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Understanding the role of humans as ‘ecosystem engineers’ requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no con-ceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional defini-tions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term – ‘Earth system engineering’ – to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate this framework using the fossil record, and show how it can be applied across the tree of life, and throughout Earth history. 

We report U-Pb age determinations of carbonate nodules from an in situ paleosol horizon in the Upper Permian Balfour Formation and from several horizons of pedogenic nodule conglomerate (PNC) in the Triassic Katberg Formation, Karoo Basin, South Africa, using laser ablation−inductively coupled plasma−mass spectrometry (LA-ICP-MS). The paleosol sample yields an age of 252 ± 3 Ma, which overlaps with a previous high-precision U-Pb zircon date from a volcanic ash deposit 2 m above the paleosol. This relationship demonstrates the reliability of using LA-ICP-MS dating techniques on terrestrial pedogenic calcite. Two PNC samples collected at the base of the Katberg Formation within the same sandstone unit yield ages of 255 ± 3 Ma and 251 ± 3 Ma. The age of 251 ± 3 Ma overlaps with the high-precision U-Pb zircon date below the PNC and is a maximum age estimate of deposition for the base of the Katberg Formation. Our results show that reworked nodules in the same concentrated conglomerate lag can be of different ages, but that similarly aged nodules are spatially associated. In addition, two PNC samples collected higher in the section yield ages of 249 ± 3 Ma and 241 ± 3 Ma, providing maximum depositional ages for the lower to middle Katberg Formation for the first time. We demonstrate that pedogenic carbonate nodules can be dated with meaningful precision, providing another mechanism for constraining the age of sedimentary sequences and studying events associated with the Permian−Triassic transition in the central Karoo Basin, even though the extinction boundary may not be preserved in this area. 

Abstract PremisePteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation‐related applications of the group—has been impaired by the relative isolation of the neo‐ and paleobotanical research communities and by the absence of large‐scale biodiversity data sources. MethodsHere we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo‐ and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal‐enabled research projects. ResultsThe data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next‐generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time. DiscussionThe PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity‐related investigations, and providing new opportunities for education and community engagement. 

The Whitehorse Group and Quartermaster Formation are extensive red-bed terrestrial sequences representing the final episode of sedimentation in the Palo Duro Basin in north-central Texas, U.S.A. Regionally, these strata record the culmination of a long-term regression sequence beginning in the middle to late Permian. The Whitehorse Group includes beds of abundant laminated to massive red quartz siltstone to fine sandstone and rare dolomite, laminated to massive gypsum, and claystones, as well as diagenetic gypsum. The Quartermaster Formation exhibits a change from nearly equal amounts of thin planar and lenticular fine sandstone and laminated to massive mudstone in its lower half to overlying strata with coarser-grained, cross-bedded sandstones indicative of meandering channels up to 7 m deep and rare overbank mudstones. Paleosols are absent in the Upper Whitehorse Group and only poorly developed in the Quartermaster Formation. Volcanic ash-fall deposits (tuffs) present in uppermost Whitehorse Group and lower Quartermaster Formation strata permit correlation among five stratigraphic sections distributed over ∼150 km and provide geochronologic age information for these rocks. Both the Whitehorse Group and Quartermaster Formation have traditionally been assigned to the late Permian Ochoan (Changhsingian) stage, and workers assumed that the Permian-Triassic boundary is characterized by a regionally significant unconformity. Chemostratigraphic or biostratigraphic evidence for this age assignment, however, have been lacking to date. Single zircon U-Pb CA-TIMS analyses from at least two distinct volcanic ash fall layers in the lower Quartermaster Formation, which were identified and collected from five different localities across the Palo Duro Basin, yield interpreted depositional ages ranging from 252.19 ± 0.30 to 251.74 ± 0.28 Ma. Single zircon U-Pb CA-TIMS analyses of detrital zircons from sandstones located only a few meters beneath the top of the Quartermaster Formation yield a range of dates from Mesoproterozoic (1418 Ma) to Middle Triassic (244.5 Ma; Anisian), the latter of which is interpreted as a maximum depositional age, which is no older than Anisian, thus indicating the Permian-Triassic boundary to lie somewhere within the lower Quartermaster Formation/upper Whitehorse Group succession. Stable carbon isotope data from 180 samples of early-burial dolomicrite cements preserve a chemostratigraphic signal that is similar among sections, with a large ∼−8‰ negative isotope excursion ∼20 m beneath the Whitehorse Group-Quartermaster Formation boundary. This large negative carbon isotope excursion is interpreted to be the same excursion associated with the end-Permian extinction and this is in concert with the new high precision radioisotopic age data presented and the fact that the excursion lies within a normal polarity stratigraphic magnetozone. Dolomite cement δ 13 C values remain less negative (between about −5 and −8 permil) into the lower part of the Quartermaster Formation before becoming more positive toward the top of the section. This long interval of negative δ 13 C values in the Quartermaster Formation is interpreted to represent the earliest Triassic (Induan) inception of biotic and ecosystem “recovery.” Oxygen isotope values of dolomicrite cements show a progressive trend toward more positive values through the boundary interval, suggesting substantially warmer conditions around the end-Permian extinction event and a trend toward cooler conditions after the earliest Triassic. Our observations on these strata show that the paleoenvironment and paleoclimate across the Permian-Triassic boundary in western, sub-equatorial Pangea was characterized by depositional systems that were not conducive to plant preservation. 

Abstract Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of $${\sim}$$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth–death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.] 

Although Siberian Trap volcanism is considered a primary driver of the largest extinction in Earth history, the end-Permian crisis, the relationship between these events remains unclear. However, malformations in fossilized gymnosperm pollen from the extinction interval suggest biological stress coinciding with pulsed forest decline. These grains are hypothesized to have been caused by enhanced ultraviolet-B (UV-B) irradiation from volcanism-induced ozone shield deterioration. We tested this proposed mechanism by observing the effects of inferred end-Permian UV-B regimes on pollen development and reproductive success in living conifers. We find that pollen malformation frequencies increase fivefold under high UV-B intensities. Surprisingly, all trees survived but were sterilized under enhanced UV-B. These results support the hypothesis that heightened UV-B stress could have contributed not only to pollen malformation production but also to deforestation during Permian-Triassic crisis intervals. By reducing the fertility of several widespread gymnosperm lineages, pulsed ozone shield weakening could have induced repeated terrestrial biosphere destabilization and food web collapse without exerting a direct “kill” mechanism on land plants or animals. These findings challenge the paradigm that mass extinctions require kill mechanisms and suggest that modern conifer forests may be considerably more vulnerable to anthropogenic ozone layer depletion than expected.