A generalized method for calculating confidence intervals on the position of the true end point of a stratigraphic range when the distributions of fossil horizons is nonrandom is presented. The method requires a quantitative measure of collecting and/or preservation biases with stratigraphic position. This fossil recovery potential function may be based on (among other variables) bedding-plane surface areas, or, given a water depth curve, an a priori estimate of the preservation potential with water depth. The approach assumes that the observed distribution of fossil horizons is consistent with the distribution predicted by the fossil recovery potential function, an assumption that must be tested before the method is applied. Unlike previous methods for calculating confidence intervals on the end points of stratigraphic ranges, this method may be applied when the number of fossil horizons is correlated with stratigraphic position. The approach should only be applied to sections that have been sampled continuously, or approximately continuously. Its efficacy will depend on how accurately fossil recovery potentials can be determined. A method is also presented for estimating the probability that a species became extinct during a major hiatus in the rock record.

The stratigraphic distribution of fossil species contains potential information about phylogeny because some phylogenetic trees are more consistent with the distribution of fossils in the rock record than others. A maximum likelihood estimator of phylogeny is derived using an explicit mathematical model of fossil preservation. The method assumes that fossil preservations within lineages follow an independent Poisson process, but can be extended to include other preservation models. The performance of the method was examined using Monte Carlo simulation. The performance of the maximum likelihood estimator of topology increases with an increase in the preservation rate. The method is biased, like other methods of phylogeny estimation, when the rate of fossil preservation is low; estimated trees tend to be more asymmetrical than the true tree. The method appears to perform well as a tree rooting criterion even when preservation rates are low. We suggest several possible extensions of the method to address other questions about the nature of fossil preservation and the process of speciation and extinction over time and space.

Morphological analysis of four higher taxa of fossil marine invertebrates shows that, over the history of paleontology, there is no general tendency for morphologically extreme or modal species and genera to be described preferentially early or late. Reconstructing the expected evolutionary sequences of morphological disparity that would have been estimated at various times during the past century and a half reveals features that are sensitive to sampling (for example, peak trilobite disparity in the Ordovician, peak of post-Paleozoic crinoid disparity in the Triassic, and peak blastoid disparity in the Permian), as well as more robust features (for example, increase in trilobite disparity from the Cambrian to the Ordovician, continued increase in trilobite disparity despite a drop in taxonomic diversity after the Early Ordovician, decrease in blastoid disparity from the Devonian to the Carboniferous, and increase in crinoid disparity from the Jurassic to the Cretaceous followed by decline during the Cretaceous). Although we still have much to learn about the evolution of form, in many respects our view of the history of biological diversity is mature.

We used radiocarbon ages on dead Holocene shells of the venerid bivalve Chione spp. to investigate how time-averaging and taphonomy in shallow marine benthic assemblages vary with sedimentary and tectonic setting. We compared shells collected from the sediment surface in five depositional environments from two regions of the Gulf of California, Mexico: Bahía Concepción, a young faulted rift basin with high rates of terrigenous and carbonate sedimentation; and Bahía la Choya, an intertidal system along a sediment-starved shelf. Frequency distributions of shell ages in all environments form a hollow curve, with a mode at young ages and a long tail toward older ages. This pattern suggests that shells are added to the taphonomically active zone (TAZ) at roughly constant rates (via continuous shell deaths), and removed from the TAZ at random, either through destruction or by achieving final burial. Shell half-lives (the amount of time to remove half the shells from the TAZ) provide a comparative measure of time-averaging. Time-averaging varies with sedimentary and tectonic setting. The lowest amounts of time-averaging (shell half-lives of 90 to 165 years) occur in Bahía Concepción, where rapid rates of terrigenous sedimentation (on fan-deltas) and carbonate sedimentation (in pocket bays) bury shells rapidly. Time-averaging is higher in the sediment-starved environments of Bahía la Choya (shell half-lives of 285 to 550 years). The highest amounts of time-averaging occur the inner tidal flats of Bahía la Choya (shell half-life of 550 years). Here the conjunction of low sedimentation rates with low rates of shell destruction (due to periodic tidal emergence) permits shells to persist in the TAZ for very long time spans.

There is no systematic relationship between a shell's age and its taphonomic condition (taphonomic grade) in any environment, probably because of the complex and random nature of burial-exhumation in the TAZ. Age variance tends to increase with increasing taphonomic alteration: highly altered shells range in age from young to several thousand years old, while less altered shells are mostly young. The correspondence between time-averaging and the taphonomic condition of entire shell assemblages is also weak, but might be resolved with further study.

These results provide quantitative data on time-averaging in benthic assemblages as a function of sedimentary and tectonic setting, and suggest some guidelines for facies appropriate for particular studies. Shallow marine rift basins like Bahía Concepción can potentially contain within-horizon fossil assemblages representing time spans of only a few hundred years—time resolution often beyond reach in paleontology. In contrast, sediment-starved shelf habitats like Bahía la Choya are unlikely to yield assemblages with time resolution finer than several thousands of years.

The degradation-resistant organic-walled cell envelopes of acritarchs are the most abundant microfossils in Proterozoic and Cambrian rocks. These microfossils reveal diversity fluctuations that illuminate the nature of the record of primary producers near the Proterozoic/Phanerozoic boundary. Neoproterozoic radiations, some 1000–542 m.y. ago, reached levels comparable to those observed in the Cambrian Period. The microbiotas from rock successions from 13 Cambrian biochrons display significant fluctuations in the total number of microfossil taxa belonging to discrete microfossil assemblages. The assemblages reveal that Cambrian protist assemblages evolved over relatively short time spans, apparently out of low-diversity remnant populations after gradual declines in diversity. The characteristic microbiotas of the terminal Neoproterozoic and the Early, Middle, and Late Cambrian blossomed over relatively narrow time ranges, subsequently collapsing to nearly the initial levels. By virtue of the decreasing time spans involved in the late Vendian, Early, Middle, and Late Cambrian respectively, the tempo of specific turnover appears to have varied considerably. Speciation levels gradually decreased during Early and Middle Cambrian times and during Early Cambrian times were accompanied by rising levels of extinction. This latter feature seems to have reversed during Middle Cambrian times, lasting well into Late Cambrian times. Acritarchs were at the base of the marine trophic chain together with bacteria and other protists that are largely unrepresented in the fossil record. For this reason, the rise of diverse Cambrian protistan plankton must have been essential for early marine metazoan differentiation. Indeed, patterns of total diversity, speciation, and extinction of Cambrian acritarchs clearly mirror those of contemporaneous marine invertebrate faunas at the generic level.

Most modern marine ecology is ultimately based on unicellular phytoplankton, yet most large animals are unable to graze directly on even relatively large net phytoplankton; the repackaging effected by herbivorous mesozooplankton thus represents a key link in marine metazoan food chains. Despite the deep taphonomic biases affecting plankton fossilization, there is a clear record of phytoplankton from at least 1800 m.y ago. Proterozoic plankton are represented by small-to medium-sized sphaeromorphic acritarchs and probably do not include many/most of the unusually large acritarchs that characterize the Neoproterozoic. The first significant shift in phytoplankton diversity was therefore the rapid radiation of small acanthomorphic acritarchs in the Early Cambrian. The coincidence of phytoplankton diversification with the Cambrian radiation of large animals points compellingly to an ecological linkage between the two, particularly in light of recently discovered filter-feeding mesozooplankton in the Early Cambrian. The introduction of planktic filter feeders would have established the second tier of the Eltonian pyramid, potentially setting off the “self-propagating mutual feedback system of diversification” now recognized as the Cambrian explosion (Stanley 1973, 1976).

By consuming significant percentages of net phytoplankton and suspending it as animal biomass and non-aggregating fecal pellets, mesozooplankton cause a net reduction in export production; a general introduction of zooplankton would therefore have reduced carbon burial and moderated the bloom and bust cycle that must have characterized Proterozoic populations of net phytoplankton. The effect of added trophic levels in Early Cambrian ecosystems can be viewed as a serial application of the trophic cascade process observed in modern lakes, whereby the introduction of higher trophic levels determines the accumulation of plant biomass at the base of the system. As such, the major biogeochemical perturbations that mark the onset of the Phanerozoic might be considered a consequence, rather than a cause, of the Cambrian explosion; reduced C export due to zooplankton expansion explains the otherwise anomalous drop in δ13C at the base of the Tommotian.

Cambrian acanthomorphic acritarchs likely derived from planktic leiosphaerids exposed to mesozooplanktic grazing pressure, the ornamentation effectively increasing vesicle size without compromising buoyancy or surface-area:volume ratios. Alternatively, they may represent an escape into the plankton through a miniaturization of the much larger Neoproterozoic acanthomorphs. An invasion of small benthic herbivores into the water column to exploit the phytoplankton accounts for the origin of the mesozooplankton and may have been the key innovation in the Cambrian explosion.