Terrestrial mass extinctions have been attributed to a wide range of causes. Some of them are external to Earth, such as bolide impacts (as widely discussed for the K/T boundary) and radiation events. Among radiation events, there are possible large solar flares, nearby supernovae, gamma-ray bursts (GRBs), and others. These have variable intensity, duration, and probability of occurrence, although some generalizations are possible in understanding their effects (Ejzak et al. 2007). Here we focus on gamma-ray bursts (Thorsett 1995; Scalo and Wheeler 2002), a proposed causal agent for the end-Ordovician extinction. These are the most remote and infrequent of events, but by virtue of their power, a threat approximately competitive with, for example, that of nearby supernovae. A GRB of the most powerful type (Woosley and Bloom 2006) is thought to result from a supernova at the end of stellar evolution for very massive stars with high rotational speed. Much of their energy is channeled into beams, or jets, which include very high energy electromagnetic energy, i.e., gamma-rays and X-rays. It is a testament to the power of these events, far across the observable universe, that they were first detected in the 1969–1970 results from monitoring satellites designed to detect nuclear explosions on Earth's surface. It was not until the 1990s, when the distance to the events became known, that their power became apparent. Several such events occur every day in the observable universe. Other kinds of events are also potentially damaging, such as so-called short bursts and solar flares, but rate information is only now beginning to clarify how much threat is likely from such sources.

Studies of ecological structure and diversity over time in extinct groups have always been challenged by the inability to observe the behavior of fossil taxa directly. The only available evidence for function, behavior, and interactions between taxa is the morphological characteristics of the preserved fossils. Recent studies on modern groups have shown that morphological analyses may give misleading results in terms of ecological pattern and diversity. An alternative approach is to focus on functionally relevant aspects of morphology through a paleobiomechanical paradigm. The purpose of this research is to examine variation in the lower jaw morphology in Late Devonian arthrodire placoderms and develop biomechanical metrics that can be used to quantify functional diversity among this fossil group. Nine functionally relevant morphological characters were collected for 94 isolated arthrodire inferognathals from the Gogo Formation in Western Australia and the Cleveland Shale in Ohio. These data were used to address aspects of functional morphology, biomechanical disparity, and ecological structure in arthrodire placoderms from the Late Devonian. Results were compared with results from previous morphometric work on the same set of jaws.

Statistical tests show a significant difference in functional characters between the two faunas. The differences may be related to phylogenetic differences between faunas, as the two major clades of arthrodire taxa included in this study are almost completely segregated between faunas. Average pairwise disparity analyses of the mechanical characters indicate that there is no significant difference in overall functional diversity between the Cleveland Shale and Gogo Reef arthrodire faunas. This result is at odds with previous results that show overall morphological disparity to be much higher in the Cleveland Shale. Clustering patterns within a multivariate function-space show tightly constrained functional groups of taxa independent of phylogenetic or shape-based morphological similarity. These functional groups illustrate a level of ecological diversity in Late Devonian arthrodires that is comparable to that in certain modern faunas.

Further statistical analysis of the morphological and functional disparity of these Late Devonian taxa shows a disjoint between the two measures. Model I regression analysis of and Spearman rank-correlation analysis of average pairwise morphological and functional disparity measures indicate no significant relationship between morphological and functional disparity among the jaws used in this study. Although function is obviously derived from morphology, these results show that morphological shape analysis is not necessarily a good proxy for eco-functional diversity.

A combination of historical, functional, and biomechanical constraints has shaped the masticatory apparatus of fossil and extant xenarthrans. Among the more notable features are the teeth: hypselodont; commonly reduced in size, complexity, and number; separated by short diastema; and composed of osteodentine. Enamel is absent, as are the cuspal patterns of other mammals. A comprehensive revision of teeth and other features of the masticatory apparatus of xenarthrans reveals that previous generalizations underestimate the morphological diversity and adaptive possibilities developed within the clade. The great diversity of forms suggests several such possibilities ranging from specialized myrmecophagous species to carrion feeders or predators among animalivores; selective browsers to bulk grazers among herbivores; and omnivores. In some cases xenarthrans represent less extreme versions of patterns developed in other major clades of mammals (marsupials, afrotheres, euarchontoglires, and laurasiatheres) clearly predetermined by a tribosphenic dental morphology, whereas in others they represent unique novelties indicative of particular biological roles. The combination of tooth features that characterize xenarthrans might be seen as the key innovation for the ecologic diversity developed at least since the Oligocene, breaking the mold of the tribosphenic condition that constrained the evolution of the other major clades of mammals.

A record of late Paleozoic foraminiferal diversity, origination and extinction frequencies, and provincialism at million-year temporal resolution and species-level taxonomic resolution has been achieved by analyzing composite standard databases. Foraminiferal species diversity increased throughout Mississippian and Pennsylvanian time leading up to its peak at the Pennsylvanian/Permian boundary. Foraminifers then experienced a steep decline in diversity during the Early Permian. Frequencies of origination and extinction broadly tracked changes in global diversity. From Late Mississippian time onward, patterns in total foraminiferal diversity were dominated by fusulinoideans. There is no clear relationship between rates of foraminiferal evolution and the alternating glacial and nonglacial intervals that characterized the late Paleozoic ice age. Rather, high rates of origination and extinction might reflect instability of neritic environments as a consequence of high-frequency, high-amplitude base-level fluctuations (cyclothemic deposition). Further, the advent of algal symbiosis in fusulinoideans was a physiologic innovation that promoted diversification as these symbiont-bearing taxa experimented with morphologic adaptations for partitioning the low-nutrient environments to which they were specialized. Growth to large size and delayed maturation in fusulinoideans might have been enabled by the late Paleozoic hyperoxic atmosphere and the widespread development of oligotrophic, carbonate platform and shelf environments. The late Paleozoic history of foraminiferal diversification was influenced also by closure of the Rheic Ocean beginning in Late Mississippian time. Foraminiferal associations on opposite sides of Pangea exhibited relatively high similarity prior to the closure, but then similarity decreased steadily after destruction of the subequatorial marine corridor. Arctic-Eurasian and North American associations were nearly isolated from one another throughout the main burst of fusulinoidean diversification, so that parallel lineages developed independently in the two regions, resulting in many instances of convergence.

The middle Carboniferous was an interval of global change when the climate was transitioning from greenhouse to icehouse conditions. Field collections of paleotropical brachiopod assemblages across the Mississippian/Pennsylvanian boundary reveal a taxonomic turnover event in which the overall diversity structure is conserved, despite an apparent regional extinction of 63% of latest Mississippian genera and an apparent regional origination of 50% of earliest Pennsylvanian. An analysis of the global ranges of the brachiopods encountered in the field reveals that turnover was driven primarily by extirpation and immigration rather than true extinctions and originations. Taxonomic richness and evenness are indistinguishable between the latest Mississippian and earliest Pennsylvanian stages. Additive diversity partitioning shows that the within-collection, between-collections (i.e., within-bed), and between-bed diversity components do not change across the Mississippian/Pennsylvanian boundary for richness or evenness. Rank-abundance plots of genera show the same distribution for both stages, but with no correlation between the Mississippian abundances of range-through genera and their abundance in the Pennsylvanian. Detrended correspondence analysis shows a major change in taxonomic composition across that Mississippian/Pennsylvanian boundary and consistency in the general gradient along which genera were distributed. An estimation of spatio-temporal heterogeneity of taxonomic composition within each stage reveals that the earliest Pennsylvanian was significantly more homogeneous. These results suggest that middle Carboniferous brachiopod assemblages from tropical shallow-water carbonate platform settings were organized by some factor that was independent of the specific taxa present. Furthermore, the increased homogeneity in taxonomic composition in the Morrowan did not affect the overall diversity structure. Strong competitive interactions among taxa do not appear to be important in determining the taxonomic compositions and abundances of brachiopod stage-level assemblages.

The excellent fossil record of conodonts represents an ideal, yet underutilized, resource for resolving fundamental issues of pattern and process in evolutionary theory. However, this potential has not been exploited because the quantitative understanding of the evolution of conodont element morphology is limited. This work applies standardized morphometric protocols to skeletal elements belonging to the conodont Pterospathodus, derived from a densely sampled section from Estonia. It has established a robust quantitative framework for morphological variation in Pterospathodus, permitting statistical analysis of the current qualitative hypotheses of evolutionary pattern within this genus for the first time. Apparent directional trends were statistically compared with patterns expected for directional evolution, an unbiased random walk and stasis, using maximum-likelihood model fitting, rescaled range analysis, and the runs test. Results confirmed the presence of trends in size and shape change through time, providing an example of convincing directional morphological change in a fossil lineage. The morphometric analyses have also allowed quantitative investigation of ontogenetic processes in Pterospathodus, suggesting that allometric repatterning was the proximal mechanism responsible for mediating the observed shifts in morphology through time. The results have demonstrated that conodonts represent an important resource for understanding evolutionary pattern and process in the fossil record.

Pterosaurs were the first flying vertebrates and formed important components of terrestrial and marginal marine ecosystems during the Mesozoic. They became extinct during the latest Cretaceous (latest Maastrichtian), at, or near, the Cretaceous/Paleogene boundary, following an apparent decline in diversity in the Late Cretaceous. This reduction in species richness has been linked to the ecological radiation of birds in the Early Cretaceous and the proposal that birds competitively excluded pterosaurs from many key niches. However, although competition is often posited as a causal mechanism for many of the clade-clade replacements observed in the fossil record, these hypotheses are rarely tested. Here we present a detailed examination of pterosaur diversity through time, including both taxic and phylogenetically corrected diversity estimates and comparison of these estimates with a model describing temporal variation in the number of pterosaur-bearing formations (a proxy for rock availability). Both taxic and phylogenetic diversity curves are strongly correlated with numbers of pterosaur-bearing formations, suggesting that a significant part of the signal contained within pterosaur diversity patterns may be controlled by geological and taphonomic megabiases rather than macroevolutionary processes. There is no evidence for a long-term decline in pterosaur diversity through the Cretaceous, although a reduction in morphological, ecological, and phylogenetic diversity does appear to have occurred in the latest Cretaceous. Competitive replacement of pterosaurs by birds is difficult to support on the basis of diversity patterns.

Numerous methods have been developed to estimate the position of a mass extinction boundary while accounting for the incompleteness of the fossil record. Here we describe the point estimator and confidence interval for the extinction that are optimal under the assumption of uniform preservation and recovery potential, and independence among taxa. First, one should pool the data from all taxa into one combined “supersample.” Next, one can then apply methods proposed by Strauss and Sadler (1989) for a single taxon. This gives the optimal point estimator in the sense that it has the smallest variance among all possible unbiased estimators. The corresponding confidence interval is optimal in the sense that it has the shortest average width among all possible intervals that are invariant to measurement scale. These optimality properties hold even among methods that have not yet been discovered. Using simulations, we show that the optimal estimators substantially improve upon the performance of other existing methods. Because the assumptions of uniform recovery and independence among taxa are strong ones, it is important to assess to what extent they are satisfied by the data. We demonstrate the use of probability plots for this purpose. Finally, we use simulations to explore the sensitivity of the optimal point estimator and confidence interval to nonuniformity and lack of independence, and we compare their performance under these conditions with existing methods. We find that nonuniformity strongly biases the point estimators for all methods studied, inflates their standard errors, and degrades the coverage probabilities of confidence intervals. Lack of independence has less effect on the accuracy of point estimates as long as recovery potential is uniform, but it, too, inflates the standard errors and degrades confidence interval coverage probabilities.

Paleobiological phylogenies often contain contrasting biological information to phylogenies based on extant species. Available software is primarily based on a present-day view of the world, however. Here, we present freeware to visualize phylogenies that is more suitable for the needs of paleobiologists, providing flexibility in how stratigraphic uncertainty, the geological timescale, and ancestor-descendant relationships are depicted.