Phanerozoic Earth system evolution and marine biodiversity

Quantifying the global biodiversity of Proterozoic eukaryotes

The global diversity of Proterozoic eukaryote fossils is poorly quantified despite its fundamental importance to the understanding of macroevolutionary patterns and dynamics on the early Earth. Here we report a new construction of fossil eukaryote diversity from the Paleoproterozoic to early Cambrian based on a comprehensive data compilation and quantitative analyses. The resulting taxonomic richness curve verifies Cryogenian glaciations as a major divide that separates the "Boring Billion" and Ediacaran periods, with the former characterized by a prolonged stasis, and the latter by greater diversity, more-rapid turnover, and multiple radiations and extinctions. These contrasting evolutionary patterns and dynamics provide a framework to test competing hypotheses on biosphere and geosphere coevolution in the Proterozoic Eon.

Sea level controls on Ediacaran-Cambrian animal radiations

The drivers of Ediacaran-Cambrian metazoan radiations remain unclear, as does the fidelity of the record. We use a global age framework [580-510 million years (Ma) ago] to estimate changes in marine sedimentary rock volume and area, reconstructed biodiversity (mean genus richness), and sampling intensity, integrated with carbonate carbon isotopes (δ13Ccarb) and global redox data [carbonate Uranium isotopes (δ238Ucarb)]. Sampling intensity correlates with overall mean reconstructed biodiversity >535 Ma ago, while second-order (~10-80 Ma) global transgressive-regressive cycles controlled the distribution of different marine sedimentary rocks. The temporal distribution of the Avalon assemblage is partly controlled by the temporally and spatially limited record of deep-marine siliciclastic rocks. Each successive rise of metazoan morphogroups that define the Avalon, White Sea, and Cambrian assemblages appears to coincide with global shallow marine oxygenation events at δ13Ccarb maxima, which precede major sea level transgressions. While the record of biodiversity is biased, early metazoan radiations and oxygenation events are linked to major sea level cycles.

Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous

Palaeontologists have long sought to explain the diversification of individual clades to whole biotas at global scales. Advances in our understanding of the spatial distribution of the fossil record through geological time, however, has demonstrated that global trends in biodiversity were a mosaic of regionally heterogeneous diversification processes. Drivers of diversification must presumably have also displayed regional variation to produce the spatial disparities observed in past taxonomic richness. Here, we analyse the fossil record of ammonoids, pelagic shelled cephalopods, through the Late Cretaceous, characterised by some palaeontologists as an interval of biotic decline prior to their total extinction at the Cretaceous-Paleogene boundary. We regionally subdivide this record to eliminate the impacts of spatial sampling biases and infer regional origination and extinction rates corrected for temporal sampling biases using Bayesian methods. We then model these rates using biotic and abiotic drivers commonly inferred to influence diversification. Ammonoid diversification dynamics and responses to this common set of diversity drivers were regionally heterogeneous, do not support ecological decline, and demonstrate that their global diversification signal is influenced by spatial disparities in sampling effort. These results call into question the feasibility of seeking drivers of diversity at global scales in the fossil record.

Unveiling the underlying drivers of Phanerozoic marine diversification

In investigating global patterns of biodiversity through deep time, many large-scale drivers of diversification have been proposed, both biotic and abiotic. However, few robust conclusions about these hypothesized effectors or their roles have been drawn. Here, we use a linear stochastic differential equation (SDE) framework to test for the presence of underlying drivers of diversification patterns before examining specific hypothesized drivers. Using a global dataset of observations of skeletonized marine fossils, we infer origination, extinction and sampling rates (collectively called fossil time series) throughout the Phanerozoic using a capture-mark-recapture approach. Using linear SDEs, we then compare models including and excluding hidden (i.e. unmeasured) drivers of these fossil time series. We find evidence of large-scale underlying drivers of marine Phanerozoic diversification rates and present quantitative characterizations of these. We then test whether changing global temperature, sea-level, marine sediment area or continental fragmentation could act as drivers of the fossil time series. We show that it is unlikely any of these four abiotic factors are the hidden drivers we identified, though there is evidence for correlative links between sediment area and origination/extinction rates. Our characterization of the hidden drivers of Phanerozoic diversification and sampling will aid in the search for their ultimate identities.

Landscape dynamics and the Phanerozoic diversification of the biosphere

The long-term diversification of the biosphere responds to changes in the physical environment. Yet, over the continents, the nearly monotonic expansion of life started later in the early part of the Phanerozoic eon1 than the expansion in the marine realm, where instead the number of genera waxed and waned over time2. A comprehensive evaluation of the changes in the geodynamic and climatic forcing fails to provide a unified theory for the long-term pattern of evolution of life on Earth. Here we couple climate and plate tectonics models to numerically reconstruct the evolution of the Earth's landscape over the entire Phanerozoic eon, which we then compare to palaeo-diversity datasets from marine animal and land plant genera. Our results indicate that biodiversity is strongly reliant on landscape dynamics, which at all times determine the carrying capacity of both the continental domain and the oceanic domain. In the oceans, diversity closely adjusted to the riverine sedimentary flux that provides nutrients for primary production. On land, plant expansion was hampered by poor edaphic conditions until widespread endorheic basins resurfaced continents with a sedimentary cover that facilitated the development of soil-dependent rooted flora, and the increasing variety of the landscape additionally promoted their development.

Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals

The deep sea (>200 m) is home to a surprisingly rich biota, which in some cases compares to that found in shallow areas. Scleractinian corals are an example of this - they are key species in both shallow and deep ecosystems. However, what evolutionary processes resulted in current depth distribution of the marine fauna is a long-standing question. Various conflicting hypotheses have been proposed, but few formal tests have been conducted. Here, we use global spatial distribution data to test the bathymetric origin and colonization trends across the depth gradient in scleractinian corals. Using a phylogenetic approach, we infer the origin and historical trends in directionality and speed of colonization during the diversification in depth. We also examine how the emergence of photo-symbiosis and coloniality, scleractinian corals' most conspicuous phenotypic innovations, have influenced this process. Our results strongly support an offshore-onshore pattern of evolution and varying dispersion capacities along depth associated with trait-defined lineages. These results highlight the relevance of the evolutionary processes occurring at different depths to explain the origin of extant marine biodiversity and the consequences of altering these processes by human impact, highlighting the need to include this overlooked evolutionary history in conservation plans.

A novel method for identifying key genes in macroevolution based on deep learning with attention mechanism

Macroevolution can be regarded as the result of evolutionary changes of synergistically acting genes. Unfortunately, the importance of these genes in macroevolution is difficult to assess and hence the identification of macroevolutionary key genes is a major challenge in evolutionary biology. In this study, we designed various word embedding libraries of natural language processing (NLP) considering the multiple mechanisms of evolutionary genomics. A novel method (IKGM) based on three types of attention mechanisms (domain attention, kmer attention and fused attention) were proposed to calculate the weights of different genes in macroevolution. Taking 34 species of diurnal butterflies and nocturnal moths in Lepidoptera as an example, we identified a few of key genes with high weights, which annotated to the functions of circadian rhythms, sensory organs, as well as behavioral habits etc. This study not only provides a novel method to identify the key genes of macroevolution at the genomic level, but also helps us to understand the microevolution mechanisms of diurnal butterflies and nocturnal moths in Lepidoptera.

Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction

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.

Earth's interior dynamics drive marine fossil diversity cycles of tens of millions of years

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.

Nickel and zinc micronutrient availability in Phanerozoic oceans

Nickel and zinc are both bio-essential micronutrients with a nutrient-like distribution in the modern ocean, but show key differences in their biological functions and geochemical behavior. Eukaryotic phytoplankton, and especially diatoms, have high Zn quotas, whereas cyanobacteria generally require relatively more Ni. Secular changes in the relative availability of these micronutrients may, therefore, have affected the evolution and diversification of phytoplankton. In this study, we use a large compilation of Ni and Zn concentration data for Phanerozoic sediments to evaluate long-term changes in Ni and Zn availability and possible links to phytoplankton evolution. Modern data suggest that organic-rich sediments capture the dissolved deep ocean Ni/Zn ratio, regardless of local depositional conditions. We use this observation to constrain Ni/Zn ratios for past oceans, based on data from the sedimentary record. This record highlights long-term changes in the relative availability of these micronutrients that can be linked to the (bio)geochemical conditions on the Earth's surface. Early Palaeozoic oceans were likely relatively Ni rich, with sedimentary Ni/Zn ratios for this interval mostly being around ~1 or higher. A comparison with Phanerozoic strontium-, carbon-, and sulfur-isotopic records suggests that the late Palaeozoic decrease in sulfidic conditions and increase in hydrothermal inputs and organic-carbon burial rates caused a shift towards more Zn-rich conditions. Mesozoic and Cenozoic sediments show relatively Zn-rich oceans for these time intervals, with sedimentary Ni/Zn ratios mostly being around ~1 or lower. These observations imply that the diversification of the dominant groups of modern eukaryotic phytoplankton occurred in relatively Zn-rich oceans and that these organisms still carry this signature in their stoichiometries. However, the Phanerozoic transition to a more Zn-rich ocean pre-dates the origin and diversification of modern eukaryotes and, therefore, this transition was likely not the main direct cause for eukaryotic diversification in the Mesozoic and Cenozoic Eras.

Global impact and selectivity of the Cretaceous-Paleogene mass extinction among sharks, skates, and rays

The Cretaceous-Paleogene event was the last mass extinction event, yet its impact and long-term effects on species-level marine vertebrate diversity remain largely uncharacterized. We quantified elasmobranch (sharks, skates, and rays) speciation, extinction, and ecological change resulting from the end-Cretaceous event using >3200 fossil occurrences and 675 species spanning the Late Cretaceous-Paleocene interval at global scale. Elasmobranchs declined by >62% at the Cretaceous-Paleogene boundary and did not fully recover in the Paleocene. The end-Cretaceous event triggered a heterogeneous pattern of extinction, with rays and durophagous species reaching the highest levels of extinction (>72%) and sharks and nondurophagous species being less affected. Taxa with large geographic ranges and/or those restricted to high-latitude settings show higher survival. The Cretaceous-Paleogene event drastically altered the evolutionary history of marine ecosystems.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth-death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.

Diversity dependence is a ubiquitous phenomenon across Phanerozoic oceans

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.

The supercontinent cycle and Earth's long-term climate

Earth's long-term climate has been profoundly influenced by the episodic assembly and breakup of supercontinents at intervals of ca. 500 m.y. This reflects the cycle's impact on global sea level and atmospheric CO2 (and other greenhouse gases), the levels of which have fluctuated in response to variations in input from volcanism and removal (as carbonate) by the chemical weathering of silicate minerals. Supercontinent amalgamation tends to coincide with climatic cooling due to drawdown of atmospheric CO2 through enhanced weathering of the orogens of supercontinent assembly and a thermally uplifted supercontinent. Conversely, breakup tends to coincide with increased atmospheric CO2 and global warming as the dispersing continental fragments cool and subside, and weathering decreases as sea level rises. Supercontinents may also influence global climate through their causal connection to mantle plumes and large igneous provinces (LIPs) linked to their breakup. LIPs may amplify the warming trend of breakup by releasing greenhouse gases or may cause cooling and glaciation through sulfate aerosol release and drawdown of CO2 through the chemical weathering of LIP basalts. Hence, Earth's long-term climatic trends likely reflect the cycle's influence on sea level, as evidenced by Pangea, whereas its influence on LIP volcanism may have orchestrated between Earth's various climatic states.

Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

Life rather than climate influences diversity at scales greater than 40 million years

The diversity of life on Earth is controlled by hierarchical processes that interact over wide ranges of timescales¹. Here, we consider the megaclimate regime² at scales ≥1 million years (Myr). We focus on determining the domains of 'wandering' stochastic Earth system processes ('Court Jester'³) and stabilizing biotic interactions that induce diversity dependence of fluctuations in macroevolutionary rates ('Red Queen'⁴). Using state-of-the-art multiscale Haar and cross-Haar fluctuation analyses, we analysed the global genus-level Phanerozoic marine animal Paleobiology Database record of extinction rates (E), origination rates (O) and diversity (D) as well as sea water palaeotemperatures (T). Over the entire observed range from several million years to several hundred million years, we found that the fluctuations of T, E and O showed time-scaling behaviour. The megaclimate was characterized by positive scaling exponents-it is therefore apparently unstable. E and O are also scaling but with negative exponents-stable behaviour that is biotically mediated. For D, there were two regimes with a crossover at critical timescale [Formula: see text] ≈ 40 Myr. For shorter timescales, D exhibited nearly the same positive scaling as the megaclimate palaeotemperatures, whereas for longer timescales it tracks the scaling of macroevolutionary rates. At scales of at least [Formula: see text] there is onset of diversity dependence of E and O, probably enabled by mixing and synchronization (globalization) of the biota by geodispersal ('Geo-Red Queen').

Terrestrial forcing of marine biodiversification

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.

Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time

The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.

Biotic and Abiotic Controls on the Phanerozoic History of Marine Animal Biodiversity

During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change.

Biodiversity across space and time in the fossil record

The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.

Dinosaur biodiversity declined well before the asteroid impact, influenced by ecological and environmental pressures

The question why non-avian dinosaurs went extinct 66 million years ago (Ma) remains unresolved because of the coarseness of the fossil record. A sudden extinction caused by an asteroid is the most accepted hypothesis but it is debated whether dinosaurs were in decline or not before the impact. We analyse the speciation-extinction dynamics for six key dinosaur families, and find a decline across dinosaurs, where diversification shifted to a declining-diversity pattern ~76 Ma. We investigate the influence of ecological and physical factors, and find that the decline of dinosaurs was likely driven by global climate cooling and herbivorous diversity drop. The latter is likely due to hadrosaurs outcompeting other herbivores. We also estimate that extinction risk is related to species age during the decline, suggesting a lack of evolutionary novelty or adaptation to changing environments. These results support an environmentally driven decline of non-avian dinosaurs well before the asteroid impact.

Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton

The latitudinal diversity gradient (LDG)-the decline in species richness from the equator to the poles-is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.

Volcanic controls on seawater sulfate over the past 120 million years

Changes in the geological sulfur cycle are inferred from the sulfur isotopic composition of marine barite. The structure of the ³⁴S/³²S record from the Mesozoic to present, which includes ∼50- and 100-Ma stepwise increases, has been interpreted as the result of microbial isotope effects or abrupt changes to tectonics and associated pyrite burial. Untangling the physical processes that govern the marine sulfur cycle and associated isotopic change is critical to understanding how climate, atmospheric oxygenation, and marine ecology have coevolved over geologic time. Here we demonstrate that the sulfur outgassing associated with emplacement of large igneous provinces can produce the apparent stepwise jumps in the isotopic record when coupled to long-term changes in burial efficiency. The record of large igneous provinces map onto the required outgassing events in our model, with the two largest steps in the sulfur isotope record coinciding with the emplacement of large igneous provinces into volatile-rich sedimentary basins. This solution provides a quantitative picture of the last 120 My of change in the ocean's largest oxidant reservoir.

The spatial structure of Phanerozoic marine animal diversity

The global fossil record of marine animals has fueled long-standing debates about diversity change through time and the drivers of this change. However, the fossil record is not truly global. It varies considerably in geographic scope and in the sampling of environments among intervals of geological time. We account for this variability using a spatially explicit approach to quantify regional-scale diversity through the Phanerozoic. Among-region variation in diversity is comparable to variation through time, and much of this is explained by environmental factors, particularly the extent of reefs. By contrast, influential hypotheses of diversity change through time, including sustained long-term increases, have little explanatory power. Modeling the spatial structure of the fossil record transforms interpretations of Phanerozoic diversity patterns and their macroevolutionary explanations. This necessitates a refocus of deep-time diversification studies.

A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity

One great challenge in understanding the history of life is resolving the influence of environmental change on biodiversity. Simulated annealing and genetic algorithms were used to synthesize data from 11,000 marine fossil species, collected from more than 3000 stratigraphic sections, to generate a new Cambrian to Triassic biodiversity curve with an imputed temporal resolution of 26 ± 14.9 thousand years. This increased resolution clarifies the timing of known diversification and extinction events. Comparative analysis suggests that partial pressure of carbon dioxide (Pco2) is the only environmental factor that seems to display a secular pattern similar to that of biodiversity, but this similarity was not confirmed when autocorrelation within that time series was analyzed by detrending. These results demonstrate that fossil data can provide the temporal and taxonomic resolutions necessary to test (paleo)biological hypotheses at a level of detail approaching those of long-term ecological analyses.

Climate cooling and clade competition likely drove the decline of lamniform sharks

Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades' evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.

Timing and periodicity of Phanerozoic marine biodiversity and environmental change

We examine how the history of Phanerozoic marine biodiversity relates to environmental change. Our focus is on North America, which has a relatively densely sampled history. By transforming time series into the time-frequency domain using wavelets, histories of biodiversity are shown to be similar to sea level, temperature and oceanic chemistry at multiple timescales. Fluctuations in sea level play an important role in driving Phanerozoic biodiversity at timescales >50 Myr, and during finite intervals at shorter periods. Subsampled and transformed marine genera time series reinforce the idea that Permian-Triassic, Triassic-Jurassic, and Cretaceous-Paleogene mass extinctions were geologically rapid, whereas the Ordovician-Silurian and Late Devonian ‘events’ were longer lived. High cross wavelet power indicates that biodiversity is most similar to environmental variables (sea level, plate fragmentation, δ¹⁸O, δ¹³C, δ³⁴S and ⁸⁷Sr/⁸⁶Sr) at periods >200 Myr, when they are broadly in phase (i.e. no time lag). They are also similar at shorter periods for finite durations of time (e.g. during some mass extinctions). These results suggest that long timescale processes (e.g. plate kinematics) are the primary drivers of biodiversity, whilst processes with significant variability at shorter periods (e.g. glacio-eustasy, continental uplift and erosion, volcanism, asteroid impact) play a moderating role. Wavelet transforms are a useful approach for isolating information about times and frequencies of biological activity and commonalities with environmental variables.

Diversity-dependent evolutionary rates in early Palaeozoic zooplankton

The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of approximately 1 Myr. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian.

Clade-specific diversification dynamics of marine diatoms since the Jurassic

Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO2) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.

Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical Illustrations

Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and $\delta^{13}C$-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.

The nearshore cradle of early vertebrate diversification

Ancestral vertebrate habitats are subject to controversy and obscured by limited, often contradictory paleontological data. We assembled fossil vertebrate occurrence and habitat datasets spanning the middle Paleozoic (480 million to 360 million years ago) and found that early vertebrate clades, both jawed and jawless, originated in restricted, shallow intertidal-subtidal environments. Nearshore divergences gave rise to body plans with different dispersal abilities: Robust fishes shifted shoreward, whereas gracile groups moved seaward. Fresh waters were invaded repeatedly, but movement to deeper waters was contingent upon form and short-lived until the later Devonian. Our results contrast with the onshore-offshore trends, reef-centered diversification, and mid-shelf clustering observed for benthic invertebrates. Nearshore origins for vertebrates may be linked to the demands of their mobility and may have influenced the structure of their early fossil record and diversification.

Inferring Evolutionary Process From Neuroanatomical Data

Brain evolution has interested neuroanatomists for over a century. These interests often fall on how free the brain is to evolve independently of the body, how free brain regions are to evolve independently of each other, and how different environmental and ecological factors affect the brain over evolutionary time. But despite major advances in phylogenetic methods, comparative neuroanatomists have tended to limit their macroevolutionary toolbox to regression-based analyses and ignored the scope of evolutionary process-based models at their disposal. This Review summarizes the history of comparative neuroanatomy and highlights the pitfalls of the methodologies traditionally used. It provides an overview of evolutionary process-based modeling approaches for investigating univariate and multivariate data, as well as more sophisticated methods that incorporate hypotheses about biotic and abiotic pressures that may drive brain evolution. The benefits of evolutionary process-based models, and shortcomings of regression-based ones, are illustrated with widely used neuroanatomical data. Ultimately, the intent of this Review is to be a guide for subsuming macroevolutionary methods not typically used in comparative neuroanatomy, in order to improve our understanding of how the brain evolves.

Nature of the sedimentary rock record and its implications for Earth system evolution

The sedimentary rock reservoir both records and influences changes in Earth's surface environment. Geoscientists extract data from the rock record to constrain long-term environmental, climatic and biological evolution, with the understanding that geological processes of erosion and rock destruction may have overprinted some aspects of their results. It has also long been recognized that changes in the mass and chemical composition of buried sediments, operating in conjunction with biologically catalyzed reactions, exert a first-order control on Earth surface conditions on geologic timescales. Thus, the construction and destruction of the rock record has the potential to influence both how Earth and life history are sampled, and drive long-term trends in surface conditions that otherwise are difficult to affect. However, directly testing what the dominant process signal in the sedimentary record is — rock construction or destruction — has rarely been undertaken, primarily due to the difficulty of assembling data on the mass and age of rocks in Earth's crust. Here, we present results on the chronological age and general properties of rocks and sediments in the Macrostrat geospatial database (https://macrostrat.org). Empirical patterns in surviving rock quantity as a function of age are indicative of both continual cycling (gross sedimentation) and long-term sediment accumulation (net sedimentation). Temporal variation in the net sedimentary reservoir was driven by major changes in the ability of continental crust to accommodate sediments. The implied history of episodic growth of sediment mass on continental crust has many attendant implications for the drivers of long-term biogeochemical evolution of Earth and life.

Sporadic sampling, not climatic forcing, drives observed early hominin diversity

The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both taxic and phylogenetically corrected diversity estimates. Unlike past studies, we compare these estimates to sampling metrics for rock availability (hominin-, primate-, and mammal-bearing formations) and collection effort, to assess the geological and anthropogenic controls on the sampling of the early hominin fossil record. Taxic diversity, primate-bearing formations, and collection effort show strong positive correlations, demonstrating that observed patterns of early hominin taxic diversity can be explained by temporal heterogeneity in fossil sampling rather than genuine evolutionary processes. Peak taxic diversity at 1.9 million years ago (Ma) is a sampling artifact, reflecting merely maximal rock availability and collection effort. In contrast, phylogenetic diversity estimates imply peak diversity at 2.4 Ma and show little relation to sampling metrics. We find that apparent relationships between early hominin diversity and indicators of climatic instability are, in fact, driven largely by variation in suitable rock exposure and collection effort. Our results suggest that significant improvements in the quality of the fossil record are required before the role of climate in hominin evolution can be reliably determined.

How has our knowledge of dinosaur diversity through geologic time changed through research history?

Assessments of dinosaur macroevolution at any given time can be biased by the historical publication record. Recent studies have analysed patterns in dinosaur diversity that are based on secular variations in the numbers of published taxa. Many of these have employed a range of approaches that account for changes in the shape of the taxonomic abundance curve, which are largely dependent on databases compiled from the primary published literature. However, how these ‘corrected’ diversity patterns are influenced by the history of publication remains largely unknown. Here, we investigate the influence of publication history between 1991 and 2015 on our understanding of dinosaur evolution using raw diversity estimates and shareholder quorum subsampling for the three major subgroups: Ornithischia, Sauropodomorpha, and Theropoda. We find that, while sampling generally improves through time, there remain periods and regions in dinosaur evolutionary history where diversity estimates are highly volatile (e.g. the latest Jurassic of Europe, the mid-Cretaceous of North America, and the Late Cretaceous of South America). Our results show that historical changes in database compilation can often substantially influence our interpretations of dinosaur diversity. ‘Global’ estimates of diversity based on the fossil record are often also based on incomplete, and distinct regional signals, each subject to their own sampling history. Changes in the record of taxon abundance distribution, either through discovery of new taxa or addition of existing taxa to improve sampling evenness, are important in improving the reliability of our interpretations of dinosaur diversity. Furthermore, the number of occurrences and newly identified dinosaurs is still rapidly increasing through time, suggesting that it is entirely possible for much of what we know about dinosaurs at the present to change within the next 20 years.

Common species link global ecosystems to climate change: dynamical evidence in the planktonic fossil record

Common species shape the world around us, and changes in their commonness signify large-scale shifts in ecosystem structure and function. However, our understanding of long-term ecosystem response to environmental forcing in the deep past is centred on species richness, neglecting the disproportional impact of common species. Here, we use common and widespread species of planktonic foraminifera in deep-sea sediments to track changes in observed global occupancy (proportion of sampled sites at which a species is present and observed) through the turbulent climatic history of the last 65 Myr. Our approach is sensitive to relative changes in global abundance of the species set and robust to factors that bias richness estimators. Using three independent methods for detecting causality, we show that the observed global occupancy of planktonic foraminifera has been dynamically coupled to past oceanographic changes captured in deep-ocean temperature reconstructions. The causal inference does not imply a direct mechanism, but is consistent with an indirect, time-delayed causal linkage. Given the strong quantitative evidence that a dynamical coupling exists, we hypothesize that mixotrophy (symbiont hosting) may be an ecological factor linking the global abundance of planktonic foraminifera to long-term climate changes via the relative extent of oligotrophic oceans.

Trophic and tectonic limits to the global increase of marine invertebrate diversity

The marine invertebrate fossil record provides the most comprehensive history of how the diversity of animal life has evolved through time. One of the main features of this record is a modest rise in diversity over nearly a half-billion years. The long-standing view is that ecological interactions such as resource competition and predation set upper limits to global diversity, which, in the absence of external perturbations, is maintained indefinitely at equilibrium. However, the effect of mechanisms associated with the history of the seafloor, and their influence on the creation and destruction of marine benthic habitats, has not been explored. Here we use statistical methods for causal inference to investigate the drivers of marine invertebrate diversity dynamics through the Phanerozoic. We find that diversity dynamics responded to secular variations in marine food supply, substantiating the idea that global species richness is regulated by resource availability. Once diversity was corrected for changes in food resource availability, its dynamics were causally linked to the age of the subducting oceanic crust. We suggest that the time elapsed between the formation (at mid-ocean ridges) and destruction (at subduction zones) of ocean basins influences the diversity dynamics of marine invertebrates and may have contributed to constrain their diversification.

The non-uniformity of fossil preservation

The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr), the origin and cessation of sedimentary basins, and long-term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non-uniform. Models of fossil preservation should reflect this non-uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829

Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change.

Controlling for the species-area effect supports constrained long-term Mesozoic terrestrial vertebrate diversification

Variation in the geographic spread of fossil localities strongly biases inferences about the evolution of biodiversity, due to the ubiquitous scaling of species richness with area. This obscures answers to key questions, such as how tetrapods attained their tremendous extant diversity. Here, we address this problem by applying sampling standardization methods to spatial regions of equal size, within a global Mesozoic-early Palaeogene data set of non-flying terrestrial tetrapods. We recover no significant increase in species richness between the Late Triassic and the Cretaceous/Palaeogene (K/Pg) boundary, strongly supporting bounded diversification in Mesozoic tetrapods. An abrupt tripling of richness in the earliest Palaeogene suggests that this diversity equilibrium was reset following the K/Pg extinction. Spatial heterogeneity in sampling is among the most important biases of fossil data, but has often been overlooked. Our results indicate that controlling for variance in geographic spread in the fossil record significantly impacts inferred patterns of diversity through time.

Species richness increases with area sampled, potentially confounding biodiversity patterns from the fossil record. Here, the authors standardize spatial sampling to control for this bias and show that terrestrial vertebrate diversification was bounded during the Mesozoic but that equilibria were reset following the K/Pg extinction.

Plate tectonic regulation of global marine animal diversity

Valentine and Moores [Valentine JW, Moores EM (1970) Nature 228:657-659] hypothesized that plate tectonics regulates global biodiversity by changing the geographic arrangement of continental crust, but the data required to fully test the hypothesis were not available. Here, we use a global database of marine animal fossil occurrences and a paleogeographic reconstruction model to test the hypothesis that temporal patterns of continental fragmentation have impacted global Phanerozoic biodiversity. We find a positive correlation between global marine invertebrate genus richness and an independently derived quantitative index describing the fragmentation of continental crust during supercontinental coalescence-breakup cycles. The observed positive correlation between global biodiversity and continental fragmentation is not readily attributable to commonly cited vagaries of the fossil record, including changing quantities of marine rock or time-variable sampling effort. Because many different environmental and biotic factors may covary with changes in the geographic arrangement of continental crust, it is difficult to identify a specific causal mechanism. However, cross-correlation indicates that the state of continental fragmentation at a given time is positively correlated with the state of global biodiversity for tens of millions of years afterward. There is also evidence to suggest that continental fragmentation promotes increasing marine richness, but that coalescence alone has only a small negative or stabilizing effect. Together, these results suggest that continental fragmentation, particularly during the Mesozoic breakup of the supercontinent Pangaea, has exerted a first-order control on the long-term trajectory of Phanerozoic marine animal diversity.

Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover

The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic-Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary 'event', which hints at a 'cascade model' of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shelf-dwelling faunas, corresponding to a significant eustatic sea-level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/K transition therefore, although not a mass extinction, represents an important transitional period in the co-evolutionary history of life on Earth.

Accelerated body size evolution during cold climatic periods in the Cenozoic

How ecological and morphological diversity accumulates over geological time is much debated. Adaptive radiation theory has been successful in testing the effects of biotic interactions on the rapid divergence of phenotypes within a clade, but this theory ignores abiotic effects. The role of abiotic drivers on the tempo of phenotypic evolution has been tested only in a few lineages or small clades from the fossil record. Here, we develop a phylogenetic comparative framework for testing if and how clade-wide rates of phenotypic evolution vary with abiotic drivers. We apply this approach to comprehensive bird and mammal phylogenies, body size data for 9,465 extant species, and global average temperature trends over the Cenozoic. Across birds and mammals, we find that the rate of body size evolution is primarily driven by past climate. Unexpectedly, evolutionary rates are inferred to be higher during periods of cold rather than warm climates in most groups, suggesting that temperature influences evolutionary rates by modifying selective pressures rather than through its effect on energy availability and metabolism. The effect of climate on the rate of body size evolution seems to be a general feature of endotherm evolution, regardless of wide differences in species' ecology and evolutionary history. These results suggest that climatic changes played a major role in shaping species' evolution in the past and could also play a major role in shaping their evolution in the future.

Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition

Crocodyliforms have a much richer evolutionary history than represented by their extant descendants, including several independent marine and terrestrial radiations during the Mesozoic. However, heterogeneous sampling of their fossil record has obscured their macroevolutionary dynamics, and obfuscated attempts to reconcile external drivers of these patterns. Here, we present a comprehensive analysis of crocodyliform biodiversity through the Jurassic/Cretaceous (J/K) transition using subsampling and phylogenetic approaches and apply maximum-likelihood methods to fit models of extrinsic variables to assess what mediated these patterns. A combination of fluctuations in sea-level and episodic perturbations to the carbon and sulfur cycles was primarily responsible for both a marine and non-marine crocodyliform biodiversity decline through the J/K boundary, primarily documented in Europe. This was tracked by high extinction rates at the boundary and suppressed origination rates throughout the Early Cretaceous. The diversification of Eusuchia and Notosuchia likely emanated from the easing of ecological pressure resulting from the biodiversity decline, which also culminated in the extinction of the marine thalattosuchians in the late Early Cretaceous. Through application of rigorous techniques for estimating biodiversity, our results demonstrate that it is possible to tease apart the complex array of controls on diversification patterns in major archosaur clades.

Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval

Reconstructing deep time trends in biodiversity remains a central goal for palaeobiologists, but our understanding of the magnitude and tempo of extinctions and radiations is confounded by uneven sampling of the fossil record. In particular, the Jurassic/Cretaceous (J/K) boundary, 145 million years ago, remains poorly understood, despite an apparent minor extinction and the radiation of numerous important clades. Here we apply a rigorous subsampling approach to a comprehensive tetrapod fossil occurrence data set to assess the group's macroevolutionary dynamics through the J/K transition. Although much of the signal is exclusively European, almost every higher tetrapod group was affected by a substantial decline across the boundary, culminating in the extinction of several important clades and the ecological release and radiation of numerous modern tetrapod groups. Variation in eustatic sea level was the primary driver of these patterns, controlling biodiversity through availability of shallow marine environments and via allopatric speciation on land.