Paleobiologists have used taxonomic data for several types of diversity studies. Some systematists have charged that this practice obfuscates actual historical patterns of clades because many traditionally defined higher taxa are not monophyletic. Some have questioned whether ranked taxa ever represent comparable units, even when monophyletic. This study contrasts diversity patterns implied by phylogenetic estimates with those implied by ranked taxa. Early Paleozoic gastropods are useful as a test case because their generic taxonomy does not reflect the phylogenetic systematic philosophy, and fewer than one third of the genera represent monophyletic clades. Phylogenetic diversity is described in two ways: (1) numbers of lineages (i.e., observed plus phylogenetically implied “ghost lineages”), and (2) numbers of monophyla (i.e., clades whose sister taxa are other clades rather than species). “Monophyla” as tallied here are monophyletic relative to their contemporaries and older clades; however, they can be paraphyletic relative to “future” monophyla. Phylogenetic diversity is tallied with both maximum and minimum “ghost lineage” interpolations in order to reflect different possible speciation patterns and timings of speciation. Phylogenetic diversity as implied by a stricter cladistic criterion (i.e., taxa that are monophyletic relative to their contemporaries, older taxa and younger taxa) is discussed also.

First differences between substage-to-substage standing diversities reveal significant congruence between generic data and both types of phylogenetic data. Taxonomic and phylogenetic data imply a major extinction event at the end of the Ordovician, although the phylogenetic data suggest greater extinction levels than do the taxonomic data. Both data sets also suggest diversity-dependent diversification reminiscent of logistic growth, which is the pattern predicted if one or a few major ecologic factors were constraining the diversification of gastropods. However, diversity described by strict Hennigian taxa is not highly congruent with diversity as described by either lineages or monophyla. Comparing subclade dynamics requires extensive redefinition of traditional orders, but lineages, monophyla and genera all suggest that the two major subclades had different logistic diversification patterns, with one (“murchisonioids”) having a higher K than the other (“euomphaloids”). The concern that phylogenetic and taxonomic data might imply very different evolutionary histories is not borne out by gastropods, despite the nonphylogenetic nature of their traditional taxonomy.

A hierarchical branching model is presented that tracks diversity of lineages and paraclades simultaneously. It is based on three parameters: (1) lineage origination within a paraclade, (2) lineage origination that founds new paraclades, and (3) lineage extinction. The model assumes stochastic constancy of evolutionary rates and, therefore, exponential growth of diversity is the null expectation. The probabilistic model can be used to generate confidence intervals for exponential growth through Monte Carlo simulation. These confidence intervals can be compared to empirical curves to test the null hypothesis of exponential growth. The analytic solution for paraclade diversity gives the statistical expectation for the probabilistic model. It can be applied to empirical diversity curves of supraspecific taxa to estimate total speciation rate, the intrinsic rate of increase, and the proportion of speciation events that found new paraclades. Two factors were identified with the model that may cause diversity curves for higher taxa (e.g., genera, families) to deviate from simple exponential growth during initial phases of diversification: (1) stochastic fluctuation at low diversity, and (2) taxonomic structure (i.e., species/genus ratio). These sources of variability should be evaluated before macroevolutionary explanations for specific diversity trends are invoked. Two kinds of evolutionary radiations were investigated with this model: (1) prolonged periods of low diversity (macroevolutionary lag) in cheilostome bryozoans and mammals prior to their main phases of diversification, and (2) rapid bursts in diversity of bivalves following the late Permian and end-Cretaceous mass extinctions. In all cases these patterns were found to deviate significantly from the null expectation of exponential growth lending support to previous macroevolutionary explanations. Finally, rates of speciation during radiations were compared to rates of speciation during background times for articulate brachiopods, cheilostome bryozoans, bivalves, and mammals. Speciation events that found new paraclades tend to make up a larger proportion of total speciation events during radiations compared to background times indicating that the opportunity for new adaptive zones to be filled at higher taxonomic levels is proportionately higher during these periods of increased evolutionary activity, and is not simply a result of an increased frequency of speciation.

Brachiopods generally have not been considered to be typical or significant faunal components of modern or ancient hydrothermal vent and cold-seep settings. The Early Cretaceous (Neocomian) rhynchonellide brachiopod Peregrinella has long been viewed as a paleontological curiosity because of its distinctive morphology, status as the largest Mesozoic brachiopod, anomalous stratigraphic associations, and widespread, yet discontinuous paleogeographic distribution. Examination of all worldwide Peregrinella occurrences (14) indicates restriction of this brachiopod to ancient cold-seeps. It is probable that Peregrinella grew to large sizes in such great abundances at fossil cold-seep sites because of a richly organic food supply generated by localized fluid seepage and bacterial chemosynthetic activity. Living brachiopods are not known to harbor chemosymbiotic bacteria in their tissues; however, direct chemoautotrophic utilization of reduced fluids by Peregrinella cannot be rejected or demonstrated at present. Peregrinella occurs at widely separated cold-seeps of Neocomian age (e.g., California, Mexico, Tibet, Europe), yet its mode of dispersal and larval development is unknown. In modern hydrothermal vents of the deep-sea, organism dispersal occurs along oceanic ridges, where benthic faunas display both planktotrophic and nonplanktotrophic larval-mode types. Peregrinella may represent a Mesozoic relic of a long-lived “lineage” of vent-seep associated rhynchonellides from the Paleozoic (e.g., ?Eoperegrinella, Dzieduszyckia), but major gaps in the stratigraphic record between these rhynchonellide occurrences, and the lack of rigorous phylogenetic analysis for these groups preclude a clear resolution of the origin(s) of vent-seep brachiopods at present.

Distributions of brachiopods from low-latitude paleogeographic settings, primarily in the Tethyan Ocean of southern Europe, with additional data from North America allow some observations on the bathymetric distribution of early Mesozoic brachiopod orders. Norian and latest Triassic (Rhaetian) brachiopod biofacies are dominated in shallowest waters by short-looped terebratulids (Terebratulidina) while spire-bearing athyrids (Athyrida) are common components of deeper-water environments in the latest Triassic. In the late Early Jurassic (Pliensbachian), shallow-water brachiopod faunas are dominated by rhynchonellids, short-looped terebratulids are commoner in relatively deeper shelf waters, and spiriferids and long-looped terebratulids (Terebratellidina) are abundant in deeper-water shelf environments.

Following the end-Triassic extinction event there appears to be niche-replacement in deep-water shelf environments of Late Triassic athyrids by spiriferids and long-looped terebratulids in the Early Jurassic. Rhynchonellids appear to have diversified into shallowest water environments; specialized short-looped terebratulids may have occupied deeper-water niches that resulted ultimately in the success of the enigmatic Pygopidae later in the Jurassic and Cretaceous.

The relative numbers of sexually and asexually recruited colonies and the proportion of brooding zooids were determined in 26 species of cheilostome bryozoans of Late Cretaceous and Early Tertiary ages. Asexual reproduction seems to be much more widespread than previously realized, although its relative importance is related to growth habit. Arborescent species of these fossil assemblages reproduce mainly asexually via fragmentation; encrusting species reproduce sexually via motile larvae. Free-living species use both methods; some reproduce sexually, whereas other species have enhanced the ability to break and reproduce predominantly asexually. Mode of reproduction was stable over a period of 3 m.y. in all species except the vinelike Columnotheca cribrosa. In this species both the proportion of asexual recruits and brooding zooids varied in accord with environmental parameters. In all cases populations dominated by asexual propagation had a significantly lower proportion of brooding zooids than populations dominated by sexual propagation.

I describe a mathematical model of shells that incorporates simple morphometric measurements, which can be obtained easily from sectioned specimens. The model reconstructs form (size and shape) by describing the path in space traversed by, and the changes in dimensions of, a shell aperture during accretionary growth. The model contains parameters that independently affect components of these two aspects of shell form in directions radially away from (or toward) and along a coiling axis. I also describe a computer program, CerioShell, that uses the mathematical model to graphically simulate shell forms. The program permits the viewing of images from different three-dimensional orientations, using various graphical representations, and provides dimensions of the images it generates. Together, the model and the program allow one to investigate the effects that changes in modes of growth would have on shell form.

Concavo-convex brachiopods are generally assumed to have lived with their convex valves against the sediment. This orientation is based primarily on the a priori assumption that the upturned commissure would prevent fouling of the brachiopods' mantle cavity. Here, I present epibiontic and taphonomic evidence from orthids and nonproductid strophomenids that concavo-convex brachiopods lived in the reverse life orientation, with the convex valve on top.

Ten testable epibiontic and taphonomic criteria are proposed to establish the uppermost valve during encrustation and whether epibionts encrusted primarily live or dead hosts. The criteria are evaluated for 11 collections of Ordovician and Devonian nonproductid concavo-convex brachiopods that contain a total of over 500 brachiopods and 4000 epibionts. In all cases, the results support a convex-up orientation and the encrustation of live hosts. Five criteria concern epibiont growth patterns and show that (1) epibionts predominate on convex valves, (2) epibionts are not restricted to shell margins, (3) distinct exposed and cryptic faunas, as predicted theoretically and described in previous studies, exist on convex and concave valves respectively, (4) epibiont colonies were often truncated by the commissures and hinges of live hosts, and (5) growth patterns of some epibionts indicate live hosts. Five taphonomic criteria show that (1) concavo-convex shells have greater epibiont cover than other morphologies, (2) internal surfaces of disarticulated specimens are rarely encrusted, (3) interiors of articulated specimens are rarely mud-filled, (4) standard taphofacies indicators suggest little postmortem exposure, and (5) sedimentological reconstructions suggest rapid burial.

Convex-up brachiopods suggest that the Paleozoic mud bottoms they lived on were probably firmer than usually assumed and that a more complex functional interpretation of concavo-convexity is required. Hydrodynamic stability was important to many concavo-convex, plano-convex, and unequally bi-convex brachiopods. Brachiopods with these morphologies probably lived in the more stable orientation on their concave or flat valve. Productid brachiopods, although also concavo-convex, lived convex valve down and are ecologically distinct from earlier concavo-convex taxa. Productids were anchored, semi-infaunally, by spines and were more similar to Mesozoic oysters in orientation and shell function.

Small terrestrial vertebrates are not capable of maintaining a constant body temperature (±2°C) without a relatively high metabolism. The amount of temperature variability during bone growth can be determined using oxygen isotopes from bone phosphate because fractionation of oxygen isotopes between body fluid and bone phosphate is dependent upon temperature. Fluctuation of body temperature during the early phase of growth in juvenile ectotherms should result in high intra- and interbone isotopic variability, whereas juvenile endotherms should have low isotopic variability resulting from the maintenance of homeothermy. Analyses of juvenile Hypacrosaurus individuals indicate a pattern of low isotopic heterogeneity suggestive of endothermy.

We report on the bone microstructure of the Late Cretaceous birds Patagopteryx deferrariisi and members of the Enantiornithes. These birds represent the most primitive birds ever studied histologically. The occurrence of growth rings indicating alternating periods of slowed and fast growth suggests that these basal birds had slower growth rates, and differed physiologically from their modern relatives. Our findings also call into question previous ideas suggesting that nonavian theropods developed a full avian degree of homeothermic endothermy, which was later inherited by birds. On the contrary, our findings suggest that birds developed classic endothermy relatively late in their phylogenetic history.