Extinctions in the fossil record

Geographic range size is one of the few traits that promoted survivorship during both mass and background extinctions, but the exact reason (or reasons) why a large geographic range confers extinction resistance remains unclear. Proposed explanations have focused on the roles of dispersal ability, climate tolerance, global abundance, and widespread ranges in predicting taxon longevities. This study uses biogeographic data for late Paleozoic brachiopod genera to test the relative contribution of these traits to genus longevities, using simple but accurate proxy measurements. The results demonstrate a strong positive relationship between genus longevity and geographic range size, which is robust to several potential errors. Further, latitudinal range, which predominantly reflects climate tolerance, was no more important than longitudinal range, which predominantly reflects dispersal ability, in predicting genus longevities. Rather, longevities were an outcome of the total number of occurrences, which estimates global abundance, and the advantages of widespread distribution, regardless of which particular traits were responsible for generating the total geographic range. The advantages of a large geographic range were apparent during both background and mass extinctions of late Paleozoic time. Although not statistically significant, there was a tendency for the greatest selectivity to occur in intervals with the lowest extinction rates. The correlation of genus longevity and geographic range size had a profound consequence for the secular pattern of global brachiopod diversity: because the diversity of genera with small geographic ranges was more volatile owing to their correspondingly shorter longevities, global diversity and mean geographic range size paralleled each other almost exactly. Given that the correlation between taxon longevity and geographic range size has also been demonstrated for other taxonomic groups and at other time intervals, these results suggest that global diversity curves compiled from taxonomic databases dominantly reflect changes in the diversity of genera with small geographic ranges.

In order to have the capability for recognizing as many of the extinction and adaptive radiations in the fossil record as possible we should take advantage of the ecostratigraphic approach in our work. This means that we will carefully collect, stratum by stratum, data about the stratigraphic ranges of the individual taxa within individual community groups, biofacies narrowly construed, as opposed to the all too customary habit of lumping taxa from varied community groups together indiscriminately. Following this procedure enables one to far more easily recognize as well, those brief intervals when portions of the ecosystem were restructured, which is important owing to the fact that such restructuring commonly coincides with extinction and adaptive radiation events. It must be recognized that major changes in supra-specific abundance are fully as useful in pin pointing extinction and adaptive radiation events as are mere taxonomic compilations. The ecostratigraphic approach also emphasizes the fact that so-called "known" stratigraphic ranges are commonly far less than "true" ranges except for the small number of abundant genera and their species. Awareness of this last relationship makes it clear that there is no such thing as a "Background Extinction Rate" within any one community group, i.e., biofacies, because the species to species name changes within the genera of each community group are merely evidence of phyletic evolution, not the termination of a lineage. Emphasis is placed on the importance of separating out the major ecosystem components, such as the level bottom from the reef complex when trying to recognize event horizons, i.e., compilations that lump taxa from such ecosystem components together tend to blur the actual nature of the units being mixed together, giving rise to an artifactual background extinction (and adaptive radiation) rate. We now need to far more carefully sample beds above and below suspected event horizons, community group by community group, in order to discover whether or not the taxa involved in radiations and extinctions undergo a sigmoidal change in abundance or not. All of this requires that we carefully evaluate our data against a sound knowledge of classical biostratigraphy, based on the evolutionarily useful data developed during the past century and more.

To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled an ecological trait data set for 18,016 species of terrestrial vertebrates and utilized phylogenetic comparative methods to test which categories of habitat association, mode of locomotion, and feeding mode best predicted extinction risk.We also examined the individual categories of the International Union for Conservation of Nature Red List extinction drivers (e.g., agriculture and logging) threatening each species and determined the greatest threats for each of the four terrestrial vertebrate groups.We then quantified the sum of extinction drivers threatening each species to provide a multistressor perspective on threat.Cave dwelling amphibians (p < 0.01), arboreal quadrupedal mammals (all of which are primates) (p < 0.01), aerial and scavenging birds (p < 0.01), and pedal (i.e., walking) squamates (p < 0.01) were all disproportionately threatened with extinction in comparison with the other assessed ecological traits.Across all threatened vertebrate species in the study, the most common risk factors were agriculture, threatening 4491 species, followed by logging, threatening 3187 species, and then invasive species and disease, threatening 2053 species.Species at higher risk of extinction were simultaneously at risk from a greater number of threat types.If left unabated, the disproportionate loss of species with certain functional traits and increasing anthropogenic pressures are likely to disrupt ecosystem functions globally.A shift in focus from species-to trait-centric conservation practices will allow for protection of at-risk functional diversity from regional to global scales.

Mass extinctions are important to macroevolution not only because they involve a sharp increase in extinction intensity over “background” levels, but also because they bring a change in extinction selectivity, and these quantitative and qualitative shifts set the stage for evolutionary recoveries. The set of extinction intensities for all stratigraphic stages appears to fall into a single right-skewed distribution, but this apparent continuity may derive from failure to factor out the well-known secular trend in background extinction: high early Paleozoic rates fill in the gap between later background extinction and the major mass extinctions. In any case, the failure of many organism-, species-, and clade-level traits to predict survivorship during mass extinctions is a more important challenge to the extrapolationist premise that all macroevolutionary processes are simply smooth extensions of microevolution. Although a variety of factors have been found to correlate with taxon survivorship for particular extinction events, the most pervasive effect involves geographic range at the clade level, an emergent property independent of the range sizes of constituent species. Such differential extinction would impose “nonconstructive selectivity,” in which survivorship is unrelated to many organismic traits but is not strictly random. It also implies that correlations among taxon attributes may obscure causation, and even the focal level of selection, in the survival of a trait or clade, for example when widespread taxa within a major group tend to have particular body sizes, trophic habits, or metabolic rates. Survivorship patterns will also be sensitive to the inexact correlations of taxonomic, morphological, and functional diversity, to phylogenetically nonrandom extinction, and to the topology of evolutionary trees. Evolutionary recoveries may be as important as the extinction events themselves in shaping the long-term trajectories of individual clades and permitting once-marginal groups to diversify, but we know little about sorting processes during recovery intervals. However, both empirical extrapolationism (where outcomes can be predicted from observation of pre- or post-extinction patterns) and theoretical extrapolationism (where mechanisms reside exclusively at the level of organisms within populations) evidently fail during mass extinctions and their evolutionary aftermath. This does not mean that conventional natural selection was inoperative during mass extinctions, but that many features that promoted survivorship during background times were superseded as predictive factors by higher-level attributes. Many intriguing issues remain, including the generality of survivorship rules across extinction events; the potential for gradational changes in selectivity patterns with extinction intensity or the volatility of target clades; the heritability of clade-level traits; the macroevolutionary consequences of the inexact correlations between taxonomic, morphological, and functional diversity; the factors governing the dynamics and outcome of recoveries; and the spatial fabric of extinctions and recoveries. The detection of general survivorship rules—including the disappearance of many patterns evident during background times—demonstrates that studies of mass extinctions and recovery can contribute substantially to evolutionary theory.

How quickly does biodiversity rebound after extinctions? Palaeobiologists have examined the temporal, taxonomic and geographic patterns of recovery following individual mass extinctions in detail, but have not analysed recoveries from extinctions throughout the fossil record as a whole. Here, we measure how fast biodiversity rebounds after extinctions in general, rather than after individual mass extinctions, by calculating the cross-correlation between extinction and origination rates across the entire Phanerozoic marine fossil record. Our results show that extinction rates are not significantly correlated with contemporaneous origination rates, but instead are correlated with origination rates roughly 10 million years later. This lagged correlation persists when we remove the 'Big Five' major mass extinctions, indicating that recovery times following mass extinctions and background extinctions are similar. Our results suggest that there are intrinsic limits to how quickly global biodiversity can recover after extinction events, regardless of their magnitude. They also imply that today's anthropogenic extinctions will diminish biodiversity for millions of years to come.

ABSTRACTUnderstanding the environmental factors determining the distribution of species with different range sizes can provide valuable insights for evolutionary ecology and conservation biology in the face of expected climate change. However, little is known about what determines the variation in geographical and elevational ranges of alpine and subalpine plant species. Here, we examined the relationship between geographical and elevational range sizes for 80 endemic rhododendron species in China using Spearman’s rank-order correlation. We ran the species distribution model – maximum entropy modelling (MaxEnt) – with 27 environmental variables. The importance of each variable to the model prediction was compared for species groups with different geographical and elevational range sizes. Our results showed that the correlation between geographical and elevational range sizes of rhododendron species was not significant. Climate-related variables were found to be the most important factors in shaping the distributional ranges of alpine and subalpine plant species across China. Species with geographically and elevationally narrow ranges had distinct niche requirements. For geographical ranges, the narrow-ranged species showed less tolerance to niche conditions than the wide-ranged species. For elevational ranges, compared with the wide-ranged species, the narrow-ranged species showed an equivalent niche breadth, but occurred at different niche position along the environmental gradient. Our findings suggest that over large spatial extents the elevational range size can be a complementary trait of alpine and subalpine plant species to geographical range size. Climatic niche breadth, especially the range of seasonal variability, can explain species’ geographical range sizes. Changes in climate may influence the distribution of rhododendrons, with the effects likely being felt most by species with either a narrow geographical or narrow elevational range.

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.

Based on fossil mammals from North America, extinction rates since the last mass extinction, but before human influences, are estimated at 0.4 species/species/million years, which implies a species typically persisted for about 2.5 million years. The background extinction rate has been punctuated by mass extinctions, which are defined as more than 75% of species in the fossil record going extinct over a relatively short period of time, the last of which was 66 million years ago. Over the past 50,000 years humans have caused extinctions of at least 30% of large mammals, and at least 30% of Pacific island bird species. Over the past 500 years, between 1% and 5% of all remaining vertebrates on continents have been lost, which is 50 to 250 times faster than the estimated background rate of fossil mammals and implies that we will reach mass extinction levels within a few thousand years. This time will be shorter if current extinction rates are underestimated, or rates increase in the future.

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.

Past, present, and future mass extinctions

The fossil record of non-marine tetrapods (amphibians, reptiles, birds and mammals) has been described by numerous authors1–3, and major ecological replacements, mass extinctions and adaptive radiations have been identified. However, most of these features of the large-scale evolution of tetrapods have been noted without numerical data of the kind assembled for marine invertebrates4–10, marine vertebrates7–10 and vascular land plants11. Much has been learnt from the record of marine invertebrates, particularly about the overall patterns of diversification with time, the performance of different major taxonomic groups at different times, and the magnitude and timing of mass extinctions. The present study tests some of the general conclusions on the basis of a new compilation of data on the fossil record of terrestrial tetrapods. I show that family diversity rose with time, and in particular from the Cretaceous to the present day. There were several mass extinction events, but none of these was associated with a statistically high extinction rate. The extinction events, including the famous terminal Cretaceous extinction, were the result of a slightly elevated extinction rate combined with a depressed origination rate, and the present evidence does not support the view that mass extinctions are statistically distinguishable from background extinctions. Further, the record of non-marine tetrapods shows an increasing total extinction rate and an only marginally decreasing probability of extinction (per-taxon rate) from the late Devonian to the present, the opposite of the findings from the record of marine animals.

Extinction in the Anthropocene.

Procedures introduced here make it possible, first, to show that background (piecemeal) extinction is recorded throughout geologic stages and substages (not all extinction has occurred suddenly at the ends of such intervals); second, to separate out background extinction from mass extinction for a major crisis in earth history; and third, to correct for clustering of extinctions when using the rarefaction method to estimate the percentage of species lost in a mass extinction. Also presented here is a method for estimating the magnitude of the Signor-Lipps effect, which is the incorrect assignment of extinctions that occurred during a crisis to an interval preceding the crisis because of the incompleteness of the fossil record. Estimates for the magnitudes of mass extinctions presented here are in most cases lower than those previously published. They indicate that only ∼81% of marine species died out in the great terminal Permian crisis, whereas levels of 90-96% have frequently been quoted in the literature. Calculations of the latter numbers were incorrectly based on combined data for the Middle and Late Permian mass extinctions. About 90 orders and more than 220 families of marine animals survived the terminal Permian crisis, and they embodied an enormous amount of morphological, physiological, and ecological diversity. Life did not nearly disappear at the end of the Permian, as has often been claimed.

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.

Wide geographic range is generally thought to buffer taxa against extinction, but the strength of this effect has not been investigated for the great majority of the fossil record. Although the majority of genus extinctions have occurred between major mass extinctions, little is known about extinction selectivity regimes during these "background" intervals. Consequently, the question of whether selectivity regimes differ between background and mass extinctions is largely unresolved. Using logistic regression, we evaluated the selectivity of genus survivorship with respect to geographic range by using a global database of fossil benthic marine invertebrates spanning the Cambrian through the Neogene periods, an interval of approximately 500 My. Our results show that wide geographic range has been significantly and positively associated with survivorship for the great majority of Phanerozoic time. Moreover, the significant association between geographic range and survivorship remains after controlling for differences in species richness and abundance among genera. However, mass extinctions and several second-order extinction events exhibit less geographic range selectivity than predicted by range alone. Widespread environmental disturbance can explain the reduced association between geographic range and extinction risk by simultaneously affecting genera with similar ecological and physiological characteristics on global scales. Although factors other than geographic range have certainly affected extinction risk during many intervals, geographic range is likely the most consistently significant predictor of extinction risk in the marine fossil record.