The history of life is punctuated by a number of major transitions in hierarchy, defined here as the degree of nestedness of lower-level individuals within higher-level ones: the combination of single-celled prokaryotic cells to form the first eukaryotic cell, the aggregation of single eukaryotic cells to form complex multicellular organisms, and finally, the association of multicellular organisms to form complex colonial individuals. These transitions together constitute one of the most salient and certain trends in the history of life, in particular, a trend in maximum hierarchical structure, which can be understood as a trend in complexity. This trend could be produced by a biased mechanism, in which increases in hierarchy are more likely than decreases, or by an unbiased one, in which increases and decreases are about equally likely. At stake is whether or not natural selection or some other force acts powerfully over the history of life to drive complexity upward.

Too few major transitions are known to permit rigorous statistical discrimination of trend mechanisms based on these transitions alone. However, the mechanism can be investigated by using “minor transitions” in hierarchy, or, in other words, changes in the degree of individuation of the upper level. This study tests the null hypothesis that the probability (or rate) of increase and decrease in individuation are equal in a phylogenetic context. We found published phylogenetic trees for clades spanning minor transitions across the tree of life and identified changes in character states associated with those minor transitions. We then used both parsimony- and maximum-likelihood-based methods to test for asymmetrical rates of character evolution. Most analyses failed to reject equal rates of hierarchical increase and decrease. In fact, a bias toward decreasing complexity was observed for several clades. These results suggest that no strong tendency exists for hierarchical complexity to increase.

An extreme, dorsally hyperextended posture of the spine (opisthotonus), characterized by the skull and neck recurved over the back, and with strong extension of the tail, is observed in many well-preserved, articulated amniote skeletons (birds and other dinosaurs, pterosaurs, and at least placental mammals). Postmortem water transport may explain some cases of spinal curvature in fossil tetrapods, but we show how these can be distinguished from causes of the opisthotonic posture, which is a biotic syndrome. Traditional biotic explanations nearly all involve postmortem causes, and have included rigor mortis, desiccation, and contraction of tendons and ligaments. However, examination of the process of rigor mortis and experimental observations of drying and salinity in carcasses of extant animals show that these explanations of the “dead bird” (opisthotonic) posture account for few or no cases. Differential contraction of cervical ligaments after death also does not produce the opisthotonic posture. It is not postmortem contraction but perimortem muscle spasms resulting from various afflictions of the central nervous system that cause these extreme postures. That is, the opisthotonic posture is the result of “death throes,” not postmortem processes, and individuals so afflicted assumed the posture before death, not afterward. The clinical literature has long recognized that such afflicted individuals perish from asphyxiation, lack of nourishment or essential nutrients, environmental toxins, or viral infections, among other causes. Accepting the actual causes of the opisthotonic posture as perimortem and not postmortem provides insights into the causes of death of fossilized specimens, and also revises interpretations of paleoenvironmental conditions of many fossil deposits. The opisthotonic posture tells us more about the circumstances surrounding death than about what happened after death. Finally, the opisthotonic posture appears to have a phylogenetic signal: it is so far reported entirely in ornithodiran archosaurs (dinosaurs and pterosaurs) and in crown-group placentals, though the distribution in mammals may expand with further study. It seems important that the opisthotonic posture has been observed extensively only in clades of animals that are known or thought to have high basal metabolic rates: hypoxia and related diseases would be most likely to affect animals with high oxygen use rates.

We use two approaches to test hypotheses regarding function in a group of extinct mammals (Family Mesotheriidae, Order Notoungulata) that lack any close extant relatives: a principle-derived paradigm method and empirically derived analog method. Metric and discrete morphological traits of mesotheriid postcranial elements are found to be consistent with the morphology predicted by a modified version of Hildebrand's paradigm for scratch diggers. Ratios of in-force to out-force lever arms based on skeletal elements indicate that the mesotheriids examined had limbs modified for high out-forces (i.e., they were “low geared”), consistent with the digging hypothesis. Other mesotheriid characters, such as cleft ungual phalanges, a curved olecranon, and a highly modified pelvis (with extra vertebrae incorporated into the sacrum and fusion between the ischium and the axial skeleton) are regarded as being functionally significant for digging and also occur in a variety of extant diggers. Analog methods indicate that mesotheriids share numerous traits common to a variety of extant diggers. Principal component analyses of postcranial elements indicate that mesotheriids consistently share morphometric space with larger extant fossorial mammals: aardvark, anteaters, wombats, and badger. Likewise, discriminant function analyses categorized mesotheriids as fossorial, though imperfectly analogous to the extant diggers analyzed. Thus, both theory-driven and empirically derived methods of estimating function in these extinct taxa support a digging hypothesis for the mesotheriids examined. Adaptations for digging in both the forelimb and sacropelvic functional complexes of mesotheriids provide independent support for the fossorial hypothesis.

Evolutionary stasis has often been explained by stabilizing selection, intrinsic constraints, or, more recently, by spatially patterned population dynamics. To distinguish which of these mechanisms explains a given case of stasis in the fossil record, stasis must first be rigorously documented in a high-resolution stratigraphic time series of fossil specimens. Furthermore, past studies of evolutionary mode in fossil mammalian lineages have often been limited to univariate traits (e.g., molar crown area). It is reasonable to assume that tooth shape, a multivariate trait, reflects important additional aspects of tooth form and function. Here we present the results of a geometric morphometric analysis of the lower dentition of the Paleocene-Eocene condylarth species Ectocion osbornianus collected from the Bighorn and Clarks Fork Basins of northwestern Wyoming. Tooth margin shape, cusp configuration, and shearing crest shape were digitized for the last lower premolar, p4, and for two lower molars, m1 and m3. Multivariate statistical tests of evolutionary mode were used to analyze the change in shape variance over time in addition to the magnitude and direction of shape change. Test results characterize the shape time series as consisting of counteracting changes with less change than expected under a random walk (i.e., stasis). The temporal structure of shape variance implies that the sampled E. osbornianus most likely represent a single population, which is not concordant with the population dynamic mechanism of stasis. Stabilizing selection and/or intrinsic constraints remain as the mechanisms that could explain stasis in the lower dental shape of E. osbornianus despite the variable environmental conditions of the Paleocene–Eocene.

If last appearances of marine animal genera are taken as reasonable proxies for true extinctions, then there is appreciable global extinction in every stage of the Phanerozoic. If, instead, backsmearing of extinctions by incomplete sampling is explicitly taken into consideration, a different view of extinction emerges, in which the pattern of extinction is much more volatile and in which quiescent time spans—with little or no global extinction for several million years—are punctuated by major extinction events that are even more extreme than is generally thought. Independent support for this alternative view comes from analysis of genus occurrence data in the Paleobiology Database, which agrees with previous estimates of sampling probability and implies that offsets between extinction and last appearance of one or more stages are quite probable.

The process of evolution hinders our ability to make large-scale ecological comparisons—such as those encompassing marine biotas spanning the Phanerozoic—because the compared entities are taxonomically and morphologically dissimilar. One solution is to focus instead on life habits, which are repeatedly discovered by taxa because of convergence. Such an approach is applied to a comparison of the ecological diversity of Paleozoic (Cambrian–Devonian) and modern marine biotas from deep-subtidal, soft-substrate habitats. Ecological diversity (richness and disparity) is operationalized by using a standardized ecospace framework that can be applied equally to extant and extinct organisms and is logically independent of taxonomy. Because individual states in the framework are chosen a priori and not customized for particular taxa, the framework fulfills the requirements of a universal theoretical ecospace. Unique ecological life habits can be recognized as each discrete, n-dimensional combination of character states in the framework. Although the basic unit of analysis remains the organism, the framework can be applied to other entities—species, clades, or multispecies assemblages—for the study of comparative paleoecology and ecology. Because the framework is quantifiable, it is amenable to analytical techniques used for morphological disparity. Using these methods, I demonstrate that the composite Paleozoic biota is approximately as rich in life habits as the sampled modern biota, but that the life habits in the modern biota are significantly more disparate than those in the Paleozoic; these results are robust to taphonomic standardization. Despite broadly similar distributions of life habits revealed by multivariate ordination, the modern biota is composed of life habits that are significantly enriched, among others, in mobility, infaunality, carnivory, and exploitation of other organisms (or structures) for occupation of microhabitats.

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.

Four independent lines of evidence, (1) the quality of specimen preservation, (2) taxonomic collection curves, (3) molecular divergence estimates, and (4) ghost lineage analysis of a genus-level cladogram, point to echinoids having a much poorer fossil record in the Triassic than in the Lower Jurassic. Furthermore, preservational differences between Triassic and Lower Jurassic echinoids have remained a consistent feature over 160 years of discovery. Differences exist in how effectively paleontologists have collected the fauna from available outcrops in the Triassic and Lower Jurassic. Collection curves suggest that rocks have been more efficiently searched for their fossils in Europe than elsewhere in the world, and that Lower Jurassic faunas are better sampled from available outcrop than Triassic faunas. The discovery of Triassic taxa has quickened in pace over the past 4 decades (though largely driven by a single Lagerstätte—the St. Cassian beds) while discoveries of new taxa from the Lower Jurassic have slowed. Molecular analysis of extant families and ghost lineage analysis of Triassic and Lower Jurassic genera both point to poorer sampling of Triassic faunas. This difference in the quality of the fossil record may be partially explained by differences in rock outcrop area, as marine sedimentary rocks are much less common in the Triassic than in the Lower Jurassic. However, improving biomechanical design of the echinoid test over this critical time interval was probably as important, and better explains observed preservational trends. Changes in the quality of the echinoid fossil record were thus driven as much by intrinsic biological factors as by sampling patterns.

Many authors have proposed scenarios for mass extinctions that consist of multiple pulses or stages, but little work has been done on accounting for the Signor-Lipps effect in such extinction scenarios. Here we introduce a method for computing confidence intervals for the time or stratigraphic distance separating two extinction pulses in a pulsed extinction event, taking into account the incompleteness of the fossil record. We base our method on a flexible likelihood ratio test framework that is able to test whether the fossil record is consistent with any extinction scenario, whether simultaneous, pulsed, or otherwise. As an illustration, we apply our method to a data set on marine invertebrates from the Permo-Triassic boundary of Meishan, China. Using this data set, we show that the fossil record of ostracodes and that of brachiopods are each consistent with simultaneous extinction, and that these two extinction pulses are separated by 720,000 to 1.2 million years with 95% confidence. With appropriate data, our method could also be applied in other situations, such as tests of origination patterns, coordinated stasis, and recovery after a mass extinction.

Two simple plate parameters, P, the height of the plate measured normal to the plate base, and α, the angle formed between the plate base and the adjacent edge of that plate, serve to model crinoid aboral cup morphology. With few exceptions, the resulting theoretical geometries replicate the range of calyx morphology observed in the natural world. A theoretical morphospace, derived from these parameters, encompasses both the realized and unrealized possibilities of crinoid calyx construction. The model and the associated morphospace demonstrate that the occupation of crinoid cup space varies non-uniformly in time and space and suggest that functional constraints and/or ecological habit are important components of the distribution of cup morphology in time.