No mass extinction for land plants at the Permian-Triassic transition

Refugium amidst ruins: Unearthing the lost flora that escaped the end-Permian mass extinction

Searching for land refugia becomes imperative for human survival during the hypothetical sixth mass extinction. Studying past comparable crises can offer insights, but there is no fossil evidence of diverse megafloral ecosystems surviving the largest Phanerozoic biodiversity crisis. Here, we investigated palynomorphs, plant, and tetrapod fossils from the Permian-Triassic South Taodonggou Section in Xinjiang, China. Our fossil records, calibrated by a high-resolution age model, reveal the presence of vibrant regional gymnospermous forests and fern fields, while marine organisms experienced mass extinction. This refugial vegetation was crucial for nourishing the substantial influx of surviving animals, thereby establishing a diverse terrestrial ecosystem approximately 75,000 years after the mass extinction. Our findings contradict the widely held belief that restoring terrestrial ecosystem functional diversity to pre-extinction levels would take millions of years. Our research indicates that moderate hydrological fluctuations throughout the crisis sustained this refugium, likely making it one of the sources for the rapid radiation of terrestrial life in the early Mesozoic.

The Micropaleoecology Framework: Evaluating Biotic Responses to Global Change Through Paleoproxy, Microfossil, and Ecological Data Integration

The microfossil record contains abundant, diverse, and well-preserved fossils spanning multiple trophic levels from primary producers to apex predators. In addition, microfossils often constitute and are preserved in high abundances alongside continuous high-resolution geochemical proxy records. These characteristics mean that microfossils can provide valuable context for understanding the modern climate and biodiversity crises by allowing for the interrogation of spatiotemporal scales well beyond what is available in neo-ecological research. Here, we formalize a research framework of "micropaleoecology," which builds on a holistic understanding of global change from the environment to ecosystem level. Location: Global. Time period: Neoproterozoic-Phanerozoic. Taxa studied: Fossilizing organisms/molecules. Our framework seeks to integrate geochemical proxy records with microfossil records and metrics, and draws on mechanistic models and systems-level statistical analyses to integrate disparate records. Using multiple proxies and mechanistic mathematical frameworks extends analysis beyond traditional correlation-based studies of paleoecological associations and builds a greater understanding of past ecosystem dynamics. The goal of micropaleoecology is to investigate how environmental changes impact the component and emergent properties of ecosystems through the integration of multi-trophic level body fossil records (primarily using microfossils, and incorporating additional macrofossil data where possible) with contemporaneous environmental (biogeochemical, geochemical, and sedimentological) records. Micropaleoecology, with its focus on integrating ecological metrics within the context of paleontological records, facilitates a deeper understanding of the response of ecosystems across time and space to better prepare for a future Earth under threat from anthropogenic climate change.

Special Issue: 100 years of scientific excavations at UNESCO World Heritage Site Monte San Giorgio and global research on Triassic marine Lagerstätten

Only a few Swiss fossil localities are known globally and of which, the UNESCO World Heritage Site Monte San Giorgio, which extends from Switzerland into Italy, is the most important one. Following the discovery of the occurrence of articulated skeletons of marine reptiles in the local mines, large excavations were organized by Bernhard Peyer from the University of Zurich starting 1924. With this collection of articles, we commemorate the successful excavations and research, which initiated the publication of a series of monographies, mostly on the vertebrates but also on the invertebrates of this locality. Especially with the discovery of several remarkably similar Konservat-Lagerstätten in China, the discoveries from Monte San Giorgio gained global relevance. New methodologies such as computed tomography produced a wealth of new data, particularly on endocranial anatomy of several tetrapods.

Thalattosauria in time and space: a review of thalattosaur spatiotemporal occurrences, presumed evolutionary relationships and current ecological hypotheses

In the wake of the greatest mass extinction in Earth's history, the End-Permian Mass Extinction, the Triassic was a time of recovery and innovation. Aided by warm climatic conditions and favorable ecological circumstances, many reptilian clades originated and rapidly diversified during this time. This set the stage for numerous independent invasions of the marine realm by several reptilian clades, such as Ichthyosauriformes and Sauropterygia, shaping the oceanic ecosystems for the entire Mesozoic. Although comparatively less speciose, and temporally and latitudinally more restricted, another marine reptile clade, the Thalattosauriformes, stands out because of their unusual and highly disparate cranial, dental and skeletal morphology. Research on Thalattosauriformes has been hampered by a historic dearth of material, with the exception of rare material from Lagerstätten and highly fossiliferous localities, such as that from the UNESCO world heritage site of Monte San Giorgio. Consequently, their evolutionary origins and paleobiology remain poorly understood. The recent influx of new material from southwestern China and North America has renewed interest in this enigmatic group prompting the need for a detailed review of historic work and current views. The earliest representatives of the group may have been present from the late Early Triassic onwards in British Columbia. By the Ladinian the group had achieved a wide distribution across the northern hemisphere, spanning the eastern Panthalassic as well as the eastern and western Tethyan provinces. Distinct morphological and likely ecological differences exist between the two major clades of Thalattosauriformes, the Askeptosauroidea and the Thalattosauroidea, with the latter showing a higher degree of cranial and skeletal morphological disparity. In-group relationships remain poorly resolved beyond this bipartition. Overall, thalattosaurs may be closely related to other marine reptile groups such as ichthyopterygians and sauropterygians. However, their exact position within Diapsida remains elusive. Future focal points should utilize modern digital paleontological approaches to explore the many fragmentary specimens of otherwise poorly sampled localities.

Swiss ichthyosaurs: a review

Switzerland is an ichthyosaur country: it has a rich record of marine reptile fossils, particularly the fish-shaped ichthyosaurs, and the according research. Here, we provide an overview over the 12 or more genera and at least 13 species plus numerous fragmentary remains of ichthyosaurs from the Triassic to the Cretaceous that have been discovered in twelve cantons thus far, of which four species are based on Swiss holotypes. This wealth of ichthyosaur species can be explained by their abundance in the Middle Triassic conservation deposits (Konservat Lagerstätte) of Monte San Giorgio, as well as occasional discoveries in strata of Middle Triassic to Early Cretaceous age. The moderate abundance of outcrops in reasonable conditions in combination with the long history of palaeontological research in Switzerland explains this good fossil record. In addition to this unique overview, we provide more data for further studies and update the knowledge of these taxa.

The contribution of the Middle Triassic fossil assemblage of Monte San Giorgio to insect evolution

The Triassic represents a critical period for understanding the turnover of insect fauna from the Paleozoic to the Mesozoic following the end-Permian mass extinctions (EPME); however, fossil deposits from the Early-Middle Triassic are scarce. The exceptionally preserved 239 million-year-old fossil insect fauna recorded at Monte San Giorgio (Switzerland), including 248 fossils representing 15 major insect clades is presented here. Besides the exceptional features, including their small size and excellent preservation, the fossils have importance in the evolutionary history of the group. The taxonomic and ecological diversity recovered, including both freshwater (dragonflies and caddisflies) and terrestrial taxa (true bugs and wasps), demonstrates that complex environments sustained a paleocommunity dominated by monurans (thought not to have survived the EPME), midges, and beetles. Interestingly, a blattodean-like fossil bearing an external ootheca was also found, important for understanding Paleozoic roachoids to extant cockroaches' transition and the evolution of maternal brood care. Moreover, the youngest and first complete specimen of †Permithonidae and the oldest sawfly fossils were discovered. Finally, round-shaped bodies, compatible with seminal capsules or lycophyte spores, were found on the abdomens of several midge-like individuals. If these are spores, non-seed-bearing plants could have been the first entomophilous plants rather than gymnosperms, as recently supposed. Altogether, these fossils contribute substantially to understanding insect evolution and Paleozoic-Mesozoic faunal turnover.

Sedimentary records of sea level fall during the end-Permian in the upper Yangtze region (southern China): Implications for the mass extinction

Sea level fall is considered one of the significant factors leading to the end-Permian mass extinction (EPME). We studied the relative sea level changes in the Beifengjing and Shangsi sections, and the results indicate that a sea level fall occurred in the Upper Yangtze region during the Permian-Triassic transition. Considering that there is no significant change in fossil abundance in the strata following the two sea level falls observed in the Beifengjing section, we conclude that the reduction in shallow marine habitat for sea level fall solely was insufficient to cause the mass extinction. However, sea level fall did exacerbate the input of terrestrial debris into the ocean, leading to the deterioration of the marine environment. We propose that the combined adverse effects of volcanic eruptions, sea level falls, and other events exceeded the threshold for biological survival, ultimately resulting in the catastrophic EPME.

Disparity of cycad leaves dispels the living fossil metaphor

The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.

The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants

Seed plants overtook ferns to become the dominant plant group during the late Carboniferous, a period in which the climate became colder and dryer1,2. However, the specific innovations driving the success of seed plants are not clear. Here we report that the appearance of suberin lamellae (SL) contributed to the rise of seed plants. We show that the Casparian strip and SL vascular barriers evolved at different times, with the former originating in the most recent common ancestor (MRCA) of vascular plants and the latter in the MRCA of seed plants. Our results further suggest that most of the genes required for suberin formation arose through gene duplication in the MRCA of seed plants. We show that the appearance of the SL in the MRCA of seed plants enhanced drought tolerance through preventing water loss from the stele. We hypothesize that SL provide a decisive selective advantage over ferns in arid environments, resulting in the decline of ferns and the rise of gymnosperms. This study provides insights into the evolutionary success of seed plants and has implications for engineering drought-tolerant crops or fern varieties.

Improving the relevance of paleontology to climate change policy

Paleontology has provided invaluable basic knowledge on the history of life on Earth. The discipline can also provide substantial knowledge to societal challenges such as climate change. The long-term perspective of climate change impacts on natural systems is both a unique selling point and a major obstacle to becoming more pertinent for policy-relevant bodies like the Intergovernmental Panel on Climate Change (IPCC). Repeated experiments on the impacts of climate change without anthropogenic disturbance facilitate the extraction of climate triggers in biodiversity changes. At the same time, the long timescales over which paleontological changes are usually assessed are beyond the scope of policymakers. Based on first-hand experience with the IPCC and a quantitative analysis of its cited literature, we argue that the differences in temporal scope are less of an issue than inappropriate framing and reporting of most paleontological publications. Accepting that some obstacles will remain, paleontology can quickly improve its relevance by targeting climate change impacts more directly and focusing on effect sizes and relevance for projections, particularly on higher-end climate change scenarios.

Dying in the Sun: Direct evidence for elevated UV-B radiation at the end-Permian mass extinction

Land plants can adjust the concentration of protective ultraviolet B (UV-B)-absorbing compounds (UACs) in the outer wall of their reproductive propagules in response to ambient UV-B flux. To infer changes in UV-B radiation flux at Earth's surface during the end-Permian mass extinction, we analyze UAC abundances in ca. 800 pollen grains from an independently dated Permian-Triassic boundary section in Tibet. Our data reveal an excursion in UACs that coincide with a spike in mercury concentration and a negative carbon-isotope excursion in the latest Permian deposits, suggesting a close temporal link between large-scale volcanic eruptions, global carbon and mercury cycle perturbations, and ozone layer disruption. Because enhanced UV-B radiation can exacerbate the environmental deterioration induced by massive magmatism, ozone depletion is considered a compelling ecological driver for the terrestrial mass extinction.

Multiple drivers and lineage-specific insect extinctions during the Permo-Triassic

The Permo-Triassic interval encompasses three extinction events including the most dramatic biological crisis of the Phanerozoic, the latest Permian mass extinction. However, their drivers and outcomes are poorly quantified and understood for terrestrial invertebrates, which we assess here for insects. We find a pattern with three extinctions: the Roadian/Wordian (≈266.9 Ma; extinction of 64.5% insect genera), the Permian/Triassic (≈252 Ma; extinction of 82.6% insect genera), and the Ladinian/Carnian boundaries (≈237 Ma; extinction of 74.8% insect genera). We also unveil a heterogeneous effect of these extinction events across the major insect clades. Because extinction events have impacted Permo-Triassic ecosystems, we investigate the influence of abiotic and biotic factors on insect diversification dynamics and find that changes in floral assemblages are likely the strongest drivers of insects' responses throughout the Permo-Triassic. We also assess the effect of diversity dependence between three insect guilds; an effect ubiquitously found in current ecosystems. We find that herbivores held a central position in the Permo-Triassic interaction network. Our study reveals high levels of insect extinction that profoundly shaped the evolutionary history of the most diverse non-microbial lineage.

Examining paleobotanical databases: Revisiting trends in angiosperm folivory and unlocking the paleoecological promise of propensity score matching and specification curve analysis

Paleobotany is at a crossroads. Long-term trends in the fossil record of plants, encompassing their interactions with herbivores and with the environment, are of the utmost relevance for predicting global change as pCO2 continues to rise. Large data compilations with the potential to elucidate those trends are increasingly easy to assemble and access. However, in contrast to modern ecology and unlike various other paleontological disciplines, paleobotany has a limited history of “big data” meta-analyses. Debates about how much data are needed to address particular questions, and about how to control for potential confounding variables, have not examined paleobotanical data. Here I demonstrate the importance of analytical best practices by applying them to a recent meta-analysis of fossil angiosperms. Two notable analytical methods discussed here are propensity score matching and specification curve analysis. The former has been used in the biomedical and behavioral sciences for decades; the latter is a more recent method of examining relationships between, and inherent biases among, models. Propensity score matching allows one to account for potential confounding variables in observational studies, and more fundamentally, provides a way to quantify whether it is possible to account for them. Specification curve analysis provides the opportunity to examine patterns across a variety of schemes for partitioning data—for example, whether fossil assemblages are binned temporally by stage, epoch, or period. To my knowledge, neither of these methods has been used previously in paleontology, however, their use permits more robust analysis of paleoecological datasets. In the example provided here, propensity score matching is used to separate latitudinal trends from differences in age, climate, and plant community composition. Specification curve analysis is used to examine the robustness of apparent latitudinal trends to the schema used for assigning fossil assemblages to latitudinal bins. These analytical methods have the potential to further unlock the promise of the plant fossil record for elucidating long-term ecological and evolutionary change.

The Invasion of the Land in Deep Time: Integrating Paleozoic Records of Paleobiology, Ichnology, Sedimentology, and Geomorphology

The invasion of the land was a complex, protracted process, punctuated by mass extinctions, that involved multiple routes from marine environments. We integrate paleobiology, ichnology, sedimentology, and geomorphology to reconstruct Paleozoic terrestrialization. Cambrian landscapes were dominated by laterally mobile rivers with unstable banks in the absence of significant vegetation. Temporary incursions by arthropods and worm-like organisms into coastal environments apparently did not result in establishment of continental communities. Contemporaneous lacustrine faunas may have been inhibited by limited nutrient delivery and high sediment loads. The Ordovician appearance of early land plants triggered a shift in the primary locus of the global clay mineral factory, increasing the amount of mudrock on the continents. The Silurian-Devonian rise of vascular land plants, including the first forests and extensive root systems, was instrumental in further retaining fine sediment on alluvial plains. These innovations led to increased architectural complexity of braided and meandering rivers. Landscape changes were synchronous with establishment of freshwater and terrestrial arthropod faunas in overbank areas, abandoned fluvial channels, lake margins, ephemeral lakes, and inland deserts. Silurian-Devonian lakes experienced improved nutrient availability, due to increased phosphate weathering and terrestrial humic matter. All these changes favoured frequent invasions to permament establishment of jawless and jawed fishes in freshwater habitats and the subsequent tetrapod colonization of the land. The Carboniferous saw rapid diversification of tetrapods, mostly linked to aquatic reproduction, and land plants, including gymnosperms. Deeper root systems promoted further riverbank stabilization, contributing to the rise of anabranching rivers and braided systems with vegetated islands. New lineages of aquatic insects developed and expanded novel feeding modes, including herbivory. Late Paleozoic soils commonly contain pervasive root and millipede traces. Lacustrine animal communities diversified, accompanied by increased food-web complexity and improved food delivery which may have favored permanent colonization of offshore and deep-water lake environments. These trends continued in the Permian, but progressive aridification favored formation of hypersaline lakes, which were stressful for colonization. The Capitanian and end-Permian extinctions affected lacustrine and fluvial biotas, particularly the invertebrate infauna, although burrowing may have allowed some tetrapods to survive associated global warming and increased aridification.

Paleoclimate-induced stress on polar forested ecosystems prior to the Permian-Triassic mass extinction

The end-Permian extinction (EPE) has been considered to be contemporaneous on land and in the oceans. However, re-examined floristic records and new radiometric ages from Gondwana indicate a nuanced terrestrial ecosystem response to EPE global change. Paleosol geochemistry and climate simulations indicate paleoclimate change likely caused the demise of the widespread glossopterid ecosystems in Gondwana. Here, we evaluate the climate response of plants to the EPE via dendrochronology snapshots to produce annual-resolution records of tree-ring growth for a succession of late Permian and early Middle Triassic fossil forests from Antarctica. Paleosol geochemistry indicates a shift in paleoclimate towards more humid conditions in the Early and early Middle Triassic relative to the late Permian. Paleosol morphology, however, supports inferences of a lack of forested ecosystems in the Early Triassic. The plant responses to this paleoclimate change were accompanied by enhanced stress during the latest Permian as determined by high-resolution paleoclimate analysis of wood growth intervals. These results suggest that paleoclimate change during the late Permian exerted significant stress on high-latitude forests, consistent with the hypothesis that climate change was likely the primary driver of the extinction of the glossopterid ecosystems.

Early evolution of beetles regulated by the end-Permian deforestation

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

Living fast in the Triassic: New data on life history in Lystrosaurus (Therapsida: Dicynodontia) from northeastern Pangea

Lystrosaurus was one of the few tetrapods to survive the Permo-Triassic mass extinction, the most profound biotic crisis in Earth’s history. The wide paleolatitudinal range and high abundance of Lystrosaurus during the Early Triassic provide a unique opportunity to investigate changes in growth dynamics and longevity following the mass extinction, yet most studies have focused only on species that lived in the southern hemisphere. Here, we present the long bone histology from twenty Lystrosaurus skeletal elements spanning a range of sizes that were collected in the Jiucaiyuan Formation of northwestern China. In addition, we compare the average body size of northern and southern Pangean Triassic-aged species and conduct cranial geometric morphometric analyses of southern and northern taxa to begin investigating whether specimens from China are likely to be taxonomically distinct from South African specimens. We demonstrate that Lystrosaurus from China have larger average body sizes than their southern Pangean relatives and that their cranial morphologies are distinctive. The osteohistological examination revealed sustained, rapid osteogenesis punctuated by growth marks in some, but not all, immature individuals from China. We find that the osteohistology of Chinese Lystrosaurus shares a similar growth pattern with South African species that show sustained growth until death. However, bone growth arrests more frequently in the Chinese sample. Nevertheless, none of the long bones sampled here indicate that maximum or asymptotic size was reached, suggesting that the maximum size of Lystrosaurus from the Jiucaiyuan Formation remains unknown.

Fossil data support a pre-Cretaceous origin of flowering plants

Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.

The rise of angiosperms pushed conifers to decline during global cooling

Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.

Plant extinction excels plant speciation in the Anthropocene

BACKGROUND

In the past several millenniums, we have domesticated several crop species that are crucial for human civilization, which is a symbol of significant human influence on plant evolution. A pressing question to address is if plant diversity will increase or decrease in this warming world since contradictory pieces of evidence exit of accelerating plant speciation and plant extinction in the Anthropocene.

RESULTS

Comparison may be made of the Anthropocene with the past geological times characterised by a warming climate, e.g., the Palaeocene-Eocene Thermal Maximum (PETM) 55.8 million years ago (Mya)-a period of "crocodiles in the Arctic", during which plants saw accelerated speciation through autopolyploid speciation. Three accelerators of plant speciation were reasonably identified in the Anthropocene, including cities, polar regions and botanical gardens where new plant species might be accelerating formed through autopolyploid speciation and hybridization.

CONCLUSIONS

However, this kind of positive effect of climate warming on new plant species formation would be thoroughly offset by direct and indirect intensive human exploitation and human disturbances that cause habitat loss, deforestation, land use change, climate change, and pollution, thus leading to higher extinction risk than speciation in the Anthropocene. At last, four research directions are proposed to deepen our understanding of how plant traits affect speciation and extinction, why we need to make good use of polar regions to study the mechanisms of dispersion and invasion, how to maximize the conservation of plant genetics, species, and diverse landscapes and ecosystems and a holistic perspective on plant speciation and extinction is needed to integrate spatiotemporally.

Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases

Ancestral sequence reconstruction and resurrection provides useful information for protein engineering, yet its alliance with directed evolution has been little explored. In this study, we have resurrected several ancestral nodes of fungal laccases dating back ∼500 to 250 million years. Unlike modern laccases, the resurrected Mesozoic laccases were readily secreted by yeast, with similar kinetic parameters, a broader stability, and distinct pH activity profiles. The resurrected Agaricomycetes laccase carried 136 ancestral mutations, a molecular testimony to its origin, and it was subjected to directed evolution in order to improve the rate of 1,3-cyclopentanedione oxidation, a β-diketone initiator commonly used in vinyl polymerization reactions.IMPORTANCE The broad variety of biotechnological uses of fungal laccases is beyond doubt (food, textiles, pulp and paper, pharma, biofuels, cosmetics, and bioremediation), and protein engineering (in particular, directed evolution) has become the key driver for adaptation of these enzymes to harsh industrial conditions. Usually, the first requirement for directed laccase evolution is heterologous expression, which presents an important hurdle and often a time-consuming process. In this work, we resurrected a fungal Mesozoic laccase node which showed strikingly high heterologous expression and pH stability. As a proof of concept that the ancestral laccase is a suitable blueprint for engineering, we performed a quick directed evolution campaign geared to the oxidation of the β-diketone 1,3-cyclopentanedione, a poor laccase substrate that is used in the polymerization of vinyl monomers.

Permo-Triassic boundary carbon and mercury cycling linked to terrestrial ecosystem collapse

Records suggest that the Permo-Triassic mass extinction (PTME) involved one of the most severe terrestrial ecosystem collapses of the Phanerozoic. However, it has proved difficult to constrain the extent of the primary productivity loss on land, hindering our understanding of the effects on global biogeochemistry. We build a new biogeochemical model that couples the global Hg and C cycles to evaluate the distinct terrestrial contribution to atmosphere-ocean biogeochemistry separated from coeval volcanic fluxes. We show that the large short-lived Hg spike, and nadirs in δ²⁰²Hg and δ¹³C values at the marine PTME are best explained by a sudden, massive pulse of terrestrial biomass oxidation, while volcanism remains an adequate explanation for the longer-term geochemical changes. Our modelling shows that a massive collapse of terrestrial ecosystems linked to volcanism-driven environmental change triggered significant biogeochemical changes, and cascaded organic matter, nutrients, Hg and other organically-bound species into the marine system.

The dynamics of stem and crown groups

The fossil record of the origins of major groups such as animals and birds has generated considerable controversy, especially when it conflicts with timings based on molecular clock estimates. Here, we model the diversity of "stem" (basal) and "crown" (modern) members of groups using a "birth-death model," the results of which qualitatively match many large-scale patterns seen in the fossil record. Typically, the stem group diversifies rapidly until the crown group emerges, at which point its diversity collapses, followed shortly by its extinction. Mass extinctions can disturb this pattern and create long stem groups such as the dinosaurs. Crown groups are unlikely to emerge either cryptically or just before mass extinctions, in contradiction to popular hypotheses such as the "phylogenetic fuse". The patterns revealed provide an essential context for framing ecological and evolutionary explanations for how major groups originate, and strengthen our confidence in the reliability of the fossil record.

A Cretaceous peak in family-level insect diversity estimated with mark-recapture methodology

The history of insects' taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the 'range through' method suggests a steady, nearly monotonic increase in family-level diversity, whereas 'shareholder quorum subsampling' suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture-mark-recapture (CMR) approach is used to estimate insects' family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.

Carbon isotopic evidence for rapid methane clathrate release recorded in coals at the terminus of the Late Palaeozoic Ice Age

The end of the Late Palaeozoic Ice Age (LPIA) ushered in a period of significant change in Earth's carbon cycle, demonstrated by the widespread occurrence of coals worldwide. In this study, we present stratigraphically constrained organic stable carbon isotope (δ¹³C_org) data for Early Permian coals (312 vitrain samples) from the Moatize Basin, Mozambique, which record the transition from global icehouse to greenhouse conditions. These coals exhibit a three-stage evolution in atmospheric δ¹³C from the Artinskian to the Kungurian. Early Kungurian coals effectively record the presence of the short-lived Kungurian Carbon Isotopic Excursion (KCIE), associated with the proposed rapid release of methane clathrates during deglaciation at the terminus of the Late Palaeozoic Ice Age (LPIA), with no observed disruption to peat-forming and terrestrial plant communities. δ¹³C_org variations in coals from the Moatize Basin are cyclic in nature on the order of 10³-10⁵ years and reflect changes in δ¹³C_org of ~±1‰ during periods of stable peat accumulation, supporting observations from Palaeozoic coals elsewhere. These cyclic variations express palaeoenvironmental factors constraining peat growth and deposition, associated with changes in base level. This study also demonstrates the effectiveness of vitrain in coal as a geochemical tool for recording global atmospheric change during the Late Palaeozoic.

Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction

Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.