The Paleobiology Database is an online, non-governmental, non-profit public resource for paleontological data. It is organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. This is the second edition of the volume designed to be a comprehensive guide for Paleobiology Database users, both General and Contributory. It covers most database uses from data retrieval and mapping to data contribution of all types. It contains numerous examples to illustrate database use as well as definitions of terms and additional links to numerous other sources. We hope that this user guide will help all users access the great volume of data in the Paleobiology Database and lead others to start and continue to add data to the system.

The physical, biogeochemical, and ecological properties of the modern seafloor are extensively shaped by the activities of burrowing and sediment-mixing animals, processes collectively known as bioturbation. Bioturbation is primarily recorded by homogenized sediments of the seafloor mixed layer and the underlying transition layer of discrete burrows. Although these two zones can be readily measured today, there has been limited understanding of how the mixed and transition layers evolved over the Phanerozoic since animals first began to extensively colonize the seafloor. Here, we provide a record for the depths of the sedimentary mixed and transition layers through the Phanerozoic. We find that although deepening of the sediment mixed layer spanned hundreds of millions of years, a deep transition layer was established as early as the Cambrian and did not further deepen until the Mesozoic-trajectories reflecting evolutionary radiations, changes in nutrient cycling, and alleviation of oxygen stress.

Understanding the role of humans as 'ecosystem engineers' requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no conceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional definitions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term - 'Earth system engineering' - to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate this framework using the fossil record, and show how it can be applied across the tree of life, and throughout Earth history.

This study analyses intriguing tubular fossils derived from the Upper Permian deposits of southern China. The fossils' structure is diagenetically altered by silicification precluding an unambiguous systematic assignment. However, the general morphology and tube architecture strongly imply a relationship with tube-dwelling organisms of different affinity such as tentaculitoids and tube-dwelling polychaetes. Due to the simple morphology of the tubes lacking any ornamentation, as well as the encrustation mode of some individuals, the investigated specimens most likely belong to early sabellids. Although calcareous sabellids persisted since the Middle Permian, their distribution and abundance during the Permian were confined to a single occurrence. If the fossils studied indeed represent sabellids, the global range and abundance of this group during the late Palaeozoic was likely more extensive than currently assumed.

There is a strong relationship between metazoan body size and extinction risk. However, the size selectivity and underlying mechanisms in foraminifera, a common marine protozoa, remain controversial. Here, we found that foraminifera exhibit size-dependent extinction selectivity, favoring larger groups (>7.4 log 10 cubic micrometer) over smaller ones. Foraminifera showed significant size selectivity in the Guadalupian-Lopingian, Permian-Triassic, and Cretaceous-Paleogene extinctions where the proportion of large genera exceeded 50%. Conversely, in extinctions where the proportion of large genera was <45%, foraminifera displayed no selectivity. As most of these extinctions coincided with oceanic anoxic events, we conducted simulations to assess the effects of ocean deoxygenation on foraminifera. Our results indicate that under suboxic conditions, oxygen fails to diffuse into the cell center of large foraminifera. Consequently, we propose a hypothesis to explain size distribution–related selectivity and Lilliput effect in animals relying on diffusion for oxygen during past and future ocean deoxygenation, i.e., oxygen diffusion distance in body.

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to ‘predict’ the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.

The Paleobiology Database is an online, non-governmental, non-profit public resource for paleontological data. It is organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. This volume is designed to be a comprehensive guide for Paleobiology Database users, both General and Contributory. It covers most database uses from data retrieval and mapping to data contribution of all types. It contains numerous examples to illustrate database use as well as definitions of terms and additional links to numerous other sources. We hope that this user guide will help all users access the great volume of data in the Paleobiology Database and lead others to start and continue to add data to the system.

AbstractUnderstanding spatial variation in origination and extinction can help to unravel the mechanisms underlying macroevolutionary patterns. Although methods have been developed for estimating global origination and extinction rates from the fossil record, no framework exists for applying these methods to restricted spatial regions. Here, we test the efficacy of three metrics for regional analysis, using simulated fossil occurrences. These metrics are then applied to the marine invertebrate record of the Permian and Triassic to examine variation in extinction and origination rates across latitudes. Extinction and origination rates were generally uniform across latitudes for these time intervals, including during the Capitanian and Permian–Triassic mass extinctions. The small magnitude of this variation, combined with the possibility of its attribution to sampling bias, cautions against linking any observed differences to contrasting evolutionary dynamics. Our results indicate that origination and extinction levels were more variable across clades than across latitudes.

The end-Permian mass extinction was triggered by geologically-rapid carbon release from enormous flood basalt eruptions, the Siberian Traps. This perturbation to the carbon cycle led to a hyperthermal event: considerable temperature increases on land and in the oceans, expansion of oceanic oxygen minimum zones, heavy metal pollution, short-term acid rain and disruption of the ozone layer, and intensification of the hydrologic cycle with shifts in rainfall patterns. If carbon release was sufficiently rapid, the oceans may have suffered a short-lived acidification event. These environmental stresses caused a severe and rapid extinction in the oceans and probably also on land. In the oceans, extinctions occurred in a single pulse lasting < 60,000 years; wiped out all corals and trilobites and most species of brachiopods, crinoids, and bryozoans; and devastated reef ecosystems. Almost no group survived unscathed, but more active organisms that could withstand temperature, oxygen, and pH changes fared better. On land, the timing and severity of extinction are less well constrained, but there was a major disruption to plant communities synchronous with the marine extinction, and likely extinctions among land vertebrates and insects. Although the end-Permian extinction was more severe than other hyperthermals, perhaps because the rate and/or magnitude of environmental disruption were larger, these events can help reveal the environmental and biological consequences of rapid carbon emissions and carbon cycle disruption.

The health of reef-building corals has declined due to climate change and pollution. However, less is known about whether giant clams, reef-dwelling bivalves with a photosymbiotic partnership similar to that found in reef-building corals, are also threatened by environmental degradation. To compare giant clam health against a prehistoric baseline, we collected fossil and modern Tridacna shells from the Gulf of Aqaba, Northern Red Sea. After calibrating daily/twice-daily growth lines from the outer shell layer, we determined that modern individuals of all three species (Tridacna maxima, T. squamosa and T. squamosina) grew faster than Holocene and Pleistocene specimens. Modern specimens also show median shell organic δ15N values 4.2‰ lower than fossil specimens, which we propose is most likely due to increased deposition of isotopically light nitrate aerosols in the modern era. Nitrate fertilization accelerates growth in cultured Tridacna, so nitrate aerosol deposition may contribute to faster growth in modern wild populations. Furthermore, colder winter temperatures and past summer monsoons may have depressed fossil giant clam growth. Giant clams can serve as sentinels of reef environmental change, both to determine their individual health and the health of the reefs they inhabit.

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects-the most diverse group of organisms on Earth-to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new dataset. Permian beetles were dominated by xylophagous stem groups with high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

In the first half of the nineteenth century, a marked shift occurred in our understanding and treatment of the chelicerate fossil record, with the differentiation and recognition of entirely extinct genera for the first time. At the heart of this taxonomic revolution were the Eurypterida (sea scorpions) and Xiphosura (horseshoe crabs), although both groups were in fact considered crustaceans until Lankester's (1881) seminal comparative anatomical study of the extant xiphosuran Limulus Müller, 1785 and modern scorpions. The oldest available eurypterid genus is Eurypterus deKay, 1825; the oldest available fossil arachnid genus name is that of the scorpion Cyclophthalmus Corda, 1835. However, there has been considerable historical confusion over the oldest available fossil xiphosuran genus name, which has been recognized alternately as Belinurus König (with a publication date of either 1820 or 1851) or the synonymous Bellinurus Pictet, 1846. Most recent treatments (e.g., Selden and Siveter, 1987; Anderson and Selden, 1997; Anderson et al., 1997; Lamsdell, 2016, 2021; Bicknell and Pates, 2020) have favored Bellinurus Pictet, 1846 as the available name; however, Haug and Haug (2020) recently argued that Belinurus König, 1820 is valid and has priority, a position then followed by Lamsdell (2020), prompting a reinvestigation of the taxonomic history of the genus. Upon review, it is clear that neither of the previously recognized authorities for Belinurus are accurate and that the two candidate type species for each genus are, in fact, synonyms. Given the convoluted and at times almost illogical history of the competing names, along with the most recent controversy as to which has priority, we present a complete history of the treatment of the genus to resolve the issue.

AbstractBrachiopods dominated the seafloor as a primary member of the Paleozoic fauna. Despite the devastating effects of the end-Permian extinction, the group recovered during the early Mesozoic only to gradually decline from the Jurassic to today. This decline likely had multiple causes, including increased predation and bioturbation-driven substrate disruption, but the role of changing substrate is not well understood. Given the importance of substrate for extant brachiopod habitat, we documented Mesozoic–Cenozoic lithologic preferences and morphological changes to assess how decreasing firm-substrate habitat may have contributed to the brachiopod decline. Compared with bivalves, Mesozoic brachiopods occurred more frequently and were disproportionately abundant in carbonate lithologies. Although patterns in glauconitic or ferruginous sediments are equivocal, brachiopods became more abundant in coarser-grained carbonates and less abundant in fine-grained siliciclastics. During the Jurassic, brachiopod species rarely had abraded beaks but tended to be more convex with a high beak, potentially consistent with a non-analogue lifestyle resting on the seafloor. However, those highly convex morphotypes largely disappeared by the Cenozoic, when more terebratulides had abraded beaks, suggesting closer attachment to hard substrates. Rhynchonellides disproportionately declined to become a minor component of Cenozoic faunas, perhaps because of less pronounced morphological shifts. Trends in lithologic preferences and morphology are consistent with bioturbation-driven substrate disruption, with brachiopods initially using firmer carbonate sediments as refugia before adapting to live primarily attached to hard surfaces. This progressive habitat restriction likely played a role in the final brachiopod decline, as bioturbating ecosystem engineers transformed benthic habitats in the Mesozoic and Cenozoic.