Although Phanerozoic increases in the global richness, local richness, and evenness of marine invertebrates are well documented, a common explanation for these patterns has been difficult to identify. Evidence is presented here from marine invertebrate communities that there is a Phanerozoic increase in the fundamental biodiversity number (θ), which describes diversity and relative abundance distributions in neutral ecological theory. If marine ecosystems behave according to the rules of Hubbell's Neutral Theory of Biodiversity and Biogeography, the Phanerozoic increase in θ suggests three possible mechanisms for the parallel increases in global richness, local richness, and evenness: (1) an increase in the per-individual probability of speciation, (2) an increase in the area occupied by marine metacommunities, and (3) an increase in the density (per-area abundance) of marine organisms. Because speciation rates have declined over time and because there is no clear evidence for an increase in metacommunity area through the Phanerozoic, the most likely of these is an increase in the spatial density of marine invertebrates over the Phanerozoic, an interpretation supported by previous studies of fossil abundance. This, coupled with a Phanerozoic rise in body size, suggests that an increase in primary productivity through time is the primary cause of Phanerozoic increases in θ, global richness, local richness, local evenness, abundance, and body size.

Multivariate methods such as cluster analysis and ordination are basic to paleoecology, but the messy nature of fossil occurrence data often makes it difficult to recover clear patterns. A recently described faunal similarity index based on the Forbes coefficient improves results when its complement is employed as a distance metric. This index involves adding terms to the Forbes equation and ignoring one of the counts it employs (that of species found in neither of the samples under consideration). Analyses of simulated data matrices demonstrate its advantages. These matrices include large and small samples from two partially overlapping species pools. In a cluster analysis, the widely used Dice coefficient and the Euclidean distance metric both create groupings that reflect sample size, the Simpson index suggests large differences that do not exist, and the corrected Forbes index creates groupings based strictly on true faunal overlap. In a principal coordinates analysis (PCoA) the Forbes index almost removes the sample-size signal but other approaches create a second axis strongly dominated by sample size. Meanwhile, species lists of late Pleistocene mammals from the United States capture biogeographic signals that standard ordination methods do recover, but the adjusted Forbes coefficient spaces the points out more sensibly. Finally, when biome-scale lists for living mammals are added to the data set and extinct species are removed, correspondence analysis misleadingly separates out the biome lists, and PCoA based on the Dice coefficient places them to the edge of the cloud of fossil assemblage data points. PCoA based on the Forbes index places them in more reasonable positions. Thus, only the adjusted Forbes index is able to recover true biological patterns. These results suggest that the index may be useful in analyzing not only paleontological data sets but any data set that includes species lists having highly variable lengths.

Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.

Scleractinian corals have two fundamentally different life strategies, which can be inferred from morphological criteria in fossil material. In the non-photosymbiotic group nutrition comes exclusively from heterotrophic feeding, whereas the photosymbiotic group achieves a good part of its nutrition from algae hosted in the coral's tissue. These ecologic differences arose early in the evolutionary history of corals but with repeated evolutionary losses and presumably also gains of symbiosis since then. We assessed the biodiversity dynamics and environmental occupancy of both ecologic groups to identify times when the evolutionary losses of symbiosis as inferred from molecular analyses might have occurred and if these can be linked to environmental change. Two episodes are likely: The first was in the mid-Cretaceous when non-symbiotic corals experienced an origination pulse and started to become more common in deeper, non-reef habitats and on siliciclastic substrates initiating a long-term offshore trend in occupancy. The second was around the Cretaceous/Paleogene boundary with another origination pulse and increased occupancy of deep-water settings in the non-symbiotic group. Environmental factors such as rapid global warming associated with mid-Cretaceous anoxic events and increased nutrient concentrations in Late Cretaceous—Cenozoic deeper waters are plausible mechanisms for the shift. Turnover rates and durations are not significantly different between the two ecologic groups when compared over the entire history of scleractinians. However, the deep-water shift of non-symbiotic corals was accompanied by reduced extinction rates, supporting the view that environmental occupancy is a prominent driver of evolutionary rates.

The latest Aalenian—early Bajocian time interval (ca. 171-169 Ma) is marked by a global reorganization of oceanic plates with the Central Atlantic opening and the formation of the Pacific plate. This time interval is also marked by a global geochemical perturbation of δ¹³C with a negative excursion at the Aalenian/Bajocian boundary and a positive excursion during the early Bajocian. Evolutionary diversifications of marine invertebrate taxa, namely ammonites, radiolarians, and coccolithophorids, are recorded at that time. Concerning coccolithophorids, this interval witnesses the diversification and expansion of the most successful Mesozoic genus: Watznaueria. In this study, we explore the potential environmental, ecological, and biological forcing at the origin of Watznaueria diversification and its effect on the coccolith assemblages through quantification of the absolute and relative abundances of calcareous nannofossils in two Middle Jurassic key sections: Cabo Mondego (Portugal) and Chaudon-Norante (France). In both sections, we find an increase in nannofossil absolute abundance and flux at the beginning of the lower Bajocian, coeval with an increase in absolute and relative abundances of Watznaueria spp., followed by a plateau in the middle and upper part of the lower Bajocian. The increase of Watznaueria spp. is synchronous with a decrease in relative abundance of other major coccolith taxa, whereas the absolute abundance of these species did not decrease. During the climatically driven early Bajocian eutrophication event, Watznaueria spp. integrated into the calcareous nannoplankton community in two successive evolutionary steps involving first W. contracta and W. colaccicchii, and second W. britannica and W. aff. manivitiae. Step 1 was driven by an increase in niche carrying capacities linked to the early Bajocian eutrophication. Step 2 was driven by specific adaptation of the newly evolved Watznaueria species to bloom in nutrient-rich environments not exploited before. These evolutionary events have initiated the 100-Myr reign of Watznaueria over the calcareous nannoplankton community.

Describing patterns of connectivity among organs is essential for identifying anatomical homologies among taxa. It is also critical for revealing morphogenetic processes and the associated constraints that control the morphological diversification of clades. This is particularly relevant for studies of organisms with skeletons made of discrete elements such as arthropods, vertebrates, and echinoderms. Nonetheless, relatively few studies devoted to morphological disparity have considered connectivity patterns as a level of morphological organization or developed comparative frameworks with proper tools. Here, we analyze connectivity patterns among apical plates in Atelostomata, the most diversified clade among irregular echinoids. The clade comprises approximately 1600 fossil and Recent species (e.g., 25% of post-Paleozoic species of echinoids) and shows high levels of morphological disparity. Plate connectivity patterns were analyzed using tools and statistics of graph theory. To describe and explore the diversity of connectivity patterns among plates, we symbolized each pattern as a graph in which plates are coded as nodes that are connected pairwise by edges. We then generated a comparative framework as a morphospace of connections, in which the disparity of plate patterns observed in nature was mapped and analyzed. Main results show that apical plate patterns are both highly disparate between and within atelostomate groups and limited in number; overall, they also constitute small, compact, and simple structures compared to possible random patterns. Main traits of the evolution of apical plate patterns reveal the existence of strong morphogenetic constraints that are phylogenetically determined. In contrast, evolutionary radiations within atelostomates were accompanied by a clear increase in disparity, suggesting a release of some constraints at the origin of clades.

Decay experiments are becoming a more widespread tool in evaluating the fidelity of the fossil record. Character interpretations of fossil specimens stand to benefit from an understanding of how decay can result in changes in morphology and, potentially, total character loss. We performed a decay experiment for the Class Enteropneusta to test the validity of anatomical interpretations of the Burgess Shale enteropneust Spartobranchus tenuis and to determine how the preservation of morphological features compares with the sequence of character decay in extant analogues. We used three species of enteropneust (Saccoglossus pusillus, Harrimania planktophilus, and Balanoglossus occidentalis) representing the two major families of Enteropneusta. Comparisons between decay sequences suggest that morphological characters decay in a consistent and predictable manner within Enteropneusta, and do not support the hypothesis of stemward slippage. The gill bars and nuchal skeleton were the most decay resistant, whereas the gill pores and pre-oral ciliary organ were unequivocally the most decay prone. Decay patterns support the identification of the nuchal skeleton, gill bars, esophageal organ, trunk, and proboscis in Spartobranchus tenuis and corroborate a harrimaniid affinity. Bias due to the taphonomic loss of taxonomically informative characters is unlikely. The morphologically simple harrimaniid body plan can be seen, therefore, to be plesiomorphic within the enteropneusts. Discrepancies between the sequence of decay in a laboratory setting and fossil preservation also exist. These discrepancies are highlighted not to discredit the use of modern decay studies but rather to underline their non-actualistic nature. Paleoenvironmental variables besides decay, such as the timeframe between death and early diagenesis as well as postmortem transport, are discussed relative to decay data. These experiments reinforce the strength of a comprehensive understanding of decay sequences as a benchmark against which to describe fossil taxa and understand the conditions leading to fossilization.

The extinct shark Carcharocles megalodon is one of the largest marine apex predators ever to exist. Nonetheless, little is known about its body-size variations through time and space. Here, we studied the body-size trends of C. megalodon through its temporal and geographic range to better understand its ecology and evolution. Given that this species was the last of the megatooth lineage, a group of species that shows a purported size increase through time, we hypothesized that C. megalodon also displayed this trend, increasing in size over time and reaching its largest size prior to extinction. We found that C. megalodon body-size distribution was left-skewed (suggesting a long-term selective pressure favoring larger individuals), and presented significant geographic variation (possibly as a result of the heterogeneous ecological constraints of this cosmopolitan species) over geologic time. Finally, we found that stasis was the general mode of size evolution of C. megalodon (i.e., no net changes over time), contrasting with the trends of the megatooth lineage and our hypothesis. Given that C. megalodon is a relatively long-lived species with a widely distributed fossil record, we further used this study system to provide a deep-time perspective to the understanding of the body-size trends of marine apex predators. For instance, our results suggest that (1) a selective pressure in predatory sharks for consuming a broader range of prey may favor larger individuals and produce left-skewed distributions on a geologic time scale; (2) body-size variations in cosmopolitan apex marine predators may depend on their interactions with geographically discrete communities; and (3) the inherent characteristics of shark species can produce stable sizes over geologic time, regardless of the size trends of their lineages.

Body size is one of the most studied phenotypic attributes because it is biologically important and easily measured. Despite a long history of study, however, the pattern of body-size change in diverse higher taxa over the Phanerozoic remains largely unknown because few relevant data sets span more than a single geological period or provide comprehensive, global coverage. In this study, we measured representative specimens of 3414 brachiopod genera illustrated in the Treatise on Invertebrate Paleontology. We applied these size data to stage-resolved stratigraphic ranges from the Treatise and the Paleobiology Database to develop a Phanerozoic record of trends in brachiopod size. Using a model comparison approach, we find that temporal variation in brachiopod size exhibits two distinct modes—a Paleozoic mode of size increase and a post-Paleozoic mode indistinguishable from a random walk. This transition reflects a change in the identities of the most diverse brachiopod orders rather than a shift in mode within any given order. Paleozoic size increase reflects a small, persistent bias toward the origination of new genera larger than those surviving from the previous stage and is identifiable as a statistically supported trend in three orders representing both Class Strophomenata (Order Productida) and Class Rhynchonellata (orders Atrypida and Spiriferida). Extinction exhibits no consistent bias with respect to size. The shift in evolutionary mode across the end-Permian mass extinction adds to long-standing evidence from studies of diversity and abundance that this biotic catastrophe suddenly and permanently altered the evolutionary history of what was, until that time, the most diverse animal phylum on Earth.