The billion-dollar case for sustaining palaeontology's digital databases.

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth‐death models has made it possible to detect their signature based on extant‐taxa phylogenies. Most birth‐death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree (“single pulse” approach), in contrast to the paleontological record, where MEEs have a time duration. Here, we explore the power of a Bayesian Birth‐Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a “time‐slice” approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on the phylogeny's size and MEE intensity. Comparisons of BDSKY with the single‐pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates.

Integrated biostratigraphy based on planktonic foraminifera and dinoflagellates across the Cretaceous/Paleogene (K/Pg) transition at the Izeh section (SW Iran)

Numerous environmental and intrinsic biotic factors have been sought to explain patterns in diversity and turnover. Using taxonomically vetted and sampling-standardized data sets of more than 50,000 taxonomic occurrences in the Paleobiology Database (PaleoDB) we tested whether habitat breadth predicts genus durations and diversity dynamics of marine Mesozoic bivalves, and whether this effect is independent of the well-known positive relationship between geographic range and longevity. We defined the habitat breadth of a genus as a function of its realized ranges in water depth, substrate type, and grain size of the substrate. Our analysis showed that mean values of extinction and origination rates are significantly higher for narrowly adapted genera compared to broadly adapted genera, with differences being evident in all analyzed stratigraphic intervals. Linear models showed that both geographic range and habitat breadth have an independent effect on genus durations and on diversity dynamics. These results reaffirm the role of geographic range and furthermore suggest that habitat breadth is an equally important key predictor of extinction risk and origination probability in Mesozoic marine bivalves. Habitat generalists, regardless of their geographic range, are generally less prone to extinction. Conversely, widely distributed genera that are more specialized may be more endangered than one would expect from their geographic range alone. Extinction rates tend to be higher for specialized genera in both background and mass extinctions, suggesting that wide habitat breadth universally buffers against extinction. The trajectories of origination rates through time differ from those of extinction rates. Whereas there is no pronounced ecological selectivity in origination in the Triassic and most of the Jurassic, Cretaceous origination rates are higher for specialized genera. This may best be explained by diversity-dependence. When diversity levels reach a critical point a further increase in diversity is achieved by elevated origination rates of more specialized forms.

Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates. We introduce divDyn, a new r package that facilitates the calculation of taxonomic richness, extinction and origination rates from time‐binned fossil data. State‐of‐the‐art counting protocols, and sampling standardization functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by environmental affinity. Using divDyn, we display Phanerozoic‐scale diversity dynamics of marine invertebrates. With the help of the core function and standard subsampling options, we revisit the hypothesis of declining taxonomic rates over time, mass extinctions and equilibrial diversity dynamics and assess their methodological dependency. Our results suggest that rates declined only over the early Phanerozoic, only three mass extinctions stand out clearly, and evidence of equilibrial dynamics is dependent on the used methods. The modular and fast implementation of published methods ensures traceability, reproducibility and comparability of future studies.

According to when they attained high diversity, major taxa of marine animals have been clustered into three groups, the Cambrian, Paleozoic, and Modern Faunas. Because the Cambrian Fauna was a relatively minor component of the total fauna after mid-Ordovician time, the Phanerozoic history of marine animal diversity is largely a matter of the fates of the Paleozoic and Modern Faunas. The fact that most late Cenozoic genera belong to taxa that have been radiating for tens of millions of years indicates that the post-Paleozoic increase in diversity indicated by fossil data is real, rather than an artifact of improvement of the fossil record toward the present.Assuming that ecological crowding produced the so-called Paleozoic plateau for family diversity, various workers have used the logistic equation of ecology to model marine animal diversification as damped exponential increase. Several lines of evidence indicate that this procedure is inappropriate. A plot of the diversity of marine animal genera through time provides better resolution than the plot for families and has a more jagged appearance. Generic diversity generally increased rapidly during the Paleozoic, except when set back by pulses of mass extinction. In fact, an analysis of the history of the Paleozoic Fauna during the Paleozoic Era reveals no general correlation between rate of increase for this fauna and total marine animal diversity. Furthermore, realistically scaled logistic simulations do not mimic the empirical pattern. In addition, it is difficult to imagine how some fixed limit for diversity could have persisted throughout the Paleozoic Era, when the ecological structure of the marine ecosystem was constantly changing. More fundamentally, the basic idea that competition can set a limit for marine animal diversity is incompatible with basic tenets of marine ecology: predation, disturbance, and vagaries of recruitment determine local population sizes for most marine species. Sparseness of predators probably played a larger role than weak competition in elevating rates of diversification during the initial (Ordovician) radiation of marine animals and during recoveries from mass extinctions. A plot of diversification against total diversity for these intervals yields a band of points above the one representing background intervals, and yet this band also displays no significant trend (if the two earliest intervals of the initial Ordovician are excluded as times of exceptional evolutionary innovation). Thus, a distinctive structure characterized the marine ecosystem during intervals of evolutionary radiation—one in which rates of diversification were exceptionally high and yet increases in diversity did not depress rates of diversification.Particular marine taxa exhibit background rates of origination and extinction that rank similarly when compared with those of other taxa. Rates are correlated in this way because certain heritable traits influence probability of speciation and probability of extinction in similar ways. Background rates of origination and extinction were depressed during the late Paleozoic ice age for all major marine invertebrate taxa, but remained correlated. Also, taxa with relatively high background rates of extinction experienced exceptionally heavy losses during biotic crises because background rates of extinction were intensified in a multiplicative manner; decimation of a large group of taxa of this kind in the two Permian mass extinctions established their collective identity as the Paleozoic Fauna.Characteristic rates of origination and extinction for major taxa persisted from Paleozoic into post-Paleozoic time. Because of the causal linkage between rates of origination and extinction, pulses of extinction tended to drag down overall rates of origination as well as overall rates of extinction by preferentially eliminating higher taxa having relatively high background rates of extinction. This extinction/origination ratchet depressed turnover rates for the residual Paleozoic Fauna during the Mesozoic Era. A decline of this fauna's extinction rate to approximately that of the Modern Fauna accounts for the nearly equal fractional losses experienced by the two faunas in the terminal Cretaceous mass extinction.Viewed arithmetically, the fossil record indicates slow diversification for the Modern Fauna during Paleozoic time, followed by much more rapid expansion during Mesozoic and Cenozoic time. When viewed more appropriately as depicting geometric—or exponential—increase, however, the empirical pattern exhibits no fundamental secular change: the background rate of increase for the Modern Fauna—the fauna that dominated post-Paleozoic marine diversity—simply persisted, reflecting the intrinsic origination and extinction rates of constituent taxa. Persistence of this overall background rate supports other evidence that the empirical record of diversification for marine animal life since Paleozoic time represents actual exponential increase. This enduring rate makes it unnecessary to invoke environmental change to explain the post-Paleozoic increase of marine diversity.Because of the resilience of intrinsic rates, an empirically based simulation that entails intervals of exponential increase for the Paleozoic and Modern Faunas, punctuated by mass extinctions, yields a pattern that is remarkably similar to the empirical pattern. It follows that marine animal genera and species will continue to diversify exponentially long into the future, barring disruption of the marine ecosystem by human-induced or natural environmental changes.

Mass extinctions are rare but catastrophic events that profoundly disrupt biodiversity. Widelyaccepted consequences of mass extinctions, such as biodiversity loss and the appearance of temporary ‘disaster taxa,’ imply that nested species-area relationships (SARs, or how biodiversity scales with area) should change dramatically across these events: specifically, both the slope (reflecting the rate of accumulation of new species with increasing area) and intercept (reflecting the density of species at local scales) of the power-law relationship should decrease. However, these hypotheses have not been tested, and the contribution of variation in the SAR to diversity dynamics in deep time has been neglected. We use fossil data to quantify nested SARs in North American terrestrial tetrapods through the Cretaceous-Paleogene (K/Pg) mass extinction (Campanian–Ypresian). SARs vary substantially through time and among groups. In the pre-extinction interval (Maastrichtian), unusually shallow SAR slopes (indicating low beta diversity or provinciality) drive low total regional diversity in dinosaurs, mammals and other tetrapods. In the immediate post-extinction interval (Danian), the explosive diversification of mammals drove high regional diversity via a large increase in SAR slope (indicating higher beta diversity or provinciality), and only a limited increase in SAR intercept (suggesting limited diversity change at small scales). This contradicts the expectation that post-extinction biotas should be regionally homogenized by the spread of disaster taxa and impoverished by diversity loss. This early post-extinction increase in SAR slope was followed in the Thanetian–Selandian (∼4.4. myr later) by increases in the intercept, indicating that diversity dynamics at local and regional scales did not change in synchrony. These results demonstrate the importance of SARs for understanding deep-time diversity dynamics, particularly the spatial dynamics of recovery from mass extinctions.

The fossil records of the Northern Caucasus (southwestern Russia) provide an exceptional opportunity to reveal the evolution of brachiopods during the Callovian-Albian time interval and to evaluate the regional evidence for a Jurassic/Cretaceous mass extinction. Stratigraphic ranges of 119 species, 52 genera, 25 families, 13 superfamilies, and 2 orders of brachiopods are considered to document the main patterns of their diversity dynamics. The total number of taxa was high in the Callovian-Oxfordian, then dropped in the Kimmeridgian, increased again in the Tithonian, decreased significantly in the Berriasian, and remained relatively low until the end of the Early Cretaceous except for a minor peak in the Barremian. Species, genera, families, and superfamilies of brachiopods declined remarkably in the Northern Caucasus in the Berriasian, which is regional evidence for a Jurassic/Cretaceous mass extinction. Both an acceleration in disappearance rate and a drop in appearance rate contributed to this collapse. Recovery began in the Valanginian-Hauterivian, but it was not completed at the level of species. Transgressions/regressions, growth of the carbonate platform, a salinity crisis, and oxygen depletion were important controls on the brachiopod diversity dynamics in the Northern Caucasus. A regressive episode around the Jurassic-Cretaceous transition seems to be a plausible cause of the relevant brachiopod decline. A comparison of changes in the total number of brachiopod taxa between the Neo-Tethys Ocean and the Alpine Tethys Ocean shows some difference, but both domains provide evidence for a Jurassic/Cretaceous mass extinction, which was less severe in the Swiss Alps and the Jura Mountains (Alpine Tethys) than in the Northern Caucasus (Neo-Tethys).

Fossils are crucial for accurately dating phylogenetic trees because their ages provide vital constraints on the timing of macroevolutionary events, and their morphological characters offer key information on evolutionary rates and phylogenetic positions. The fossilized birth-death (FBD) process is a diversification model that incorporates both extant and extinct species, serving as a tree prior that seamlessly integrates fossils into phylogenetic inference. While the FBD model can account for mass extinctions, which caused rapid, widespread organismal loss, few studies have utilized FBD models incorporating these events in phylogenetic inference. This is likely because the detectability of mass extinctions and their impact on phylogenetic inference remain unclear. Through simulations, we assessed the influence of mass extinctions on divergence time and topology inference and evaluated the detectability of mass extinction signals in total-evidence dating. We examined three FBD tree priors: without mass extinction, with known mass extinction time and survival probability, and with known mass extinction time but unknown survival probability. Our results show that the FBD model with known mass extinction time and unknown survival probability was able to reliably detect mass extinctions when they occurred, and correctly refrained from detecting mass extinctions when they were absent. Moreover different FBD models generate similar divergence time and tree topology errors. Even when the FBD model used for tree inference did not explicitly account for mass extinction events, signals of mass extinction were still detectable on the resulting MCC trees. The accuracy of the detection was similar to the one obtained from MCC trees inferred using an FBD model that includes mass extinction parameters. We also reduced the fossilization rate and the number of morphological characters, obtaining results consistent with the aforementioned findings. However, reducing the fossilization rate decreased the accuracy of detecting mass extinctions when they occurred, and reducing the number of morphological characters decreased the accuracy of divergence time inference. Furthermore, we adjusted the priors for the existence of mass extinction and the survival probability of mass extinction. We found that the prior for the existence of mass extinction had no effect on inference, whereas the prior for the survival probability of mass extinction significantly influenced both the detection of mass extinctions and the estimation of survival probabilities. It should be noted that our simulations represent a largely best-case scenario with constant diversification rates; empirical datasets with more complex evolutionary histories may present additional challenges for mass extinction detection. Finally, we applied these models to an empirical dataset of crinoids and found that, consistent with our simulation results, the inclusion of a mass extinction event in the tree prior had a negligible impact on the inferred topologies and divergence times at the whole-tree level, although small variations on individual node estimates were observed in the empirical analyses.

Four Commentaries on the Pope’s Message on Climate Change and Income Inequality. IV. Pope Francis’ Encyclical Letter Laudato Si’, Global Environmental Risks, and the Future of Humanity.

Diversity dynamics of the Permian–Triassic land plants in South China are studied by analyzing paleobotanical data. Our results indicate that the total diversity of land-plant megafossil genera and species across the Permian/Triassic boundary (PTB) of South China underwent a progressive decline from the early Late Permian (Wuchiapingian) to the Early-Middle Triassic. In contrast, the diversity of land-plant microfossil genera exhibited only a small fluctuation across the PTB of South China, showing an increase at the PTB. Overall, land plants across the PTB of South China show a greater stability in diversity dynamics than marine faunas. The highest extinction rate (90.91%) and the lowest origination rate (18.18%) of land-plant megafossil genera occurred at the early Early Triassic (Induan), but the temporal duration of the higher genus extinction rates (>60%) in land plants was about 23.4 Myr, from the Wuchiapingian to the early Middle Triassic (Anisian), which is longer than that of the coeval marine faunas (3–11 Myr). Moreover, the change of genus turnover rates in land-plant megafossils steadily fluctuated from the late Early Permian to the Late Triassic. More stable diversity and turnover rate as well as longer extinction duration suggest that land plants near the PTB of South China may have been involved in a gradual floral reorganization and evolutionary replacement rather than a mass extinction like those in the coeval marine faunas.

Over 40years ago, Raup and Sepkoski identified five episodes of elevated extinction in the marine fossil record that were thought to be statistically distinct, thus warranting the term the "Big Five" mass extinctions. Since then, the term has become part of standard vocabulary, especially with the naming of the current biodiversity crisis as the "sixth mass extinction." However, there is no general agreement on which time intervals should be viewed as mass extinctions, in part because the Big Five turn out not to be statistically distinct from background rates of extinction, and in part, because other intervals of time have even higher extinction rates, in the Cambrian and early Ordovician. Nonetheless, the Big Five represent the five largest events since the early Ordovician, including in analyses that attempt to compensate for the incompleteness of the fossil and rock records. In the last 40years, we have learned a great deal about the causes of many of the major and minor extinction events and are beginning to unravel the mechanisms that translated the initial environmental disturbances into extinction. However, for many of the events, further understanding will require going back to the outcrop, where the patchy distribution of environments and pervasive temporal gaps in the rock record challenge our ability to establish true extinction patterns. As for the current biodiversity crisis, there is no doubt that the rate of extinction is among the highest ever experienced by the biosphere, perhaps the second highest after the end-Cretaceous bolide impact. However (and fortunately), the absolute number of extinctions is still relatively small - there is still time to prevent this becoming a genuine mass extinction. Given the arbitrariness of calling out the Big Five, perhaps the current crisis should be called the "incipient Anthropocene mass extinction" rather than the "sixth mass extinction."

<p>After 42 years, the debate over the end-Cretaceous mass extinction still rages with arguments made for Chicxulub impact and Deccan volcanism as the real cause of this catastrophe. We briefly review the evidence for the pre-KPB age of the Chicxulub impact based on the primary impact spherule layer, which we link to Deccan volcanism based on the global mercury (Hg) fallout from Deccan eruptions. Mercury from volcanic eruptions is distributed around the world during its atmospheric residence time of 6 months to one year, after which it rains out over land and oceans. Major pulsed volcanic eruptions yield high Hg concentrations during fallout, which we termed Extreme Events (EE). We identified 20 of these Hg extreme events during the last 550 ky of the late Maastrichtian in sequences from Tunisia, Israel, Egypt and Mexico. At Elles, Tunisia, we dated these events (EE1 to EE20) based on orbital cyclicity and biostratigraphy with precision of one cycle (20 ky) with an error margin of 10-20 ky (Keller et al., 2020). We linked these dates to U-Pb zircon ages of the Deccan Traps with similarly high precision (Schoene et al., 2019). The resulting mercury stratigraphy yielded excellent age control linking Deccan eruption pulses across the globe. Results from two localities in NE Mexico revealed the Chicxulub impact crashed into Yucatan above the base of the <em>Plummerita hantkeninoides</em> zone CF1 and EE6 at about 200 ky prior to the KPB mass extinction. This deposit is unlike any other of the over 100 reworked spherule layers mixed with abundant shallow water debris. This oldest and primary impact spherule layer consists of compressed pure melt rock glass and glass spherules that settled rapidly to the deep seafloor. The environmental effects of this large impact were short-lived and caused no species extinctions. The effects of this 10 km-sized bolide impact had been vastly overrated.</p><p>The KPB mass extinction was identified between the longest lava flows across India to the Krishna-Godavari Basin and into the Bay of Bengal. Based on peak Hg fallout, we identified these volcanic eruptions as the largest most rapid sequence of pulsed events in Tunisia, Israel, Egypt and Mexico, all coinciding with the rapid mass extinction observed in India. The mass extinction began with the onset and ramp-up of pulsed Deccan eruptions resulting in toxic and acidic waters that caused 50% species extinctions. Extremely rapid large pulsed eruptions followed and resulted in the longest lave flows and hyperthermal warming that caused the rapid demise of all but one species, the disaster opportunist <em>Guembelitria cretacea</em>. Deccan eruptions quickly diminished after the mass extinction and climate cooled rapidly giving rise to the first new species. Volcanic eruptions remained low and cool temperatures persisted through the early Paleocene interrupted by a smaller eruption phase about 100 ky after the mass extinction.  These data reveal that Deccan volcanism caused the KPB mass extinction without any extraterrestrial aid.</p><p>Keywords: Chicxulub, Deccan Volcanism, Mass Extinction, Mercury Stratigraphy, Age control</p><p> </p>

Knowledge gaps and missing links in understanding mass extinctions: Can mathematical modeling help?

Extinction in the Anthropocene.

In this paper, I develop efficient tools to simulate trees with a fixed number of extant species. The tools are provided in my open source R-package TreeSim available on CRAN. The new model presented here is a constant rate birth-death process with mass extinction and/or rate shift events at arbitrarily fixed times 1) before the present or 2) after the origin. The simulation approach for case (2) can also be used to simulate under more general models with fixed events after the origin. I use the developed simulation tools for showing that a mass extinction event cannot be distinguished from a model with constant speciation and extinction rates interrupted by a phase of stasis based on trees consisting of only extant species. However, once we distinguish between mass extinction and period of stasis based on paleontological data, fast simulations of trees with a fixed number of species allow inference of speciation and extinction rates using approximate Bayesian computation and allow for robustness analysis once maximum likelihood parameter estimations are available.