We offer an alternative interpretation of the Kingdom Vendobionta as a monophyletic sister group to the Eumetazoa. We hypothesize that the Vendobionta are cnidarian-like organisms that lacked cnidae. Cnidarians are held to have arisen by acquisition of cnidae by symbiosis with a microsporidian. Our analysis differs from existing interpretations of the Ediacaran fossils as ancestors of extant cnidarians in that we do not regard any of these forms as either polypoid or medusoid. This interpretation requires the erection of a new metazoan phylum, the Vendobionta.

Molecular data are becoming an indispensable tool for the reconstruction of phylogenies. Fossil molecular data remain scarce, but have the potential to resolve patterns of deep branching and provide empirical tests of tree reconstruction techniques. A total evidence approach, combining and comparing complementary morphological, molecular and stratigraphical data from both recent and fossil taxa, is advocated as the most promising way forward because there are several well-established problems that can afflict the analysis of molecular sequence data sometimes resulting in spurious tree topologies. The integration of evidence allows us to: (1) choose suitable taxa for molecular phylogenetic analysis for the question at hand; (2) discriminate between conflicting hypotheses of taxonomic relationship and phylogeny; (3) evaluate procedures and assumptions underlying methods of building trees; and (4) estimate rates of molecular evolution in the geological past. Paleontology offers a set of independent data for comparison and corroboration of analyses and provides the only direct means of calibrating molecular trees, thus giving insight into rates of molecular evolution in the geological past.

We compared phylogenies derived from morphological data for two cheilostome bryozoan genera, Stylopoma and Metrarabdotos, with genetic differences between species (Stylopoma) and the stratigraphic occurrence of fossils (both genera). Correspondence between species of Stylopoma defined by protein electrophoresis and on preservable skeletal morphology is excellent, despite great morphological variability within colonies and the predominance of quantitative over discrete characters. Moreover, agreement between genetic and morphological classifications increased greatly when morphological discrimination was pushed to the limit, despite inability to consistently assign all specimens to species with high confidence. This “splitting” strategy also maximized the correlation between genetic distances and the distances between species in cladistically derived phylogenies.

Fossil and living species of both genera are sufficiently abundant and widespread to provide credible limits for inferred ancestral relationships. Inclusion of fossils in cladistic analyses of Stylopoma increased the consistency of cladistic hypotheses by up to 30% and provided a more effective means of rooting trees than comparison with living species of the most closely related genus (“outgroup”). Moreover, in the case of Metrarabdotos, failure to incorporate stratigraphic information turned the cladogram virtually upside down, so that postulated ancestors first appear in the fossil record 6–16 m.y. after their putative descendants became extinct.

Stratigraphically rooted trees suggest that most well-sampled Metrarabdotos and Stylopoma species originated fully differentiated morphologically and persisted unchanged for > 1 to > 16 m.y., typically alongside their putative ancestors. Moreover, the tight correlation between phenetic, cladistic, and genetic distances among living Stylopoma species suggests that changes in all three variables occurred together during speciation. All of these observations support the punctuated equilibrium model of speciation.

Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics).

The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa.

Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.

Many areas of paleobiological research require reliable extinction metrics. Branching-and-extinction simulations and data on Phanerozoic marine families and genera are used to investigate the relationship between interval length and commonly used extinction metrics. Normalization of extinction metrics for interval length is problematic, even when interval length is known without error, because normalization implicitly assumes some model of variation in extinction risk within an interval. If extinction risk within an interval were constant, or if it varied but played no role in the definition of stratigraphic intervals, then Van Valen's time-normalized extinction metric would provide a measure of average extinction risk that is effectively unbiased by interval length. When extinction risk varies greatly within an interval and interval boundaries are drawn at times of heavy extinction, extinction metrics that normalize for interval length are negatively correlated with interval length. Despite its intuitive appeal, the per-taxon extinction rate (proportional extinction per million years) is biased by interval length under a wide range of extinction models.

Empirically, time-normalized extinction metrics for Phanerozoic families and genera are negatively correlated with interval length. This is consistent with an extinction model in which many times of very low risk are punctuated by a few times of very high risk which in turn determine stage boundaries. Origination and extinction patterns are similar, but origination intensity varies less among stages than extinction intensity. This observation has at least two plausible explanations: that origination episodes are more protracted than extinction episodes, and that biologic groups do not respond in unison to origination opportunities the way they seem to respond during extinction events. For families and genera, there is enough variation in extinction intensity among stages that stage length can be ignored when studying certain extinction patterns over the entire Phanerozoic.

The mid-Mesozoic time was characterized by massive reorganization of the ecological structure of benthic marine communities. Although the general pattern of this “Mesozoic Marine Revolution” has been extensively documented, little is known about how it affected the taxonomic and morphologic diversities of individual lineages of organisms. Here I document group-level dynamics of the Mesozoic change using the fossil record of aporrhaid gastropods, a diverse and widespread family during that time. Using data gathered through field and museum work and extensive literature search, I compare and contrast patterns of taxonomic and morphologic change during the Jurassic and Cretaceous within a geographic framework. I also examine how the changes were manifested at different ecological and geographic scales.

The Mesozoic history of the Aporrhaidae includes two major radiations separated by a period of overall stability. While both radiations increased the taxonomic diversity of the family, they had very different morphologic consequences, resulting in a striking discordance between morphologic and taxonomic diversity patterns. The initial radiation during Bajocian-Bathonian times established two large morphologic groups within the aporrhaids based mainly on differences in the shape of the apertural margin. The second, post-Albian, radiation saw higher origination rates and increased taxonomic and morphologic diversity among genera having simpler apertural margins, while genera with elaborate multidigitate apertures declined in taxonomic diversity but not in morphologic diversity. During post-Albian times the group with simpler apertural margins also tended to be more widespread compared to the group with multidigitate apertures. Comparison of regional and global taxonomic diversities reveals a discordance between regional and global taxonomic patterns: while diversities within certain geographic areas increased in concert with the global radiation, those for other areas decreased substantially, resulting in a remarkably constant average taxonomic diversity within geographic areas.

The same three subtypes of derived multiserial Hunter-Schreger bands are found in the incisor enamel of African phiomorph rodents from the late Eocene-early Oligocene and the oldest South American Caviomorpha from the Deseadan (late Oligocene). The synapomorphies contained therein, especially arrangement and orientation of interprismatic matrix, make an African origin of the Caviomorpha very probable. A North American origin of the Caviomorpha is thus rejected, as only primitive pauciserial Hunter-Schreger bands have been observed in possible ischyromyoid caviomorph ancestors. A multiserial Schmelzmuster apparently never evolved in the North American rodent fauna.

Modern marine plankton communities include a broad diversity of metazoans that are suspension-feeding or micropredatory as adults. Many benthic marine species have larval stages that reside, and often feed, in the plankton for brief to very long periods of time, and most marine benthic communities include large numbers of suspension-feeders. This has not always been the case. Cambrian benthic communities included relatively few suspension-feeders. Similarly, there were few metazoan clades represented in the plankton, either as adult suspension-feeders or as larvae. Review of the fossil record suggests that the diversification of the plankton and suspension-feeding marine animals began in the Late Cambrian and continued into the Ordovician. These changes were accompanied by, and probably influenced, concurrent major changes in the marine realm, including an increase in tiering within benthic communities, the replacement of the Cambrian fauna by the Paleozoic fauna, and a general taxonomic diversification. The ultimate cause of these changes is uncertain, but it appears likely that the plankton was and is a refuge from predation and bioturbation for adults and larvae alike. The expansion in plankton biomass thus provided increased ecological opportunities for suspension-feeders in the plankton and benthos.

The number of cell types required for the construction of a metazoan body plan can serve as an index of morphological (or anatomical) complexity; living metazoans range from four (placozoans) to over 200 (hominids) somatic cell types. A plot of the times of origin of body plans against their cell type numbers suggests that the upper bound of complexity has increased more or less steadily from the earliest metazoans until today, at an average rate of about one cell type per 3 m.y. (when nerve cell types are lumped). Computer models in which increase or decrease in cell type number was random were used to investigate the behavior of the upper bound of cell type number in evolving clades. The models are Markovian; variance in cell type number increases linearly through time. Scaled to the fossil record of the upper bound of cell type numbers, the models suggest that early rates of increase in maximum complexity were relatively high. The models and the data are mutually consistent and suggest that the Metazoa originated near 600 Ma, that the metazoan “explosion” near the Precambrian/Cambrian transition was not associated with any important increase in complexity of body plans, and that important decreases in the upper bound of complexity are unlikely to have occurred.

Benthic foraminifera have attained gigantic sizes many times throughout geologic history. To understand the selective processes underlying foraminiferal gigantism, we used a computer-based, three-dimension, solid finite element model to analyze the mechanical strength of different discoid forms, including two of the largest living foraminifera—Cycloclypeus carpenteri Brady and Marginopora vertebralis Quoy and Gaimard. These two species enlarge by cyclic, planar growth, resulting in slightly biconvex (C. carpenteri) and slightly biconcave (M. vertebralis) forms. As the tests enlarge, the maximum stresses induced by a standard bending moment decrease in both species. Such stress-reducing growth plans apparently allow growth to extraordinarily large sizes and allow volume to increase with minimal lowering of the surface-to-volume ratio, a critical functional factor in ensuring increased surface area for photosynthesis by endosymbionts contained within the tests and for chemical exchange by the foraminifera with the external environment. Of the two species, M. vertebralis has a stronger construction and a lower surface-to-volume ratio. These features indicate optimal constructional solutions to environmental constraints (degree of turbulence and light availability) in their disparate natural habitats: M. vertebralis in the mechanically rigorous inter- to subtidal, and C. carpenteri on the light-minimal and hydraulically quieter, deeper sea beds. We conclude that morphological design in larger foraminifera is constrained by a biomechanical factor, and that gigantism and biomechanical optimization are demonstrably related.

The well-known decline of global background extinction intensity was caused by the sorting of higher taxonomic groups. Two factors were responsible. First, probabilities of familial origination and extinction in these groups (taxonomic orders) were highly correlated. Groups whose families had high probabilities of origination and extinction tended to have highly volatile diversity paths and, consequently, short life spans. Second, orders with high probabilities of familial origination and extinction were rarely replaced by new high-turnover orders. Thus, because high-turnover orders tended to become extinct without replacement, the global background extinction intensity declined. Since familial origination and extinction probabilities are correlated, global background origination intensity inevitably declined as well. As a consequence of these processes, virtually all groups of organisms now living have low probabilities of familial origination and extinction.

Simulations of branching evolution were used to obtain the expected relationships among probabilities (of origination and extinction), volatilities, and longevities for the entire range of possible probabilities, and these relationships were compared to those obtained from the empirical record. In the simulations, only the probabilities of origination and extinction were specified, so volatilities and clade longevities were determined entirely by the probabilities. The similarity between results obtained by simulation and those obtained by analysis of the empirical record further supports the inference that the observed decline of background extinction (and origination) intensity can be explained largely by the loss of high-probability groups to induced volatility.

The equations for calculating classical confidence intervals on the end points of stratigraphic ranges are based on the restrictive assumption of randomly distributed fossil finds. Herein, a method is presented for calculating confidence intervals on the end-points of stratigraphic ranges that partially relaxes this assumption: the method will work for any continuous distribution of gap sizes, not just those generated by random processes. The price paid for the generality of the new approach is twofold: (1) there are uncertainties associated with the sizes of the confidence intervals, and (2) for large confidence values (e.g., 95%) a rich fossil record is required to place upper bounds on the corresponding confidence intervals. This new method is not universal; like the method for calculating classical confidence intervals it is based on the assumption that there is no correlation between gap size and stratigraphic position. The fossil record of the Neogene Caribbean bryozoan Metrarabdotos is analyzed with the new approach. The equations developed here, like those for classical confidence intervals, should not be applied to stratigraphic ranges based on discrete sampling regimes, such as those typically established from deep-sea drilling cores, though there are exceptions to this rule.

Arm autotomy was induced in a living specimen of Metacrinus rotundus (Echinodermata: Crinoidea). An arm was autotomized at a ligamentary articulation known as a cryptosyzygy, following incision by scissors distal to the break point. Although sessile stalked crinoids cannot entirely escape from a predatory attack by arm autotomy and they do not have an active defense, arm autotomy at cryptosyzygies reduces damage and arm loss by effective distribution, and by minimizing trauma and facilitating subsequent regeneration.

The paradigmatic distribution of cryptosyzygies in which arm loss is set at a minimum, compared with the actual distribution, shows that these two patterns are similar and that actual specimens successfully reduce arm loss by the effective distribution of cryptosyzygies. The crinoid branching pattern also affects arm loss, and two different paradigms are discussed: anti-predatory and harvesting. Arm branching patterns of various isocrinids have tended toward the anti-predatory configuration from the Jurassic to the Recent, suggesting that the isocrinids have coped with increased predation. Shallow-water comatulids generally adopt the anti-predatory paradigm in their branching pattern, whereas many deep-water, stalked crinoids adopt a harvesting paradigm, reflecting that shallow-water comatulids receive more predatory attacks than do deep-water crinoids.

It has been argued that many clades originating in the early Paleozoic filled their design space rapidly while still at low taxonomic diversity. Standardization of morphology for analytical purposes facilitates testing of this claim. Here I document evolutionary patterns of morphological disparity in Ordovician-Devonian crinoids, using a set of 75 discrete characters covering the principal features of the crinoid stem, cup, tegmen, and arms. Disparity is measured as the average dissimilarity among species, the range of morphospace occupied, and the number of realized character-state combinations. Comparison with generic richness reveals that the full range of form was essentially attained by the early part of the Caradocian, long before the time of maximal taxonomic diversity. Despite subsequent taxonomic diversification, the variety of crinoid form did not expand appreciably; increased diversity was accommodated by the evolution of variations upon the spectrum of designs established earlier. The data discussed here do not definitively imply specific sources of constraint, but the effective stasis in disparity supports previous arguments that some morphological limits were reached early in crinoid history.

It is now widely recognized that a large number of Cretaceous planktic foraminiferal species are commonly found associated with fully Danian faunas in many K/T boundary sections and deep-sea cores. This “Cretaceous” fauna has traditionally been regarded as representing the reworking of older Cretaceous sediments into younger strata, though recent isotopic data from some species indicates that, at least in these instances, the reworking hypothesis is false. To further test this reworking hypothesis the biogeography of this “Cretaceous” fauna is compared to the underlying uppermost Maastrichtian biogeography and to the biogeography of lowermost Danian planktic foraminiferal faunas. Results show that there is no regular decline in species richness, extinction, or faunal co-occurrence values for this “Cretaceous” fauna at progressively higher (=younger) Danian stratigraphic horizons. Moreover, there is no compelling association between the stratigraphic persistence of this “Cretaceous” fauna and shallow depositional settings. Instead, this fauna is characterized by: (1) a close (and predictive) association between “Cretaceous” and indigenous Danian species richness values throughout the lower Danian, (2) a close numerical and geographic correspondence between Danian speciation and the disappearance of “Cretaceous” species from the Danian fossil record, and (3) a pronounced similarity between changes in the general biogeographic structures of the “Cretaceous” and associated Danian faunas throughout the study interval. These data suggest that the K/T planktic foraminiferal extinction event exhibited a marked geographic structure with low and middle latitude faunas experiencing differentially high extinction rates in the lowermost Danian zones P0 and P1a and high latitude survivor faunas persisting more or less unchanged into the overlying zone, P1b and P1c. Taken together, these results challenge the traditional concept of an instantaneous uppermost Cretaceous planktic foraminiferal mass extinction and its proposed causal connection to bolide impact.

Detailed analysis of the stratigraphic ranges of Devonian rugose coral genera within the Old World and Eastern Americas Realms gives new information on faunal extinctions and other bioevents in both realms. Various origination and extinction metrics are calculated from tabulations of occurrences in each stage. The most significant faunal changes were near or at the ends of the Lochkovian and Frasnian stages. The former marks the gradual transition from dominance by Silurian families and genera to the characteristic Devonian coral assemblages; the latter marks the virtual extinction of the Devonian families and genera. Other coral events are related to the two major changes.

The data provide new bases for comparing the histories of the two realms. Most of the events are recorded in both, giving support to previous suggestions that the causes were worldwide. The coral record shows an increase (probably episodic) in environmental deterioration persisting through the Middle Devonian and culminating in extinction at the end of the Frasnian. Eustatic sea level fluctuations may have caused the precursor events and a bolide impact may have caused the end-Frasnian extinction.

The age of first occurrence of taxa remains an underutilized source of information in phylogenetic analysis. In this paper I develop a method whereby one can measure the fit of the stratigraphic record to an estimated phylogenetic tree. The method works as follows: (1) each of the internal nodes excluding the root node of a phylogenetic tree is visited, (2) the oldest age of first occurrence for the taxa above the node is compared to the oldest age of first occurrence for the sister node, and (3) if the age above the node is the same age or younger than the age below the node, then the node is stratigraphically consistent. A measure of the total fit of the stratigraphic record to the tree is the proportion of nodes that are stratigraphically consistent (expressed as the stratigraphic consistency index, SCI). This measure of stratigraphic fit is sensitive to errors in phylogenetic estimation as well as to missing lineages (or parts of lineages). The significance of the fit of the stratigraphic record to the tree can be determined through a permutation approach that generates the null distribution for SCI under the hypothesis that the stratigraphic fit is no better than would be expected at random. The method is applied to several studies taken from the literature. Almost all published trees had significant SCI values, meaning the trees fit the stratigraphic record quite well. Applications of stratigraphic consistency for determining the confidence that should be placed in a phylogenetic estimate, for determining the root of a tree, and as a modified optimality criterion for estimating phylogenetic trees are discussed.

Specimens of Nautilus species caught in the wild show a marked increase in oxygen isotopic composition between embryonic and postembryonic septa. The significance of this increase in terms of the early life history of Nautilus has been unclear. To help explain this pattern, we analyzed the isotopic composition of the septa of three specimens of Nautilus belauensis raised in aquariums under controlled temperature conditions. Our results indicate that both embryonic and postembryonic septa are secreted with the same temperature-dependent fractionation of aragonite relative to water as that of other aragonite-secreting molluscs (Grossman and Ku 1986). The δ18O values of the septa thus provide a reliable means of determining the water temperature in which the septa form. Calculated temperatures based on oxygen isotopic data from specimens caught in the wild reveal that embryonic development occurs at 22°-24° corresponding to a depth of 100-200 m depending on the location. The increase in δ18O in postembryonic septa reflects a migration into colder, deeper water after hatching. In Cretaceous nautilids, a systematic shift in δ18O is not present, indicating that these animals probably did not change their habitat after hatching. This is consistent with the likelihood that they lived in shallower environments than that of modern Nautilus.

Macroevolutionary change from the Middle to the Late Paleozoic crinoid fauna was not the result of mass extinction. The presumption that the decline of the middle Paleozoic crinoid fauna was from a single mass extinction event was tested using seriation, multidimensional scaling (MDS), binomial analysis, and bootstrapping simulations on a data set which is a comprehensive revision of old faunal lists. The data for these analyses were based on temporal distributions of 214 species from 69 late Osagean and early Meramecian localities from the midcontinental United States. The time under consideration is subdivided into seven informal intervals using MDS in conjunction with biostratigraphy. Seriation of species ranges into these intervals results in a gradual pattern of faunal turnover, and sampling bias can be eliminated as a cause for this more gradual pattern. MDS analysis of the crinoid range data is similar to MDS simulations using data with continuous, monotonic species turnover and dissimilar to a simulated mass extinction. Binomial analysis and bootstrapping demonstrate that the observed number of extinctions at the putative extinction boundary were not unusually high. All methods agree that extinctions throughout this time were high but spanned several time intervals and that rapid, monotonic faunal turnover describes the data better than mass extinction. Macroevolutionary processes other than mass extinction and microevolutionary processes must have dictated the character and composition of this remarkable faunal transition among the Crinoidea.