Taxonomic databases are important tools in the study of faunal diversity and evolution. The usefulness of the inferences drawn from these databases is diminished when the role of environment is not considered. Analysis of the foraminiferal database at the genus and family levels is used to demonstrate the effect of water depth on presumed changes in taxonomic diversity and evolutionary turnover rates.

This paleoenvironmental effect is particularly noticeable when foraminiferal faunas of the late Paleozoic and the Mesozoic and Cenozoic intervals are compared. The late Paleozoic fauna is dominated by the Fusulinina and shallow-water (0–200 m) Textularuna. Standing diversity fluctuates greatly, and evolutionary turnover is high. This reflects short-term fluctuations in sea level which led to the rapid formation and destruction of narrow ecological niches. Evolutionary turnover appears to be related to reef growth during this time. This trend may also reflect an increased number of k-selected specialists which serve as proxy indicators for a slow-circulating oligotrophic ocean system. Shallow-water taxa may also be predisposed to extinction due to their reliance on symbiotic algae. The extinction event at the end of the Permian resulted in the loss of almost 70% of the standing generic diversity. This included the complete loss of the Fusulinina as well as a number of shallow-water textularids. Cohort survivorship curves are steep and taxon ages short during this time.

The diversity increase over the past 245 million years has largely been due to the addition of deep-water (200-10,000 m) taxa. This was particularly true during the Late Cretaceous and early Eocene, and may reflect the relatively high eustatic sea level during those intervals. The relationship between reef development and evolutionary turnover rates is less clear during this time interval. Although the extinction event that marked the end of the Cretaceous resulted in a greater loss in absolute taxonomic diversity than occurred at the end of the Permian, the relative loss in generic diversity was only about 21% due to the large number of deep-water taxa. When the entire fauna is considered, cohort survivorship curves are less steep and taxon ages are longer than in the late Paleozoic, but when only the shallow-water taxa are considered, the results are similar to those for the late Paleozoic.

The Bilk Creek Limestone of the Black Rock Terrane in northwestern Nevada and the McCloud Limestone of the Eastern Klamath Terrane in northern California contain a diverse and abundant Permian brachiopod fauna currently under study. The composite rock record of both limestones spans the Wolfcampian and Leonardian stages of the Permian, during which both terranes were part of a volcanic arc separated from the North American continent by a marginal basin of unknown dimension. Brachiopods of this volcanic arc provide important evidence bearing on current hypotheses of Permian paleobiogeography and paleogeography.

The Bilk Creek/ McCloud brachiopods are best characterized as an endemic fauna of a unique province and not as a mixed, “Tethyan” and North American fauna. The central problem of these arc faunas is not how similar they are to faunas of the Tethyan basin but why they are so dissimilar from North American faunas. Overlying rock units in both terranes contain Guadalupian brachiopod faunas that are North American in character. The paleobiogeographic pattern is one of decreasing levels of endemism throughout the Wolfcampian and Leonardian, to ultimate deprovincialization during the Guadalupian. This is not consistent with a pantropic dispersal hypothesis.

The temporal pattern is consistent with a paleogeographic hypothesis of initial, long-distance separation of arc and continent with convergence of the arc toward the North American continental margin. The dissimilarity of the arc brachiopod faunas to coeval, same-environment faunas of North America suggests that the marginal basin that separated the two must have been several thousand kilometers wide during the Early Permian, producing the endemic fauna. A Japan-style model, with arc and continent in close proximity is not supported.

Chaetetids have recently emerged from relative obscurity on two fronts. On one, they have achieved a certain notoriety in their reclassification from tabulate corals to a recently erected class of sponges; on the other, they are becoming appreciated as locally significant faunal elements and bioherm framebuilders.

Mass extinctions profoundly affect patterns of diversification and skeletal innovation in the succeeding radiation. For instance, promising adaptations may be removed permitting traits of the few survivors to proliferate. Consequently, patterns of survivorship could control directions of radiation following the extinction event. Alternatively, selection during radiation may be quite different from extinction conditions. The founders may be quickly superseded by taxa with wholely new innovations that are built upon, but are distinct from, the founding morphologies.

Planktic foraminifera nearly became extinct at the end of the Cretaceous. Of the two or three lineages that survived, perhaps only one founded the bulk of the Paleocene radiation of Globigerinacea. In addition, there was little habitat diversification within the surviving lineages. Nearly all the morphological and ecological innovations occur in a single clade that diverged rapidly from the ancestral stock.

Neither of the best known surviving lineages diversified much after the Cretaceous. Hedbergella monmouthensis is the ancestor of Danian Globanomalina archaeocompressa. The two taxa are nearly identical in both morphology and in isotopic signature. Significantly, the globanomalinids displayed very little diversification, like their Cretaceous ancestors before them. Instead, species were replaced one after another in an anagenetic trend and consistently occupied a moderately deep-water habitat. Similarly, triserial Guembelitria gave rise to only a modest radiation of biserial species in the earliest Danian primarilly within near surface water habitats.

Cladistic analysis suggests that the major part of the Cenozoic radiation was founded by one or two Cretaceous taxa. Most Danian trochospiral species abruptly radiated into two main stocks in the earliest Danian. All of them are probably derived from Hedbergella, but they rapidly became morphologically differentiated from this Cretaceous survivor. Alternatively, many of the features of the Danian species may have been inherited from another Cretaceous survivor–possibly a species of Rugoglobigerina–as suggested by comparative studies of early ontogeny. In either case, the group split rapidly into two main lineages. One, rooted in non-spinose ‘Morozovella’ taurica, led to the major diversification of the muricate-walled morozovellids. Isotopic data suggest this lineage spread from a moderately deep water habitat into the near-surface waters where the major diversification occurred. The other lineage developed spinose wall texture and gave rise to the diverse subbotinid radiation. Stable isotopic data suggests the subbotinids grew consistently in the coldest and presumably deepest waters. Their spinose wall texture suggests they were at least partly carnivorous, by analogy with living spinose taxa.

These patterns of morphological and ecological diversification suggest that the immediate survivors did not radiate markedly but retained the evolutionary rates and habitats of their Cretaceous ancestors. Most of the radiation occurred in a clade whose innovations evolved during the Danian, rather than simply retooling traits of their founder. Likewise, the radiation occurred principally in surface and deep water habitats, both largely vacated by the extinction event. The intermediate depth habitats were continuously occupied by the persistent hedbergellid-globanomalinid lineage. Their habitat was not invaded by other radiating clades. Evidently, survival alone does not confer the capacity for subsequent diversification upon a founding species. Innovation seems to be the key to dominance rather than mere persistence through an episode of heightened extinction.

The past decade has seen many advances in research on vertebrate faunas of the Triassic period. The end of the Triassic now is cited widely as the dawn of modern terrestrial ecosystems, and currently the earliest mammals, turtles, lissamphibians (frogs, toads and salamanders), lizards, and crocodiles are all documented from this period. Admittedly many of these early members of present day higher order taxa were very different from their modern counterparts. For instance, the earliest crocodiles were highly active cursorial forms (e.g., Crush, 1984), and the mammals were very different to the living placentals and marsupials. Nevertheless, they possessed many of the key morphological characteristics that diagnose the group and that may well have contributed to their ultimate success. However, the Triassic was also a time of bizarre and enigmatic tetrapods, some of whose relationships are the subject of considerable debate. Indeed, in the last year this debate has reached new heights with suggestions that certain rather unusual Triassic non-dinosaurian tetrapods may have more bearing on bird origins than theropod dinosaurs. This debate has been fueled by the discoveries of feathered dinosaurs from China which, on the face of it, one might expect to dampen the search for alternative hypotheses regarding bird origins.

It is generally accepted that the extraordinary preservation of fossils in the Burgess Shale is at least partly due to the exclusion of large metazoan scavengers through rapid burial in an inimical environment. Disruption of individual organisms appears to have been largely the result of mechanical processes and/or microbial decay. The absence of bioturbation through much of the classic section, including Walcott's Phyllopod Bed, supports these arguments. However, macroscopic traces are known from other horizons within the Burgess Shale section and from lateral equivalents in the Stephen Formation a short distance south of the main locality.

The sparse ichnoassemblage includes bedding-plane exposures of portions of compacted, parallel-sided burrows containing skeletal debris comprising fragmented and disarticulated hyoliths, small trilobites, and bracniopods. Walcott originally figured one such trace as Planolites sp. ? and noted, but offered no evidence for, an association with the archaeopriapulid Ottoia prolifica. This notion was subsequently rejected by Conway Morris.

A recently collected specimen, from talus south of the main locality, contains a poorly preserved but recognizable body fossil of Ottoia within the outline of a “Planolites”. Although this juxtaposition may be accidental, a number of features of the association, and a consideration of the burrowing behaviour of modern priapulids, suggest that Ottoia could have been the generator of “Planolites”-like traces.

Pleistocene-Holocene sedimentary rocks, which outcrop along the northern Gulf of California coast in the vicinity of Puerto Peñasco, Sonora, have a very heterogeneous, mixed carbonateclastic composition. Carbonate grains are primarily molluscan, echinoderm, bryozoan and calcareous algal fragments. Terrigenous grains are primarily silicate minerals (e.g., quartz and feldspar) derived from three nearby igneous prominences (the basaltic Punta Peñasco and Cerro Prieto and the granitic Punta Pelicano).

Porosity of the sedimentary rocks, which commonly exceeds 50% in many units, may be intergranular and/or moldic. Cements in eolianite, precipitated within the vadose zone, are mainly of the meniscus spar type at grain contacts. Cements in beachrock, precipitated within the intertidal or shallow subtidal zone, include isopachous calcite spar and/or acicular aragonite.

In this paper, I discuss issues of time resolution and time-averaging in fossil megafloras from Late Cretaceous (Cenomanian) to Oligocene age. The sites are predominantly from North America with some examples from other continents. The purpose of this paper is to explicate the methods used to resolve the age and duration of fossil floras and to discuss the uncertainties associated with these methods. The age of floras is most important for their evolutionary, paleoclimatic and paleoaltitudinal applications, while the duration of floras (here defined as the time represented by individual assemblages, florules, or quarries) is critical for paleoecological and paleoenvironmental applications. Levels of time resolution of both the age and the duration of fossil floras are subject to time-averaging. Behrensmeyer et al. (1992, p. 75) have defined two types of time-averaging: analytical time-averaging which is artificial and results from techniques of analysis and taphonomic time-averaging which is natural and results from the taphonomic history of the assemblage.

Applications of commonly used numerical techniques in diatom-based paleoecology are reviewed including: approaches used to model diatom taxa to important limnological variables; ordination and other commonly used multivariate approaches; and the myriad of approaches that are now being explored to infer environmental variables based on diatom assemblages.

Modelling the response of individual diatom taxa to limnologically important variables is consistent with ecological theory and has been largely accomplished using approaches based on generalized linear models. These techniques have established that strong and significant relationships exist between the numerically dominant diatom taxa and important limnological variables (e.g., pH, nutrients, salinity). Null modelling approaches have also been used. However, inclusion of rare taxa in null models results in high rates of type-II errors, and consequently spurious claims that only a minority of diatoms have significant relationships to important limnological variables such as lakewater pH and nutrients.

A variety of ordination techniques are widely used in diatom-based paleolimnological studies to aid in summarizing the main directions of variation in diatom assemblages, and to identify limnological variables that are strongly correlated to the diatom assemblages, both in time and space. More advanced ordination techniques, such as partial ordinations, are increasingly being used to assess the shared and unique variance attributable to groups of important limnological variables. Further, diatom-based approaches based on experimental designs with control lakes and appropriate multivariate statistics are now becoming increasingly common to assess, for example, the impact of forestry on water quality.

A number of different diatom-based inference models based on the present-day relationships between diatom assemblages and limnological variables are now available for inferring important limnological variables. These approaches vary from simple approaches such as weighted-averaging to more complex approaches involving curve fitting and maximum likelihood, neural networks, and Bayesian statistics. All of these approaches have been shown to result in strong inference models, each using aspects of ecological information available from the diatom assemblages.

Extensive species-level, marine biotic turnover is recorded across the Cenomanian-Turonian (C-T) Stage boundary in the western interior of the United States (Fig. 1) and intercontinentally (e.g., Wright and Kennedy, 1981; Elder, 1987; Jarvis et al., 1988). Widespread intensification and expansion of the oxygen minimum zone have been widely proposed as a causal mechanism for the organic-rich deposits and biotic extinctions found in strata of this age (e.g., Schlanger et al., 1987; Jarvis et al., 1988). Accompanying these extinctions were large-scale reorganizations of community compositions and trophic structures. In the western interior, repeated community replacement was associated with widespread cyclic sedimentation, and long-term community turnover was related to extended periods of dysaerobia and possibly low salinity conditions. Community compositions and distributions were therefore largely controlled by physical rather than biological factors. This paper will document how these oceanographic and sedimentologic factors affected community patterns across the C-T boundary.

The Pliocene uplift of the Panamanian isthmus isolated previously contiguous Caribbean and eastern Pacific marine faunas, and initiated the development of different selective regimes on opposing sides of the barrier. Contrasting environmental conditions provided the context for different rates and kinds of evolutionary change on either side of the isthmus. The goal of our study is to characterize the rates and types of these paleoenvironmental changes; we employ stable isotopic profiles of venerid bivalve shells from the Miocene-Recent deposits of Panama and Costa Rica.

We analyzed geographic and depth variation in Recent shells as a means of calibrating the fossil analyses. Results from Recent venerids highlight the differences between the Caribbean and eastern Pacific shallow marine environments. Pacific shells typically exhibit strong annual fluctuations in δ18O, associated with seasonal upwelling and its associated cool waters. In shallow, near-shore habitats, freshwater runoff during the rainy season also contributes significantly to annual δ18O cycles. Caribbean shells exhibit negligible annual cyclicity.

We analyzed fossil shells from the Miocene Gatun Formation, and the Pliocene Cayo Agua, Escudo de Veraguas, and Rio Banano Formations from the Caribbean coast, and the Plio-Pleistocene Charco Azul Group from the Pacific coast. Results from fossil shells indicate that annual cycles are well-preserved, and not obscured by diagenesis or other alteration. A strong annual signal in δ18O (amplitude >1.5‰) is found back at least to the Early Pleistocene along the Pacific coast. Some post-uplift Caribbean samples exhibit stronger seasonality than that observed in similar habitats today.

Following rediscovery of the sclerosponges (Hartman 1969, 1979; Hartman and Goreau, 1970, 1975) and recognition of their similarities to the stromatoporoids (Hartman and Goreau, 1970, p. 221–228), classification and interpretation of fossil Porifera have undergone major revisions during the past ten years. Our interpretation of the “edges” of the phylum have been considerably expanded.

When Charles Darwin wrote that “Our classifications will come to be, as far as they may be so made, genealogies…we have to discover and trace the many diverging lines of descent in our natural genealogies by characters…which have long been inherited” (Darwin, 1859), he presciently laid down aims and objectives of systematics that have become attainable only since the development of genetics and of molecular approaches to systematics. Genetics elucidates the heredity of characters; molecular systematics measures the degrees of relationship between diverging lineages (Griffiths et al., 1993; Page and Holmes, 1998; Graur and Li, 2000). This article attempts to review these essential aids to the art and science of brachiopod classification as they stand today. Every step so far taken to promote molecular approaches to brachiopod systematics has yielded new, unexpected, and valuable information, but there remains massive scope for new work and new workers.