the main nerve trunk in chordates is dorsal, rather than being ventral as in protostomes.