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Dynamics of origination and extinction in the marine fossil record
Abstract
The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.
... However, such an interpretation requires caution as the negative relationship between diversity and origination rate also affected bivalves themselves (Fig. 5c). In fact, this negative correlation is largely caused by the rebounded origination after the extinction when diversity is low 43,51,63,64 . For brachiopods and bivalves, this 'diversity-dependent' pattern is only prominent in the aftermaths of mass extinctions. ...
... Similar to the result described above (Fig. 5a-d), the new results also indicate that 'diversity-dependence' is an important mechanism that regulates their origination rates (Fig. 5e-j): the infaunal bivalve diversity strongly and negatively correlated with origination rates of all three groups. This 'diversity-dependence', or the elevated origination rate after mass extinction, is a ubiquitous phenomenon across multiple marine clades 43,51,63,64,68 , which has been attributed to weakened competition 43 , extinction of predators 51 , or others. Regardless of specific ecological meaning, these correlations again suggest that the long-term (i.e., Permian-Jurassic) diversification dynamics of the three groups were largely governed by comparable factors, and bivalves (or specifically, epifaunal bivalves) were not competitors of brachiopods over macroevolutionary scales. ...
... In addition to Bayesian model-based methods which estimate continuous rates, we also analysed the diversification dynamics of global brachiopods and bivalves using traditional methods (e.g., per-capita 41 , three-timer 63 , and its improved versions, gap-filler 135 and second-forthird 136 ), which are based on discrete time bins. The workflow was identical to that of Kocsis et al. 40 . ...
Certain times of major biotic replacement have often been interpreted as broadly competitive, mediated by innovation in the succeeding clades. A classic example was the switch from brachiopods to bivalves as major seabed organisms following the Permian-Triassic mass extinction (PTME), ~252 million years ago. This was attributed to competitive exclusion of brachiopods by the better adapted bivalves or simply to the fact that brachiopods had been hit especially hard by the PTME. The brachiopod-bivalve switch is emblematic of the global turnover of marine faunas from Palaeozoic-type to Modern-type triggered by the PTME. Here, using Bayesian analyses, we find that unexpectedly the two clades displayed similar large-scale trends of diversification before the Jurassic. Insight from a multivariate birth-death model shows that the extinction of major brachiopod clades during the PTME set the stage for the brachiopod-bivalve switch, with differential responses to high ocean temperatures post-extinction further facilitating their displacement by bivalves. Our study strengthens evidence that brachiopods and bivalves were not competitors over macroevolutionary time scales, with extinction events and environmental stresses shaping their divergent fates.
... Sampling probability is also termed detection or encounter probability in the CMR literature, and we use these interchangeably here. Although other methods have been independently developed to account for sampling probabilities, origination and extinction rates simultaneously (Foote, 2003;Alroy, 2008), they do not have the generality or convenience of CMR methods, as we will discuss at appropriate points later in the chapter. ...
... Note that this is equivalent to Alroy's "two-timers" (Alroy 2008), although he calculates sampling probability differently. ...
... We need to begin to account for incomplete sampling in our models. Standardization may alleviate some problems of uneven sampling (Alroy et al., 2001;Alroy et al., 2008), but standardization necessarily involves sources of variation in detection processes that we can identify and control. Unfortunately, there are many likely sources of variation that we cannot identify and control. ...
We rely on observations of occurrences of fossils to infer the rates and timings of origination and extinction of taxa. These estimates can then be used to shed light on questions such as whether extinction and origination rates have been higher or lower at different times in earth history or in different geographical regions, etc. and to investigate the possible underlying causes of varying rates. An inherent problem in inference using occurrence data is one of incompleteness of sampling. Even if a taxon is present at a given time and place, we are guaranteed to detect or sample it less than 100% of the time we search in a random outcrop or sediment sample that should contain it, either because it was not preserved, it was preserved but then eroded, or because we simply did not find it. Capture-mark-recapture (CMR) methods rely on replicate sampling to allow for the simultaneous estimation of sampling probability and the parameters of interest (e.g. extinction, origination, occupancy, diversity). Here, we introduce the philosophy of CMR approaches especially as applicable to paleontological data and questions. The use of CMR is in its infancy in paleobiological applications, but the handful of studies that have used it demonstrate its utility and generality. We discuss why the use of CMR has not matched its development in other fields, such as in population ecology, as well as the importance of modelling the sampling process and estimating sampling probabilities. In addition, we suggest some potential avenues for the development of CMR applications in paleobiology.
... An alternative approach, developed at the inception of the PBDB, was to combine stages as needed to obtain intervals of approximately equal duration, approximately 10-11 million years. This was the resolution used in the first analyses with the PBDB (Alroy et al., 2001), which continues to be used on occasion (Alroy, 2008;Alroy et al., 2008;Kocsis et al., 2019). ...
... We (John Alroy and I) initiated the PBDB to make these data web-accessiblethe PBDB is collections based, where for each published fossil collection (locality), the taxa present, its location, available stratigraphic, taphonomic, tectonic data, etc., can be entered. Thus, the PBDB affords the opportunity to measure collection intensity (e.g., the number of occurrences for each taxon temporally and spatially), making it possible to standardize sampling when assessing marine diversity dynamics (Miller and Foote, 1996;Alroy et al., 2001;Alroy, 2008;Close et al., 2018;Kocsis et al., 2019). Now, some 20 years later, the PBDB has a substantial amount of data and has become a standard starting point for large-scale analyses of the fossil record. ...
... At about that time the PBDB was being established (we ran the first planning meeting at the National Center for Ecological Analysis and Synthesis [NCEAS] in 1998). In 2008 Alroy (2008) published the first sample standardized analysis of marine origination and extinction rates with the PBDB using the 11-million-year timescale. He confirmed that the post-early Ordovician intervals with the five highest extinction rates correspond to the Big Five, as well as confirming that the extinction intensities were consistent with one distribution of rates: the Big Five remained Type 4 mass extinctions. ...
Over 40 years 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 40 years, 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.”
... The efforts of paleontologists in the last centuries have generated ultra-scale data sets of high spatial resolution, and some might even include some spatiotemporal analyses themselves (e.g., PBDB). These 'big data' must be used to answer 'big questions' in paleontology (Alroy, 2008;Nürnberg and Aberhan, 2013;Foote, 2014). Hence, a tool to exploit such huge spatiotemporal data is needed. ...
... In addition, amplified integration of geographic visualization and/or geo-computation is essential to address many environmental concerns (Varela et al., 2011(Varela et al., , 2015Abdelhady and Abdalla, 2018). Ecologists and climatologists now focus more and more on understanding climate changes over a broader range of time and space scales via paleontological data from the fossil record (Alroy, 2008). ...
A systematic horizon scanning was undertaken to identify the up-to-date perspectives on paleontological research. A summarized evaluation (applicability and acceptability) was also provided to identify the challenges and opportunities of paleontological techniques. Present-day advances in molecular analyses and scanning techniques generate valuable new data to test old and recent systematic problems and provide a revolution in systematic paleontology. Integrating non-destructive high-resolution virtual solutions such as X-ray computed tomography and 3D-laser scanning with machine learning can be widely used for the analysis of internal features of fossils and more efficiently for automated taxonomy. The slow pace of the revolution in paleontological techniques can be attributed to the limited advanced statistical training and the cost of the instruments, software, and hardware needed for digitization and imaging. In addition, molecular techniques offer a unique source of information (e.g., biomarkers), however, costs and difficulties are limiting their applications. Sclerochronology using carbonate shells of well-preserved fossils (e.g., mollusks, corals, and fish) has the potential to reconstruct the paleoclimate at very high resolution (daily, seasonal, and annual). These approaches are revolutionary and will grow continuously to substitute traditional methods and will reduce time and human efforts.
... It is obvious that both nutrients and tectonics aspects are intimately related and must be considered together for better understanding of life evolution and biodiversity distribution. It is important to point out that timescales of biological evolution estimated based on the analysis of phylogenies and/or fossils are rather long and comparable to geodynamic timescales (Alroy, 2008;Marshall, 2017). In a constant rate birth-death model (Kendall, 1949), new species originate with speciation rate, and species become extinct with extinction rate, typically expressed as rates per lineage per million years (L -1 Myr -1 ). ...
... Typically, estimates of speciation and extinction rates fall within the range 0 to 1 L -1 Myr -1 (Marshall, 2017) and rarely exceed 1 L -1 Myr -1 , except within intervals of crisis (Alroy, 2008). The timescales of biological evolution are therefore similar to the timescales of tectono-magmatic lithospheric and mantle processes in Hagen et al. (2021) presented the next generation biogeographical modelling tool GEN3SIS aimed at simulating eco-evolutionary processes coupled to plate tectonics and long-term climate variations. ...
Understanding the interactions between surface and deep Earth processes is important for research in many diverse scientific areas including climate, environment, energy, georesources and biosphere. The TOPO-EUROPE initiative of the International Lithosphere Program serves as a pan-European platform for integrated surface and deep Earth sciences, synergizing observational studies of the Earth structure and fluxes on all spatial and temporal scales with modelling of Earth processes. This review provides a survey of scientific developments in our quantitative understanding of coupled surface-deep Earth processes achieved through TOPO-EUROPE. The most notable innovations include (1) a process-based understanding of the connection of upper mantle dynamics and absolute plate motion frames; (2) integrated models for sediment source-to-sink dynamics, demonstrating the importance of mass transfer from mountains to basins and from basin to basin; (3) demonstration of the key role of polyphase evolution of sedimentary basins, the impact of pre-rift and pre-orogenic structures, and the evolution of subsequent lithosphere and landscape dynamics; (4) improved conceptual understanding of the temporal evolution from back-arc extension to tectonic inversion and onset of subduction; (5) models to explain the integrated strength of Europe’s lithosphere; (6) concepts governing the interplay between thermal upper mantle processes and stress-induced intraplate deformation; (7) constraints on the record of vertical motions from high-resolution data sets obtained from geo-thermochronology for Europe’s topographic evolution; (8) recognition and quantifications of the forcing by erosional and/or glacial-interglacial surface mass transfer on the regional magmatism, with major implications for our understanding of the carbon cycle on geological timescales and the emerging field of biogeodynamics; and (9) the transfer of insights obtained on the coupling of deep Earth and surface processes to the domain of geothermal energy exploration. Concerning the future research agenda of TOPO-EUROPE, we also discuss the rich potential for further advances, multidisciplinary research and community building across many scientific frontiers, including research on the biosphere, climate and energy. These will focus on obtaining a better insight into the initiation and evolution of subduction systems, the role of mantle plumes in continental rifting and (super)continent break-up, and the deformation and tectonic reactivation of cratons; the interaction between geodynamic, surface and climate processes, such as interactions between glaciation, sea level change and deep Earth processes; the sensitivity, tipping points, and spatio-temporal evolution of the interactions between climate and tectonics as well as the role of rock melting and outgassing in affecting such interactions; the emerging field of biogeodynamics, that is the impact of coupled deep Earth – surface processes on the evolution of life on Earth; and tightening the connection between societal challenges regarding renewable georesources, climate change, natural geohazards, and novel process-understanding of the Earth system.
... T he Great Ordovician Biodiversification Event was the greatest accumulation of marine metazoan richness in Earth's history 1 . Two widely different views on the onset and duration of the GOBE has been proposed: A slow, continues rise in richness over >40 million years through the Cambrian-Ordovician periods is observed based on broadly binned temporal analyses of early Paleozoic fossil occurrences 2,3 . Opposing this view stands studies conducted with high temporal resolution that show a rapid radiation that started during the Middle Ordovician 1,4,5 . ...
... Generic richness increased four-fold during the Middle-early Late Ordovician 11,12 and there was a complete restructuring of trophic relationships [1][2][3] . The first complex marine ecosystems with deeper tiering, intricate trophic cascades and ecospace partitioning were established 13 . ...
The Great Ordovician Biodiversification Event (GOBE) represents the greatest increase in marine animal biodiversity ever recorded. What caused this transformation is heavily debated. One hypothesis states that rising atmospheric oxygen levels drove the biodiversification based on the premise that animals require oxygen for their metabolism. Here, we present uranium isotope data from a Middle Ordovician marine carbonate succession that shows the steepest rise in generic richness occurred with global marine redox stability. Ocean oxygenation ensued later and could not have driven the biodiversification. Stable marine anoxic zones prevailed during the maximum increase in biodiversity (Dapingian–early Darriwilian) when the life expectancy of evolving genera greatly increased. Subsequently, unstable ocean redox conditions occurred together with a marine carbon cycle disturbance and a decrease in relative diversification rates. Therefore, we propose that oceanic redox stability was a factor in facilitating the establishment of more resilient ecosystems allowing marine animal life to radiate.
... In synoptic studies, e.g., Sepkoski ([1986]) or Alroy ([2008]), time bins are coarse (~10 million years) or sometimes uneven. However, as the use of databases increases, scientists can use finer time bins. ...
... As discussed in section 4, marine environments represent most of the past ecological information, as shelled marine species fossilise easily. In synoptic studies of mass extinctions meant to generate diversity curves (like Sepkoski [1982], [2002] and Alroy [2008]), these taxa tend to be over-represented. On the contrary, upland-environment and tropical species are under-represented (Barnosky et al. [2011], p. 52) and do not take central stage in paleodiversity curves, but are of high importance for comparative studies since most contemporary species loss is allegedly occurring in the tropics, which house most of Earth's current species diversity. ...
In both scientific and popular circles it is often said that we are in the midst of a sixth mass extinction. Although the urgency of our present environmental crises is not in doubt, such claims of a present mass extinction are highly controversial scientifically. Our aims are, first, to get to the bottom of this scientific debate by shedding philosophical light on the many conceptual and methodological challenges involved in answering this scientific question, and, second, to offer new philosophical perspectives on what the value of asking this question has been — and whether that value persists today. We show that the conceptual challenges in defining ‘mass extinction’, uncertainties in past and present diversity assessments, and data incommensurabilities undermine a straightforward answer to the question of whether we are in, or entering, a sixth mass extinction today. More broadly we argue that an excessive focus on the mass extinction framing can be misleading for present conservation efforts and may lead us to miss out on the many other valuable insights that Earth’s deep time can offer in guiding our future.
... Extinctions on land (e.g., non-avian dinosaurs, flying reptiles, and 30-80% of plants) and in the oceans (an estimated 47-53% extinction of genera, extrapolated to ~76% extinction of species [Jablonski, 1994;Alroy, 2008], e.g., rudists, ammonites, mosasaurs, and >90% of the species of planktonic foraminifera and coccolithophores [e.g., Lowery et al., 2020]) were selective, and there was an abrupt, global biological turnover (see Schulte et al., 2010, for a review). ...
... Russell (1977Russell ( , 1979) postulated a species extinction rate of 75% (likewise extrapolated from genus extinction rates) for the end Cretaceous, which included marine and terrestrial species, plants, and animals. Alroy (2008) provides a more recent genus extinction rate of 53%, but only for marine invertebrates. ...
This volume pays tribute to the great career and extensive and varied scientific accomplishments of Walter Alvarez, on the occasion of his 80th birthday in 2020, with a series of papers related to the many topics he covered in the past 60 years: Tectonics of microplates, structural geology, paleomagnetics, Apennine sedimentary sequences, geoarchaeology and Roman volcanics, Big History, and most famously the discovery of evidence for a large asteroidal impact event at the Cretaceous–Tertiary (now Cretaceous–Paleogene) boundary site in Gubbio, Italy, 40 years ago, which started a debate about the connection between meteorite impact and mass extinction. The manuscripts in this special volume were written by many of Walter’s close collaborators and friends, who have worked with him over the years and participated in many projects he carried out. The papers highlight specific aspects of the research and/or provide a summary of the current advances in the field.
... The evolutionary history of crinoids was significantly altered by the Late Ordovician extinctions, the secondmost severe biosphere collapse in Earth's history (e.g., Sepkoski 1996;Alroy 2008Alroy , 2010aAlroy , 2010bHarper et al. 2014). Recent research has focused on understanding the tempo and mode of the extinction and recovery of crinoids during this period (e.g., Peters and Ausich 2008;Ausich and Deline 2012;Kozik et al. 2022). ...
... As a precaution against spurious features of sampling patterns (see Fig. S8), we focus on comparing numbers of regional two-timer species, that is, species that were observed in a region for at least two time bins consecutively (Fig. 5) 79 . These are the better-sampled species, whose observed responses may be more reliable. ...
A mismatch of species thermal preferences to their environment may forewarn that some assemblages will undergo greater reorganization, extirpation, and possibly extinction, than others under climate change. Here, we examined the effects of regional warming on marine benthic species occupancy and assemblage composition over one-million-year time steps during the Early Jurassic. Thermal bias, the difference between modelled regional temperatures and species’ long-term thermal optima, predicted species responses to warming in an escalatory order. Species that became extirpated or extinct tended to have cooler temperature preferences than immigrating species, while regionally persisting species fell midway. Larger regional changes in summer seawater temperatures (maximum + 10°C) strengthened the relationship between species thermal bias and the escalatory order of responses, which was also stronger for brachiopods than bivalves, but the relationship was overridden by severe seawater deoxygenation. At + 3°C seawater warming, our models estimate that around 5% of an assemblage’s pre-existing benthic species was extirpated, and around one-fourth of the new assemblage being immigrated species. Our results validate thermal bias as an indicator of future extinction, persistence, and immigration of marine species under modern magnitudes of climate change.
... For instance, research spanning development, genetics, genomics, organismal studies and ecology, has together contributed to identifying the genetic and developmental basis of colour pattern variation and its role in lineage divergence and isolation in organisms as diverse as Heliconius butterflies (Mallet and A c c e p t e d M a n u s c r i p t Barton 1989;Reed et al. 2011;The Heliconius Genome Consortium 2012;Martin et al. 2013;Van Belleghem et al. 2023) and Mimulus wildflowers (Bradshaw et al. 1998;Schemske and Bradshaw 1999;Liang et al. 2023). Likewise, the integration of paleontological and paleoenvironmental data with DNA sequence data of extant organisms has allowed estimation of past rates of diversification and extinction, while implicating specific phenotypic traits as drivers of speciation and diversification (Benton 1995;Alroy 2008;Quental and Marshall 2010;Pyron, Burbrink and Wiens 2013) (see Section 5). Interdisciplinary work can also reveal key knowledge gaps (see Section 4), which in itself can drive major advances in addressing or bridging them (Coyne and Orr 1989;Rabosky and Matute 2013). ...
Speciation research–the scientific field focused on understanding the origin and diversity of species–has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research–(i) scientific integration, through the bringing together of ideas, data and approaches, and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (1) the multidisciplinary nature of speciation research, (2) the complex language of speciation, (3) a bias toward certain study systems, (4) the challenges of working across scales, and (5) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.
... The hypothesis of diversity-dependence predicts a negative correlation between diversity residuals and diversificationrate residuals. Given the general statistical phenomenon of regression to the mean, diversity and diversification rate tend be negatively correlated even if rates are independent of diversity [54,55]. We therefore use a randomization procedure [6,7] to determine whether observed correlations are stronger than would be expected for a diversity-independent process. ...
Rigorous analysis of diversity-dependence—the hypothesis that the rate of proliferation of new species is inversely related to standing diversity—requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment–water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.
... Analyses accounting for variable sampling rates over time suggest that global Guadalupian extinction rates among marine taxa are well within background rates for the Phanerozoic (Foote, 2007;Alroy, 2008). Sampling-standardized analyses by Clapham et al. (2009) suggested that the EGE may have been driven by suppressed origination rather than by elevated extinction, or was a 'depletion event' (sensu Stigall, 2019). ...
The transition from the middle to late Permian (Guadalupian–Lopingian) is claimed to record one or more extinction events that rival the ‘Big Five’ in terms of depletion of biological diversity and reorganization of ecosystem structure. Yet many questions remain as to whether the events recorded in separate regions were synchronous, causally related, or were of a magnitude rivaling other major crises in Earth’s history. In this paper, we survey some major unresolved issues related to the Guadalupian–Lopingian transition and offer a multidisciplinary approach to advance understanding of this under-appreciated biotic crisis by utilizing records in Southern Hemisphere high-palaeolatitude settings. We focus on the Bowen-Gunnedah-Sydney Basin System (BGSBS) as a prime site for analyses of biotic and physical environmental change at high palaeolatitudes in the middle and terminal Capitanian. Preliminary data suggest the likely position of the mid-Capitanian event is recorded in regressive deposits at the base of the Tomago Coal Measures (northern Sydney Basin) and around the contact between the Broughton Formation and the disconformably overlying Pheasants Nest Formation (southern Sydney Basin). Initial data suggest that the end-Capitanian event roughly correlates to the transgressive “Kulnura Marine Tongue” in the middle of the Tomago Coal Measures (northern Sydney Basin) and strata bearing dispersed, ice-rafted gravel in the Erins Vale Formation (southern Sydney Basin). Preliminary observations suggest that few plant genera or species disappeared in the transition from the Guadalupian to Lopingian, and the latter interval saw an increase in floristic diversity.
... Although the ecological devastation is well-constrained in faunal extinctions (Benton, 1990;Benton, 1995;Alroy, 2008), taxonomic losses in the plant-kingdom are more ambiguous and locally restricted with a selective impact, varying globally between 17 and 73%, based on spore and pollen taxa (McElwain and Punyasena, 2007;Mander et al., 2010;Lindström, 2016). Many detailed studies have focused on the link between CAMP-induced carbon cycle perturbations and the active destruction and/or extirpation of terrestrial vegetation during the ETME and lowermost Hettangian, mostly at northern hemisphere sites (McElwain et al., 1999;McElwain and Punyasena, 2007;van de Schootbrugge et al., 2009;Mander et al., 2010;Bonis and Kürschner, 2012;Li et al., 2016;Peng et al., 2018;Lindström et al., 2019;Li et al., 2020;Lindström, 2021;Lindström et al., 2021). ...
Disturbances in terrestrial vegetation across the end-Triassic mass-extinction (ETME) and earliest Jurassic (~201.5 - 201.3 Ma) have previously been linked to carbon cycle perturbations induced by the Central Atlantic Magmatic Province. Large-scale volcanic degassing has been proposed to have affected the terrestrial realm through various mechanisms. However, the effects of long-term “super greenhouse” climate variability on vegetation dynamics following the mass-extinction remain poorly understood. Based on a 10-million-year long multi-proxy record of northern Germany (Schandelah-1, Germany, paleolatitude of ~41 °N) spanning the late Rhaetian to the Sinemurian (~201.5 – 190.8 Ma), we aim to assess mechanistic links between carbon cycle perturbations, climate change, and vegetation dynamics.
Based on a high-resolution palynofloral record a two-phased extinction emerges, confirming extinction patterns seen in other studies. The first phase is associated with a decline in arborescent conifers, coinciding with a negative carbon isotope excursion and an influx of aquatic palynomorphs. Following this decline, we find a stepwise rise of ferns at the cost of trees during the latest Rhaetian, culminating with the extinction of tree taxa at the Triassic-Jurassic boundary. The rise in ferns is accompanied by an increase in reworked organic matter and charcoal, suggestive of erosion and wildfires. Furthermore, the Hettangian (201.3 – 199.3 Ma) vegetation in NW Europe shows evidence of long-term disturbance reflected by the periodic resurgence of fern taxa, similarly accompanied by increases in reworking and charcoal. This periodicity is linked to the 405-kyr eccentricity cycle indicating a biome that responded to astronomically induced variability in hydrology. A transition into an apparently more stable biome starts during the early Sinemurian, where palynofloral assemblages become dominated by bisaccate pollen taxa, mainly derived from conifers.
The ETME was clearly forced by the effects of volcanogenic emissions, such as SO2, CO2 and other pollutants, acting on both short (0.1 – 10 kyrs) and long timescales (10 – 100 kyrs). In contrast, charcoal and detrital input indicators show that the disturbances during the Hettangian were driven by periodic shifts in the regional hydrological regime. This was forced by the effects of orbital insolation variation and potentially exacerbated by increased atmospheric pCO2. The cyclic progression of ecosystem disturbance was similar to that of the ETME and only recovered during the early Sinemurian. Atmospheric pCO2 remained elevated after CAMP-activity had subsided due to a collapse of terrestrial biomass and carbonate producers. This inability to store carbon on long timescales could therefore have impeded global recovery.
... Interestingly, other major events highlighted as having potentially impacted insect evolution (during the Late Pennsylvanian, Late Jurassic, and later Early Cretaceous) 10 do not overlap with the five mass extinctions of the marine realm. 11 In summary, the main drivers of biodiversity dynamics on emerged lands, and for insects in particular, remain inadequately explored in the deep time because of a lack of resolution and, to some extent, a dearth of taxonomic expertise. 10 The fossil record of insects has essentially been investigated using diversity metrics, resting on units based on taxonomic rank, usually the genus, whose attribution is subjective. ...
Owing to their prevalence in nowadays terrestrial ecosystems, insects are a relevant group to assess the impact of mass extinctions on emerged land. However, limitations of the insect fossil record make it difficult to assess the impact of such events based on taxonomic diversity alone. Therefore, we documented trends in morphological diversity, i.e., disparity, using wings of Permian to Jurassic Odonata as model. Our results show a decreasing trend in disparity while species richness increased. Both the Permian-Triassic and Triassic-Jurassic transitions are revealed as important events, associated with strong morphospace restructuring due to selective extinction. In each case, a recovery was assured by the diversification of new forms compensating the loss of others. Early representatives of Odonata continuously evolved new shapes, a pattern contrasting with the classical assertion of a morphospace fulfilled early and followed by selective extinctions and specialization within it.
... However, raw percentages are strongly biased by variations in sampling intensity, and quantifying extinction rates over the late Ediacaran is fraught with other difficulties stemming from the character of the Ediacaran fossil record, and ongoing difficulties with stratigraphic correlation and subdivision. For example, from our occurrence dataset (Figure 1; taxa and references provided in Supplementary Material) we can argue for major extinctions across the White Sea-Nama and E-C boundaries utilizing a simple proportion of extinct genera, but we do not have much confidence in Ediacaran per capita extinction rates using common methods such as Foote (1999), Alroy (2008), or Alroy (2014). The principal issue is that these methods utilize the proportion of taxa crossing boundaries for their extinction rate estimates in various patterns (e.g., boundary crossers, 3-timers, and gap fillers spanning 3 intervals with no detections in the middle) and the Ediacaran is dominated by taxa that occur in a single assemblage zone. ...
Since the 1980s, the existence of one or more extinction events in the late Ediacaran has been the subject of debate. Discussion surrounding these events has intensified in the last decade, in concert with efforts to understand drivers of global change over the Ediacaran–Cambrian transition and the appearance of the more modern-looking Phanerozoic biosphere. In this paper we review the history of thought and work surrounding late Ediacaran extinctions, with a particular focus on the last 5 years of paleontological, geochemical, and geochronological research. We consider the extent to which key questions have been answered, and pose new questions which will help to characterize drivers of environmental and biotic change. A key challenge for future work will be the calculation of extinction intensities that account for limited sampling, the duration of Ediacaran ‘assemblage’ zones, and the preponderance of taxa restricted to a single ‘assemblage’; without these data, the extent to which Ediacaran bioevents represent genuine mass extinctions comparable to the ‘Big 5’ extinctions of the Phanerozoic remains to be rigorously tested. Lastly, we propose a revised model for drivers of late Ediacaran extinction pulses that builds off recent data and growing consensus within the field. This model is speculative, but does frame testable hypotheses that can be targeted in the next decade of work.
... This late addition of volatiles by impacts may have been essential in creating a habitable planet that ultimately enabled the emergence of life on Earth. It is ironic that a similar collision of an extraterrestrial projectile with the Earth has been identified as the cause of the Cretaceous-Paleogene (K-Pg, formerly K-T) mass extinction about~65.5 million years ago (Alroy, 2008). The anomalously high abundance of Ir and other platinum group elements (PGEs) in the K-Pg boundary clay and impact ejecta (spherules, shocked minerals, etc.) deposits led to the discovery of the~180-to 200-km-diameter Chicxulub impact structure on the Yucatan Peninsula, Mexico (Alvarez et al., 1982;Hildebrand et al., 1991;Smit & Klaver, 1981). ...
The Dhala structure in north‐central India is a confirmed complex impact structure of Paleoproterozoic age. The presence of an extraterrestrial component in impactites from the Dhala structure was recognized by geochemical analyses of highly siderophile elements and Os isotopic compositions; however, the impactor type has remained unidentified. This study uses Cr isotope systematics to identify the type of projectile involved in the formation of the Dhala structure. Unlike the composition of siderophile elements (e.g., Ni, Cr, Co, and platinum group elements) and their inter‐element ratios that may get compromised due to the extreme energy generated during an impact, Cr isotopes retain the distinct composition of the impactor. The distinct ε ⁵⁴ Cr value of −0.31 ± 0.09 for a Dhala impact melt breccia sample (D6‐57) indicates inheritance from an impactor originating within the non‐carbonaceous reservoir, that is, the inner Solar System. Based on the Ni/Cr ratio, Os abundance, and Cr isotopic composition of the samples, the impactor is constrained to be of ureilite type. Binary mixing calculations also indicate contamination of the target rock by 0.1–0.3 wt% of material from a ureilite‐like impactor. Together with the previously identified impactors that formed El'gygytgyn, Zhamanshin, and Lonar impact structures, the Cr isotopic compositions of the Dhala impactites argue for a much more diverse source of the objects that collided with the Earth over its geological history than has been supposed previously.
... ϵ(t) is a noise term that includes the data's uncertainty and the effect of the approximation, e.g., other features affecting diversity besides supernovae and shallow marine areas. Figure Permian-Triassic mass-extinction size (Alroy, 2008). Including this time scale and using the fact that the diversity N(t) can only depend on past changes of SN(t) leads to the simple function The area function can be expressed as a function of sea level using Equation (2) as where 0 is the sea level at t = 0 (present time). ...
It is an open question what has constrained macroevolutionary changes in marine animal diversity on the time scale of the Phanerozoic. Here, we will show that supernovae appear to have significantly influenced the biodiversity of life. After normalizing diversity curves of major animal marine genera by the changes in the area of shallow marine margins, a close correlation between supernovae frequency and biodiversity is obtained. The interpretation is that supernovae influence Earth's climate, which controls the ocean and atmospheric circulation of nutrients. With this, supernovae influence ocean bioproductivity and are speculated to affect genera-level diversity. The implication is a surprisingly influential role of stellar processes on evolution.
... Specifically, the total extinction rate (family extinctions per million years) was greatest during the Cambrian but gradually decreased over the next 500 million years. Subsequent studies that better account for possible sampling biases have also observed this decrease in extinction rate (e.g., Foote, 2003;Alroy, 2008;Kocsis et al., 2019). Various causal mechanisms have been proposed to explain the decrease in extinction rates, including increased ecological complexity, ecological resistance to extinction, taxonomic structure (increase in the number of species per clade over time), lineage durations, variability of the rock record, and stabilization of the carbon cycle as a result of decreased shallow-marine anoxia (reviewed by Payne et al., 2020). ...
Oxygen levels in the atmosphere and ocean have changed dramatically over Earth history, with major impacts on marine life. Because the early part of Earth’s history lacked both atmospheric oxygen and animals, a persistent co-evolutionary narrative has developed linking oxygen change with changes in animal diversity. Although it was long believed that oxygen rose to essentially modern levels around the Cambrian period, a more muted increase is now believed likely. Thus, if oxygen increase facilitated the Cambrian explosion, it did so by crossing critical ecological thresholds at low O2. Atmospheric oxygen likely remained at low or moderate levels through the early Paleozoic era, and this likely contributed to high metazoan extinction rates until oxygen finally rose to modern levels in the later Paleozoic. After this point, ocean deoxygenation (and marine mass extinctions) is increasingly linked to large igneous province eruptions—massive volcanic carbon inputs to the Earth system that caused global warming, ocean acidification, and oxygen loss. Although the timescales of these ancient events limit their utility as exact analogs for modern anthropogenic global change, the clear message from the geologic record is that large and rapid CO2 injections into the Earth system consistently cause the same deadly trio of stressors that are observed today. The next frontier in understanding the impact of oxygen changes (or, more broadly, temperature-dependent hypoxia) in deep time requires approaches from ecophysiology that will help conservation biologists better calibrate the response of the biosphere at large taxonomic, spatial, and temporal scales.
... There are records of species from the early Miocene very similar to the extant ones (Woodrings, 1982), which can go back to the origin of the current diversity before the rise of the isthmus. These events coupled with relatively low post-Miocene marine extinction rates (Alroy, 2008;Foster et al., 2020;Harnik et al., 2012) may explain the high diversity of Eurytellina, as well as serve as a test of hypothesis for other transisthmian genera in Tellinidae. ...
One of the main questions of phylogenetic systematics has recently focused on the reliability and robustness of taxonomic
data. Many recent studies are devoted almost exclusively to the molecular-morphological couplet. However, in many metazoan
taxa, the presence of skeletal parts or poorly preserved soft parts is dominant in collections, making it difficult to extract
genetic material. This is the case with many invertebrates and unfortunately a very common situation in mollusk collections.
Herein we carry out a phylogenetic analysis of the transisthmian American tellinid bivalve genus Eurytellina based
on anatomical and morphometric characters, using different ways to analyze the morphometric data under parsimony-based
methods. Species in this genus are recognized as deep infaunal burrowers and present a strong filter-feeding apparatus. We
included 144 taxonomically important morphoanatomical and morphometric characters and 19 landmark characters. The
main results are a) Tellinota (formerly a synonym of Eurytellina) is confirmed as a taxon restricted to Africa; b) Eurytellina
lineata is confirmed as sister group to all the other members of the genus; c) there is strong evidence for three robust clades,
here named as groups trinitatis, nitens and punicea; d) some transisthmian sister species hypotheses are confirmed—although
the pattern of speciation and radiation may be related to a complex long-term elevation of the Panama Isthmus and previous
events (probably since the early Cenozoic). Furthermore, several new anatomical characters are described within the Order
Tellinoidea, which should be considered in future studies.
The search for drivers of hominin speciation and extinction has tended to focus on the impact of climate change. Far less attention has been paid to the role of interspecific competition. However, research across vertebrates more broadly has shown that both processes are often correlated with species diversity, suggesting an important role for interspecific competition. Here we ask whether hominin speciation and extinction conform to the expected patterns of negative and positive diversity dependence, respectively. We estimate speciation and extinction rates from fossil occurrence data with preservation variability priors in a validated Bayesian framework and test whether these rates are correlated with species diversity. We supplement these analyses with calculations of speciation rate across a phylogeny, again testing whether these are correlated with diversity. Our results are consistent with clade-wide diversity limits that governed speciation in hominins overall but that were not quite reached by the Australopithecus and Paranthropus subclade before its extinction. Extinction was not correlated with species diversity within the Australopithecus and Paranthropus subclade or within hominins overall; this is concordant with climate playing a greater part in hominin extinction than speciation. By contrast, Homo is characterized by positively diversity-dependent speciation and negatively diversity-dependent extinction—both exceedingly rare patterns across all forms of life. The genus Homo expands the set of reported associations between diversity and macroevolution in vertebrates, underscoring that the relationship between diversity and macroevolution is complex. These results indicate an important, previously underappreciated and comparatively unusual role of biotic interactions in Homo macroevolution, and speciation in particular. The unusual and unexpected patterns of diversity dependence in Homo speciation and extinction may be a consequence of repeated Homo range expansions driven by interspecific competition and made possible by recurrent innovations in ecological strategies. Exploring how hominin macroevolution fits into the general vertebrate macroevolutionary landscape has the potential to offer new perspectives on longstanding questions in vertebrate evolution and shed new light on evolutionary processes within our own lineage.
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Although some authors have suggested that the clade experienced a decline in diversity, potentially starting millions of years before the end-Cretaceous mass extinction, others have suggested that the group remained highly diverse right up until the Cretaceous-Paleogene (K-Pg) boundary. Our results show that model assumptions, likely with respect to incomplete sampling, have a large impact on whether dinosaurs appear to have experienced a long-term decline or not. The results are also highly sensitive to the topology and branch lengths of the phylogeny used. Developing comprehensive models of sampling bias, and building larger and more accurate phylogenies, are likely to be necessary steps for us to determine whether dinosaur diversity was or was not in decline before the end-Cretaceous mass extinction.
Within the uncertainties of involved astronomical and biological parameters, the Drake Equation typically predicts that there should be many exoplanets in our galaxy hosting active, communicative civilizations (ACCs). These optimistic calculations are however not supported by evidence, which is often referred to as the Fermi Paradox. Here, we elaborate on this long-standing enigma by showing the importance of planetary tectonic style for biological evolution. We summarize growing evidence that a prolonged transition from Mesoproterozoic active single lid tectonics (1.6 to 1.0 Ga) to modern plate tectonics occurred in the Neoproterozoic Era (1.0 to 0.541 Ga), which dramatically accelerated emergence and evolution of complex species. We further suggest that both continents and oceans are required for ACCs because early evolution of simple life must happen in water but late evolution of advanced life capable of creating technology must happen on land. We resolve the Fermi Paradox (1) by adding two additional terms to the Drake Equation: foc (the fraction of habitable exoplanets with significant continents and oceans) and fpt (the fraction of habitable exoplanets with significant continents and oceans that have had plate tectonics operating for at least 0.5 Ga); and (2) by demonstrating that the product of foc and fpt is very small (< 0.00003–0.002). We propose that the lack of evidence for ACCs reflects the scarcity of long-lived plate tectonics and/or continents and oceans on exoplanets with primitive life.
Coral reefs are rapidly declining due to global climate change ¹ . Alongside environmental protection, gene engineering technologies are essential in protecting reef-building (stony) corals ²⁻⁷ . Precise multi-omics backgrounds are crucial for gene technique application ⁸⁻¹³ and understanding stony coral biology ²⁻⁵ . However, high heterozygosity 4,14 and exogenous sequence contamination ¹⁵⁻¹⁷ impede high-quality stony coral genome assembly. To address this, we developed a workflow for stony coral genome assembly, achieving four high-quality chromosome-level genomes ( Acropora muricata , Montipora foliosa , M. capricornis , and Pocillopora verrucosa ). A global synteny analysis of chromosomes and homeobox genes highlighted the highly conserved features of Scleractinia stony coral genomes, even after an evolutionary divergence 250 million years ago (mya). Single-cell RNA sequencing (scRNA-seq), combined with a pan-genomic analysis, aided our understanding of symbiosis and calcification, both issues of conservation concern. A dynamics simulation of the mechanism of systemic RNA interference defective protein 1 transmembrane family member 1 (SIDT1) tetramer offered a potential approach to observe gene impacts on stony corals. This work enhances understanding of the evolutionary, molecular, and cellular aspects of stony corals and provides a detailed dataset for applying gene engineering technologies in response to global climate challenges.
Marine redox conditions (that is, oxygen levels) impact a wide array of biogeochemical cycles, but the main controls of marine redox since the start of the Phanerozoic about 538 million years ago are not well established. Here we combine supervised machine learning with shale-hosted trace metal concentrations to reconstruct a near-continuous record of redox conditions in major marine depositional settings. We find synchronously opposite redox changes in upper ocean versus deep shelf and (semi-)restricted basin settings ('redox anticouples', nomen novum) in several multi-million-year intervals, which can be used to track the positions of oxygen-minimum zones and the primary locations of organic burial through time. These changes coincided with biological innovations that altered large-scale oxidant-reductant fluxes (mid-Palaeozoic spread of land plants; Mesozoic plankton revolution) and tectonic upheavals that regulated sea-level elevation (Pangaea amalgamation and break-up). We find that the pre-Devonian deep shelf was buffered at a largely anoxic state probably by dissolved organic matter, switched to a transitional state during the Devonian–Carboniferous interval characterized by the inception of persistent oxygen-minimum zones and subsequently shifted to a redox regime featuring thin oxygen-minimum zones ballasted probably by particulate organic matter. Deep shelf redox changes are correlated with background extinction rates of marine animals, and mass extinctions during major redox transitions generally were more severe.
The marine losses during the Permo-Triassic mass extinction were the worst ever experienced. All groups were badly affected, especially amongst the benthos (e.g. brachiopods, corals, bryozoans, foraminifers, ostracods). Planktonic populations underwent a fundamental change with eukaryotic algae being replaced by nitrogen-fixing bacteria, green-sulphur bacteria, sulphate-reducing bacteria and prasinophytes. Detailed studies of boundary sections, especially those in South China, have resolved the crisis to a ∼55 kyr interval straddling the Permo-Triassic boundary. Many of the losses occur at the beginning and end of this interval painting a picture of a two-phase extinction. Improved knowledge of the extinction has been supported by numerous geochemical studies that allow diverse proposed extinction mechanisms to be studied. A transition from oxygenated to anoxic-euxinic conditions is seen in most sections globally, although the intensity and timing shows regional variability. Decreased ocean ventilation coincides with rapidly rising temperatures and many extinction scenarios attribute the losses to both anoxia and high temperatures. Other kill mechanisms include ocean acidification for which there is conflicting support from geochemical proxies and, even less likely, siltation (burial under a massive influx of terrigenous sediment) which lacks substantive sedimentological evidence. The ultimate driver of the catastrophic changes at the end of the Permian was likely Siberian Trap eruptions and their associated carbon dioxide emissions with consequences such as warming, ocean stagnation and acidification. Volcanic winter episodes stemming from Siberian volcanism have also been linked to the crisis, but the short-term nature of these episodes (<decades) and the overwhelming evidence for rapid warming during the crisis makes this an unlikely cause. Finally, whilst the extinction is well studied in equatorial latitudes, a different history is found in northern Boreal latitudes including an earlier crisis which merits further study in order to fully understand the course and cause of the Permo-Triassic extinctions.
The evolution of herbicide resistance in weeds is a problem affecting both food production and ecosystems. Numerous factors affect selection towards herbicide resistance, making it difficult to anticipate where, under what circumstances, and under what timeframe, herbicide resistance is likely to appear. Using the International Herbicide-Resistant Weed Database to provide data on locations and situations where resistance has occurred, we trained models to predict where resistance is most likely in future. Validation of the global models with historical data found a prediction accuracy of up to 78%, while for well-sampled regions, such as Australia, the model correctly predicted more than 95% of instance of resistance and sensitivity. Applying the models to predict instances of resistance over the next decade, future hotspots were detected in North and South America and Australia. Species such as Conyza canadensis, Eleusine indica, and Lactuca serriola are expected to show substantial increases in the number of resistance occurrences. The results highlight the potential of machine-learning approaches in predicting future resistance hotspots and urge more efforts in resistance monitoring and reporting to enable improved predictions. Future work incorporating dimensions such as weed traits, phylogeny, herbicide chemistry, and farming practices could improve the predictive power of the models.
Understanding palaeodiversity dynamics through time and space is a central goal of macroevolution. Estimating palaeodiversity dynamics has been historically addressed with fossil data because it directly reflects the past variations of biodiversity. Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful to estimate diversification dynamics. Recent methodological developments have unlocked the possibility to investigate palaeodiversity dynamics by using phylogenetic birth‐death models with non‐homogeneous rates through time and across clades. One of them seems particularly promising to detect clades whose diversity has declined through time. However, empirical applications of the method have been hampered by the lack of a robust, accessible implementation of the whole procedure, therefore requiring users to conduct all the steps of the analysis by hand in a time‐consuming and error‐prone way.
Here we propose an automation of Morlon et al. (2011) clade‐shift model with additional features accounting for recent developments, and we implement it in the R package RPANDA. We also test the approach with simulations focusing on its ability to detect shifts of diversification and to infer palaeodiversity dynamics. Finally, we illustrate the automation by investigating the palaeodiversity dynamics of Cetacea, Vangidae, Parnassiinae and Cycadales.
Simulations showed that we accurately detected shifts of diversification although false shift detections were higher for time‐dependent diversification models with extinction. The median global error of palaeodiversity dynamics estimated with the automated model is low, showing that the method can capture diversity declines. We detected shifts of diversification for three of the four empirical examples considered (Cetacea, Parnassiinae and Cycadales). Our analyses unveil a waxing‐and‐waning pattern due to a phase of negative net diversification rate embedded in the trees after isolating recent radiations.
Our work makes it possible to easily apply non‐homogeneous models of diversification in which rates can vary through time and across clades to reconstruct palaeodiversity dynamics. By doing so, we detected palaeodiversity declines among three of the four groups tested, highlighting that such periods of negative net diversification might be common. We discuss the extent to which this approach might provide reliable estimates of extinction rates, and we provide guidelines for users.
The major obstacle to Martian colonization is the mission cost which requires significant reduction. From the structural engineering point of view, importing materials and structural elements from Earth or massive excavations on the surface of Mars require an enormous amount of energy; thus, inflatable and under-surface structures as the main options for Martian colonization seem unrealistically expensive. Construction of affordable buildings onsite using only in situ sources may represent an ideal solution for Martian colonization. On the other hand, solar energy, at the early stage of colonization, would be the only available, practical, and low-cost energy source on Mars. Though, for sustainable and broad colonization, the energy required for construction and the construction cost should be minimized. Here, we propose three types of simple (relatively optimized), perforated, and algorithmic shape-optimized Martian structures to minimize the material and energy required for construction as well as the construction cost using only in situ resources. These structural forms can be considered remarkable steps towards sustainable structural construction and colonization on Mars. Also, these innovative structures were designed to minimize the tensile stress (maximize the compressive stress) and enable the use of in situ concrete. Our data indicate that compared to our previous study, the material and energy required for construction as well as the construction cost can be reduced by more than 50%. Acceptance criteria and limitations appropriate to the Martian environment, and desirable structural and material behaviors were defined to evaluate whether or not the behavior of a structure under the applied loads and conditions will be acceptable. To detect potential issues for onsite construction and evaluate the geometry of the models, a 1:200 3D model of the best structural form was printed.
The body size of marine ectotherms is often negatively correlated with ambient water temperature, as seen in many clades during the hyperthermal crisis of the end-Permian mass extinction (c. 252 Ma). However, in the case of ostracods, size changes during ancient hyperthermal events are rarely quantified. In this study, we evaluate the body size changes of ostracods in the Aras Valley section (northwest Iran) in response to the drastic warming during the end-Permian mass extinction at three taxonomic levels: class, order, species. At the assemblage level, the warming triggers a complete species turnover in the Aras Valley section, with larger, newly emerging species dominating the immediate post-extinction assemblage for a short time. Individual ostracod species and instars do not show dwarfing or a change in body size as an adaptation to the temperature stress during the end-Permian crisis. This may indicate that the ostracods in the Aras Valley section might have been exceptions to the temperature–size rule (TSR), using an adaptation mechanism that does not involve a decrease in body size. This adaptation might be similar to the accelerated development despite constant instar body sizes that can be observed in some recent experimental studies of ostracod responses to thermal stress.
The fossil record reveals that biotic diversity has fluctuated quasi-cyclically through geological time. However, the causal mechanisms of biotic diversity cycles remain unexplained. Here, we highlight a common, correlatable 36 ± 1 Myr (million years) cycle in the diversity of marine genera as well as in tectonic, sea-level, and macrostratigraphic data over the past 250 Myr of Earth history. The prominence of the 36 ± 1 Myr cycle in tectonic data favors a common-cause mechanism, wherein geological forcing mechanisms drive patterns in both biological diversity and the preserved rock record. In particular, our results suggest that a 36 ± 1 Myr tectono-eustatically driven sea-level cycle may originate from the interaction between the convecting mantle and subducting slabs, thereby pacing mantle-lithospheric deep-water recycling. The 36 ± 1 Myr tectono-eustatic driver of biodiversity is likely related to cyclic continental inundations, with expanding and contracting ecological niches on shelves and in epeiric seas.
Understanding 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.
One of the many contributions paleontology makes to our understanding of the biosphere and its evolution is a direct temporal record of biotic events. However, assuming fossils have been correctly identified and accurately dated, stratigraphic ranges underestimate true temporal ranges: observed first occurrences are too young, and observed last occurrences are too old. Here I introduce the techniques developed for placing confidence intervals on the end-points of stratigraphic ranges. I begin with the analysis of single taxa in local sections – with the simplest of assumptions – random fossilization. This is followed by a discussion of the methods developed to handle the fact that the recovery of fossils is often non-random in space and time. After discussion of how confidence intervals can be used to test for simultaneous origination and extinctions, I conclude with an example application of confidence intervals to unravel the relative importance of background extinction, environmental change and mass extinction of ammonite species at the end of the Cretaceous in western Tethys.
By comparing detrended estimates of diversity (taxonomic richness) and rates of origination, extinction, and net diversification, I show that at the global scale over the course of the Phanerozoic eon, rates of diversification and origination are negatively correlated with diversity. By contrast, extinction rates are only weakly correlated with diversity for the most part. These results hold for both genus- and species-level data and for many alternative analytical protocols. The asymmetry between extinction on the one hand and origination and net diversification on the other hand supports a model whereby extinction is largely driven by abiotic perturbations, with subsequent origination filling the void left by depleted diversity. Diversity dependence is somewhat weaker, but still evident, if the initial Ordovician radiation or rebounds from major mass extinctions are omitted from analysis; thus, diversity dependence is influenced, but not dominated, by these special intervals of Earth history. In the transition from Paleozoic to post-Paleozoic time, diversity dependence of origination weakens while that of extinction strengthens; however, diversity dependence of net diversification barely changes in strength. Despite nuances, individual clades largely yield results consistent with those for the aggregate data on all animals. On the whole, diversity-dependent diversification appears to be a pervasive factor in the macroevolution of marine animal life.
Unlabelled:
The Smithian-Spathian boundary (SSB) crisis played a prominent role in resetting the evolution and diversity of the nekton (ammonoids and conodonts) during the Early Triassic recovery. The late Smithian nektonic crisis culminated at the SSB, ca. 2.7 Myr after the Permian-Triassic boundary mass extinction. An accurate and high-resolution biochronological frame is needed for establishing patterns of extinction and re-diversification of this crisis. Here, we propose a new biochronological frame for conodonts that is based on the Unitary Associations Method (UAM). In this new time frame, the SSB can thus be placed between the climax of the extinction and the onset of the re-diversification. Based on the study of new and rich conodont collections obtained from five sections (of which four are newly described here) in the Nanpanjiang Basin, South China, we have performed a thorough taxonomical revision and described one new genus and 21 new species. Additionally, we have critically reassessed the published conodont data from 16 other sections from South China, and we have used this new, standardized dataset to construct the most accurate, highly resolved, and laterally reproducible biozonation of the Smithian to early Spathian interval for South China. The resulting 11 Unitary Association Zones (UAZ) are intercalibrated with lithological and chemostratigraphical (δ13Ccarb) markers, as well as with ammonoid zones, thus providing a firm basis for an evolutionary meaningful and laterally consistent definition of the SSB. Our UAZ8, which is characterized by the occurrence of Icriospathodus ex gr. crassatus, Triassospathodus symmetricus and Novispathodus brevissimus, is marked by a new evolutionary radiation of both conodonts and ammonoids and is within a positive peak in the carbon isotope record. Consequently, we propose to place the SSB within the separation interval intercalated between UAZ7 and UAZ8 thus leaving some flexibility for future refinement and updating.
Supplementary information:
The online version contains supplementary material available at 10.1186/s13358-022-00259-x.
Recent advances in Artificial Intelligence (AI), particularly the rise of deep learning, are revolutionizing data collection and analysis in many aspects of the Earth Sciences, including paleontology. Rapid digital transformation of paleontological information enables automation of various paleontological tasks using AI technology. One such task is identifying and classifying skeletal grains at different levels of the Linnaean taxonomic hierarchy, both macro- and microscopically. Unfortunately, fossil classification remains largely untouched by AI due to the expertise and time required to generate high-quality, large-scale labeled training data. This task is particularly challenging when part of the compositional analysis of limestone, where three-dimensional objects (i.e., skeletal grains) are observed in a two-dimensional cross-section. It is compounded by the imbalanced data and limited number of images available, approximately four orders smaller than the number necessary to train deep neural networks. Recent efforts to classify such fossil images using deep learning returned a single output/label classification, limiting the information output from the model, and hindering its further applications to replicate paleontologist-level identification. Here, we couple a multi-head deep convolutional neural network architecture called TaxonNet that adopts the Branch Convolutional Neural Networks and advanced image augmentation to overcome these barriers. This model uses prior knowledge of hierarchical category relationships to output multiple hierarchical taxonomic predictions from a single petrographic image. In this study, we developed and evaluated four different strategies of hierarchical classification: (i) forward (coarse to fine); (ii) reverse (fine to coarse); (iii) parallel (coarse and fine simultaneously), and (iv) hybrid. The forward and reverse strategies yield the most accurate prediction of ~95 % accuracy for coarse-level and fine-level recognitions across major fossil types in carbonate petrographic images, including algae, mollusks, and corals. These results represent an important step toward applying AI to advance fossil grain classification and exhibit a promising real-world geological application of a hierarchical network in paleontology, sedimentary petrography, and other image-based geological analysis requiring hierarchical, multilabel output.
Biodiversity on Earth is shaped by abiotic perturbations and rapid diversifications. At the same time, there are arguments that biodiversity is bounded and regulated via biotic interactions. Evaluating the role and relative strength of diversity regulation is crucial for interpreting the ongoing biodiversity changes. We have analyzed Phanerozoic fossil record using public databases and new approaches for identifying the causal dependence of origination and extinction rates on environmental variables and standing diversity. While the effect of environmental factors on origination and extinction rates is variable and taxon specific, the diversity dependence of the rates is almost universal across the studied taxa. Origination rates are dependent on instantaneous diversity levels, while extinction rates reveal delayed diversity dependence. Although precise mechanisms of diversity dependence may be complex and difficult to recover, global regulation of diversity via negative diversity dependence of lineage diversification seems to be a common feature of the biosphere, with profound consequences for understanding current biodiversity crisis.
Quantitative phylogenetic inference estimates the probability of observed character distributions given trees and rates. Most available programs for doing this assume (tacitly or explicitly) that the sampled taxa are contemporaneous. However, paleontologists usually sample taxa over a clade's history. Thus, we must estimate the probability of observed character-state distributions over time given trees and rates. When we include information about sampling intensity, then we really are estimating the probability of the observed record given trees and rates. Some additional problems that should be issues for neontologists, but which are much more obvious concerns for paleontologists include: 1) ancestor-descendant relationships; 2) punctuated versus continuous morphological change; and, 3) the effects of extinction and speciation rates on prior probabilities of trees. Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, our tests of phylogeny are really tests of evolutionary histories.
The Triassic-Jurassic boundary is one of the most important geological boundaries in the Earth's evolutionary history. Previous paleoclimate studies focused primarily on Tethys realm at low and middle latitudes, while the northern hemisphere has yet to be studied. Here, we report Mg-Zn-Cu isotopic data for a continuous terrestrial sedimentary section in the southern margin of the Junggar Basin to constrain chemical weathering intensity and climatic change during this critical interval at high latitude. This section is enriched in heavy Mg isotopes with δ²⁶Mg ranging from 0.08‰ to 0.43‰. It displays a decreasing Zn isotopic composition with δ⁶⁶Zn ranging from −0.05‰ to 0.24‰, as well as limited Cu isotope fractionation (δ⁶⁵Cu = −0.06‰ to 0.09‰). These isotopic results, combined with major and trace elemental variations, suggest a reduced sedimentary environment and increasingly intensive chemical weathering across the boundary, responding to a warmer and more humid paleoclimate. Compared with other places located around Tethys, this regional climatic change in high latitude areas can be linked to known global climate change during this period. Our study provides new insights from high-latitude Asia to reconstruct the global pattern of climate change at the Triassic-Jurassic boundary.
The assumption that exoplanets are ‘in equilibrium’ with their surroundings has not given way to life's transmissivity on large spatial scales. The spread of human diseases and the life recovery rate after mass extinctions on our planet, on the other hand, may exhibit spatial and temporal scaling as well as distribution correlations that influence the mappable range of their characteristics. We model hypothetical bio-dispersal within a single Galactic region using the stochastic infection dynamics process, which is inspired by these local properties of life dispersal on Earth. We split the population of stellar systems into different categories regarding habitability and evolved them through time using probabilistic cellular automata rules analogous to the model. As a dynamic effect, we include the existence of natural dispersal vectors (e.g. dust, asteroids) in a way that avoids assumptions about their agency (i.e. questions of existence). Moreover, by assuming that dispersal vectors have a finite velocity and range, the model includes the parameter of ‘optical depth of life spreading’. The effect of the oscillatory infection rate ( $b( t,\; \, d)$ ) on the long-term behaviour of the dispersal flux, which adds a diffusive component to its progression, is also taken into account. The life recovery rate ( $g( t,\; \, d)$ ) was only included in the model as a link to macrofaunal diversity data, which shows that all mass extinctions have a 10 Myr ‘speed rate’ in diversity recovery. This parameter accounts for the repopulation of empty viable niches as well as the formation of new ones, without ruling out the possibility of genuine life reemergence on other habitable worlds in the Galaxy that colossal extinctions have sterilized. All life-transmission events within the Galactic patch have thus been mapped into phase space characterized by parameters $b$ and $g$ . We found that phase space is separated into subregions of long-lasting transmission, rapidly terminated transmission, and a transition region between the two. We observed that depending on the amplitude of the oscillatory life-spreading rate, life-transmission in the Galactic patch might take on different geometrical shapes (i.e. ‘waves’). Even if some host systems are uninhabited, life transmission has a certain threshold, allowing a patch to be saturated with viable material over a long period. Although stochastic fluctuations in the local density of habitable systems allow for clusters that can continuously infect one another, the spatial pattern disappears when life transmission is below the observed threshold, so that transmission process is not permanent in time. Both findings suggest that a habitable planet in a densely populated region may remain uninfected.
Over the past decade, a new set of methods for estimating dated trees has emerged. Originally referred to as the fossilized birth–death (FBD) process, this single model has expanded to a family of models that allows researchers to coestimate evolutionary parameters (e.g., diversification, sampling) and patterns alongside divergence times for a variety of applications from paleobiology to real-time epidemiology. We provide an overview of this family of models. We explore the ways in which these models correspond to methods in quantitative paleobiology, as the FBD process provides a framework through which neontological and paleontological approaches to phylogenetics and macroevolution can be unified. We also provide an overview of challenges associated with applying FBD models, particularly with an eye toward the fossil record. We conclude this piece by discussing several exciting avenues for the inclusion of fossil data in phylogenetic analyses.
Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 53 is November 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
The “Agriopleura event”, which expresses the regional extinction, in northwestern Europe, of the rudist genus Agriopleura, is associated with environmental and biological changes. This event marks the boundary between two distinctive late Barremian regional rudist assemblages, the pre-event Brouzet-les-Alès and post-event Orgon faunas. The succeeding Palorbitolina episode is coeval with a rudist eclipse. The ensuing Rustrel fauna identifies the phase of post-extinction recovery. The last occurrence of Agriopleura, the stem genus of the Radiolitidae, coincides with the extinction of 41% of the pre-event Requieniidae and Monopleuridae. The recovery phase is characterized by new species and a low extinction pattern. This phase is marked by a burst of speciation, in part indigenous and in part due to immigrants i.e. Caprinidae. The key morphotypes, clingers, elevators and recumbents record contrasting changes in specific diversity, clingers being dominant due to the substantial diversity of Requieniidae and Monopleuridae. During the extinction event elevators decrease and suffered a reduction in size, large size species being selectively eliminated. The entry of the Caprinidae identifies the recovery phase and accounts for size increase and an important contribution of recumbent. The main agent of the extinction, combines cooling, anoxia, platform exposure and a trophic factor assumed to account for the selective removal of the elevators. A dual partition in feeding behavior of clingers and elevators is suggested: elevators exploiting the phytoplankton flux and the re-suspended bottom biodeposits; and clingers feeding on the benthic boundary layer. Significant community changes are associated with Agriopleura extinction and its aftermath, which clearly respond to changes in taxonomic composition. Elevator dominated communities with the Agriopleura are replaced by polytaxic requieniid rich communities then by caprinids. The Palorbitolina episode, records a trophic peak, cooling and a deepening trend. The recovery phase mainly records an aragonitic pulse coupled with temperature increase.
During the mid-Palaeozoic, vascular land plants (i.e., tracheophytes) underwent a great radiation that triggered the development of the land biosphere – the so-called Silurian–Devonian terrestrial revolution. However, little is known about how different plant groups impacted this process. A newly constructed dataset of plant macrofossil genera is used to characterize the tempo and mode of development of Silurian–Devonian vegetation and how it spread out over subaerial habitats. Important fluctuations of diversity and evolutionary rates of vegetation are linked to the diversity dynamics of particular tracheophyte groups. Despite a general increase of taxonomic richness through the Devonian, there was a clear stepwise pattern of origination and extinction events that resulted in the main floral transitions over time, such as the change to a forested landscape. To test if sampling bias may be affecting the observed diversity patterns, the latter were compared with the number of plant macrofossil localities as a proxy for sampling effort. This suggested a highly significant correlation between observed diversity and sampling effort, but it was not homogeneous, suggesting that at least some diversity fluctuations have a potential biological explanation. The sampling-corrected pattern of standing diversity suggests a clear increase of plant richness in the Pragian (Early Devonian) and Givetian (Middle Devonian), which may be related to the early expansion of the tracheophyte clades and the initial diversification of forested ecosystems, respectively. Further works should be focused on elucidate the impact of rock record on our understanding of Devonian plant diversification.
The diversification of the three major marine faunas during the Phanerozoic was intimately coupled to the evolution of the biogeochemical cycles of carbon and nutrients via nutrient runoff from land and the diversification of phosphorus-rich phytoplankton. Nutrient input to the oceans has previously been demonstrated to have occurred in response to orogeny and fueling marine diversification. Although volcanism has typically been associated with extinction, the eruption of continental Large Igneous Provinces (LIPs) is also a very significant, but previously overlooked, source of phosphorus involved in the diversification of the marine biosphere. We demonstrate that phosphorus input to the oceans peaked repeatedly following the eruption and weathering of LIPs, stimulating the diversification of nutrient-rich calcareous and siliceous phytoplankton at the base of marine food webs that in turn helped fuel diversification at higher levels. These developments were likely furthered by the evolution of terrestrial floras. Results for the Meso-Cenozoic hold implications for the Paleozoic Era. Early-to-middle Paleozoic diversity was, in contrast to the Meso-Cenozoic, limited by nutrient-poor phytoplankton resulting from less frequent tectonism and poorly-developed terrestrial floras. Nutrient runoff and primary productivity during the Permo-Carboniferous likely increased, based on widespread orogeny, the spread of deeper-rooting forests, the fossil record of phytoplankton, and biogeochemical indices. Our results suggest that marine biodiversity on geologic time scales is unbounded (unlimited), provided sufficient habitat, nutrients, and nutrient-rich phytoplankton are also available in optimal amounts and on optimal timescales.
The dynamics of extinction and diversification determine the long-term effects of extinction episodes. If rapid bursts of extinction are offset by equally rapid bursts of diversification, their biodiversity consequences will be transient. But if diversification rates cannot accelerate rapidly enough, pulses of extinction will lead to long-lasting depletion of biodiversity. Here I use spectral analysis of the fossil record to test whether diversification rates can accelerate as much as extinction rates, over both short and long spans of geological time. I show that although the long-wavelength variability of diversification rates equals or exceeds that of extinctions, diversification rates are markedly less variable than extinction rates at wavelengths shorter than roughly 25 million years. This implies that there are intrinsic speed limits that constrain how rapidly diversification rates can accelerate in response to pulses of extinction.
In post-Cambrian time, five events—the end-Ordovician, end-Frasnian in the Late De-vonian, end-Permian, end-Triassic, and end-Cretaceous—are commonly grouped as the ''big five'' global intervals of mass extinction. Plotted by magnitude, extinction intensities for all Phanerozoic substages show a continuous distribution, with the five traditionally recognized mass extinctions located in the upper tail. Plotted by time, however, proportional extinctions clearly divide the Phan-erozoic Eon into six stratigraphically coherent intervals of alternating high and low extinction in-tensity. These stratigraphic neighborhoods provide a temporal context for evaluating the intensity of extinction during the ''big five'' events. Compared with other stages and substages in the same neighborhood, only the end-Ordovician, end-Permian, and end-Cretaceous extinction intensities appear as outliers. Moreover, when origination and extinction are considered together, only these three of the ''big five'' events appear to have been generated exclusively by elevated extinction. Low origination contributed more than high extinction to the marked loss of diversity in the late Fras-nian and at the end of the Triassic. Therefore, whereas the ''big five'' events are clearly times when diversity suffered mass depletion, only those at the end of the Ordovician, Permian, and Cretaceous periods unequivocally qualify as globally distinct mass extinctions. Each of the three has a unique pattern of extinction, and the diversity dynamics of these events differ, as well, from the other two major diversity depletions. As mass depletions of diversity have no common effect, common cau-sation seems unlikely.
Recent Fourier analyses of fossil extinction data have indicated that
the power spectrum of extinction during the Phanerozoic may take the
form of 1/f noise, a result which, it has been suggested, could be
indicative of the presence of "critical dynamics" in the processes
giving rise to extinction. In this paper we examine extinction power
spectra in some detail, using family-level data from a variety of
different sources. We find that although the average form of the power
spectrum roughly obeys the 1/f law, the spectrum can be represented more
accurately by dividing it into two regimes: a low-frequency one which is
well fit by an exponential, and a high-frequency one in which it follows
a power law with a 1/f^2 form. We give explanations for the occurrence
of each of these behaviours and for the position of the cross-over
between them.
Paleobiologists have used taxonomic data for several types of diversity studies. Some systematists have charged that this practice obfuscates actual historical patterns of clades because many traditionally defined higher taxa are not monophyletic. Some have questioned whether ranked taxa ever represent comparable units, even when monophyletic. This study contrasts diversity patterns implied by phylogenetic estimates with those implied by ranked taxa. Early Paleozoic gastropods are useful as a test case because their generic taxonomy does not reflect the phylogenetic systematic philosophy, and fewer than one third of the genera represent monophyletic clades. Phylogenetic diversity is described in two ways: (1) numbers of lineages (i.e., observed plus phylogenetically implied “ghost lineages”), and (2) numbers of monophyla (i.e., clades whose sister taxa are other clades rather than species). “Monophyla” as tallied here are monophyletic relative to their contemporaries and older clades; however, they can be paraphyletic relative to “future” monophyla. Phylogenetic diversity is tallied with both maximum and minimum “ghost lineage” interpolations in order to reflect different possible speciation patterns and timings of speciation. Phylogenetic diversity as implied by a stricter cladistic criterion (i.e., taxa that are monophyletic relative to their contemporaries, older taxa and younger taxa) is discussed also.
First differences between substage-to-substage standing diversities reveal significant congruence between generic data and both types of phylogenetic data. Taxonomic and phylogenetic data imply a major extinction event at the end of the Ordovician, although the phylogenetic data suggest greater extinction levels than do the taxonomic data. Both data sets also suggest diversity-dependent diversification reminiscent of logistic growth, which is the pattern predicted if one or a few major ecologic factors were constraining the diversification of gastropods. However, diversity described by strict Hennigian taxa is not highly congruent with diversity as described by either lineages or monophyla. Comparing subclade dynamics requires extensive redefinition of traditional orders, but lineages, monophyla and genera all suggest that the two major subclades had different logistic diversification patterns, with one (“murchisonioids”) having a higher K than the other (“euomphaloids”). The concern that phylogenetic and taxonomic data might imply very different evolutionary histories is not borne out by gastropods, despite the nonphylogenetic nature of their traditional taxonomy.
The dynamical processes underlying evolution over geological timescales
remain unclear,. Analyses of time series of the fossil record have
highlighted the possible signature of periodicity in mass extinctions,,
perhaps owing to external influences such as meteorite impacts. More
recently the fluctuations in the evolutionary record have been proposed
to result from intrinsic nonlinear dynamics for which self-organized
criticality provides an appropriate theoretical framework. A consequence
of this controversial conjecture is that the fluctuations should be
self-similar, exhibiting scaling behaviour like that seen in other
biological and socioeconomic, systems. The self-similar character is
described by a 1/f power spectrum P(f), which measures the contributions
of each frequency f to the overall time series. If self-similarity is
present, then P(f) ~ f - β with 0 < β <2.
This idea has not been sufficiently tested, however, owing to a lack of
adequate data. Here we explore the statistical fluctuation structure of
several time series obtained from available palaeontological data bases,
particularly the new `Fossil Record 2'. We find that these data indeed
show self-similar fluctuations characterized by a 1/f spectrum. These
findings support the idea that a nonlinear response of the biosphere to
perturbations provides the main mechanism for the distribution of
extinction events.
Statistical analyses of the fossil record seek to discover the mechanisms controlling biotic diversity throughout the Earth's history. Solé et al.1 reported that many extinction time series are statistically self-similar, with 1/f power spectra, suggesting that extinctions are driven by self-organized criticality or by other scale-free internal dynamics of the biosphere. Here we show that the apparent self-similarity and 1/f scaling reported by Solé et al. are artefacts of their interpolation methods. Extinction records that are not interpolated show no evidence of fractal scaling.
Many features of global diversity compilations have proven robust to continued sam- pling and taxonomic revision. Inherent biases in the stratigraphic record may nevertheless sub- stantially affect estimates of global taxonomic diversity. Here we focus on short-term (epoch-level) changes in apparent diversity. We use a simple estimate of the amount of marine sedimentary rock available for sampling: the number of formations in the stratigraphic Lexicon of the United States Geological Survey. We find this to be positively correlated with two independent estimates of rock availability: global outcrop area derived from the Paleogeographic Atlas Project (University of Chi- cago) database, and percent continental flooding. Epoch-to-epoch changes in the number of for- mations are positively correlated with changes in sampled Phanerozoic marine diversity at the genus level. We agree with previous workers in finding evidence of a diversity-area effect that is substantially weaker than the effect of the amount of preserved sedimentary rock. Once the mutual correlation among change in formation numbers, in diversity, and in area flooded is taken into consideration, there is relatively little residual correlation between change in diversity and in the extent of continental flooding. These results suggest that much of the observed short-term variation in marine diversity may be an artifact of variation in the amount of rock available for study. Pre- liminary results suggest the same possibility for terrestrial data. Like the comparison between change in number of formations and change in sampled diversity, which addresses short-term variation in apparent diversity, the comparison between absolute val- ues of these quantities, which relates to longer-term patterns, also shows a positive correlation. Moreover, there is no clear temporal trend in the residuals of the regression of sampled diversity on number of formations. This raises the possibility that taxonomic diversity may not have in- creased substantially since the early Paleozoic. Because of limitations in our data, however, this question must remain open.
During the Ordovician Radiation, domination of benthic marine communities shifted away from trilobites, toward articulate brachiopods, and, to a lesser degree, toward bivalves and gastropods. In this paper, we identify the patterns in origination and extinction probabilities that gave rise to these transitions. Using methods adapted from capture-mark-recapture (CMR) pop-ulation studies, we estimate origination, extinction, and sampling probabilities jointly to avoid con-founding patterns in turnover rates with temporal variation in the quality of the fossil record. Not surprisingly, higher extinction probabilities in trilobites relative to articulate brachiopods, bivalves, and gastropods were partly responsible for relative decreases in trilobite diversity. However, ar-ticulate brachiopods also had higher origination probabilities than trilobites, indicating that rela-tive increases in articulate brachiopod diversity would have occurred even in the absence of be-tween-class differences in extinction probabilities. This contrasts with inferences based on earlier Phanerozoic-scale, long-term averages of turnover probabilities, and it indicates that a major cause of this faunal transition has been overlooked.
Short-term variations in rates of taxonomic extinction and origination in the fossil record may be the result of true changes in rates of turnover, variable rates of fossil preservation, or some combination of the two. Here, positive extinction and origination rate excursions among Phaner-ozoic marine animal genera are reexpressed in terms of the amount of normal, background time they represent. In addition to providing a background-adjusted calibration of rate intensities, this reexpression determines the durations of sampling gaps that would be required to explain entirely all observed rate excursions as sampling artifacts. This possibility is explored by analyzing a new compilation of the timing and duration of sedimentary hiatuses in North America. Hiatuses spanning more than approximately one million years (Myr) in the marine sedimentary rock record have a mean duration of 73 Myr. There are two major hiatus types—those that form in response to long-duration tectonic cycles and that bound the major Sloss-scale sequences (mean duration 200 Myr), and those that form in response to shorter-duration changes in sediment ac-commodation space and that occur within major Sloss-scale sequences (mean duration less than 23 Myr). The latter are approximately exponentially distributed and have a mean duration that is comparable to the mean duration of intervening sedimentary rock packages. Although sedimentary hiatuses are generally long enough in duration to accommodate the hy-pothesis that short-term variations in rates of genus origination and extinction are artifacts of sam-pling failures at major unconformities (''Unconformity Bias'' hypothesis), the observed evolution-ary rates are not correlated with hiatus durations. Moreover, hiatuses that follow the major mass extinctions are not long in comparison to most other non–mass extinction intervals. These results do not support the hypothesis that hiatuses at major unconformities alone have artificially clustered genus first and last occurrences, thereby causing many of the documented statistical similarities between the temporal structure of the sedimentary rock record and macroevolutionary patterns. Instead, environmental changes related to the expansion and contraction of marine environments may have been the primary forcers of both biological turnover and the spatio-temporal pattern of sediment accumulation. Fully testing this ''Common Cause'' hypothesis requires quantifying and overcoming lingering taxonomic, biostratigraphic, facies, and numerous other biases that are both inherent in geologic data and imposed by imperfect knowledge of the fossil record.
A simple equilibrial model for the growth and maintenance of Phanerozoic global marine taxonomie diversity can be constructed from considerations of the behavior of origination and extinction rates with respect to diversity. An initial postulate that total rate of diversification is proportional to number of taxa extant leads to an exponential model for early phases of diversification. This model appears to describe adequately the “explosive” diversification of known metazoan orders across the Precambrian-Cambrian Boundary, suggesting that no special event, other than the initial appearance of Metazoa, is necessary to explain this phenomenon. As numbers of taxa increase, the rate of diversification should become “diversity dependent.” Ecological factors should cause the per taxon rate of origination to decline and the per taxon rate of extinction to increase. If these relationships are modeled as simple linear functions, a logistic description of the behavior of taxonomie diversity through time results. This model appears remarkably consistent with the known pattern of Phanerozoic marine ordinal diversity as a whole. Analysis of observed rates of ordinal origination also indicates these are to a large extent diversity dependent; however, diversity dependence is not immediately evident in rates of ordinal extinction. Possible explanations for this pattern are derived from considerations of the size of higher taxa and from simulations of their diversification. These suggest that both the standing diversity and the pattern of origination of orders may adequately reflect the behavior of species diversity through time; however, correspondence between rates of ordinal and species extinction may deteriorate with progressive loss of information resulting from incomplete sampling of the fossil record.
Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.
The kinetic model of taxonomic diversity predicts that the long-term diversification of taxa within any large and essentially closed ecological system should approximate a logistic process controlled by changes in origination and extinction rates with changing numbers of taxa. This model is tested with a new compilation of numbers of metazoan families known from Paleozoic stages (including stage-level subdivisions of the Cambrian). These data indicate the occurrence of two intervals of logistic diversification within the Paleozoic. The first interval, spanning the Vendian and Cambrian, includes an approximately exponential increase in families across the Precambrian-Cambrian Boundary and a “pseudo-equilibrium” through the Middle and Late Cambrian, caused by diversity-dependent decrease in origination rate and increase in extinction rate. The second interval begins with a rapid re-diversification in the Ordovician, which leads to a tripling of familial diversity during a span of 50 Myr; by the end of the Ordovician diversity attains a new dynamic equilibrium that is maintained, except for several extinction events, for nearly 200 Myr until near the end of the Paleozoic. A “two-phase” kinetic model is constructed to describe this heterogeneous pattern of early Phanerozoic diversification. The model adequately describes the “multiple equilibria,” the asymmetrical history of the “Cambrian fauna,” the extremely slow initial diversification of the later “Paleozoic fauna,” and the combined patterns of origination and extinction in both faunas. It is suggested that this entire pattern of diversification reflects the early success of ecologically generalized taxa and their later replacement by more specialized taxa.
The per-stage extinction rate is the product of the per-taxon extinction rate and stage length, and the per-stage origination rate is defined similarly. These rates decline from ancient to recent times because of the pull of the Recent, because there is more young than old fossiliferous rock, and because average stage length increases from the recent to the past. More specifically, the present model assumes that the graphs of ln(per-stage extinction rate) and ln(per-stage origination rate) versus geologic time have slope zero in the absence of sampling biases, and shows how sampling biases cause both these graphs to appear to have slope min( h,q ) + s in the distant past, where h and q are the fossil loss and actual per-taxon extinction rates, and the stratigraphic constant, s, quantifies how stage length changes through time.
Although the per-stage rates of bivalve families and marine invertebrate genera decline toward the recent, the magnitudes of these declines are entirely consistent with what the present model predicts sampling biases will produce. Hence there is no need to postulate a biological explanation for these patterns.
The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.
On the basis of about 70,000 species citations in the Zoological Record , it is estimated that about 190,000 fossil invertebrate species were described and named through 1970. The true figure may be higher because of incompleteness of the Zoological Record or lower because the estimate does not account for synonymy.
About 70% of the species were described from USSR, Europe, and North America. About 42% are Paleozoic, 28% Mesozoic, and 30% Cenozoic. In the Cambrian part of the sample, 75% of the species are trilobites. In the Mesozoic and Cenozoic, about 70% are either molluscs or protozoans.
When the data are normalized for absolute time, diversity (species per million years) shows a Paleozoic high in the Devonian which is approximately four-tenths of the Cenozoic level.
The fossil record of Phanerozoic brachiopod genera and Late Cenozoic New World mammal genera is examined for evidence of evolutionary equilibria. One necessary (but insufficient) condition is met: within temporal intervals, numbers of originations correlate with numbers of extinctions. Eliminating temporally short-ranging brachiopods, however, reduces the correlation so that it explains only 16% of the variation. More decisive tests of the equilibrium hypothesis appear impossible with available data. Difficulties of temporal and geographic scale, taxonomic level, and ecological consistency must be resolved before equilibrium models can be applied in paleontology for other than inspiration.
During the Ordovician Radiation, domination of benthic marine communities shifted away from trilobites, toward articulate brachiopods, and, to a lesser degree, toward bivalves and gastropods. In this paper, we identify the patterns in origination and extinction probabilities that gave rise to these transitions. Using methods adapted from capture-mark-recapture (CMR) population-studies, we estimate origination, extinction, and sampling probabilities jointly to avoid confounding patterns in turnover rates with temporal variation in the quality of the fossil record. Not surprisingly, higher extinction probabilities in trilobites relative to articulate brachiopods, bivalves, and gastropods were partly responsible for relative decreases in. trilobite diversity. However, articulate brachiopods also had higher origination probabilities than trilobites, indicating that relative increases in articulate brachiopod diversity would have occurred even in the absence of between-class differences in extinction probabilities. This contrasts with inferences based on earlier Phanerozoic-scale, long-term averages of turnover probabilities, and it indicates that a major cause of this faunal transition has been overlooked.
Time series of global diversity and extinction intensity measured from data on stratigraphic ranges of marine animal genera show the impact of bio-events on the fauna of the world ocean. Measured extinction intensities vary greatly, from major mass extinctions that eradicated 39 to 82% of generic diversity to smaller events that had substantially less impact on the global fauna. Many of the smaller extinction events are clearly visible only after a series of filters are applied to the data. Still, most of these extinction events are also visible in a smaller set of data on marine families. Although many of the episodes of extinction seen in the global data are well known from detailed biostratigraphic investigations, some are unstudied and require focused attention for confirmation or refutation.
Tropical countries have many times more species of most taxa than temperate ones, and small areas in the tropics have a smaller multiple of the number of species of small temperate areas. Where many species are present, abundances tend to be more equal and geographic distributions more spotty. Most tropical environments are less seasonal and more productive, and the dry areas and mountains which are relatively more seasonal and less productive have fewer species. The species which have reached offshore islands are often much commoner there and occupy expanded habitats.
To account for these relations, the following general hypothesis seems necessary:species interactions are important and the tropics have a head start on speciation. The head start, or greater rate, allows extra species to pile up in the tropics, but because of the importance of competition, no single area becomes as greatly enriched. Rather, faunal differences between areas increase. The lesser excess of tropical species in small areas is largely due to greater productivity and reduced seasonality which make marginal ways of life profitable. With more overlap in resources, the closely packed tropical species have more uniform abundances and the coexistence of these species is more precarious, causing the spotty geographic distributions.
Neither the species diversity of the food supply nor the longer breeding season (supposedly allowing staggered nesting seasons with an early shift and a later shift) is relevant to bird species diversity.
Changes in genus diversity within higher taxa of marine animals on the temporal scale of a few million years are more strongly correlated with changes in extinction rate than with chang- es in origination rate during the Paleozoic. After the Paleozoic the relative roles of origination and extinction in diversity dynamics are reversed. Metazoa as well as individual higher taxa shift from one mode of diversity dynamics to the other. The magnitude of taxonomic rates, the relative var- iance of origination and extinction rates, and the presence or absence of a long-term secular in- crease in diversity all fail to account for the shift in importance of origination and extinction in diversity changes. Origination and extinction rates both tend to be diversity-dependent, but dif- ferent modes of diversity-dependence may contribute to the change in diversity dynamics from the Paleozoic to the post-Paleozoic. During the Paleozoic, there is a weak tendency for extinction rates to be more diversity-dependent than origination rates, whereas after the Paleozoic the two rates are about equally diversity-dependent on average.
Patterns of origination within taxa, and patterns of dominance diversity among taxa are examined to distinguish nonrandom from random components. Numbers of first appearances per stage are sporadic and tend to be distributed nonrandomly through time. However, many taxa show a randomly distributed order of stages containing first appearances. A stochastic model of origination only partially reflects the patterns seen in the fossil record. Levels of dominance diversity among many taxa vary synchronously and at the same rates. The Phanerozoic is characterized by a succession of groups of taxa. Such associations are not predicted by a random model of diversity change. The fossil record is examined for evidence of an evolutionary equilibrium with constant taxonomic turnover. Fossil extinction and origination rates do not support the assumption of a static evolutionary equilibrium. Taxonomic and morphological evidence is consistent with a model of progressive specialization through the Phanerozoic.
Biotic mixing is becoming very wide-spread from human activities and is recognized as a potential threat to native biodiversity. In theory, species-area curves can be used to predict the ultimate biodiversity loss and homogenization occurring from faunal mixing. One way to test this empirically at coarse spatial and temporal scales is to quantify past episodes of faunal mixing in the fossil record. Analysis of diversity changes following the origin of the Isthmus of Panama indicates that marine biodiversity change was similar to that predicted by species-area patterns: the isolating effects of the Isthmus produced a roughly 45-60% increase in total biodiversity in the Atlantic and Pacific regions nearby. Conversely, if the isolating effects of the Isthmus were to disappear through the Panama Canal and other human activities, a decrease of about 31-38% of current species diversity might be expected. Extrapolation of these results to global scales indicate that global marine species diversity may decrease by about 58% if worldwide biotic mixing occurs. This supports previous estimates based on terrestrial biotas that predict global decreases from 35 to 71%, with a mean decrease of 55%.
To quantify the 'emptiness' of adaptive space a mathematical model of diversification is derived which makes explicit the relationship between maximum species capacity and realized diversity. The proportion of niches empty at equilibrium is a function only of the intrinsic rates of species origination and extinction. Estimates of these rates for 8 marine invertebrate groups suggest that the mean proportion of empty niches is somewhere in the range of 12-54%. Evolution in such an open adaptive space should be characterized by unremitting taxonomic turnover and continuous faunal change (but only occasional adaptive improvements), and should permit the rapid establishment of new morphospecies. These expectations are qualitatively borne out by the fossil record. -from Authors
The well-known decline of global background extinction intensity was caused by the sorting of higher taxonomic groups. Two factors were responsible. First, probabilities of familial origination and extinction in these groups (taxonomic orders) were highly correlated. Groups whose families had high probabilities of origination and extinction tended to have highly volatile diversity paths and, consequently, short life spans. Second, orders with high probabilities of familial origination and extinction were rarely replaced by new high-turnover orders. Thus, because high-turnover orders tended to become extinct without replacement, the global background extinction intensity declined. Since familial origination and extinction probabilities are correlated, global background origination intensity inevitably declined as well. As a consequence of these processes, virtually all groups of organisms now living have low probabilities of familial origination and extinction.
Simulations of branching evolution were used to obtain the expected relationships among probabilities (of origination and extinction), volatilities, and longevities for the entire range of possible probabilities, and these relationships were compared to those obtained from the empirical record. In the simulations, only the probabilities of origination and extinction were specified, so volatilities and clade longevities were determined entirely by the probabilities. The similarity between results obtained by simulation and those obtained by analysis of the empirical record further supports the inference that the observed decline of background extinction (and origination) intensity can be explained largely by the loss of high-probability groups to induced volatility.
Time-dependent sampling biases affect the per-taxon origination and extinction rates computed from the fossil record. In this paper, I assume that the actual per-taxon origination and extinction rates are constant through time, and show that the observed per-taxon origination and extinction rates will decrease from the distant past to the Recent because there is less old than young fossiliferous rock and because extant taxa are nearly 100% known but extinct taxa are not.
I apply the results to the bivalve families, and argue that the decrease of the observed per-family origination and extinction rates of bivalves from the Paleozoic to the Recent is consistent with the actual per-family origination and extinction rates of bivalves having been constant during this time span. The decrease through time of the observed per-taxon extinction and origination rates of marine families reported by Van Valen (1984) and Van Valen & Maiorana (1985), and of non-marine tetrapod families reported by Benton (1985) may also be sampling artefacts.
The evolutionary pattern of speciation and extinction in any biologic group may be described by a variety of mathematical models. These models provide a framework for describing the history of taxonomic diversity (clade shape) and other aspects of large evolutionary patterns. The simplest model assumes time homogeneity; that is, speciation and extinction probabilities are constant through time and within taxonomic groups. In some cases, the homogeneous model provides a good fit to real world paleontological data, but in other cases the model serves only as a null hypothesis that must be rejected before more complex models can be applied. In cases where the homogeneous model does not fit the data, time-inhomogeneous models can be formulated that specify change, regular or episodic, in speciation and extinction probabilities. An appendix provides a list of the most useful equations based on the homogeneous model.-Author
Approximate periodicity for peak rates of global extinction during the past 250 m.y. may have resulted from delayed recovery following major extinction events. Two components can be envisioned for such delays: persistence of inimical environmental conditions for some time after the onset of the crisis, and slow restoration of vulnerable taxa. This general hypothesis is consistent with statistical evidence of linkage between measured rates of extinction of marine invertebrate genera for contiguous stages and substages of the geologic column. The nine broad valleys between the "periodic' peak rates for the past 250 m.y. exhibit only three trivial secondary peaks, indicating that, if the pattern is not artifactual, trends in global rates of extinction have not readily been abruptly reversed. The late Neogene record of bivalve molluscs in the Western Atlantic offers a more detailed picture of delayed recovery. -from Author
Every form of behaviour is shaped by trial and error. Such stepwise adaptation can occur through individual learning or through natural selection, the basis of evolution. Since the work of Maynard Smith and others, it has been realised how game theory can model this process. Evolutionary game theory replaces the static solutions of classical game theory by a dynamical approach centred not on the concept of rational players but on the population dynamics of behavioural programmes. In this book the authors investigate the nonlinear dynamics of the self-regulation of social and economic behaviour, and of the closely related interactions between species in ecological communities. Replicator equations describe how successful strategies spread and thereby create new conditions which can alter the basis of their success, i.e. to enable us to understand the strategic and genetic foundations of the endless chronicle of invasions and extinctions which punctuate evolution. In short, evolutionary game theory describes when to escalate a conflict, how to elicit cooperation, why to expect a balance of the sexes, and how to understand natural selection in mathematical terms.
Most recent explanations for extinctions have focused on abiotic mechanisms such as climatic change, bolide impact, and eustatic sea-level change. The structure and dynamics of the ecological systems that are responding to these disturbances have generally been overlooked. The authors used percolation theory to examine how disturbances propagate among interconnected nodes on lattices. Models suggest that the magnitude of ecosystem response to disturbance is strongly non-linear. Small disturbances can produce large extinctions and large disturbances small extinctions, depending on the degree of interdependency within the system. Disturbances may act to maintain ecosystems at low levels of overall integration. Paleontological and neontological evidence for long-term ecosystem stability, co-evolutionary interactions, and mass extinction selectivity all emphasize the potential importance of interdependence in ancient and modern ecosystems. -from Authors
Using Sepkoski's compendium of fossil marine families (1982a, and updates), we have analyzed the changing pace of familial origination and extinction within 55 extinct and 44 extant higher taxa of marine organisms. Eight different metrics were calculated, and least-squares regression analysis was used to identify within-taxon trends in the data. All metrics and analyses gave essentially the same results. Origination metrics decline significantly with time during the histories of higher taxa, while extinction metrics increase significantly. The number of statistically significant declines of origination metric, however, substantially and invariably exceeds the number of statistically significant increases of extinction metric for each pair of corresponding metrics analyzed. It follows, therefore, that temporal trends in the pace of origination and extinction within higher taxa are highly asymmetrical.
Further analysis shows that truncating data from temporal endpoints has little effect upon the intensity of origination trends, implying that declining pace of origination is a sustained property of the long term histories of taxa. Such truncation, however, reduces the intensity of extinction trends to statistical insignificance and confirms Van Valen's (1985a) suggestion that extinction behaves largely as a stationary process. If the histories of higher taxa are characterized by substantial declines in the pace of origination while the pace of extinction remains largely stationary, it follows that declining pace of origination is an important controlling factor in long term taxic evolution.
Many areas of paleobiological research require reliable extinction metrics. Branching-and-extinction simulations and data on Phanerozoic marine families and genera are used to investigate the relationship between interval length and commonly used extinction metrics. Normalization of extinction metrics for interval length is problematic, even when interval length is known without error, because normalization implicitly assumes some model of variation in extinction risk within an interval. If extinction risk within an interval were constant, or if it varied but played no role in the definition of stratigraphic intervals, then Van Valen's time-normalized extinction metric would provide a measure of average extinction risk that is effectively unbiased by interval length. When extinction risk varies greatly within an interval and interval boundaries are drawn at times of heavy extinction, extinction metrics that normalize for interval length are negatively correlated with interval length. Despite its intuitive appeal, the per-taxon extinction rate (proportional extinction per million years) is biased by interval length under a wide range of extinction models.
Empirically, time-normalized extinction metrics for Phanerozoic families and genera are negatively correlated with interval length. This is consistent with an extinction model in which many times of very low risk are punctuated by a few times of very high risk which in turn determine stage boundaries. Origination and extinction patterns are similar, but origination intensity varies less among stages than extinction intensity. This observation has at least two plausible explanations: that origination episodes are more protracted than extinction episodes, and that biologic groups do not respond in unison to origination opportunities the way they seem to respond during extinction events. For families and genera, there is enough variation in extinction intensity among stages that stage length can be ignored when studying certain extinction patterns over the entire Phanerozoic.
Temporal patterns of origination and extinction are essential components of many paleontological studies, but it has been difficult to obtain accurate rate estimates because the observed record of first and last appearances is distorted by the incompleteness of the fossil record. Here I analyze observed first and last appearances of marine animal and microfossil genera in a way that explicitly takes incompleteness and its variation into consideration. This approach allows estimates of true rates of origination and extinction throughout the Phanerozoic. Substantial support is provided for the proposition that most rate peaks in the raw data are real in the sense that they do not arise as a consequence of temporal variability in the overall quality of the fossil record. Even though the existence of rate anomalies is supported, their timing is nevertheless open to question in many cases. If one assumes that rates of origination and extinction are constant through a given stratigraphic interval, then peaks in revised origination rates tend to be displaced backward and extinction peaks forward relative to the peaks in the raw data. If, however, one assumes a model of pulsed turnover, with true originations concentrated at lower interval boundaries and true extinctions concentrated at upper interval boundaries, the apparent timing of extinction peaks is largely reliable at face value. Thus, whereas rate anomalies may well be real, precisely when they occurred is a question that cannot be answered definitively without independent support for a model of smooth versus pulsed rate variation. The pattern of extinction, particularly the major events, is more faithfully represented in the fossil record than that of origination. There is a tendency for the major extinction events to occur during stages in which the quality of the record is relatively high and for recoveries from extinctions to occur when the record is less complete. These results imply that interpretations of origination and extinction history that depend only on the existence of rate anomalies are fairly robust, whereas interpretations of the timing of events and the temporal covariation between origination and extinction may require substantial revision.
A decline in the total and per-family extinction rate of marine families1,2 during the Phanerozoic has been attributed to progressive improvements in the ecological properties of species. We believe this is not necessarily the case and suggest that the lower family extinction rates may reflect increases in the number of species per family, on the geological time scale, with higher species/family ratios being an inevitable consequence of the increase in species richness3 and the geometry of the branching evolutionary tree4. Because species-rich families are more likely to survive the stochastically constant background probabilities of species extinction, the biosphere has gradually accumulated species-rich clades and the total and per-family rates of extinction have consequently declined.
Mathematical modeling of cladogenesis and fossil preservation is used to explore the expected behavior of commonly used measures of taxonomic diversity and taxonomic rates with respect to interval length, quality of preservation, position of interval in a stratigraphic succession, and taxonomic rates themselves. Particular attention is focused on the independent estimation of origination and extinction rates. Modeling supports intuitive and empirical arguments that single-interval taxa, being especially sensitive to variation in preservation and interval length, produce many undesirable distortions of the fossil record. It may generally be preferable to base diversity and rate measures on estimated numbers of taxa extant at single points in time rather than to adjust conventional interval-based measures by discarding single-interval taxa. A combination of modeling and empirical analysis of fossil genera supports two major trends in marine animal evolution. (1) The Phanerozoic decline in taxonomic rates is unlikely to be an artifact of secular improvement in the quality of the fossil record, a point that has been argued before on different grounds. (2) The post-Paleozoic rise in diversity may be exaggerated by the essentially complete knowledge of the living fauna, but this bias is not the principal cause of the pattern. The pattern may partly reflect a secular increase in preservation nevertheless. Apparent temporal variation in taxonomic rates can be produced artificially by variation in preservation rate. Some empirical arguments suggest, however, that much of the short-term variation in taxonomic rates observed in the fossil record is real. (1) For marine animals as a whole, the quality of the fossil record of a higher taxon is not a good predictor of its apparent variability in taxonomic rates. (2) For a sample data set covering a cross-section of higher taxa in the Ordovician, most of the apparent variation in origination and extinction rates is not statistically attributable to independently measured variation in preservation rates. (3) Previous work has shown that standardized sampling to remove effects of variable preservation and sampling yields abundant temporal variation in estimated taxonomic rates. While modeling suggests which rate measures are likely to be most accurate in principle, the question of how best to capture true variation in taxonomic rates remains open.
The study of evolution has increasingly incorporated considerations of history, scale, and hierarchy, in terms of both the origin of variation and the sorting of that variation. Although the macroevolutionary exploration of developmental genetics has just begun, considerable progress has been made in understanding the origin of evolutionary novelty in terms of the potential for coordinated morphological change and the potential for imposing uneven probabilities on different evolutionary directions. Global or whole-organism heterochrony, local heterochrony (affecting single structures, regions, or organ systems) and heterotopies (changes in the location of developmental events), and epigenetic mechanisms (which help to integrate the developing parts of an organism into a functional whole) together contribute to profound nonlinearities between genetic and morphologic change, by permitting the generation and accommodation of evolutionary novelties without pervasive, coordinated genetic changes; the limits of these developmental processes are poorly understood, however. The discordance across hierarchical levels in the production of evolutionary novelties through time, and among latitudes and environments, is an intriguing paleontological pattern whose explanation is controversial, in part because separating effects of genetics and ecology has proven difficult. At finer scales, species in the fossil record tend to be static over geologic time, although this stasis—to which there are gradualistic exceptions—generally appears to be underlain by extensive, nondirectional change rather than absolute invariance. Only a few studies have met the necessary protocols for the analysis of evolutionary tempo and mode at the species level, and so the distribution of evolutionary patterns among clades, environments, and modes of life remains poorly understood. Sorting among taxa is widely accepted in principle as an evolutionary mechanism, but detailed analyses are scarce; if geographic range or population density can be treated as traits above the organismic level, then the paleontological and macroecological literature abounds in potential raw material for such analyses. Even if taxon sorting operates on traits that are not emergent at the species level, the differential speciation and extinction rates can shape large-scale evolutionary patterns in ways that are not simple extrapolations from short-term evolution at the organismal level. Changes in origination and extinction rates can evidently be mediated by interactions with other clades, although such interactions need to be studied in a geographically explicit fashion before the relative roles of biotic and physical factors can be assessed. Incumbency effects are important at many scales, with the most dramatic manifestation being the postextinction diversifications that follow the removal of incumbents. However, mass extinctions are evolutionarily important not only for the removal of dominant taxa, which can occur according to rules that differ from those operating during times of lower extinction intensity, but also for the dramatic diversifications that follow upon the removal or depletion of incumbents. Mass extinctions do not entirely reset the evolutionary clock, so survivors can exhibit unbroken evolutionary continuity, trends that suffer setbacks but then resume, or failure to participate in the recovery.
The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.
A three-phase kinetic model with time-specific perturbations is used to describe large-scale patterns in the diversification of Phanerozoic marine families. The basic model assumes that the Cambrian, Paleozoic, and Modern evolutionary faunas each diversified logistically as a consequence of early exponential growth and of later slowing of growth as the ecosystems became filled; it also assumes interaction among the evolutionary faunas such that expansion of the combined diversities of all three faunas above any single fauna's equilibrium caused that fauna's diversity to begin to decline. This basic model adequately describes the diversification of the evolutionary faunas through the Paleozoic Era as well as the asymmetrical rise and fall of background extinction rates through the entire Phanerozoic. Declines in diversity and changes in faunal dominance associated with mass extinctions can be accommodated in the model with short-term accelerations in extinction rates or declines in equilibria. Such accelerations, or perturbations, cause diversity to decline exponentially and then to rebound sigmoidally following release. The amount of decline is dependent on the magnitude and duration of the perturbation, the timing of the perturbation with respect to the diversification of the system, and the system's initial per-taxon rates of diversification and turnover. When applied to the three-phase model, such perturbations describe the changes in diversity and faunal dominance during and after major mass extinctions, the long-term rise in total diversity following the Late Permian and Norian mass extinctions, and the peculiar diversification and then decline of the remnants of the Palaeozoic fauna during the Mesozoic and Cenozoic Eras. The good fit of this model to data on Phanerozoic familial diversity suggests that many of the large-scale patterns of diversification seen in the marine fossil record of animal families are simple consequences of nonlinear interrelationships among a small number of parameters that are intrinsic to the evolutionary faunas and are largely (but not completely) invariant through time. -Author
Virtually all plant and animal species that have ever lived on the earth are extinct. For this reason alone, extinction must
play an important role in the evolution of life. The five largest mass extinctions of the past 600 million years are of greatest
interest, but there is also a spectrum of smaller events, many of which indicate biological systems in profound stress. Extinction
may be episodic at all scales, with relatively long periods of stability alternating with short-lived extinction events.
Most extinction episodes are biologically selective, and further analysis of the victims and survivors offers the greatest
chance of deducing the proximal causes of extinction. A drop in sea level and climatic change are most frequently invoked
to explain mass extinctions, but new theories of collisions with extraterrestrial bodies are gaining favor. Extinction may
be constructive in a Darwinian sense or it may only perturb the system by eliminating those organisms that happen to be susceptible
to geologically rare stresses.
A global database of gastropod sizes from the Permian through the Middle Triassic doc-uments trends in gastropod shell size and permits tests of the suggestion that Early Triassic gas-tropods were everywhere unusually small. Analysis of the database shows that no specimens of unambiguous Early Triassic age larger than 2.6 cm have been reported, in contrast to common 5– 10-cm specimens of both Permian and Middle Triassic age. The loss of large gastropods is abrupt even at a fine scale of stratigraphic resolution, whereas the return of larger individuals in the Mid-dle Triassic appears gradual when finely resolved. Taphonomic and sampling biases do not ade-quately explain the absence of large Early Triassic gastropods. Examination of size trends by genus demonstrates that the size decrease across the Permian/Triassic boundary is compatible with both size-selective extinction at the species level and anagenetic size change within lineages. Size in-crease in the Middle Triassic resulted from the origination of large species within genera that have Early Triassic fossil records and the occurrence of new genera containing large species during the Middle Triassic. Genera recorded from the Permian and Middle Triassic but not the Early Triassic (''Lazarus taxa'') do not contribute to observed size increase in the Middle Triassic. Moreover, Laz-arus taxa lack large species and exhibit low species richness during both the Permian and the Mid-dle Triassic, suggesting that they survived as small, rare forms rather than existing at large sizes in Early Triassic refugia. The ecological opportunities and selective pressures that produced large gastropods during most intervals of the Phanerozoic evidently did not operate in Early Triassic oceans. Whether this reflects low predation or competitive pressure, r-selection facilitated by high primary production, or physical barriers to large size remains poorly understood.
For more than two decades, Jack Sepkoski's hypothesis of three great 'evolutionary faunas' has dominated thinking about the Phanerozoic evolution of marine animals. This theory combines pattern description with process modelling: diversity trajectories of major taxonomic groups are sorted into three categories, and the trajectories are predicted by coupled logistic equations. Here I use a re-creation of Sepkoski's classic three-phase coupled logistic model and an empirical analysis of his genus-level compendium to re-examine his claims about diversity dynamics. I employ a 'focal-group' variant of the proportional volatility G-statistic to deter-mine whether variation in turnover rates of focal taxonomic groups can be explained by the average rates for each group through time combined with average rates across all groups within each temporal bin. If growth is exponential and ecological interactions between pairs of groups are always similarly strong, then groups will wax and wane very predictably, and these statistics will always be insignificant. If instead growth is density-dependent and there are no inter-actions, significant volatility should be confined to periods of rapid radiations, such as those following major mass extinctions. Finally, if unusually strong pairwise interactions directly cause certain groups to succeed or fail, then significant volatility in each competing group should be present during replacement episodes that are not tied to overall radiations or extinctions. Additionally, if clustering groups into faunas is informative, then summed faunal diversity histories will replicate the observed volatility of all groups treated separately. To illustrate the focal-group method, I apply it to diversity data for the major groups of Cenozoic North American mammals. Surprisingly, the tests show that although some orders experience significant radiations and extinctions, orders with visually similar trajectories such as archaic, mostly Paleocene mammals fail to share dynamic properties. Volatility is far greater in Sepkoski's marine data, with almost every class showing significant and strong deviations from background turnover rates. However, Sepkoski's three-phase model predicts these patterns inconsistently. As expected, the Cambrian and Paleozoic faunas show high volatility during the hand-off between them. However, the hypothesized twin late Paleozoic and Jurassic/early Cretaceous hand-offs between the Paleozoic and Modern faunas are not marked by excessively rapid declines and increases. Instead, the Modern evolutionary fauna shows highly unusual dynamic behaviour starting in the mid-Cretaceous, coincident with the Mesozoic marine revolution and well after the Paleozoic fauna's decline. Sepkoski's categorization also generally fails to summarize overall volatility during long stretches of the Paleozoic and Mesozoic. Consult the copyright statement on the inside front cover for non-commercial copying policies.
This paper documents a series of methodological innovations that are relevant to mac-roevolutionary studies. The new methods are applied to updated faunal and body mass data sets for North American fossil mammals, documenting several key trends across the late Cretaceous and Cenozoic. The methods are (1) A maximum likelihood formulation of appearance event or-dination. The reformulated criterion involves generating a maximally likely hypothesized relative ordering of first and last appearances (i.e., an age range chart). The criterion takes faunal occur-rences, stratigraphic relationships, and the sampling probability of individual genera and species into account. (2) A nonparametric temporal interpolation method called ''shrink-wrapping'' that makes it possible to employ the greatest possible number of tie points without violating monoto-nicity or allowing abrupt changes in slopes. The new calibration method is used in computing pro-visional definitions of boundaries among North American land mammal ages. (3) Additional meth-ods for randomized subsampling of faunal lists, one weighting the number of lists that have been drawn by the sum of the square of the number of occurrences in each list, and one further modi-fying this approach to account for long-term changes in average local species richness. (4) Foote's new equations for instantaneous speciation and extinction rates. The equations are rederived and used to generate time series, confirm that logistic dynamics result from the diversity dependence of speciation but not extinction, and define the median duration of species (i.e., 2.6 m.y. for Eocene– Pleistocene mammals). (5) A method employing the G likelihood ratio statistic that is used to quan-tify the volatility of changes in the relative proportion of species falling in each of several major taxonomic groups. (6) Univariate measures of body mass distributions based on ordinary moment statistics (mean, standard deviation, skewness, kurtosis). These measures are favored over the method of cenogram analysis. Data are presented showing that even diverse individual fossil col-lections merely yield a noisy version of the same pattern seen in the overall continental data set. Peaks in speciation rates, extinction rates, proportional volatility, and shifts in body mass distri-butions occur at different times, suggesting that environmental perturbations do not have simple effects on the biota.
The coordinated stasis model has far-reaching implications. Among them are three important predictions concerning diversity dynamics that I test here against the Cenozoic fossil record of terrestrial North American mammals. First, origination and extinction rates should be correlated; second, turnover should be a composite function of very low background rates and occasional, dramatic turnover pulses; and finally, stasis should result from ecological (niche) incumbency, with the domains of incumbent species being defined by ecological similarity, which in the case of mammals corresponds closely with taxonomic affinity. The data used to test these hypotheses are standing diversity levels and counts of originations and extinctions for 1193 genera and 3161 species. Instead of relying on a traditional time scale comprised of “ages” having uneven and unpredictable durations, the diversity curve is computed directly from a multivariate ordination of 3870 faunal lists, and then sectioned into 1.0 m.y. intervals. The lists span the late Cretaceous through late Pleistocene interval, exclusive of the Wisconsinan, and are taxonomically standardized to remove junior synonyms, out-dated combinations, and nomina dubia. Because Cretaceous and Paleocene diversity dynamics are idiosyncratic, only the last 55 intervals (Eocene-Pleistocene: 55-0.01 Ma) are analyzed. The test of origination and extinction rates shows that an apparent correlation between them is a statistical artifact related to the necessary coincidence of first and last appearances for taxa known from just one interval. The test of variation in turnover shows that most of the observed extinction rates could be generated by a single, invariant underlying rate, wheras origination rates show many well-defined pulses. Furthermore, origination pulses within particular orders are not fully coincident. The very largest pulses of origination therefore seem to be mediated by key adaptations within particular groups, not by the general opportunity to fill niches opened up by extinction. Both of these tests argue against the idea of sweeping “reorganization” intervals bounding placid “stasis” intervals, and against Vrba's turnover pulse hypothesis. Finally, tests for niche incumbency, based on plots of per-taxon turnover rates against standing diversity, show that incumbency is widespread and mediated by the suppression of origination at high diversity levels in all groups. Extinction is a far less important controlling factor. Because orders are ecologically distinct, but random subsamples of the entire data set actually show stronger controls than groupings based on ordinal affinity, it appears that niche space has little or no important ecological substructuring. Therefore, mammalian diversity seems to be integrated at the highest possible taxonomic level, in opposition to the coordinated stasis concept of static guilds. On balance, the results indicate that although the data are robust and provide strong support for the niche incumbency model and the idea of diversity equilibrium, they generally disconfirm the unique predictions of coordinated stasis.
All groups for which data exist go extinct at a rate that is constant for a given group. When this is recast in ecological form (the effective environment of any homogeneous, group of organisms deteriorates at a stochasti- cally constant rate), no definite exceptions exist although a few are possible. Extinction rates are similar within some very broad categories and vary regularly with size of area inhabited. A new unit of rates for discrete phenomena, the macarthur, is introduced. Laws are appropriate in evolutionary biology. Truth needs more than correct predictions. The Law of Extinction is evidence for ecological significance and comparability of taxa. A ncn- Markovian hypothesis to explain the law invokes mutually incompatible optima within an adaptive zone. A self-perpetuating fluctuation results which can be stated in terms of an unstudied aspect of zero-sum game theory. The hypothesis can be derived from a view that momentary fitness is the amount of control of resources, which remain constant in total amount. The hypothesis implies that long-term fitness has only two components and that events of mutualism are rare. The hypothesis largely explains the observed pattern of
molecular evolution.