The evolution of powered flight has traditionally been associated with the origin of birds, the most successful clade of modern tetrapods, as exemplified by the nearly 10,000 species alive today. Flight requires a suite of morphological changes to skeletal anatomy to create a light yet resistant framework for an airfoil and advanced nervous motor control. Given the level of morphological integration necessary to create a suitable aerofoil, the origin of flight may be intuitively assumed to be coupled with high evolutionary rates of wing-related morphologies. Here we show that the origin of birds is associated with little or no evolutionary change to the skeletal anatomy of the forelimb, and thus Archaeopteryx is unlikely to be the “Rosetta Stone” for the origin of flight it was once believed to be. Using comparative statistics and time-series analyses on a data set constructed from all known forelimb skeletal anatomy of non-avian theropod dinosaurs and a diverse assemblage of early birds, we demonstrate three focused peaks of rapid forelimb evolution at Tetanurae, Eumaniraptora, and Ornithothoraces. The peaks are not associated with missing data and remain stable under multiple perturbations to the phylogenetic arrangements. Different regions of the forelimbs are demonstrated to have undergone asynchronous periods of evolutionary peaks and stasis. Our results evince a more complicated stepwise mode of forelimb evolution before and after the origin of Aves than previously supposed.

The mammal fauna of the Willwood Formation, central Bighorn Basin, Wyoming, is ideal for paleoecological analysis because it is extensive, well studied, and continuously distributed over sediments representing the first 3 Myr of the early Eocene. The geology of the Bighorn Basin is also well known, providing a precise temporal framework and climatic context for the Willwood mammals. Previous analysis identified three “biohorizons,” based on simple counts of the first and last appearances of species. This study uses species diversity and appearance rates calculated from more extensive collections to approximate the ecological dynamic of the ancient fauna and assess whether the biohorizons were significant turnover events related to recently described climatic variation. Diversity and appearance data collected for this project are extensively corrected for uneven sampling, which varies by two orders of magnitude. Observed, standardized appearance and diversity estimates are subsequently compared with predicted background frequencies to identify significant variation. Important coincident shifts in the biotic parameters demonstrate that ecological change was concentrated in two discrete intervals ≤300 Kyr each that correspond with two of the original biohorizons. The intervals coincide with the onset and reversal of an episode of climate cooling identified directly from Bighorn Basin floras and sediments. Ecological changes inferred from the diversity and turnover patterns at and following the two biohorizons suggest short- and long-term faunal response to shifts in mean annual temperature on the order of 5–8°C.

The end-Guadalupian extinction, at the end of the Middle Permian, is thought to have been one of the largest biotic crises in the Phanerozoic. Previous estimates suggest that the crisis eliminated 58% of marine invertebrate genera during the Capitanian stage and that its selectivity helped the Modern evolutionary fauna become more diverse than the Paleozoic fauna before the end-Permian mass extinction. However, a new sampling-standardized analysis of Permian diversity trends, based on 53731 marine invertebrate fossil occurrences from 9790 collections, indicates that the end-Guadalupian “extinction” was actually a prolonged but gradual decrease in diversity from the Wordian to the end of the Permian. There was no peak in extinction rates; reduced genus richness exhibited by all studied invertebrate groups and ecological guilds, and in different latitudinal belts, was instead driven by a sharp decrease in origination rates during the Capitanian and Wuchiapingian. The global diversity decrease was exacerbated by changes in beta diversity, most notably a reduction in provinciality due to the loss of marine habitat area and a pronounced decrease in geographic disparity over small distances. Disparity over moderate to large distances was unchanged, suggesting that small-scale beta diversity changes may have resulted from compression of bathymetric ranges and homogenization of onshore-offshore faunal gradients stemming from the spread of deep-water anoxia around the Guadalupian/Lopingian boundary. Although tropical invertebrate genera were no more likely than extratropical ones to become extinct, the marked reduction in origination rates during the Capitanian and Wuchiapingian is consistent with the effects of global cooling (the Kamura Event), but may also be consistent with other environmental stresses such as anoxia. However, a gradual reduction in diversity, rather than a sharp end-Guadalupian extinction, precludes the need to invoke drastic extinction mechanisms and indicates that taxonomic loss at the end of the Paleozoic was concentrated in the traditional end-Permian (end-Changhsingian) extinction, which eliminated 78% of all marine invertebrate genera.

Recent research has corroborated the long-held view that the diversity of genera within benthic marine communities has increased from the Paleozoic to the Cenozoic as much as three-to fourfold, after mitigating for such biasing influences as secular variation in time-averaging and environmental coverage. However, these efforts have not accounted for the considerable increase in the availability of unlithified fossiliferous sediments in strata of late Mesozoic and Cenozoic age. Analyses presented here on the Cenozoic fossil record of New Zealand demonstrate that unlithified sediments not only increase the amount of fossil material and hence the observed diversity therein, but they also preserve a pool of taxa that is compositionally distinct from lithified sediments. The implication is that a large component of the difference in estimates of within-community diversity between Paleozoic and Cenozoic assemblages may relate to the increased availability of unlithified sediments in the Cenozoic.

Biophysical modeling and morphologic data from the fossil record were used to investigate the functional significance of changes in thallus morphology during the early evolutionary history of dasycladalean algae (dasyclads), a clade of benthic marine macroalgae. Modeling results indicate that the addition of cylindrical appendages (laterals) to an upright main axis, a key morphological innovation in the evolution of dasyclad thallus form, can provide for large gains in light interception efficiency, near-maximum gains in this regard being achieved when the ratio of total lateral surface area to main axis surface area is 4 or greater. Among the 13 early Paleozoic study taxa, all but one was found to exceed this value. Modeling of surface area to volume ratios for early Paleozoic dasyclads indicates that laterals for these forms conveyed only modest gains in this regard and, therefore, likely played little role in improving nutrient uptake. For survivorship, it appears that increasing thallus complexity by developing laterals conveyed important benefits by imparting both compartmentalization and redundancy, thereby increasing the likelihood that lateral-bearing forms would survive attacks by early mesograzers. Trends and patterns in the fossil record support such a survival-enhancing role for laterals and are consistent with the initial evolution of these structures as an early manifestation of an evolutionary arms race between macroalgae and herbivores initiated near the Proterozoic/Phanerozoic boundary.

The marine faunas of tropical America underwent substantial evolutionary turnover in the past 3 to 4 million years in response to changing environmental conditions associated with the rise of the Isthmus of Panama, but the ecological signature of changes within major clades is still poorly understood. Here we analyze the paleoecology of faunal turnover within the family Pectinidae (scallops) over the past 12 Myr. The fossil record for the southwest Caribbean (SWC) is remarkably complete over this interval. Diversity increased from a low of 12 species ca. 10–9 Ma to a maximum of 38 species between 4 and3 Ma and then declined to 22 species today. In contrast, there are large gaps in the record from the tropical eastern Pacific (TEP) and diversity remained low throughout the past 10 Myr. Both origination and extinction rates in the SWC peaked between 4 and 3 Ma, and remained high until 2–1 Ma, resulting in a 95% species level turnover between 3.5 and 2 Ma. The TEP record was too incomplete for meaningful estimates of origination and extinction rates. All living species within the SWC originated within the last 4 Myr, as evidenced by a sudden jump in Lyellian percentages per faunule from nearly zero up to 100% during this same interval. However, faunules with Lyellian percentages near zero occurred until 1.8 Ma, so that geographic distributions were extraordinarily heterogeneous until final extinction occurred. There were also striking differences in comparative diversity and abundance among major ecological groups of scallops. Free-swimming scallops constituted the most diverse guild throughout most of the last 10 Myr in the SWC, and were always moderately to very abundant. Leptopecten and Argopecten were also highly diverse throughout the late Miocene and early Pliocene, but declined to very few species thereafter. In contrast, byssally attaching scallops gradually increased in both diversity and abundance since their first appearance in our samples from 8–9 Ma and are the most diverse group today. Evolutionary turnover of scallops in the SWC was correlated with strong ecological reorganization of benthic communities that occurred in response to declining productivity and increased development of corals reefs.

Despite extensive paleoecological analyses of spatial and temporal turnover in species composition, the fidelity with which time-averaged death assemblages capture variation in species composition and diversity partitioning of living communities remains unexplored. Do death assemblages vary in composition between sites to a lesser degree than do living assemblages, as would be predicted from time-averaging? And is the higher number of species observed in death relative to living assemblages reduced with increasing spatial scale? We quantify the preservation of spatial and temporal variation in species composition using 11 regional data sets based on samples of living molluscan communities and their co-occurring time-averaged death assemblages. (1) Compositional dissimilarities among living assemblages (LA) within data sets are significantly positively rank-correlated to dissimilarities among counterpart pairs of death assemblages (DA), demonstrating that pairwise dissimilarity within a study area has a good preservation potential in the fossil record. Dissimilarity indices that downplay the abundance of dominant species return the highest live-dead agreement of variation in species composition. (2) The average variation in species composition (average dissimilarity) is consistently smaller in DAs than in LAs (9 of 11 data sets). This damping of variation might arise from DAs generally having a larger sample size, but the reduction by ∼10–20% mostly persists even in size-standardized analyses (4 to 7 of 11 data sets, depending on metric). Beta diversity expressed by the number of compositionally distinct communities is also significantly reduced in death assemblages in size-standardized analyses (by ∼25%). This damping of variation and reduction in beta diversity is in accord with the loss of temporal resolution expected from time-averaging, without invoking taphonomic bias (from differential preservation or postmortem transportation) or sample-size effects. The loss of temporal resolution should directly reduce temporal variation, and assuming time-for-space substitution owing to random walk within one habitat and/or temporal habitat shifting, it also decreases spatial variation in species composition. (3) DAs are more diverse than LAs at the alpha scale, but the difference is reduced at gamma scales because partitioning of alpha and beta components differs significantly between LAs and DAs. This indicates that the effects of time-averaging are reduced with increasing spatial scale. Thus, overall, time-averaged molluscan DAs do capture variation among samples of the living assemblage, but they tend to damp the magnitude of variation, making them a conservative means of inferring change over time or variation among regions in species composition and diversity. Rates of temporal and spatial species turnover documented in the fossil record are thus expected to be depressed relative to the turnover rates that are predicted by models of community dynamics, which assume higher temporal resolution. Finally, the capture by DAs of underlying variation in the LA implies little variation in the net preservation potential of death assemblages across environments, despite the different taphonomic pathways suggested by taphofacies studies.

Although only a few studies have explicitly evaluated live-dead agreement of species and community responses to environmental and spatial gradients, paleoecological analyses implicitly assume that death assemblages capture these gradients accurately. We use nine data sets from modern, relatively undisturbed coastal study areas to evaluate how the response of living molluscan assemblages to environmental gradients (water depth and seafloor type; “environmental component” of a gradient) and geographic separation (“spatial component”) is captured by their death assemblages. We find that:

1. Living assemblages vary in composition either in response to environmental gradients alone (consistent with a species-sorting model) or in response to a combination of environmental and spatial gradients (mass-effect model). None of the living assemblages support the neutral model (or the patch-dynamic model), in which variation in species abundance is related to the spatial configuration of stations alone. These findings also support assumptions that mollusk species consistently differ in responses to environmental gradients, and suggest that in the absence of postmortem bias, environmental gradients might be accurately captured by variation in species composition among death assemblages. Death assemblages do in fact respond uniquely to environmental gradients, and show a stronger response when abundances are square-root transformed to downplay the impact of numerically abundant species and increase the effect of rare species.

2. Species' niche positions (position of maximum abundance) along bathymetric and sedimentary gradients in death assemblages show significantly positive rank correlations to species positions in living assemblages in seven of nine data sets (both square-root-transformed and presence-absence data).

3. The proportion of compositional variation explained by environmental gradients in death assemblages is similar to that of counterpart living assemblages. Death assemblages thus show the same ability to capture environmental gradients as do living assemblages. In some instances compositional dissimilarities in death assemblages show higher rank correlation with spatial distances than with environmental gradients, but spatial structure in community composition is mainly driven by spatially structured environmental gradients.

4. Death assemblages correctly identify the dominance of niche metacommunity models in mollusk communities, as revealed by counterpart living assemblages. This analysis of the environmental resolution of death assemblages thus supports fine-scale niche and paleoenvironmental analyses using molluscan fossil records. In spite of taphonomic processes and time-averaging effects that modify community composition, death assemblages largely capture the response of living communities to environmental gradients, partly because of redundancy in community structure that is inherently associated with multispecies assemblages. The molluscan data sets show some degree of redundancy as evidenced by the presence of at least two mutually exclusive subsets of species that replicate the community structure, and simple simulations show that between-sample relationships can be preserved and remain significant even when a large proportion of species is randomly removed from data sets.

Since David Raup's seminal 1976 work, paleontologists have been aware of the relationship between outcrop area and diversity. By incorporating lithologic data derived from Alexander Ronov and coworkers into our own data on areas of mapped outcrops from worldwide geologic maps, we are able to establish a quantitative connection between area of sedimentary rock exposure and diversity from the same general depositional environments. Significant power-law relations are observed at both global and continental scales of consideration. The addition of data on areas of habitable area estimated from paleogeographic maps does not substantially affect these correlations between outcrop area and diversity, indicating that the relation between outcrop area and diversity is primarily a function of sampling and not a common cause such as sea level. We observe a significant diversity-area effect, first noted by Jack Sepkoski in the marine realm. Unlike Sepkoski's, however, our diversity-area effect appears to play a substantial role in influencing diversity through time; a true global diversity signal appears to be contained in the rock record despite the impacts of variable sampling.

Greater outcrop area can serve to increase estimated diversity by increasing both the sample size and the range of habitats and biogeographic provinces sampled. After standardizing for pure sampling intensity by rarefying the number of taxon occurrences, outcrop area continues to explain a substantial portion of global marine diversity. This indicates that coverage, or sampling from multiple habitats and biogeographic provinces, is even more important than sampling intensity. If we remove the effect of outcrop area from our estimate of global biodiversity, we do not observe a net increase in diversity toward the present, lending support to other studies that have not supported a substantial, long-term global increase in biodiversity during the Phanerozoic.