The evolutionary history of scleractinian corals, based on morphological taxonomy and inferences from the fossil record, has been poorly understood. Molecular techniques developed over the past ten years are now being used to gain a new perspective on scleractinian phylogeny. DNA sequences, mitochondrial genome structure, and morphological characters support a basal position for the Anthozoa in the phylum Cnidaria. Mitochondrial and nuclear DNA sequences suggest a relatively derived position of the order Scleractinia within the class Anthozoa. Mitochondrial and nuclear DNA sequences have provided a new hypothesis for evolution within the Scleractinia that is different from hypotheses based on morphological characters of extant and fossil taxa. Groupings within the two major lineages defined by molecular data do not correspond to morphological suborder groupings although groupings of genera within families do correspond to traditional taxonomy. This new molecular hypothesis suggests that the Scleractinia are represented by two major lineages that diverged from each other before the appearance of the scleractinian skeleton in the fossil record. This divergence time supports the hypotheses that the Scleractinia are not related to the Rugosa of the Paleozoic and that the scleractinian skeleton has evolved more than once. These two major lineages may represent two architectural strategies within the Scleractinia that have led to their great morphological diversity.

Perhaps the one structural feature of the molluscan shell which has historically attracted the most attention from biologists and paleobiologists alike is the banding or growth increment variation associated with so many molluscan species. Such growth patterns are often prominently displayed on the external surfaces of shells and have long been the focus of serious biological and paleontological research (see reviews by Clark, 1974; Lutz and Rhoads, 1980). The usefulness of external shell growth patterns in ecological or paleoecological contexts is limited, however, by both the inability to distinguish true periodic features from random disturbance marks and by the extreme crowding of growth lines near the margins of mature shells. In the last two decades these problems have been surmounted with the recognition of periodic growth patterns within molluscan shells. Internal shell growth patterns are known from all classes of mollusks, but those in the Bivalvia have been studied most extensively. This is a result of the relative ease with which a complete ontogenetic growth record can be obtained by sectioning a shell along the axis of maximum growth (Rhoads and Pannella, 1970). Analogous ontogenetic records are very difficult, if not impossible, to obtain from coiled or spiral shells (e.g., gastropods) using current techniques (Lutz and Rhoads, 1980). This chapter, then, aims to review the major types of internal shell growth patterns described within molluscan shells (mainly bivalves) and to discuss their origin and applications in ecology and paleoecology. Also taken up in this chapter is a brief consideration of geochemical variations (stable oxygen and carbon isotopes and trace and minor elements) within molluscan shells. Physical-chemical, environmental, and physiological influences on shell chemistry are discussed in relation to how biogeochemical variations in the shell may be used to reconstruct paleoenvironmental conditions.

Though long suspected to be critical to the understanding of the evolution of the pelecypod subclass Pteriomorphia, the mid-Palaeozoic family Rhombopteriidae was too poorly known to allow clarification of its relationships. Furthermore, numerous species were assigned to the nominate genus, Rhombopteria, many of which belong in other genera or even other subclasses. Consequently, the morphologic concept entailed by Rhombopteria was confused as were functional morphologic investigations.

Silicified rhombopteriids discovered in the Lower Devonian of Australia are referred to a new genus, and reveal internal shell characters essential for understanding rhombopteriid relationships. The family Rhombopteriidae is revised to include only three genera, Rhombopteria, Prantliella and the new Australian genus.

New data provided by the Australian material indicate that rhombopteriids were non-byssate, dimyarian pteriomorphs that lived pleurothetically on the left valve as do gryphaeid oysters. The Rhombopteriidae are assigned to the Ostreina and are the sister group of all other ostreinans including the Ostreoidea, Pseudomonotidae and Terquemiidae. Important characters common to rhombopteriids and gryphaeid oysters include: 1) left-sided pleurothetic habit; 2) absence of byssal notch or sinus throughout ontogeny; 3) Quenstedt muscle scar; 4) proximal gill weal; 5) circumferential curb; 6) commissural shelf; and 7) posteroventral palliobranchial fusion as evidenced by a branchitellum and posterior radial fold and sulcus. Outgroup comparison with Umburridae indicate that characters 1–4 are symplesiomorphic for the Order Ostreoida. Characters 5–7 are autapomorphies for a clade including the Rhombopteriidae, Pseudomonotidae, Terquemiidae and Ostreoidea.

Rhombopteriids were probably derived from left-sided pleurothetic, umburrid-like ancestors which, in turn, descended from primitive, equivalved, orthothetic prionodonts. Thus, a right-sided pleurothetic stage was never part of the evolutionary pathway of oysters. The inequivalved shell of eupteriomorphs evolved initially for a left-sided pleurothetic semi-infaunal habit. Retained as an adaptation in rhombopteriids and oysters, the inequivalved shell is an exaptation in Pterioida (winged shells), Pectinina (scallops) and Pseudomonotidae, having been coopted for a right-sided pleurothetic orientation, and having the effect of enhancing stability in an epifaunal habit. Evolution of right-sided pleurothetic pteriomorphs, including the Pseudomonotidae, Pectinina and Pterioida, from separate left-sided pleurothetic rhombopteriid-like or umburrid-like ancestors, is explicable by paedomorphic retention of the byssus and epifaunal habit of the early post-larva. A right-sided pleurothetic orientation would follow ‘automatically’ owing to hydrodynamic and mechanical constraints on the already evolved, inequivalved shell, byssally attached by the anterior margin on the substrate surface.

Since Barrande (1852) first illustrated a trilobite larva, aspects of trilobite ontogeny and early development have received a great deal of attention (see Beecher, 1895; Størmer, 1942; Whittington, 1957; Hu, 1971; Chatterton, 1980). Much of this literature, however, is purely descriptive and very little has been done to incorporate these works into a biological synthesis. During the past several decades a great deal has been learned about the role of larval ecology in monitoring biogeographic distributions, cohort survivorship and taxonomic longevity among modern marine invertebrates. This growing body of knowledge has provided the basis for many new insights regarding patterns of extinction and survivorship and macroevolution evident within the fossil record (see Jablonski, 1986; Jablonski and Lutz, 1983).

We review two foundations of statistical inference, the theory of likelihood and the Bayesian paradigm. We begin by applying principles of likelihood to generate point estimators (maximum likelihood estimators) and hypothesis tests (likelihood ratio tests). We then describe the Bayesian approach, focusing on two controversial aspects: the use of prior information and subjective probability. We illustrate these analyses using simple examples.

The minerals pyrite and marcasite (broadly termed pyritic minerals) are iron sulfides that are common if not ubiquitous in sedimentary rocks, especially in association with organic materials (Berner, 1970). In most marine sedimentary associations, pyrite and marcasite are associated with organic sediments rich in dissolved sulfate and iron minerals. Because of the rapid consumption of sulfate in freshwater environments, however, pyrite formation is more restricted in nonmarine sediments (Berner, 1983). The origin of the sulfur in nonmarine environments must lie within pre-existing rocks or volcanic detritus; a relatively small, but significant contribution may derive from plant and animal decomposition products.

In November of 1995, the Alabama Department of Education required all biology textbooks used in the state to display a disclaimer informing the young reader that

This textbook discusses evolution, a controversial theory some scientists present as a scientific explanation for the origin of living things, such as plants, animals and humans. No one was present when life first appeared on earth, therefore, any statement about life's origins should be considered as theory, not fact.

Of the 50 thousand or more species descriptions that exist in my reference library, there is very little change over 130 years in the basic vocabulary used to describe the shape or the ornament of the ostracode valves. Although there have been some modifications (Sylvester-Bradley and Benson, 1971) following the availability of the SEM, arguably the most important change in ostracodology will come when we are able to describe the outside form of the carapace in functional terms, as we do the inside. It is here where the future of learning about their adaptive history lies (Benson, 1974, 1975, 1981, 1983).

Studies of paleobiogeography have changed markedly in recent decades transforming a once static subject into one which now has great potential as a useful counterpart to systematic and ecological studies in the interpretation of the geological history of organisms. This has resulted, in large part, from the emergence of plate tectonic models which, in turn, have been used as the bases for extremely sophisticated paleoclimatic modeling. As a result, paleobiogeography has attained a level of precision comparable to that of the studies of paleoecology and systematic paleontology. It is now possible to consider causes for global patterns of origin and dispersal of organisms on a much more realistic level than was previously possible.

Movies are the myths of late-20th century western culture. Because of the power of films like ET to capture our imagination, we are more likely than past generations to accept the possibility that life exists elsewhere in our galaxy. Such a myth can be used to sketch the main themes of this chapter, which concern the origin of life on the Earth.

Imagine that 4 billion years ago, intelligent beings evolved on an Earth-like planet in the solar system of a neighboring star. After ten million years of evolution, they have solved the problems of interstellar travel and aging. Virtually immortal family groups set out to explore the galaxy and almost immediately discover a solar system associated with a nearby star only 80 light years away from their home planet. They find that the third planet is rich in the primary elements of life - carbon, hydrogen, oxygen and nitrogen - which are present in the atmosphere in the form of carbon dioxide (CO2), molecular nitrogen (N2) and water vapor (H2O). They decide to spend a few centuries studying this planet, which they consider to be a possible model of their own primordial world as it was four billion years in their past.

High quality (>2% TOC) Upper Devonian source rocks are developed in several sequence types. The commonest type, accounting for 70% of the studied examples is the transgressive sequence with a basal hiatus. Others include shallowing upward sequences (12%), lacustrine sequences in fault-controlled basins (7%), distal slope sequences (7%), and evaporite capped sequences (4%).

Starting from the synthesis of Johnson, Klapper, and Sandberg (1985) it has been possible to demonstrate correlativity of Upper Devonian transgressive episodes globally. The marked association of epeiric sea Upper Devonian source rocks with transgressions heightens interest in their causation. Could they have been produced by glacio-eustatic sea-level change as Stanley (1984; 1988) implies? Quantitative paleoclimate modeling and isotopic paleotemperatures for the Upper Devonian suggest not. Modeling using CCM1 at NCAR, including five year seasonal cycles, suggests the absence of any large southern hemisphere ice volume. Because much of the Upper Devonian land mass was either in equatorial or high latitude regions, there was little development of monsoonal climates. Midlatitude cyclonic activity was also much less than at present, meaning less polar transport of moisture and drier polar areas. Precipitation maxima largely coincided with topographic elevations. In contrast to the Late Ordovician to earliest Silurian, there was no Upper Devonian perennial snow cover even over the high latitude southern land mass. This was in spite of winter land temperatures as low as -40°. in eastern Gondwana. In that area and elsewhere, there was thin winter snow cover which melted in late spring resulting in no build-up of snow cover to produce glaciation. This was mainly the consequence of low winter precipitation in Gondwana. High latitude sea surface temperatures were certainly cold enough to displace or exclude some organisms. However, in low latitude areas where Upper Devonian extinctions also took place, modeled sea surface temperatures range between 27° and 34°. Such areas would have been refuges for any organisms displaced by cold, high latitude waters. The higher temperature values of low latitudes are convergent with the isotopic paleotemperatures determined by Brand (1989) using well preserved Upper Devonian brachiopods. Brand's determinations suggest temperatures even reaching lethal values for many plankton (37°). The extinction of reefs by the close of Frasnian time could have been partly a result of such elevated temperatures. Stacked extinctions of conodonts (Ziegler and Lane, 1987) and acritarchs may have been a further result. The loss of reefs, an important consumer of plankton, may have permitted a relative increase in plankton abundance crossing from more oceanic areas into epeiric seas, possibly contributing to high quality source rock deposition.

Lately, we proposed a hypothesis that the ancestral angiosperm was a diminutive, rhizomatous to scrambling perennial herb with small simple flowers. Our phylogenetic studies suggest that arborescent to shrubby magnolialians with large, multiparted, complex flowers are derived, rather ancestral as commonly thought. We suggest that the early angiosperm, due to its rhizomatous habit, would have been able to survive in more ephemeral habitats. A test of this idea would be to examine the sedimentological context of early angiosperms.

Despite a number of reports of early angiosperm megafossils from Barremian to middle Albian (mid- to late Early Cretaceous) age sediments, only the Potomac Group of the eastern U.S.A. has provided a stratigraphic sequence of early angiosperm diversification. Furthermore, study of this sequence has also linked observations on floristic assemblages to the lithofacies in which they occur, leading Doyle and Hickey to report an ecological expansion of early angiosperms from relatively near-channel environments to a much broader range of flood plain sites during the Barremian/Aptin to latest Albian/early Cenomanian interval represented by Potomac Group deposition. From this those authors inferred that the early angiosperms were “riparian weeds” that grew on moderately unstable, near-channel sites subject to periodic flooding and episodes of alluviation.

We recently expanded on these inferences by examining the sedimentology of Dutch Gap, an early angiosperm site at the earliest level of the Potomac Group (Barremain/Aptian-Pollen Zone I) near Richmond, VA. Sediments here appear to represent the meander belt of a fluvial setting. A series of multi-storied channel units at the site are filled with arkosic, medium to coarse, sub-angular sand with pebble- to boulder-size clasts of gneiss, claystone and mudstone concentrated at channel bases, reactivation surfaces, and on lateral accretion surfaces. These channels are cut into inferred levee and splay deposits that consist of thin interbeds of sand and silt alternating with dark grey, micaceous mudstone to claystone. This sequence fines in an inferred distal direction from the channels and the mudstone/claystone interbeds thicken at the expense of the coarser units until they coalesce into relatively thick, dark grey clay beds with only thin silty laminae. These beds are thought to represent floodbasin deposits.

The megafossil plants recovered from our studies at Dutch Gap exhibit a clear pattern of association with each other and with these lithofacies. Angiosperms (Celastrophyllum, Rogersia, and an unnamed new form) together with ferns are found in relatively silty interbeds that lie in what appear to be distal levee settings, while the backswamp was dominated by the bennittitalean Dioonites buchianus. Conifers of diverse kinds are dominant only in pinkish, silty clay clasts that are inferred to have been transported from drier flood-plain environments.

This study provides added evidence of an association between early angiosperms and moderately unstable, channel-margin sites and, in addition, calls attention to the potential that detailed sedimentological investigations have of providing important evidence on early angiosperm paleoecology.

Herbivorous tetrapods make their first appearance in Upper Carboniferous fossil assemblages but only become abundant and diverse in Upper Permian ones. During the Late Carboniferous-Early Permian interval, herbivory appeared independently at least five times: in diadectids, bolosaurids, captorhinids, edaphosaurids and caseids. These animals ranged from small forms with aptitudes for collection and processing of low-fiber plant tissues (as well as terrestrial invertebrates) to giants particularly apt for utilization of high-fiber tissues. Our report focuses on the latter group since the development of high-fiber herbivory has had a critical impact on evolution of terrestrial plants and animals as well as on the organization of terrestrial ecosystems.

The low abundance and diversity of early, high-fiber herbivores reflect on one hand, sampling biases toward habitats suboptimal for herbivory, and on the other, the limited ecological capabilities of the animals themselves. Most of the Permo-Carboniferous assemblages derive from wet-land swamp and forest ecosystems where plant tissues would have been relatively rare and/or inaccessible and predation relatively intense. The likely herbivores appear apt for life in wet-land ecosystems; there they probably utilized localized patchs of productive shrub and herb along rivers and around lakes as refuges from disturbance (desiccation, temperature extremes and predation) as well as sources of food. Their low metabolic levels and growth rates minimized nutritional requirements but along with large size provided adequately for adult maintenance and for reproduction. High adult survivorship and production of a large number of eggs through a long adult lifespan would have offset high egg and juvenile mortality.

Only a few Late Carboniferous and Early Permian assemblages sample drier woodland and shrub habitats where conditions would have been more favorable for high-fiber herbivory, but by Late Permian such assemblages occur in much greater numbers and diversity. The high-fiber herbivores in these dry-land ecosystems had ecological aptitudes comparable to wet-land forms but were relatively more abundant and diverse, reflecting both a greater abundance and extent of shrubby vegetation and a lower incidence of predation.

Clusters of ammonoid embryonic shells have been discovered in several carbonate concretions from a dysoxic, relatively deep water shale (Heebner Shale-Oread Formation) of Virgilian (U. Carboniferous) age near the community of Pomona, Kansas. The concretions from a single outcrop display four distinct units. Unit 1 is the lowest unit and has an evenly laminated fabric with scattered embryonic and juvenile ammonoids, gastropods, and bivalves. The bedding fabric of this unit is interrupted and truncated by a series of pits that form the base of Unit 2, which is a sharply bounded discontinuity. Within the pits there are embryonic ammonoid clusters up to 2.5 cm thick containing as many as 250 individuals per cm3. Some juvenile ammonoids and shell fragments (mostly of ammonoids) are also present. These clusters are capped by Unit 3 which has a gradational boundary with Unit 2. Unit 3 consists in places of a packstone of fossil debris including ammonoid body chamber and phragmocone fragments, three genera of juvenile ammonoids, embryonic ammonoids, and more rarely brachiopods, bivalves, and orthoconic nautiloids. Elsewhere, fossils of Unit 3 are well separated by matrix, which lacks the bedding fabric characteristic of Unit 1. The ammonoids in Unit 3 include mature to sub-mature fragments of Aristoceras and sub-mature phragmocones of Glaphyrites and Shumardites. The brachiopods (articulate and inarticulate) and the bivalves are probably sub-mature or mature. Planktonic bivalves are extremely rare. The number of shell fragments of embryonic and postembryonic ammonoids and other shell fragments decreases upwards from the upper contact of Unit 2. The boundary of Units 3 and 4 is more-or-less gradational; Unit 4 has a sedimentary fabric and faunal content like that observed in Unit 1.

One set of hypotheses to explain the embryo clusters in Unit 2 emphasizes sedimentological processes such as selective transportation and accumulation by currents, turbidity transport and storm deposits. Another set of hypotheses favors biological activities such as reproductive activity and egg-laying. If this second set of hypotheses is correct, these clusters would provide the first documentation of ammonoid reproductive activity and would represent a find as significant in its way as that of the nests of embryo bearing dinosaur eggs.

New material of Mixosaurus nordenskioeldii from the Middle Triassic Sulphur Mountain Formation of Wapiti Lake, British Columbia, includes cranial elements with complete upper and lower dentitions, and associated post-cranial material. It demonstrates that skulls with a Phalarodon-like dentition are associated with a Mixosaurus type of post-cranium. The upper and lower dentitions differ in the degree of anteroposterior elongation of the molariform teeth and in the rate of tooth differentiation. These new specimens demonstrate that the separation of the Svalbard material into Phalarodon and Mixosaurus (Merriam, 1911; Wiman, 1916) represents a separation of upper and lower dentitions and confirms that Phalarodon fraasi is the junior synonym of Mixosaurus nordenskioeldii.

Mixosaurus nordenskioeldii is more derived than M. cornalianus in the following characters: 1) Anterior end of both jaws edentulous, 2) Posterior crushing teeth laterally compressed domes, elongate anterolaterally, 3) Skull with large parietal crest, extending well forward between the orbits, 4) Sixth digit present in manus (developed from a neomorph in M. cornalianus).

A well preserved stapes is present in the new material of Mixosaurus from British Columbia. This is one of the oldest preserved ichthyosaur stapes and demonstrates that this element was primitively long and slender in the Ichthyopterygia.

The cheek region in Mixosaurus is formed by two large bones traditionally identified as the quadratojugal and the squamosal. The homologies of these elements are reinterpreted as the squamosal and the supratemporal.