Stratigraphic paleobiology uses a modern understanding of the construction of the stratigraphic record—from beds to depositional sequences to sedimentary basins—to interpret patterns and guide sampling strategies in the fossil record. Over the past 25 years, its principles have been established primarily through forward numerical modeling, originally in shallow-marine systems and more recently in nonmarine systems. Predictions of these models have been tested through outcrop-scale and basin-scale field studies, which have also revealed new insights. At multi-basin and global scales, understanding the joint development of the biotic and sedimentary records has come largely from macrostratigraphy, the analysis of gap-bound packages of sedimentary rock. Here, we present recent advances in six major areas of stratigraphic paleobiology, including critical tests in the Po Plain of Italy, mass extinctions and recoveries, contrasts of shallow-marine and nonmarine systems, the interrelationships of habitats and stratigraphic architecture, large-scale stratigraphic architecture, and the assembly of regional ecosystems. We highlight the potential for future research that applies stratigraphic paleobiological concepts to studies of climate change, geochemistry, phylogenetics, and the large-scale structure of the fossil record. We conclude with the need for more stratigraphic thinking in paleobiology.

A fundamental question in paleobiology is whether ecology is correlated with evolutionary history. By combining time-calibrated phylogenetic trees with genus occurrence data through time, we can understand how environmental preferences are distributed on a tree and evaluate support for models of ecological similarity. Exploring parameters that lend support to each evolutionary model will help address questions that lie at the nexus of the evolutionary and ecological sciences. We calculated ecological difference and phylogenetic distance between species pairs for 83 taxa used in recent phylogenetic revisions of the brachiopod order Strophomenida. Ecological difference was calculated as the pairwise distance along gradients of water depth, carbonate, and latitudinal affinity. Phylogenetic distance was calculated as the pairwise branch length between tips of the tree. Our results show no relationship between ecological affinity and phylogeny. Instead results suggest an ecological burst during the initial radiation of the clade. This pattern likely reflects scaling at the largest macroevolutionary and macroecological scales preserved in the fossil record. Hierarchical scaling of ecological and evolutionary processes is complex, but phylogenetic paleoecology is an avenue for better evaluating these questions.

Mass extinctions affect the history of life by decimating existing diversity and ecological structure and creating new evolutionary and ecological pathways. Both the loss of diversity during these events and the rebound in diversity following extinction had a profound effect on Phanerozoic evolutionary trends. Phylogenetic trees can be used to robustly assess the evolutionary implications of extinction and origination.

We examine both extinction and origination during the Late Ordovician mass extinction. This mass extinction was the second largest in terms of taxonomic loss but did not appear to radically alter Paleozoic marine assemblages. We focus on the brachiopod order Strophomenida, whose evolutionary relationships have been recently revised, to explore the disconnect between the processes that drive taxonomic loss and those that restructure ecological communities.

A possible explanation for this disconnect is if extinction and origination were random with respect to morphology. We define morphospace using principal coordinates analysis (PCO) of character data from 61 Ordovician–Devonian taxa and their 45 ancestral nodes, defined by a most parsimonious reconstruction in Mesquite. A bootstrap of the centroid of PCO values indicates that genera were randomly removed from morphospace by the Late Ordovician mass extinction, and new Silurian genera were clustered within a smaller previously unoccupied region of morphospace. Diversification remained morphologically constrained throughout the Silurian and into the Devonian. This suggests that the recovery from the Late Ordovician mass extinction resulted in a long-term shift in strophomenide evolution. More broadly, recovery intervals may hold clues to understanding the evolutionary impact of mass extinctions.

Using museum and literature data, we characterize faunal turnover in bivalves and brachiopods of the North American Midcontinent over approximately 12.5 Myr spanning the Pennsylvanian/Permian boundary. The two groups experienced indistinguishable rates of background faunal turnover but differed in the type and timing of elevated turnover episodes. Bivalves underwent an episode of elevated first appearance in the Missourian Series whereas brachiopods underwent an episode of elevated disappearance in the Wolfcampian Series. In neither group does turnover history strongly correlate to long-term changes in basinal lithofacies, which reflect evolution of regional climate. Comparison with other time intervals and basins suggests that magnitude and frequency of turnover episodes during the late Paleozoic was intermediate between the more episodic early Paleozoic and less episodic Mesozoic.

Understanding what drives global diversity requires knowledge of the processes that control diversity and turnover at a variety of geographic and temporal scales. This is of particular importance in the study of mass extinctions, which have disproportionate effects on the global ecosystem and have been shown to vary geographically in extinction magnitude and rate of recovery.

Here, we analyze regional diversity and turnover patterns for the paleocontinents of Laurentia, Baltica, and Avalonia spanning the Late Ordovician mass extinction and Early Silurian recovery. Using a database of genus occurrences for inarticulate and articulate brachiopods, bivalves, anthozoans, and trilobites, we show that sampling-standardized diversity trends differ for the three regions. Diversity rebounded to pre-extinction levels within 5 Myr in the paleocontinent of Laurentia, compared with 15 Myr or longer for Baltica and Avalonia. This increased rate of recovery in Laurentia was due to both lower Late Ordovician extinction rates and higher Early Silurian origination rates relative to the other continents. Using brachiopod data, we dissected the Rhuddanian recovery into genus origination and invasion. This analysis revealed that standing diversity in the Rhuddanian consisted of a higher proportion of invading taxa in Laurentia than in either Baltica or Avalonia. Removing invading genera from diversity counts caused Rhuddanian diversity to fall in Laurentia. However, Laurentian diversity still rebounded to pre-extinction levels within 10 Myr of the extinction event, indicating that genus origination rates were also higher in Laurentia than in either Baltica or Avalonia. Though brachiopod diversity in Laurentia was lower than in the higher-latitude continents prior to the extinction, increased immigration and genus origination rates made it the most diverse continent following the extinction. Higher rates of origination in Laurentia may be explained by its large size, paleogeographic location, and vast epicontinental seas. It is possible that the tropical position of Laurentia buffered it somewhat from the intense climatic fluctuations associated with the extinction event, reducing extinction intensities and allowing for a more rapid rebound in this region. Hypotheses explaining the increased levels of invasion into Laurentia remain largely untested and require further scrutiny. Nevertheless, the Late Ordovician mass extinction joins the Late Permian and end-Cretaceous as global extinction events displaying an underlying spatial complexity.

Biotic invasions in the fossil record provide natural experiments for testing hypotheses of niche stability, speciation, and the assembly and diversity of regional biotas. We compare ecological parameters (preferred environment, occupancy, median abundance, rank abundance) of genera shared between faunal provinces during the Richmondian Invasion in the Late Ordovician on the Laurentian continent. Genera that spread from one faunal province to the other during the invasion (invading shared genera) have high Spearman rank correlations (>0.5) in three of four ecological parameters, suggesting a high level of niche stability among invaders. Genera that existed in both regions prior to and following the invasion (noninvading shared genera) have low correlations (<0.3) and suggest niche shift between lineages that diverged at least 8 Myr earlier. Niche shift did not accumulate gradually over this time interval but appears to have occurred in a pulse associated with the onset of the Taconic orogeny and the switch from warm-water to cool-water carbonates in southern Laurentia.

The late Mesozoic through early Cenozoic is an interval of significant biologic turnover and ecologic reorganization within marine assemblages, but the timing and causes of these changes remain poorly understood. Here, we quantify the pattern and timing of shifts in the diversity (richness and evenness) and ecology of local (i.e., sample level) mollusk-dominated assemblages during this critical interval using field-collected and published data sets from the U.S. Gulf Coastal Plain. We test whether the biologic and ecologic patterns observed primarily at the global level during this time are also expressed at the local level, and whether the end-Cretaceous (K/Pg) mass extinction and recovery moderated these trends. To explore whether environment had any effect on these patterns, we examine data from shallow subtidal and offshore settings.

Assemblages from both settings recovered to pre-extinction diversity levels rapidly, in less than 7 million years. Following initial recovery, diversity remained unchanged in both settings. The trajectory of ecological restructuring was distinct for each setting in the wake of the K/Pg extinction. In offshore assemblages, the abundance and number of predatory carnivorous taxa dramatically increased, and surficial sessile suspension feeders were replaced by more active suspension feeders. In contrast, shallow subtidal assemblages did not experience ecological reorganization following the K/Pg extinction. The distinct ecological patterns displayed in each environment follow onshore-offshore patterns of innovation, whereby evolutionary novelties first appear in onshore settings relative to offshore habitats. Increased predation pressure may explain the significant ecological restructuring of offshore assemblages, whereby the explosive radiation of predators drove changes in their prey. Habitat-specific ecological restructuring, and its occurrence solely during the recovery interval, implies that disturbance and incumbency were also key in mediating these ecological changes.

Long-term diversity equilibria, ecological incumbency, and widespread recurrent fossil assemblages have each been cited as evidence that local processes, such as competition, played an important role in structuring communities over geologic time. We analyze the relationship between local and regional diversity in tropical marine communities spanning approximately 13 Myr of the Late Ordovician to test for the role of local processes in structuring local communities. We find a significant and strong positive relationship between local and regional diversity, indicating that local communities were not saturated with species and that local processes did not exert a dominant influence on local diversity. Rather, local diversity was influenced more by regional oceanographic processes that governed the size of the regional species pool. This evidence for unsaturated communities is consistent with the Walker and Valentine hierarchically structured niche model of global diversification. These results come at the beginning of the 200-Myr Paleozoic plateau in both local and global diversity and therefore raise the question whether local communities were ever saturated with species during the Paleozoic. Similar studies need to be conducted during other times in the Paleozoic to determine if this is indeed the case.

Accurate interpretation of origination and extinction of fossil species is crucial to answering a variety of questions in paleontology. Fossil datums, the observed age of first or last occurrences, are subject to sampling error as a result of preservation and low abundances near range endpoints. This sampling error can cause local range offset, an age difference between the observed first or last occurrence of a species and its true origination or extinction. Here, we develop and test a new technique, the Probable Datum Method (PDM), that can be used to assess the extent of local range offset for nannofossil species. The PDM estimates the original abundance of a taxon and its probable true age of first or last occurrence. The PDM uses a model in which original abundance is related to count abundance through preservation and the counting process. This model is empirically parameterized, including an experimental determination of false positive and error rates of a nannofossil count. The model is simulated then inverted to estimate likely original abundance and true datum age from count abundance data. We first test the PDM in a positive control experiment with known parameter values. This experiment shows that the PDM is robust and returns known values accurately. Next we apply the method to the origination of nannoplankton after the Cretaceous/Paleogene boundary to test whether first occurrences were synchronous between widely spaced locations. The PDM results suggest that observed diachrony of K/Pg originations cannot be explained by the effects of local range offset; rather, in some cases they indicate truly diachronous first occurrences between localities. Although the technique was developed to analyze nannoplankton ranges, the statistical nature of the PDM, its experimentally derived parameters, and its parsimonious nature should make it applicable to many micropaleontological studies that interpret patterns of origination and extinction.

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.

A compilation of species occurrences in a chronostratigraphic framework of depositional sequences from a 250,000 km2 area in the eastern United States is used to test for coordinated stasis in Middle and Upper Ordovician articulate brachiopods. Two rapid pulses of turnover in brachiopod species separate three periods of relatively lower turnover (ecologic-evolutionary [EE] subunits) that range from 3 to 9 m.y. in duration. Turnover within these EE subunits is characterized by high levels of percent species origination (ca. 60%) and percent species extinction (ca. 80%) and low levels of percent species persistence (<10%), all of which fall outside the range reported for coordinated stasis. Turnover between EE subunits is characterized by low levels of percent species holdover and percent species carryover (ca. 10% or less) and is consistent with coordinated stasis, although turnover pulses are driven largely by pulses in either extinction or origination, and not by pulses in both, as reported for coordinated stasis. Taken together, although these data display a marked bimodality in turnover, high levels of turnover within EE subunits is inconsistent with a pattern of coordinated stasis. Turnover rates within these EE subunits are much higher than previous global estimates for Cambro-Ordovician brachiopods or Phanerozoic marine species and indicate that local extirpation and migration play a significant role in regional biodiversity dynamics. Despite the high level of turnover observed within these EE subunits, some level of ecologic stability occurs because abundant genera persist throughout entire EE subunits. Ordovician species in this study behaved relatively independently of other taxa and were not tightly integrated as suggested by the broadly overlapping taxon abundance curves, the shifting habitat preference of some taxa, the piecemeal turnover between EE subunits, and the continuous creation of new species associations due to background levels of turnover within EE subunits. Turnover within EE subunits was associated with relatively stable or only mildly fluctuating environments. Rapid turnover between EE subunits was caused by extreme perturbations to the regional or possibly global ocean-climate system.

The earliest Paleocene record of calcareous nannoplankton presents a unique opportunity to understand the evolutionary recovery of life from mass extinction. Nannoplankton were devastated at the Cretaceous/Paleogene boundary and their subsequent recovery can be studied in great detail because of their abundance in sediments, continuous stratigraphic occurrence, and near global distribution. Here we determine when and where new species of nannoplankton originated and how they dispersed following the Cretaceous/Paleogene mass extinction. Initially, we focus our efforts on North Pacific and South Atlantic deep sea sites with orbital age control to compare the precise timing and dynamics of the recovery between the locations. We then broaden our investigation to six sites from different basins and a variety of environments to study global patterns of the initial recovery. Our results show that many taxa in key Paleogene lineages originated in the North Pacific Ocean and that assemblages comprised primarily of new Paleogene taxa were not observed at other sites for several hundred thousand years. Survivors that were adapted to eutrophic post extinction conditions rapidly expanded in Southern Hemisphere sites where they dominated assemblages for most of the initial recovery. We therefore hypothesize that groups of survivors formed regionally incumbent assemblages in the Southern Hemisphere that limited diversification and dispersal of new Paleogene taxa. The end of survivor dominance correlates to the recovery of the biologic pump and subsequent decrease in surface ocean nutrient concentration 300–400 Kyr after the boundary. Only after survivors were removed did new Paleogene nannoplankton assemblages become abundant globally. Our results indicate that competition from regionally incumbent survivors was as an important control on the K/Pg recovery of nannoplankton.

Biotic invasions are a common feature of the fossil record, yet remarkably little is known about them, given their enormous potential to reveal the processes that regulate local and regional diversity over long time scales. We used additive diversity partitioning to examine how diversity structure changed as a result of a marine biotic invasion in tropical, shallow and deep subtidal environments spanning approximately 4 Myr in the Late Ordovician. The biotic invasion increased richness in the regional ecosystem by nearly 40%. Within-habitat turnover diversity accounts for most of the increase in richness, with between-habitat turnover diversity contributing a lesser amount. Increases in these components of diversity were accommodated by increased packing of species along a depth gradient and increased habitat heterogeneity. Diversity metrics that incorporate taxon abundance (Shannon information, Simpson's D) show similar patterns and reveal that many invading taxa were locally abundant and widespread in their occurrence. Extinction of incumbent taxa did not foster the invasion; rather the invasion appears to be linked to a regional or global warming event. Taken together, these observations indicate that these Late Ordovician marine communities were open to invasion and not saturated with species. Moreover, the increase in species diversity caused by the invasion was not ephemeral; instead it lasted for at least 1 Myr. Similar studies of other biotic invasions in the fossil record are necessary to determine (1) the factors, such as extinction of incumbents or resource limitation, that may facilitate or inhibit invasion in ancient ecosystems; (2) how local and regional ecosystems respond to invasion; and (3) the extent to which biotic invasions play a substantial role in ecosystem change through geologic time.

The Paleocene-Eocene Thermal Maximum (PETM; ca. 55.8 Ma) is thought to coincide with a profound but entirely transient change among nannoplankton communities throughout the ocean. Here we explore the ecology of nannoplankton during the PETM by using multivariate analyses of a global data set that is based upon the distribution of taxa in time and space. We use these results, coupled with stable isotope data and geochemical modeling, to reinterpret the ecology of key genera. The results of the multivariate analyses suggest that the community was perturbed significantly in coastal and high-latitudes sites compared to the open ocean, and the relative influence of temperature and nutrient availability on the assemblage varies regionally. The open ocean became more stratified and less productive during the PETM and the oligotrophic assemblage responded primarily to changes in nutrient availability. Alternatively, assemblages at the equator and in the Southern Ocean responded to temperature more than to nutrient reduction. In addition, the assemblage change at the PETM was not merely transient—there is evidence of adaptation and a long-term change in the nannoplankton community that persists after the PETM and results in the disappearance of a high-latitude assemblage. The long-term effect on communities caused by transient warming during the PETM has implications for modern-day climate change, suggesting similar permanent changes to nannoplankton community structure as the oceans warm.

Articulate brachiopods underwent a major taxonomic and morphologic diversification during the Ordovician, yet remarkably little is known about the environmental, ecologic, and biogeographic contexts surrounding this event. An exception is Lockley's (1983) synthesis of brachiopod-dominated paleocommunities from the Welsh Basin. His study focused on a small geographic area dominated by siliciclastic sediments that was positioned at high paleo-latitudes during the Ordovician. North America, in contrast, was positioned at the equator and was the site of extensive carbonate platform development. A factor analysis of 165 North American assemblages was undertaken for comparison to Lockley's summary. The comparison suggests that the radiation of articulate brachiopods varied latitudinally, with different superfamilies radiating and achieving dominance in different biogeographic provinces. This pattern is also expressed by the relative abundance relationships among dominant genera making up the biofacies and therefore suggests that adaptation to local environmental parameters may have been an important governing factor.

The analysis of North American assemblages indicates that the composition of brachiopod biofacies changed dramatically as the Ordovician radiation unfolded. Ibexian and early Whiterockian shelf environments were dominated by orthaceans with porambonitaceans important in nearshore Ibexian environments. In the late Whiterockian a major turnover in biofacies composition occurred that marked the appearance and/or diversification of several new articulate superfamilies. Late Whiterockian through Cincinnatian offshore environments were characterized by plectambonitaceans and enteletaceans with strophomenaceans also moderately important. Nearshore environments were dominated by strophomenaceans, orthaceans, and rhynchonellaceans. Atrypaceans appeared nearshore in the Mohawkian but shifted their center of dominance offshore by the Cincinnatian. Deep basin environments were rarely inhabited by articulate brachiopods and were dominated throughout the Ordovician by inarticulates (lingulaceans). There was no major change in composition of the deep-water inarticulate biofacies that paralleled the turnover seen among articulates on the platforms.

The Welsh Basin biofacies described by Lockley are broadly similar to the North American biofacies. Orthaceans characterized Arenigian (late Ibexian and early Whiterockian) shelf environments. Orthaceans and strophomenaceans dominated Llanvirnian through Caradocian (early Whiterockian - early Cincinnatian) nearshore environments and plectambonitaceans and enteletaceans dominated offshore environments. Inarticulates were dominant in deep basin environments throughout the Ordovician. In contrast to North America, rhynchonellaceans and porambonitaceans, although present in the Welsh Basin, apparently never formed a distinct biofacies. In the case of the porambonitaceans, this may reflect poor sampling of Lower Ordovician strata. Enteletaceans, on the other hand, appeared earlier (Arenig) in the Welsh Basin than in North America and eventually diversified to become dominant in a broader range of environments that included the nearshore.