Stable metal anodes enabled by a labile organic molecule bonded to a reduced graphene oxide aerogel

Metallic anodes (lithium, sodium, and zinc) are attractive for rechargeable battery technologies but are plagued by an unfavorable metal–electrolyte interface that leads to nonuniform metal deposition and an unstable solid–electrolyte interphase (SEI). Here we report the use of electrochemically labile molecules to regulate the electrochemical interface and guide even lithium deposition and a stable SEI. The molecule, benzenesulfonyl fluoride, was bonded to the surface of a reduced graphene oxide aerogel. During metal deposition, this labile molecule not only generates a metal-coordinating benzenesulfonate anion that guides homogeneous metal deposition but also contributes lithium fluoride to the SEI to improve Li surface passivation. Consequently, high-efficiency lithium deposition with a low nucleation overpotential was achieved at a high current density of 6.0 mA cm⁻². A Li|LiCoO₂ cell had a capacity retention of 85.3% after 400 cycles, and the cell also tolerated low-temperature (−10 °C) operation without additional capacity fading. This strategy was applied to sodium and zinc anodes as well.

Rechargeable batteries based on metal anodes including lithium (Li), sodium (Na), and zinc (Zn) show great promise in achieving high energy density (1–3). Unfortunately, the electrochemical interface of the metal anodes is not favorable for metal deposition. Metal nucleation is inhomogeneous at the surface, leading to the growth of metal dendrites (4–7) and the formation of an unstable solid–electrolyte interphase (SEI) that is incapable of protecting metals from the side reactions with the electrolyte (8–12).Substantial efforts have been devoted to stabilizing the interface of metal anodes, especially for Li metal. These include the design of artificial protective layers (13–17), alternative electrolytes (18–24), and sacrificial additives (25–30) to stabilize the metal–electrolyte interface, the development of mechanically robust coatings (31–34) to block Li dendrite growth, and the use of structured scaffolds to host dendrite-free Li deposition by reducing local current densities (35–43). However, the performance of metal anodes remains poor under high-current or low-temperature conditions. This is because the inhomogeneous Li nucleation and unstable SEI problems have not been well addressed, and these problems at the interface are even exacerbated under critical operating conditions, especially high-current densities and low temperatures (5, 6, 44).Toward this end, we report a simple molecular approach for regulating the electrochemical interface of metal anodes, which enables even Li deposition and stable SEI formation in a conventional electrolyte. This was realized by bonding a labile organic molecule, benzenesulfonyl fluoride (BSF), to a reduced graphene oxide (rGO) aerogel surface as the Li anode host (Fig. 1A). During Li deposition, BSF molecules electrochemically decompose at the interface and generate benzenesulfonate anions bonded to the rGO aerogel (Fig. 1B). The conjugated anions have a strong binding affinity for Li, serving as lithiophilic sites on the rGO surface to synergistically induce homogeneous Li nucleation of Li on the rGO surface. At the same time, BSF molecules contribute LiF to the SEI layer, which facilitates Li surface passivation (Fig. 1C). As a result, high-efficiency (99.2%) Li deposition was achieved at a Li deposition amount of 6.0 mAh cm⁻² and a current density of 6.0 mA cm⁻²; the barrier to Li nucleation was markedly reduced, as evidenced by the low nucleation overpotentials at high-current density (6.0 mA cm⁻²) or at a low temperature (−10 °C). A 400-cycle life with a capacity retention of 83.6% was achieved for a Li|LiCoO₂ (LCO) cell in a conventional carbonate electrolyte. Moreover, with the organic molecule-tuned interface, the Li|LCO cell can be stably cycled at a low operating temperature (−10 °C). This approach was applied to Na and Zn metal anodes as well.Open in a separate windowFig. 1.Illustration of a stable interface for Li deposition using a labile organic molecule, benzenesulfonyl fluoride (BSF). (A) Covalently bonded BSF on the rGO aerogel surface. (B) In situ generation of a lithiophilic conjugated anion (benzenesulfonate) and LiF on the surface during Li deposition. (C) Li nucleation preferentially occurs at the conjugated anion sites owing to the strong Li binding affinity, which leads to uniform Li deposition. In addition, the LiF that is formed is in the SEI layer and passivates the Li surface.     

Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters

ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K⁺ channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease.

ATP binding cassette (ABC) proteins are a large family of membrane proteins found in all kingdoms of life (1, 2). ABC proteins have a core structure composed of two transmembrane (TM) domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2) (Fig. 1A and SI Appendix, Fig. S1A) (3–5). Through ATP binding and hydrolysis at the NBDs, ABC proteins actively transport solutes across cell membranes, regulate activities of other proteins, or function as channels (1, 2). Thus, ABC proteins are involved in many biological processes, including lipid homeostasis, cellular metal trafficking, and antigen peptide transport. Mutations in human ABC proteins cause diseases such as Tangier disease, adenoleukodystrophy, cystic fibrosis, Dubin–Johnson syndrome, and pseudoxanthoma elasticum (PXE) (1, 2). Furthermore, the export of a wide range of cancer chemotherapeutics, antibiotics, and anti-fungal drugs by ABC transporters confers multidrug resistance to tumor cells, bacteria, and fungal pathogens, respectively (1, 2, 6, 7).Open in a separate windowFig. 1.Ycf1p structure. (A) Ycf1p domain arrangement. TMD, transmembrane domain; L0, L0 linker; NBD, nucleotide binding domain; and R, regulatory (R) region. The Pep4p proteolytic digestion site within the luminal loop 6 of TMD1 is denoted by a pink “*.” Phosphorylation sites in the L0 linker (S251) and R region (S908 and T911) are depicted with a “P” circled in red. (B) Cryo-EM density of Ycf1p with domains colored as in A. (C) Example of the atomic model for individual TM helices in TMD0 and the R region fit into the corresponding map densities. (D) Schematic ribbon diagram of Ycf1p colored as in A and B and with the proteolytic digestion site denoted by a pink “*.”Human ABC proteins are divided into seven subfamilies (A to G) based in part on the sequence of their NBDs and TMDs in the core ABC structure (1, 2). The C-subfamily is the most diverse and includes the cystic fibrosis transmembrane conductance regulator (CFTR), the sulphonylurea receptors that form regulatory subunits in ATP-sensitive K⁺ (K_ATP) channels, and the multidrug resistance proteins (MRPs). In addition to the ABC core, ABCC proteins contain an N-terminal extension that is either composed of an additional TM domain (TMD0) and L0 linker (Fig. 1A, orange and tan, respectively, and SI Appendix, Fig. S1A) or just an L0 tail (5, 8). A TMD0, but not L0 linker, is also found in some ABCB proteins (3, 5). These N-terminal extensions are involved in trafficking, endosomal recycling, protein interactions, and/or regulation of ABC activity (9–18). The existence of disease-causing mutations in TMD0 and the L0 linker of different ABCC proteins (8, 13, 18) indicates that these regions play important roles in protein function when present.High-resolution structural information for TMD0 is available only for the atypical ABCC protein SUR1 (19, 20), which is part of the large hetero-octameric K_ATP channel complex. In contrast, structures of monomeric ABC transporters showed only low-resolution density for TMD0 that was insufficient for building a full atomic model or lacked density for the domain altogether (14, 21–24). The vacuolar ABCC protein yeast cadmium factor 1 (Ycf1p) from Saccharomyces cerevisiae is a close homolog of human MRPs and a model for ABCC proteins that function as monomers. Ycf1p transports glutathione-conjugated heavy metals, such as Cd²⁺, from the cytosol into the vacuole, detoxifying the cell (25, 26). Human MRP1 can rescue Cd²⁺ transport activity in a YCF1 deletion strain (27).Like other ABCC proteins, Ycf1p contains a relatively long and mostly disordered linker that connects NBD1 and TMD2 (25, 28, 29) (Fig. 1A and SI Appendix, Fig. S1A). This linker contains stimulatory phosphorylation sites (25, 28), similar to the phospho-regulatory (R) region in the ABCC protein CFTR (30–32). Ycf1p also contains an inhibitory phosphorylation site in the L0 linker (33). However, how the R region interacts with the ABCC core and how its phosphorylation modulates protein function remain poorly understood for most ABCC proteins. Structural studies of Ycf1p presented here reveal how TMD0 and the R region exert their regulatory functions in MRP-like ABCC proteins.     

Observation of non-Hermitian topology and its bulk–edge correspondence in an active mechanical metamaterial

Topological edge modes are excitations that are localized at the materials’ edges and yet are characterized by a topological invariant defined in the bulk. Such bulk–edge correspondence has enabled the creation of robust electronic, electromagnetic, and mechanical transport properties across a wide range of systems, from cold atoms to metamaterials, active matter, and geophysical flows. Recently, the advent of non-Hermitian topological systems—wherein energy is not conserved—has sparked considerable theoretical advances. In particular, novel topological phases that can only exist in non-Hermitian systems have been introduced. However, whether such phases can be experimentally observed, and what their properties are, have remained open questions. Here, we identify and observe a form of bulk–edge correspondence for a particular non-Hermitian topological phase. We find that a change in the bulk non-Hermitian topological invariant leads to a change of topological edge-mode localization together with peculiar purely non-Hermitian properties. Using a quantum-to-classical analogy, we create a mechanical metamaterial with nonreciprocal interactions, in which we observe experimentally the predicted bulk–edge correspondence, demonstrating its robustness. Our results open avenues for the field of non-Hermitian topology and for manipulating waves in unprecedented fashions.

The inclusion of non-Hermitian features in topological insulators has recently seen an explosion of activity. Exciting developments include tunable wave guides that are robust to disorder (1–3), structure-free systems (4, 5), and topological lasers and pumping (6–10). In these systems, active components are introduced to typically 1) break time-reversal symmetry to create topological insulators with unidirectional edge modes (1–5) and 2) pump topologically protected edge modes, thus harnessing Hermitian topology in non-Hermitian settings (6–9, 11). In parallel, extensive theoretical efforts have generalized the concept of a topological insulator to truly non-Hermitian phases that cannot be realized in Hermitian materials (12–14). However, such non-Hermitian topology and its bulk–edge correspondence remain a matter of intense debate. On the one hand, it has been argued that the usual bulk–edge correspondence breaks down in non-Hermitian settings, while on the other hand, new topological invariants specific to non-Hermitian systems have been proposed to capture particular properties of their edge modes (15–20).Here, focusing on a non-Hermitian version of the Su–Schrieffer–Heeger (SSH) model (15–17, 21) with an odd number of sites (Fig. 1A), we find that a change in the bulk non-Hermitian topological invariant is accompanied by a localization change in the zero-energy edge modes. This finding suggests the existence of a bulk–edge correspondence for this type of truly non-Hermitian topology. We further construct a mechanical analogue of the non-Hermitian quantum model (Fig. 1B) and create a mechanical metamaterial (Fig. 1C) in which we observe the predicted correspondence between the non-Hermitian topological invariant and the topological edge mode. In particular, we report that the edge mode in the non-Hermitian topological phase has a peculiar nature, as it is localized on the rigid rather than the floppy side of the mechanical metamaterial.Open in a separate windowFig. 1.Quantum-to-classical mapping of a chain with non-Hermitian topology. (A) An SSH chain with two sublattices, A (in red) and B (in blue), augmented with nonreciprocal variations in the hopping amplitudes (indicated by ±ε). (B) The nonreciprocal classical analog of the augmented SSH chain, in which the classical masses (in red) correspond to the A sites in the quantum model, while the nonreciprocal springs (in blue) are analogous to the B sites. (C) Picture of the mechanical metamaterial realizing the nonreciprocal classical analogue of the augmented SSH model.     

From the Cover: Evidence from South Africa for a protracted end-Permian extinction on land

Earth’s largest biotic crisis occurred during the Permo–Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa’s Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using sample-standardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The “disaster taxon” Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

Mass extinctions are major perturbations of the biosphere resulting from a wide range of different causes including glaciations and sea level fall (1), large igneous provinces (2), and bolide impacts (3, 4). These events caused permanent changes to Earth’s ecosystems, altering the evolutionary trajectory of life (5). However, links between the broad causal factors of mass extinctions and the biological and ecological disturbances that lead to species extinctions have been difficult to characterize. This is because ecological disturbances unfold on timescales much shorter than the typical resolution of paleontological studies (6), particularly in the terrestrial record (6–8). Coarse-resolution studies have demonstrated key mass extinction phenomena including high extinction rates and lineage turnover (7, 9), changes in species richness (10), ecosystem instability (11), and the occurrence of disaster taxa (12). However, finer time resolutions are central to determining the association and relative timings of these effects, their potential causal factors, and their interrelationships. Achieving these goals represents a key advance in understanding the ecological mechanisms of mass extinctions.The end-Permian mass extinction (ca. 251.9 Ma) was Earth’s largest biotic crisis as measured by taxon last occurrences (13–15). Large outpourings from Siberian Trap volcanism (2) are the likely trigger of calamitous climatic changes, including a runaway greenhouse effect and ocean acidification, which had profound consequences for life on land and in the oceans (16–18). An estimated 81% of marine species (19) and 89% of tetrapod genera became extinct as established Permian ecosystems gave way to those of the Triassic. In the ocean, this included the complete extinction of reef-forming tabulate and rugose corals (20, 21) and significant losses in previously diverse ammonoid, brachiopod, and crinoid families (22). On land, many nonmammalian synapsids became extinct (16), and the glossopterid-dominated floras of Gondwana also disappeared (23). Stratigraphic sequences document a global “coral gap” and “coal gap” (24, 25), suggesting reef and forest ecosystems were rare or absent for up to 5 My after the event (26). Continuous fossil-bearing deposits documenting patterns of turnover across the Permian–Triassic transition (PTT) on land (27) and in the oceans (28) are geographically widespread (29, 30), including marine and continental successions that are known from China (31, 32) and India (33). Continental successions are known from Russia (34), Australia (35), Antarctica (36), and South Africa’s Karoo Basin (Fig. 1 and 37–40), the latter providing arguably the most densely sampled and taxonomically scrutinized (41–43) continental record of the PTT. The main extinction has been proposed to occur at the boundary between two biostratigraphic zones with distinctive faunal assemblages, the Daptocephalus and Lystrosaurus declivis assemblage zones (Fig. 1), which marks the traditional placement of the Permian–Triassic geologic boundary [(37) but see ref. 44]. Considerable research has attempted to understand the anatomy of the PTT in South Africa (38, 39, 45–52) and to place it in the context of biodiversity changes across southern Gondwana (53, 54) and globally (29, 31, 32, 44, 47, 55).Open in a separate windowFig. 1.Map of South Africa depicting the distribution of the four tetrapod fossil assemblage zones (Cistecephalus, Daptocephalus, Lystrosaurus declivis, Cynognathus) and our two study sites where fossils were collected in this study (sites A and B). Regional lithostratigraphy and biostratigraphy within the study interval are shown alongside isotope dilution–thermal ionization mass spectrometry dates retrieved by Rubidge et al., Botha et al., and Gastaldo et al. (37, 44, 80). The traditional (dashed red line) and associated PTB hypotheses for the Karoo Basin (37, 44) are also shown. Although traditionally associated with the PTB, the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary is defined by first appearances of co-occurring tetrapod assemblages, so its position relative to the three PTB hypotheses is unchanged. The Ripplemead member (*) has yet to be formalized by the South African Committee for Stratigraphy.Decades of research have demonstrated the richness of South Africa’s Karoo Basin fossil record, resulting in hundreds of stratigraphically well-documented tetrapod fossils across the PTT (37, 39, 56). This wealth of data has been used qualitatively to identify three extinction phases and an apparent early postextinction recovery phase (39, 45, 51). Furthermore, studies of Karoo community structure and function have elucidated the potential role of the extinction and subsequent recovery in breaking the incumbency of previously dominant clades, including synapsids (11, 57). Nevertheless, understanding patterns of faunal turnover and recovery during the PTT has been limited by the scarcity of quantitative investigations. Previous quantitative studies used coarsely sampled data (i.e., assemblage zone scale, 2 to 3 Ma time intervals) to identify low species richness immediately after the main extinction, potentially associated with multiple “boom and bust” cycles of primary productivity based on δ¹³C variation during the first 5 My of the Triassic (41, 58). However, many details of faunal dynamics in this interval remain unknown. Here, we investigate the dynamics of this major tetrapod extinction at an unprecedented time resolution (on the order of hundreds of thousands of years), using sample-standardized methods to quantify multiple aspects of regional change across the Cistecephalus, Daptocephalus, and Lystrosaurus declivis assemblage zones.     

Dimensions of invasiveness: Links between local abundance,geographic range size,and habitat breadth in Europe’s alien and native floras

Understanding drivers of success for alien species can inform on potential future invasions. Recent conceptual advances highlight that species may achieve invasiveness via performance along at least three distinct dimensions: 1) local abundance, 2) geographic range size, and 3) habitat breadth in naturalized distributions. Associations among these dimensions and the factors that determine success in each have yet to be assessed at large geographic scales. Here, we combine data from over one million vegetation plots covering the extent of Europe and its habitat diversity with databases on species’ distributions, traits, and historical origins to provide a comprehensive assessment of invasiveness dimensions for the European alien seed plant flora. Invasiveness dimensions are linked in alien distributions, leading to a continuum from overall poor invaders to super invaders—abundant, widespread aliens that invade diverse habitats. This pattern echoes relationships among analogous dimensions measured for native European species. Success along invasiveness dimensions was associated with details of alien species’ introduction histories: earlier introduction dates were positively associated with all three dimensions, and consistent with theory-based expectations, species originating from other continents, particularly acquisitive growth strategists, were among the most successful invaders in Europe. Despite general correlations among invasiveness dimensions, we identified habitats and traits associated with atypical patterns of success in only one or two dimensions—for example, the role of disturbed habitats in facilitating widespread specialists. We conclude that considering invasiveness within a multidimensional framework can provide insights into invasion processes while also informing general understanding of the dynamics of species distributions.

Human socioeconomic activities are altering species’ global distributions, bridging natural dispersal barriers through the accidental and intentional relocation of organisms, and opening opportunities for them to expand into new regions beyond their historic native ranges (1). The outcome of any given introduction event, however, is dependent on ecological and stochastic processes, and many introduced alien species fail to establish and persist (2, 3). Even species that do achieve persistent, self-sustaining populations (i.e., become naturalized sensu ref. 4) show varying degrees of success (i.e., invasiveness) in newly occupied regions. This has been true for natural colonization events throughout Earth’s history [e.g., on islands (5, 6) and during continental biotic interchanges (7–9)] and is certainly the case for the ongoing surge of human-mediated introductions (10–12). Disentangling the factors that lead to invasion success provides an opportunity not only for anticipating and mediating future anthropogenic invasions but also for better understanding the dynamics underlying natural range expansions (13).Quantifying a species’ success in invading the alien range is complex, a fact reflected in the diverse criteria applied by different authorities when deciding whether or not to classify naturalized species as invasive (14). Recent efforts have therefore recognized that invasiveness cannot be captured by a single metric but rather encompasses multiple aspects of ecological success and impact (15, 16). Some proposed metrics, such as spread rate and socioeconomic impacts, are difficult to quantify for large numbers of species (4, 17). However, Rabinowitz’s three-dimensional scheme for characterizing the rarity or commonness of species in their native distributions (18, 19) has been successfully co-opted as a valuable perspective for better understanding the success of alien species (16, 20, 21). Applied in the context of introduced species, this framework recognizes the potential for established aliens to vary along at least three demographic dimensions of invasiveness: 1) in local abundance within the naturalized range, 2) in geographic range size or extent of the naturalized range, and 3) in habitat breadth in the naturalized range (16). We subsequently distinguish these metrics as dimensions of invasiveness when measured in the naturalized distributions of alien species and dimensions of commonness when measured in species native distributions.Considering invasiveness within a multidimensional framework is particularly important if species vary independently among different dimensions (16, 21). Such a scenario opens the possibility for aliens to achieve invasion success in many different ways (Fig. 1). In other words, there could exist different forms of invasiveness, similar to the different forms of rarity or commonness originally proposed by Rabinowitz (19). On the other hand, theoretical concepts and empirical examples suggest correlations between Rabinowitz’s dimensions of commonness among species in their native distributions (6, 22, 23). For example, a positive relationship between local abundance and extent of geographic occurrence or range size has been documented at various scales for numerous taxa (24–26), including plants (24, 27–31), with niche breadth proposed as a linking mechanism (24, 26, 32). If the processes that generate these patterns in native distributions act similarly in species alien distributions, some of the forms of invasiveness outlined in Fig. 1 should be less likely to occur than others. More specifically, if the invasiveness dimensions are correlated, species should vary from excelling (abundant, widespread, generalists; form AWG in Fig. 1) to performing poorly (scarce, restricted, specialists; form 0 in Fig. 1) in all three invasiveness dimensions (33). On the other hand, these macroecological patterns are not without exception, and a recent assessment found little support for correlations among commonness dimensions in Europe’s native flora (34). Alien distributions may further differ because aliens vary in their residence time, and particularly recently introduced species may be in disequilibrium and still increasing along one or more of the invasiveness dimensions (21, 35–37). In line with these alternatives, a continuum from overall poor invaders to species succeeding in all three dimensions has been documented for the regional alien flora of French grassland communities (20), while associations among dimensions were found to be low for the herbaceous alien flora of Southeast Australia (16). The correspondence among different invasiveness dimensions at broader geographic scales has yet to be assessed.Open in a separate windowFig. 1.Conceptual diagram outlining the eight different forms of invasiveness depending on success in zero, one, two, or three dimensions of invasiveness (based on refs. 16, 18, and 20). Forms of invasiveness within the cyan polygon are associated with high naturalized abundance, within the magenta polygon with widespread naturalized geographic extent, and within the yellow polygon with high naturalized habitat breadth. The overlap between magenta and cyan is blue, between cyan and yellow is green, between magenta and yellow is red, and between all three is black. The forms of invasiveness are comparable to analogous forms of commonness used to describe species in their native distributions, and we refer to the same abbreviations in both cases.Functional traits play a role in mediating invasion processes, but efforts to identify characteristics of successful invaders have generally resulted in few or inconsistent associations (38, 39). However, distinguishing between different components of invasiveness may provide additional clarity if each is influenced by different traits or if the same trait has contrasting effects on different dimensions (15, 16, 21, 40, 41). For example, many plant traits are associated with general trade-offs between rapid growth (i.e., acquisitive growth strategies) versus stress tolerance and survival (i.e., conservative growth strategies) (42–44), and one can hypothesize scenarios where these divergent strategies are associated with success in different dimensions of invasiveness (40, 41). Another example are specialized adaptations for long-distance dispersal that may promote rapid range expansion, both in extent and into new habitats, but likely do not provide any advantages that would influence local abundances (45, 46). For habitat specialists, their specific habitat associations may additionally be important for determining whether or not they become widespread (31).A number of hypotheses for invasion success additionally emphasizes the importance of unique ecological dynamics that emerge when species are decoupled from constraints experienced in their native environments (47). For example, because species are able to occupy unfilled niches where introduced [i.e., Darwin’s naturalization hypothesis (48, 49)] or because they leave behind important herbivores, competitors, or pathogens that limit populations in the native distribution [i.e., enemy release (50, 51)]. These mechanisms may be less likely when species expand into areas near the native range, for example, during natural range expansions or intracontinental introductions, as the alien individuals are more likely to encounter conditions similar to those that limited their native distribution compared to species introduced from further abroad (e.g., those with extracontinental origins) (52–54).Here, we combine vegetation plot data covering Europe (55) with databases of alien and native distributions (56, 57), plant traits (58, 59), and historical dates of introduction (60) to provide a comprehensive assessment of multidimensional invasion success for the European alien seed plant flora. First, we test for correlations among local abundance, geographic extent, and habitat breadth of alien species in their naturalized distributions and classify species into one of the eight forms of invasiveness (Fig. 1). We ask whether some forms of invasiveness rarely occur and specifically whether species tend to fit along a continuum ranging from generally poor invaders to super invaders—species excelling in all three dimensions. In addition, we compare relationships among dimensions of invasiveness to those among dimensions of commonness measured for Europe’s native flora, assessing similarities and differences in patterns of distribution between contexts. Next, we explore likely drivers of each invasiveness dimension, testing whether the year of first alien occurrence in Europe, functional traits related to ecological strategies, specialized adaptations for long-distance dispersal, habitat associations, and region of origin explain different forms of invasion success.     

Structure,self-assembly,and properties of a truncated reflectin variant

Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant’s hierarchical assembly, and establish a direct correlation between the protein’s structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells’ color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.

Materials from naturally occurring and recombinant proteins are frequently employed for the study of fundamental biological processes and leveraged for applications in fields as diverse as electronics, optics, bioengineering, medicine, and fashion (1–13). Such broad utility is enabled by the numerous advantageous characteristics of protein-based materials, which include sequence modularity, controllable self-assembly, stimuli-responsiveness, straightforward processability, inherent biological compatibility, and customizable functionality (1–13). Within this context, unique structural proteins known as reflectins have recently attracted substantial attention because of their key roles in the fascinating color-changing capabilities of cephalopods, such as the squid shown in Fig. 1A, and have furthermore demonstrated their utility for unconventional biophotonic and bioelectronic technologies (11–40). For example, in vivo, Bragg stack-like ultrastructures from reflectin-based high refractive index lamellae (membrane-enclosed platelets) are responsible for the angle-dependent narrowband reflectance (iridescence) of squid iridophores, as shown in Fig. 1B (15–20). Analogously, folded membranes containing distributed reflectin-based particle arrangements within sheath cells lead to the mechanically actuated iridescence of squid chromatophore organs, as shown in Fig. 1C (15, 16, 21, 22). Moreover, in vitro, films processed from squid reflectins not only exhibit proton conductivities on par with some state-of-the-art artificial materials (23–27) but also support the growth of murine and human neural stem cells (28, 29). Additionally, morphologically variable coatings assembled from different reflectin isoforms can enable the functionality of chemically and electrically actuated color-changing devices, dynamic near-infrared camouflage platforms, and stimuli-responsive photonic architectures (27, 30–34). When considered together, these discoveries and demonstrations constitute compelling motivation for the continued exploration of reflectins as model biomaterials.Open in a separate windowFig. 1.(A) A camera image of a D. pealeii squid for which the skin contains light-reflecting cells called iridophores (bright spots) and pigmented organs called chromatophores (colored spots). Image credit: Roger T. Hanlon (photographer). (B) An illustration of an iridophore (Left), which shows internal Bragg stack-like ultrastructures from reflectin-based lamellae (i.e., membrane-enclosed platelets) (Inset). (C) An illustration of a chromatophore organ (Left), which shows arrangements of reflectin-based particles within the sheath cells (Inset). (D) The logo of the 28-residue-long N-terminal motif (RMN), which depicts the constituent amino acids (Upper) and their predicted secondary structures (Lower). (E) The logo of the 28-residue-long internal motif (RMI), which depicts the constituent amino acids (Upper) and their predicted secondary structures (Lower). (F) The logo of the 21-residue-long C-terminal motif (RMC), which depicts the constituent amino acids (Upper) and their predicted secondary structures (Lower). (G) The amino acid sequence of full-length D. pealeii reflectin A1, which contains a single RMN motif (gray oval) and five RMI motifs (orange ovals). (H) An illustration of the selection of the prototypical truncated reflectin variant (denoted as RfA1TV) from full-length D. pealeii reflectin A1.Given reflectins’ demonstrated significance from both fundamental biology and applications perspectives, some research effort has been devoted to resolving their three-dimensional (3D) structures (30, 31, 35–39). For example, fibers drawn from full-length Euprymna scolopes reflectin 1a and films processed from truncated E. scolopes reflectin 1a were shown to possess secondary structural elements (i.e., α-helices or β-sheets) (30, 31). In addition, precipitated nanoparticles and drop-cast films from full-length Doryteuthis pealeii reflectin A1 have exhibited β-character, which was seemingly associated with their conserved motifs (35, 36). Moreover, nanoparticles assembled from both full-length and truncated Sepia officinalis reflectin 2 variants have demonstrated signatures consistent with β-sheet or α-helical secondary structure, albeit in the presence of surfactants (38). However, such studies were made exceedingly challenging by reflectins’ atypical primary sequences enriched in aromatic and charged residues, documented extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for poorly controlled aggregation (12, 14, 15, 30–32, 34–39). Consequently, the reported efforts have all suffered from multiple drawbacks, including the need for organic solvents or denaturants, the evaluation of only polydisperse or aggregated (rather than monomeric) proteins, a lack of consensus among different experimental techniques, inadequate resolution that precluded molecular-level insight, imperfect agreement between computational predictions and experimental observations, and/or the absence of conclusive correlations between structure and optical functionality. As such, there has emerged an exciting opportunity for investigating reflectins’ molecular structures, which remain poorly understood and the subject of some debate.Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a robust methodology for controlling this variant’s hierarchical assembly, and establish a direct correlation between its structural characteristics and optical properties. We first rationally select a prototypical reflectin variant expected to recapitulate the behavior of its parent protein by using a bioinformatics-guided approach. We next map the conformational and energetic landscape accessible to our selected protein by means of all-atom molecular dynamics (MD) simulations. We in turn produce our truncated reflectin variant with and without isotopic labeling, develop solution conditions that maintain the protein in a monomeric state, and characterize the variant’s size and shape with small-angle X-ray scattering (SAXS). We subsequently resolve our protein’s dynamic secondary and tertiary structures and evaluate its backbone conformational fluctuations with NMR spectroscopy. Finally, we demonstrate a straightforward mechanical agitation-based approach to controlling our truncated reflectin variant’s secondary structure, hierarchical self-assembly, and bulk refractive index distribution. Overall, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells’ color-changing functionalities, and appear poised to inform new directions across biochemistry, cellular biology, bioengineering, and optics.     

Paleocene latitude of the Kohistan–Ladakh arc indicates multistage India–Eurasia collision

We report paleomagnetic data showing that an intraoceanic Trans-Tethyan subduction zone existed south of the Eurasian continent and north of the Indian subcontinent until at least Paleocene time. This system was active between 66 and 62 Ma at a paleolatitude of 8.1 ± 5.6 °N, placing it 600–2,300 km south of the contemporaneous Eurasian margin. The first ophiolite obductions onto the northern Indian margin also occurred at this time, demonstrating that collision was a multistage process involving at least two subduction systems. Collisional events began with collision of India and the Trans-Tethyan subduction zone in Late Cretaceous to Early Paleocene time, followed by the collision of India (plus Trans-Tethyan ophiolites) with Eurasia in mid-Eocene time. These data constrain the total postcollisional convergence across the India–Eurasia convergent zone to 1,350–2,150 km and limit the north–south extent of northwestern Greater India to <900 km. These results have broad implications for how collisional processes may affect plate reconfigurations, global climate, and biodiversity.

Classically, the India–Eurasia collision has been considered to be a single-stage event that occurred at 50–55 million years ago (Ma) (1, 2). However, plate reconstructions show thousands of kilometers of separation between India and Eurasia at the inferred time of collision (3, 4). Accordingly, the northern extent of Greater India was thought to have protruded up to 2,000 km relative to present-day India (5, 6) (Fig. 1). Others have suggested that the India–Eurasia collision was a multistage process that involved an east–west trending Trans-Tethyan subduction zone (TTSZ) situated south of the Eurasian margin (7–9) (Fig. 1). Jagoutz et al. (9) concluded that collision between India and the TTSZ occurred at 50–55 Ma, and the final continental collision occurred between the TTSZ and Eurasia at 40 Ma (9, 10). This model reconciles the amount of convergence between India and Eurasia with the observed shortening across the India–Eurasia collision system with the addition of the Kshiroda oceanic plate. Additionally, the presence of two subduction systems can explain the rapid India–Eurasia convergence rates (up to 16 mm a⁻¹) that existed between 135 and 50 Ma (9), as well as variations in global climate in the Cenozoic (11).Open in a separate windowFig. 1.The first panel is an overview map of tectonic structure of the Karakoram–Himalaya–Tibet orogenic system. Blue represents India, red represents Eurasia, and the Kohistan–Ladakh arc (KLA) is shown in gray. The different shades of blue highlight the deformed margin of the Indian plate that has been uplifted to form the Himalayan belt, and the zones of darker red within the Eurasian plate highlight the Eurasian continental arc batholith. Thick black lines denote the suture zones which separate Indian and Eurasian terranes. The tectonic summary panels illustrate the two conflicting collision models and their differing predictions of the location of the Kohistan–Ladakh arc. India is shown in blue, Eurasia is shown in red, and the other nearby continents are shown in gray. Active plate boundaries are shown with black lines, and recently extinct boundaries are shown with gray lines. Subduction zones are shown with triangular tick marks.While the existence of the TTSZ in the Cretaceous is not disputed, the two conflicting collision models make distinct predictions about its paleolatitude in Late Cretaceous to Paleocene time; these can be tested using paleomagnetism. In the single-stage collision model, the TTSZ amalgamated with the Eurasian margin prior to ∼80 Ma (12) at a latitude of ≥20 °N (13, 14). In contrast, in the multistage model, the TTSZ remained near the equator at ≤10 °N, significantly south of Eurasia, until collision with India (9) (Fig. 1).No undisputed paleomagnetic constraints on the location of the TTSZ are available in the central Himalaya (15–17). Westerweel et al. (18) showed that the Burma Terrane, in the eastern Himalaya, was part of the TTSZ and was located near the equator at ∼95 Ma, but they do not constrain the location of the TTSZ in the time period between 50 and 80 Ma, which is required to test the two collision hypotheses. In the western Himalaya, India and Eurasia are separated by the Bela, Khost, and Muslimbagh ophiolites and the 60,000 km² intraoceanic Kohistan Ladakh arc (19, 20) (Fig. 1). These were obducted onto India in the Late Cretaceous to Early Paleocene (19), prior to the closure of the Eocene to Oligocene Katawaz sedimentary basin (20) (Fig. 1). The Kohistan–Ladakh arc contacts the Eurasian Karakoram terrane in the north along the Shyok suture and the Indian plate in the south along the Indus suture (21) (Fig. 1). Previous paleomagnetic studies suggest that the Kohistan–Ladakh arc formed as part of the TTSZ near the equator in the early Cretaceous but provide no information on its location after 80 Ma (22–25). While pioneering, these studies lack robust age constraints, do not appropriately average paleosecular variation of the geodynamo, and do not demonstrate that the measured magnetizations have not been reset during a subsequent metamorphic episode.     

Intolerance of uncertainty modulates brain-to-brain synchrony during politically polarized perception

Political partisans see the world through an ideologically biased lens. What drives political polarization? Although it has been posited that polarization arises because of an inability to tolerate uncertainty and a need to hold predictable beliefs about the world, evidence for this hypothesis remains elusive. We examined the relationship between uncertainty tolerance and political polarization using a combination of brain-to-brain synchrony and intersubject representational similarity analysis, which measured committed liberals’ and conservatives’ (n = 44) subjective interpretation of naturalistic political video material. Shared ideology between participants increased neural synchrony throughout the brain during a polarizing political debate filled with provocative language but not during a neutrally worded news clip on polarized topics or a nonpolitical documentary. During the political debate, neural synchrony in mentalizing and valuation networks was modulated by one’s aversion to uncertainty: Uncertainty-intolerant individuals experienced greater brain-to-brain synchrony with politically like-minded peers and lower synchrony with political opponents—an effect observed for liberals and conservatives alike. Moreover, the greater the neural synchrony between committed partisans, the more likely that two individuals formed similar, polarized attitudes about the debate. These results suggest that uncertainty attitudes gate the shared neural processing of political narratives, thereby fueling polarized attitude formation about hot-button issues.

Countries around the world are experiencing the strain of growing political polarization (1–5). Opposing partisans come to see the world through different eyes. Where one sees the freedom to choose, another sees murder; where one sees the right to protest, another sees violent conduct (6–8). Such a polarized perception of reality hampers bipartisan cooperation and can even undermine the basic principles of democracy (8, 9).How does polarization arise? One popular theory posits that a need to have certain, structured, and stable beliefs about the world drives people toward political extremes (10–13). Rather than seeing the world in nuanced shades of gray, cognitively rigid individuals perceive information in black and white, painting the world in categorical and predictable terms (14)—a view that dovetails with the immutable taxonomy of political ideologues (15–19). The rigid mind is characterized by a trait-like tendency to find unpredictable and uncertain events aversive and threatening (14, 20, 21) and has long been theorized to play an outsized role in shaping polarized perceptions (22–26). Although recent work suggests that uncertainty can impact the evaluation of political candidates (27) and policy positions (28, 29) and is a major factor contributing to political conservatism (30, 31), the link between uncertainty and political polarization remains unclear. Here, we examine whether individual differences in intolerance of uncertainty (IUS) (20, 21) shape how naturalistic political information is processed in the brain at the time of perception. We test the hypothesis that uncertainty-intolerant individuals interpret polarizing political information through an ideologically biased, subjective “lens” that produces clear-cut judgments of the issue at hand (20, 32). We further examine whether the neural fingerprint of these uncertainty-driven polarized perceptions—that is, increased brain-to-brain synchrony between like-minded partisans—predicts the formation of polarized attitudes.We combine two techniques to measure polarized perceptions of political information. First, intersubject correlation [ISC (33)] provides a direct measure of the similarity in subjective interpretations of naturalistic social stimuli (e.g., video narratives) among participants (34, 35). This technique capitalizes on the neural processes triggered by incoming auditory and visual information. If two individuals exhibit similar neural profiles when processing the same incoming information (e.g., synchronized blood oxygen level-dependent [BOLD] responses in functional MRI [fMRI]), they likely have a shared perception and understanding of that information (36–40). Given that ISC offers an established metric to gauge whether individuals are processing information in a similar way, we can use it to test whether two individuals who share the same political ideology also have similar subjective perceptions of political information, which circumvents issues with demand characteristics and explicit self-report (41). Second, to make neural synchrony analyses sensitive to more subtle differences along the ideological continuum than simple left–right groupings and to test for interactive effects between ideology and intolerance to uncertainty, we combine ISC with intersubject representational similarity analysis [IS-RSA (42–44)]. This versatile approach enables us to leverage continuous individual differences and test whether uncertainty attitudes exacerbate the processing of political information in the brain to fuel polarized political attitude formation.Using a combination of targeted online and field recruiting (n = 360), we invited 22 liberals and 22 conservatives to participate in a study on political cognition (Fig. 1A). While undergoing fMRI, participants viewed three types of videos: a neutrally worded news segment on a politically charged topic (abortion; taken from Public Broadcasting Service [PBS] News), an inflammatory debate segment (police brutality and immigration; taken from the 2016 Cable News Network [CNN] Vice-Presidential debate), and a nonpolitical nature video (taken from British Broadcasting Corporation [BBC] Earth; Fig. 1B). Neural data analysis consisted of time locking the fMRI BOLD signal to the onset of the videos and computing voxel-wise time course correlations between each possible pairing of subjects across the entire participant pool, resulting in a “neural synchrony” measurement that indexes shared subjective interpretations of dynamic, naturalistic stimuli (35, 45, 46). We first analyzed behavioral responses to the videos to test whether ideology, IUS, or both predicted similarities in attitude formation about the presented political videos. Next, we analyzed variation in neural synchrony across participant dyads using IS-RSA (Fig. 1D) to test three interrelated hypotheses: 1) shared ideology between subjects will predict brain-to-brain synchrony during the perception of political stimuli, 2) IUS will modulate this neural synchrony in committed partisans, and 3) increasing neural synchrony will predict the subsequent expression of shared polarized attitudes about the political stimuli.Open in a separate windowFig. 1.(A) Participants underwent fMRI and behavioral testing as part of a larger study on political cognition. (B) Participants viewed three videos in a fixed order while undergoing fMRI. (C) Participants were clearly divided on political ideology. (D) Analytical approach. We tested for variation in neural synchrony as a function of ideology and IUS. The statistical map slice is taken from Fig. 2C.     

A solution to a sex ratio puzzle in Melittobia wasps

The puzzling sex ratio behavior of Melittobia wasps has long posed one of the greatest questions in the field of sex allocation. Laboratory experiments have found that, in contrast to the predictions of theory and the behavior of numerous other organisms, Melittobia females do not produce fewer female-biased offspring sex ratios when more females lay eggs on a patch. We solve this puzzle by showing that, in nature, females of Melittobia australica have a sophisticated sex ratio behavior, in which their strategy also depends on whether they have dispersed from the patch where they emerged. When females have not dispersed, they lay eggs with close relatives, which keeps local mate competition high even with multiple females, and therefore, they are selected to produce consistently female-biased sex ratios. Laboratory experiments mimic these conditions. In contrast, when females disperse, they interact with nonrelatives, and thus adjust their sex ratio depending on the number of females laying eggs. Consequently, females appear to use dispersal status as an indirect cue of relatedness and whether they should adjust their sex ratio in response to the number of females laying eggs on the patch.

Sex allocation has produced many of the greatest success stories in the study of social behaviors (1–4). Time and time again, relatively simple theory has explained variation in how individuals allocate resources to male and female reproduction. Hamilton’s local mate competition (LMC) theory predicts that when n diploid females lay eggs on a patch and the offspring mate before the females disperse, the evolutionary stable proportion of male offspring (sex ratio) is (n − 1)/2n (Fig. 1) (5). A female-biased sex ratio is favored to reduce competition between sons (brothers) for mates and to provide more mates (daughters) for those sons (6–8). Consistent with this prediction, females of >40 species produce female-biased sex ratios and reduce this female bias when multiple females lay eggs on the same patch (higher n; Fig. 1) (9). The fit of data to theory is so good that the sex ratio under LMC has been exploited as a “model trait” to study the factors that can constrain “perfect adaptation” (4, 10–13).Open in a separate windowFig. 1.LMC. The sex ratio (proportion of sons) is plotted versus the number of females laying eggs on a patch. The bright green dashed line shows the LMC theory prediction for the haplodiploid species (5, 39). A more female-biased sex ratio is favored in haplodiploids because inbreeding increases the relative relatedness of mothers to their daughters (7, 32). Females of many species adjust their offspring sex ratio as predicted by theory, such as the parasitoid Nasonia vitripennis (green diamonds) (82). In contrast, the females of several Melittobia species, such as M. australica, continue to produce extremely female-biased sex ratios, irrespective of the number of females laying eggs on a patch (blue squares) (15).In stark contrast, the sex ratio behavior of Melittobia wasps has long been seen as one of the greatest problems for the field of sex allocation (3, 4, 14–21). The life cycle of Melittobia wasps matches the assumptions of Hamilton’s LMC theory (5, 15, 19, 21). Females lay eggs in the larvae or pupae of solitary wasps and bees, and then after emergence, female offspring mate with the short-winged males, who do not disperse. However, laboratory experiments on four Melittobia species have found that females lay extremely female-biased sex ratios (1 to 5% males) and that these extremely female-biased sex ratios change little with increasing number of females laying eggs on a patch (higher n; Fig. 1) (15, 17–20, 22). A number of hypotheses to explain this lack of sex ratio adjustment have been investigated and rejected, including sex ratio distorters, sex differential mortality, asymmetrical male competition, and reciprocal cooperation (15–18, 20, 22–26).We tested whether Melittobia’s unusual sex ratio behavior can be explained by females being related to the other females laying eggs on the same patch. After mating, some females disperse to find new patches, while some may stay at the natal patch to lay eggs on previously unexploited hosts (Fig. 2). If females do not disperse, they can be related to the other females laying eggs on the same host (27–31). If females laying eggs on a host are related, this increases the extent to which relatives are competing for mates and so can favor an even more female-biased sex ratio (28, 32–35). Although most parasitoid species appear unable to directly assess relatedness, dispersal behavior could provide an indirect cue of whether females are with close relatives (36–38). Consequently, we predict that when females do not disperse and so are more likely to be with closer relatives, they should maintain extremely female-biased sex ratios, even when multiple females lay eggs on a patch (28, 35).Open in a separate windowFig. 2.Host nest and dispersal manners of Melittobia. (A) Photograph of the prepupae of the leaf-cutter bee C. sculpturalis nested in a bamboo cane and (B) a diagram showing two ways that Melittobia females find new hosts. The mothers of C. sculpturalis build nursing nests with pine resin consisting of individual cells in which their offspring develop. If Melittobia wasps parasitize a host in a cell, female offspring that mate with males inside the cell find a different host on the same patch (bamboo cane) or disperse by flying to other patches.We tested whether the sex ratio of Melittobia australica can be explained by dispersal status in a natural population. We examined how the sex ratio produced by females varies with the number of females laying eggs on a patch and whether or not they have dispersed before laying eggs. To match our data to the predictions of theory, we developed a mathematical model tailored to the unique population structure of Melittobia, where dispersal can be a cue of relatedness. We then conducted a laboratory experiment to test whether Melittobia females are able to directly access the relatedness to other females and adjust their sex ratio behavior accordingly. Our results suggest that females are adjusting their sex ratio in response to both the number of females laying eggs on a patch and their relatedness to the other females. However, relatedness is assessed indirectly by whether or not they have dispersed. Consequently, the solution to the puzzling behavior reflects a more-refined sex ratio strategy.     

Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB

The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon–carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys–Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]²⁺ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys–Trp radical (Lys–Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys–Trp• intermediate by the redox-tuned [4Fe-4S]²⁺ AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon–carbon bond-forming reactions.

The radical S-adenosylmethionine (rSAM) enzyme superfamily is the largest known in nature, with over 570,000 annotated and predominantly uncharacterized members spanning all domains of life (1–4). The uniting feature of rSAM enzymes is a [4Fe-4S] cluster, usually bound by a CX₃CX₂C motif that catalyzes reductive cleavage of SAM to form L-Met and a strongly oxidizing 5′-deoxyadenosyl radical (5′-dA•) (5–7). Recent studies on a suite of rSAM enzymes have revealed the presence of a previously unknown organometallic intermediate in this process, termed Ω, in which the 5′-C of 5′-dA• is bound to the unique iron of the [4Fe-4S] cluster (Fig. 1A) (8, 9). Homolysis of the Fe–C bond ultimately liberates 5′-dA•, which abstracts a hydrogen atom from substrate to initiate a profoundly diverse set of chemical reactions in both primary and secondary metabolism, including DNA, cofactor, vitamin, and antibiotic biosynthesis (5, 10–13).Open in a separate windowFig. 1.(A) Accepted scheme for radical initiation in rSAM enzymes. (B) X-ray crystal structure of SuiB (PDB ID: 5V1T). The RS domain, SPASM domain, and RiPP recognition element are rendered blue, green, and pink, respectively. [4Fe-4S] clusters are shown as spheres with the distances separating them indicated. (C) Lys–Trp cross-link formation (20) catalyzed by SuiB. The carbon–carbon bond installed by SuiB is shown in red. (D and E) Previously proposed EAS (D) and rEAS (E) mechanisms for SuiB-catalyzed Lys–Trp cross-link formation.Of the 570,000 rSAM enzyme superfamily members, over a quarter (∼165,000 genes from the Enzyme Function Initiative-Enzyme Similarity Tool) possess C-terminal extensions, called SPASM and twitch domains, which bind auxiliary Fe-S clusters (4, 14–19). The SPASM domain typically binds two auxiliary Fe-S clusters and is named after the rSAM enzymes involved in the synthesis of subtilosin, pyrroloquinoline quinone, anaerobic sulfatase, and mycofactocin. The twitch domain is a truncated SPASM domain and only binds one auxiliary cluster (15). Despite the wide prevalence of these domains and the characterization of several different SPASM/twitch rSAM enzymes by spectroscopic and structural studies, direct evidence for their catalytic function(s) has remained elusive.We previously performed functional and structural characterization on the SPASM rSAM enzyme SuiB (Fig. 1B), which is involved in the biosynthesis of a ribosomal peptide natural product in human and mammalian microbiome streptococci (14, 20–22). SuiB introduces an unusual carbon–carbon bond onto its substrate peptide, SuiA, between the sidechains of Lys2 and Trp6 (Fig. 1C). The mechanism for this transformation is of broader relevance, as a number of enzymes, such as RrrB, PqqE, and MqnC (2, 23, 24), are known to join unactivated aliphatic and aromatic carbons to generate sp³-sp² cross-links. A general mechanistic paradigm for this class of transformations is not yet available. For SuiB, two pathways have been proposed (20), one through a typical electrophilic aromatic substitution (EAS) mechanism, which is involved in other enzyme-catalyzed indole modifications, such as indole prenylation or flavin adenine dinucleotide (FAD)-enzyme-dependent indole chlorination (25–27). In this pathway, the 5′-dA• generates an alkyl radical, which upon a second one-electron oxidation, creates an α,β-unsaturated amide electrophile with which the indole sidechain reacts via Michael addition (Fig. 1D). Lanthionine cross-links observed in diverse lanthipeptides are built by this general scheme, though via heterolytic chemistry, with Cys acting as the nucleophile (28, 29). Alternatively, a radical electrophilic aromatic substitution (rEAS) reaction has been proposed, wherein the alkyl radical, formed by 5′-dA•, would react with the indole sidechain to generate a radical σ complex, a cross-linked Lys–Trp radical (Lys–Trp•), which upon oxidation and rearomatization would yield product (Fig. 1E). In both mechanisms, AuxI is proposed as an oxidant. Although this role for an rSAM auxiliary cluster has been previously suggested (30, 31), it has yet to be directly demonstrated experimentally. Mechanistic studies have favored the rEAS pathway (20); however, intermediates in the reaction of SuiB and enzymes that catalyze similar reactions have not yet been detected (15).In the current work, we sought to differentiate between the proposed mechanisms by trapping intermediates in the catalytic cycle of SuiB and characterizing them using electron paramagnetic resonance (EPR) spectroscopy. We report observation of three transient reaction intermediates, most importantly the sought-after Lys–Trp•, which is fundamentally different from previously characterized Trp radicals, as it is cross-linked and carries an indole tetrahedral center. We also provide evidence for AuxI as the oxidant of the Lys–Trp• intermediate as well as insights into redox potential changes of Fe-S clusters in SuiB that accompany SuiA binding. Together, our findings support the rEAS pathway for formation of the sp³-sp² cross-link and carry important implications for other enzymes that catalyze related transformations.     

Developmental influence on evolutionary rates and the origin of placental mammal tooth complexity

Development has often been viewed as a constraining force on morphological adaptation, but its precise influence, especially on evolutionary rates, is poorly understood. Placental mammals provide a classic example of adaptive radiation, but the debate around rate and drivers of early placental evolution remains contentious. A hallmark of early dental evolution in many placental lineages was a transition from a triangular upper molar to a more complex upper molar with a rectangular cusp pattern better specialized for crushing. To examine how development influenced this transition, we simulated dental evolution on “landscapes” built from different parameters of a computational model of tooth morphogenesis. Among the parameters examined, we find that increases in the number of enamel knots, the developmental precursors of the tooth cusps, were primarily influenced by increased self-regulation of the molecular activator (activation), whereas the pattern of knots resulted from changes in both activation and biases in tooth bud growth. In simulations, increased activation facilitated accelerated evolutionary increases in knot number, creating a lateral knot arrangement that evolved at least ten times on placental upper molars. Relatively small increases in activation, superimposed on an ancestral tritubercular molar growth pattern, could recreate key changes leading to a rectangular upper molar cusp pattern. Tinkering with tooth bud geometry varied the way cusps initiated along the posterolingual molar margin, suggesting that small spatial variations in ancestral molar growth may have influenced how placental lineages acquired a hypocone cusp. We suggest that development could have enabled relatively fast higher-level divergence of the placental molar dentition.

Whether developmental processes bias or constrain morphological adaptation is a long-standing question in evolutionary biology (1–4). Many of the distinctive features of a species derive from pattern formation processes that establish the position and number of anatomical structures (5). If developmental processes like pattern formation are biased toward generating only particular kinds of variation, adaptive radiations may often be directed along developmental–genetic “lines of least resistance” (2, 4, 6, 7). Generally, the evolutionary consequences of this developmental bias have been considered largely in terms of how it might influence the pattern of character evolution (e.g., refs. 1, 2, 8–10). But development could also influence evolutionary rates by controlling how much variation is accessible to natural selection in a given generation (11).For mammals, the dentition is often the only morphological system linking living and extinct species (12). Correspondingly, tooth morphology plays a crucial role in elucidating evolutionary relationships, time calibrating phylogenetic trees, and reconstructing adaptive responses to past environmental change (e.g., refs. 13–15). One of the most pervasive features of dental evolution among mammals is an increase in the complexity of the tooth occlusal surface, primarily through the addition of new tooth cusps (16, 17). These increases in tooth complexity are functionally and ecologically significant because they enable more efficient mechanical breakdown of lower-quality foods like plant leaves (18).Placental mammals are the most diverse extant mammalian group, comprising more than 6,000 living species spread across 19 extant orders, and this taxonomic diversity is reflected in their range of tooth shapes and dietary ecologies (12). Many extant placental orders, especially those with omnivorous or herbivorous ecologies (e.g., artiodactyls, proboscideans, rodents, and primates), convergently evolved a rectangular upper molar cusp pattern from a placental ancestor with a more triangular cusp pattern (19–21). This resulted from separate additions in each lineage of a novel posterolingual cusp, the "hypocone'''' [sensu (19)], to the tritubercular upper molar (Fig. 1), either through modification of a posterolingual cingulum (“true” hypocone) or another posterolingual structure, like a metaconule (pseudohypocone) (19). The fossil record suggests that many of the basic steps in the origin of this rectangular cusp pattern occurred during an enigmatic early diversification window associated with the divergence and early radiation of several placental orders (20, 21; Fig. 1). However, there remains debate about the rate and pattern of early placental divergence (22–24). On the one hand, most molecular phylogenies suggest that higher-level placental divergence occurred largely during the Late Cretaceous (25, 26), whereas other molecular phylogenies and paleontological analyses suggest more rapid divergence near the Cretaceous–Paleogene (K–Pg) boundary (21, 24, 27–29). Most studies agree that ecological opportunity created in the aftermath of the K–Pg extinction probably played an important role in ecomorphological diversification within the placental orders (30, 31). But exactly how early placentals acquired the innovations needed to capitalize on ecological opportunity remains unclear. Dental innovations, especially those which facilitated increases in tooth complexity, may have been important because they would have promoted expansion into plant-based dietary ecologies left largely vacant after the K–Pg extinction event (32).Open in a separate windowFig. 1.Placental mammal lineages separately evolved complex upper molar teeth with a rectangular cusp pattern composed of two lateral pairs of cusps from a common ancestor with a simpler, triangular cusp pattern. Many early relatives of the extant placental orders, such as Eritherium, possessed a hypocone cusp and a more rectangular primary cusp pattern. Examples of complex upper molars are the following: Proboscidea, the gomphothere Anancus; Rodentia, the wood mouse Apodemus; and Artiodactyla, the suid Nyanzachoerus.Mammalian tooth cusps form primarily during the “cap” and “bell” stage of dental development, when signaling centers called enamel knots establish the future sites of cusp formation within the inner dental epithelium (33, 34). The enamel knots secrete molecules that promote proliferation and changes in cell–cell adhesion, which facilitates invagination of the dental epithelium into an underlying layer of mesenchymal cells (34, 35). Although a range of genes are involved in tooth cusp patterning (36–38), the basic dynamics can be effectively modeled using reaction–diffusion models with just three diffusible morphogens: an activator, an inhibitor, and a growth factor (39–41). Candidate activator genes in mammalian tooth development include Bmp4, Activin A, Fgf20, and Wnt genes, whereas potential inhibitors include Shh and Sostdc, and Fgf4 and Bmp2 have been hypothesized to act as growth factors (38, 40–43). In computer models of tooth development, activator molecules up-regulated in the underlying mesenchyme stimulate differentiation of overlying epithelium into nondividing enamel knot cells. These in turn secrete molecules that inhibit further differentiation of epithelium into knot cells, while also promoting cell proliferation that creates the topographic relief of the cusp (40). Although many molecular, cellular, and physical processes have the potential to influence cusp formation, and thereby tooth complexity (35, 37), parameters that control the strength and conductance of the activator and inhibitor signals, the core components of the reaction–diffusion cusp patterning mechanism (39, 40) are likely to be especially important.Here, we integrate a previous computer model of tooth morphogenesis called ToothMaker (41), with simulations of trait evolution and data from the fossil record (Fig. 2), to examine the developmental origins of tooth complexity in placental mammals. Specifically, we ask the following: 1) What developmental processes can influence how many cusps form? 2) How might these developmental processes influence the evolution of tooth cusp number, especially rates? And 3) what developmental changes may have been important in the origins of the fourth upper molar cusp, the hypocone, in placental mammal evolution?Open in a separate windowFig. 2.Workflow for simulations of tooth complexity evolution. (A) Tooth shape is varied for five signaling and growth parameters in ToothMaker. (B) From an ancestral state, each parameter is varied in 2.5% increments up to a maximum of ± 50% of the ancestral state. (C) Tooth complexity and enamel knot (EK) pattern were quantified for each parameter combination. Tooth complexity was measured using cusp number/EK number and OPC. ToothMaker and placental upper second molars were classified into categories based on EK/cusp pattern. (D) The parameter space was populated with pattern and tooth complexity datums to build a developmental landscape. (E) Tooth complexity evolution was simulated on each developmental landscape. (F) Resulting diversity and pattern of tooth complexity was compared with placental mammal molar diversity.     

Mechanosensitive remodeling of the bacterial flagellar motor is independent of direction of rotation

Motility is important for the survival and dispersal of many bacteria, and it often plays a role during infections. Regulation of bacterial motility by chemical stimuli is well studied, but recent work has added a new dimension to the problem of motility control. The bidirectional flagellar motor of the bacterium Escherichia coli recruits or releases torque-generating units (stator units) in response to changes in load. Here, we show that this mechanosensitive remodeling of the flagellar motor is independent of direction of rotation. Remodeling rate constants in clockwise rotating motors and in counterclockwise rotating motors, measured previously, fall on the same curve if plotted against torque. Increased torque decreases the off rate of stator units from the motor, thereby increasing the number of active stator units at steady state. A simple mathematical model based on observed dynamics provides quantitative insight into the underlying molecular interactions. The torque-dependent remodeling mechanism represents a robust strategy to quickly regulate output (torque) in response to changes in demand (load).

Many bacteria swim through aqueous environments to acquire resources, to disperse progeny, and to infect hosts (1, 2). The rotation of flagella (3, 4), powered by the bidirectional flagellar motor (5–7), drives motility in many bacteria. In Escherichia coli, the flagellar motor consists of over 20 different proteins that self-assemble at the cell wall in varying copy numbers (8–10). Motor structure (Fig. 1A) includes a rotor embedded in the inner cell membrane, a drive shaft, and a flexible hook that transmits torque to the filament (10, 11). The cytoplasmic ring (C ring), which contains copies of the proteins FliG, FliM, and FliN, is mounted on the cytoplasmic face of the rotor and is responsible for directional switching of the motor (12). The rotor is driven by up to 11 ion-powered MotA5B2 stator units (13–16) that surround the rotor and generate torque. MotA engages FliG, whereas MotB is mounted on the rigid framework of the peptidoglycan cell wall (17–20). Motor-bound units exchange with a pool of unbound units in the inner membrane (10, 21).Open in a separate windowFig. 1.Bacterial flagellar motor’s structure and its T-S curve. (A) Schematic representation of the flagellar motor of Gram-negative bacteria. The rotor consists of the MS ring (M for membranous and S for supramembranous) embedded in the inner membrane (IM) and the C ring embedded in the cytoplasm. Stator units (MotA–MotB complexes) that span the inner membrane bind to the peptidoglycan (PG) layer and apply torque on the C ring. The torque is transmitted via a rod (driveshaft) and a flexible hook (universal joint) to the flagellar filament. L and P rings (L for lipopolysaccharide and P for peptidoglycan) are embedded in the outer membrane (OM) and the peptidoglycan, respectively, and act as bushings. Inset shows the outline of an E. coli cell with a square demarcating the region that is represented in detail. (B) T-S curve of the CCW (solid orange) and CW (dashed blue) rotating flagellar motors compared in this study. Data are from refs. 31 and 58. See Materials and Methods for details.Motor function is regulated by inputs from the environment. Detection of specific ligands by chemoreceptors drives a two-component signaling cascade that controls the direction of rotation of the motor (22–24). Upon binding the response regulator CheY-P, the C ring undergoes a concerted conformational change that reverses motor rotation from counterclockwise (CCW) to clockwise (CW), as viewed from outside the cell. This change in the direction of rotation is the basis of run-and-tumble motility in E. coli (CCW = run, CW = tumble). Changes in viscous load trigger remodeling of the stator (25–27), whereby, at high loads, the number of motor-bound stator units increases, and vice versa. Dynamics of stator remodeling have only been quantified in CCW rotating motors, using electrorotation (28) and magnetic tweezers (29, 30). The observed dynamics were rationalized using the CCW torque–speed (T-S) relationship (Fig. 1B) (28). CCW and CW rotating motors have different T-S relationships (Fig. 1B), likely due to differences in stator–rotor interactions (31–33). How the differences in T-S relationship affect stator remodeling in CW motors is unknown. Additionally, the molecular mechanisms underlying the load-dependent remodeling phenomenon remain poorly understood.Here, we use electrorotation to study the dynamics of load-dependent stator remodeling in CW rotating motors. We find that, just like CCW motors, CW rotating flagellar motors release their stator units when the motor torque is low, and recruit stator units when the torque increases again. The rates of stator unit release and recruitment in CW and CCW motors collapse onto a single curve when plotted against torque, despite their dissimilar T-S relationships. The collapse of remodeling data suggests a universal model for torque dependence in the mechanically regulated remodeling of the bacterial flagellar motor. Our in vivo measurements of stator assembly dynamics advance the understanding of a large protein complex with multiple parts.     

High-throughput developability assays enable library-scale identification of producible protein scaffold variants

Proteins require high developability—quantified by expression, solubility, and stability—for robust utility as therapeutics, diagnostics, and in other biotechnological applications. Measuring traditional developability metrics is low throughput in nature, often slowing the developmental pipeline. We evaluated the ability of 10 variations of three high-throughput developability assays to predict the bacterial recombinant expression of paratope variants of the protein scaffold Gp2. Enabled by a phenotype/genotype linkage, assay performance for 10⁵ variants was calculated via deep sequencing of populations sorted by proxied developability. We identified the most informative assay combination via cross-validation accuracy and correlation feature selection and demonstrated the ability of machine learning models to exploit nonlinear mutual information to increase the assays’ predictive utility. We trained a random forest model that predicts expression from assay performance that is 35% closer to the experimental variance and trains 80% more efficiently than a model predicting from sequence information alone. Utilizing the predicted expression, we performed a site-wise analysis and predicted mutations consistent with enhanced developability. The validated assays offer the ability to identify developable proteins at unprecedented scales, reducing the bottleneck of protein commercialization.

A common constraint across diagnostic, therapeutic, and industrial proteins is the ability to manufacture, store, and use intact and active molecules. These protein properties, collectively termed developability, are often associated to quantitative metrics such as recombinant yield, stability (chemical, thermal, and proteolytic), and solubility (1–5). Despite this universal importance, developability studies are performed late in the commercialization pipeline (2, 4) and limited by traditional experimental capacity (6). This is problematic because 1) proteins with poor developability limit practical assay capacity for measuring primary function, 2) optimal developability is often not observed with proteins originally found in alternative formats [such as display or two-hybrid technologies (7)], and 3) engineering efforts are limited by the large gap between observation size (∼10²) and theoretical mutational diversity (∼10²⁰). Thus, efficient methods to measure developability would alleviate a significant bottleneck in the lead selection process and accelerate protein discovery and engineering.Prior advances to determine developability have focused on calculating hypothesized proxy metrics from existing sequence and structural data or developing material- and time-efficient experiments. Computational sequence-developability models based on experimental antibody data have predicted posttranslational modifications (8, 9), solubility (10, 11), viscosity (12), and overall developability (13). Structural approaches have informed stability (14) and solubility (10, 15). However, many in silico models require an experimentally solved structure or suffer from computational structure prediction inaccuracies (16). Additionally, limited developability information allows for limited predictive model accuracy (17). In vitro methods have identified several experimental protocols to mimic practical developability requirements [e.g., affinity-capture self-interaction nanoparticle spectroscopy (18) and chemical precipitation (19) as metrics for solubility]. However, traditional developability quantification requires significant amounts of purified protein. Noted in both fronts are numerous in silico and/or in vitro metrics to fully quantify developability (1, 5).We sought a protein variant library that would benefit from isolation of proteins with increased developability and demonstrate the broad applicability of the process. Antibodies and other binding scaffolds, comprising a conserved framework and diversified paratope residues, are effective molecular targeting agents (20–24). While significant progress has been achieved with regards to identifying paratopes for optimal binding strength and specificity (25, 26), isolating highly developable variants remains plagued. One particular protein scaffold, Gp2, has been evolved into specific binding variants toward multiple targets (27–29). Continued study improved charge distribution (30), hydrophobicity (31), and stability (28). While these studies have suggested improvements for future framework and paratope residues (including a disulfide-stabilized loop), a poor developability distribution is still observed (32) (Fig. 1 A and B). Assuming the randomized paratope library will lack similar primary functionality, the Gp2 library will simulate the universal applicability of the proposed high-throughput (HT) developability assays.Open in a separate windowFig. 1.HT assays were evaluated for the ability to identify protein scaffold variants with increased developability. (A and B) Gp2 variant expression, commonly measured via low-throughput techniques such as the dot blot shown, highlights the rarity of ideal developability. (C and D) The HT on-yeast protease assay measures the stability of the POI by proteolytic extent. (E and F) The HT split-GFP assay measures POI expression via recombination of a genetically fused GFP fragment. (G and H) The HT split β-lactamase assay measures the POI stability by observing the change in cell-growth rates when grown at various antibiotic concentrations. (I and J) Assay scores, assigned to each unique sequence via deep sequencing, were evaluated by predicting expression (Fig. 3). (K and L) HT assay capacity enables large-scale developability evaluation and can be used to identify beneficial mutations (Fig. 4).We sought HT assays that allow protein developability differentiation via cellular properties to improve throughput. Variations of three primary assays were examined: 1) on-yeast stability (Fig. 1 C and D)—previously validated to improve the stability of de novo proteins (33), antimicrobial lysins (34), and immune proteins (35)—measures proteolytic cleavage of the protein of interest (POI) on the yeast cell surface via fluorescence-activated cell sorting (FACS). We extend the assay by performing the proteolysis at various denaturing combinations to determine if different stability attributes (thermal, chemical, and protease specificity) can be resolved; 2) Split green fluorescent protein (GFP, Fig. 1 E and F)—previously used to determine soluble protein concentrations (36)—measures the assembled GFP fluorescence emerging from a 16–amino acid fragment (GFP₁₁) fused to the POI after recombining with the separably expressed GFP_1-10. We extend the assay by utilizing FACS to separate cells with differential POI expression to increase throughput over the plate-based assay; and 3) Split β-lactamase (Fig. 1 G and H)—previously used to improve thermodynamic stability (37) and solubility (38)—measures cell growth inhibition via ampicillin to determine functional lactamase activity achieved from reconstitution of two enzyme fragments flanking the POI. We expand assay capacity by deep sequencing populations grown at various antibiotic concentrations to relate change in cell frequency to functional enzyme concentration.In this paper, we determined the HT assays’ abilities to predict Gp2 variant developability. We deep sequenced the stratified populations and calculated assay scores (correlating to hypothesized developability) for ∼10⁵ Gp2 variants (Fig. 1I). We then converted the assay scores into a traditional developability metric by building a model that predicts recombinant yield (Fig. 1J). The assays’ capacity enabled yield evaluations for >100-fold traditional assay capacity (Fig. 1K, compared to Fig. 1B) and provide an introductory analysis of factors driving protein developability by observing beneficial mutations via predicted developable proteins (Fig. 1L).     

Plant species richness at archaeological sites suggests ecological legacy of Indigenous subsistence on the Colorado Plateau

Humans have both intentional and unintentional impacts on their environment, yet identifying the enduring ecological legacies of past small-scale societies remains difficult, and as such, evidence is sparse. The present study found evidence of an ecological legacy that persists today within an semiarid ecosystem of western North America. Specifically, the richness of ethnographically important plant species is strongly associated with archaeological complexity and ecological diversity at Puebloan sites in a region known as Bears Ears on the Colorado Plateau. A multivariate model including both environmental and archaeological predictors explains 88% of the variation in ethnographic species richness (ESR), with growing degree days and archaeological site complexity having the strongest effects. At least 31 plant species important to five tribal groups (Navajo, Hopi, Zuni, Ute Mountain Ute, and Apache), including the Four Corners potato (Solanum jamesii), goosefoot (Chenopodium sp.), wolfberry (Lycium pallidum), and sumac (Rhus trilobata), occurred at archaeological sites, despite being uncommon across the wider landscape. Our results reveal a clear ecological legacy of past human behavior: even when holding environmental variables constant, ESR increases significantly as a function of past investment in habitation and subsistence. Consequently, we suggest that propagules of some species were transported and cultivated, intentionally or not, establishing populations that persist to this day. Ensuring persistence will require tribal input for conserving and restoring archaeo-ecosystems containing “high-priority” plant species, especially those held sacred as lifeway medicines. This transdisciplinary approach has important implications for resource management planning, especially in areas such as Bears Ears that will experience greater visitation and associated impacts in the near future.

Local resource abundance is important for determining where in a given landscape humans decide to live. Nearby water, game, soil, and plants provide readily available wild resources for foraging and conditions that allow for cultivation (1–5). However, humans also modify their surrounding environments in order to increase the abundance and diversity of local plant (6–11) and animal (12–15) resources. Such “human niche construction” is a hallmark of ancient and modern societies (16, 17), having positive and negative impacts on global biodiversity while possibly creating enduring ecological legacies (18–21). This may be especially true for more sedentary and dense populations (22, 4) that are more likely to find investment worthwhile (23) and to produce unintentional impacts. Thus, variation in contemporary ecological diversity may in part reflect past land use dynamics and, therefore, be revealed through coupled archaeological and ecological research (24–33).Coupled ecological and archaeological research has led to the discovery of altered patterns of succession resulting from 1) forest clearing and changes in canopy light regime (34, 35), 2) alterations of soil especially linked to food refuse (36, 37), 3) changes in fire regimes (38, 39), and, more rarely, 4) the importation of plant propagules from distant sites of collection (40, 41). Identifying such long-lost dynamics between humans and landscapes can inform conservation aimed at restoring site-specific artifacts, features, and the associated resource base past and present, here termed “archaeo-ecosystems” (42, 43). This would greatly facilitate cross-cultural management of public lands (44) in ways that promote Indigenous health, cultural reclamation, and sovereignty (7, 45). The linkages, however, between ecological legacies, archaeo-ecosystem restoration and cross-cultural management have yet to be systematically tested or practically applied.Here, we offer a formal evaluation of this archaeo-ecosystem approach by using paired archaeological and ecological survey data focused on Puebloan occupation of a region known as Bears Ears on the Colorado Plateau in southeastern Utah (Fig. 1). Puebloan populations modified their environment by constructing terraces and check dams, developing blinds and wing traps, importing exogenous species, and setting fires (4, 22, 46), but investments were not uniform across the region. We test the hypothesis that locations with greater investment indicated by larger and more complex archaeological sites should today have higher richness of culturally significant plant species, here termed ethnographic species richness (ESR), as an enduring legacy of past investment. Our study expands previous work on ecological legacies by using field surveys to develop an explanatory model applied to 265 sites across one million acres of semiarid public lands. It documents the occurrence of uncommon and ethnographically significant plant species associated with those sites and infuses traditional ecological knowledge into proposed management actions for conserving these archaeo-ecosystems. Controlling for underlying environmental variation, our results indicate that past human habitation increases the diversity of plant species important for Indigenous subsistence.Open in a separate windowFig. 1.Location of Bears Ears National Monument in southeastern Utah. The predicted ESR at 265 known archaeological sites across the original and reduced monument boundaries and surrounding region are shown.     

Bistability in the redox chemistry of sediments and oceans

For most of Earth’s history, the ocean’s interior was pervasively anoxic and showed occasional shifts in ocean redox chemistry between iron-buffered and sulfide-buffered states. These redox transitions are most often explained by large changes in external inputs, such as a strongly altered delivery of iron and sulfate to the ocean, or major shifts in marine productivity. Here, we propose that redox shifts can also arise from small perturbations that are amplified by nonlinear positive feedbacks within the internal iron and sulfur cycling of the ocean. Combining observational evidence with biogeochemical modeling, we show that both sedimentary and aquatic systems display intrinsic iron–sulfur bistability, which is tightly linked to the formation of reduced iron–sulfide minerals. The possibility of tipping points in the redox state of sediments and oceans, which allow large and nonreversible geochemical shifts to arise from relatively small changes in organic carbon input, has important implications for the interpretation of the geological rock record and the causes and consequences of major evolutionary transitions in the history of Earth’s biosphere.

The modern oceans are pervasively oxygenated, with anoxia being restricted to oxygen minimum zones and a few poorly ventilated basins such as the Black Sea (1). In contrast, during the Precambrian and early Phanerozoic Eon, the ocean interior is thought to have been pervasively anoxic (Fig. 1). Reconstruction of the redox evolution of the deep ocean is challenging prior to the Cretaceous due to a lack of rock records that can be unambiguously attributed to deposition in deep-sea environments. Still, redox reconstructions of intermediate water depths are available from a number of localities in the Precambrian and early Phanerozoic Eon, and these data suggest that oceanic basins—or at least subbasins—have alternated spatially and temporally between predominant iron-rich (ferruginous) and sulfide-rich (euxinic) conditions (2–9) (Fig. 1B). Recent evidence also suggests that periodic basin-scale transitions between ferruginous and euxinic conditions occurred during the “oceanic anoxic events” during the predominantly oxygenated Mesozoic (10, 11) (Fig. 1B). These two contrasting redox states imply a very different chemical environment for marine life, as any shift between them also entails a critical change in the concentrations of limiting elements (such as phosphorus, iron, and molybdenum) that sustain marine productivity and energy flow through the ocean biosphere (12–15).Open in a separate windowFig. 1.The evolving redox chemistry of the oceans against the backdrop of atmospheric oxygenation. (A) The estimates of the partial pressure of atmospheric oxygen (pO₂) relative to the PAL (43). The upward arrows during the Archaean denote possible transient episodes of ocean-atmosphere oxygenation just prior to the “Great Oxidation Event” (GOE). (B) The first-order features of evolving redox in surface, middepth, and deep ocean. The pattern of surface ocean oxygenation displayed is based on isotopic data (44, 45) and equilibration with atmospheric pO_2. Note, however, that surface ocean oxygenation was likely spatially variable (46). The records for intermediate (middepth) settings are after ref. 7, supplemented with observations from refs. 2, 4–6, 8, 10. The insets in B schematically depict reported oscillations between ferruginous and sulfidic conditions during the late Archean (47) (Left) and during the Cretaceous Thermal Maximum (11) (Right). The redox conditions in the deep ocean are tentative. Although a “background” state of ferruginous conditions for the deep ocean is consistent with available data from the sedimentary record, existing empirical constraints are not of sufficiently high fidelity to rule out pervasively euxinic deposition in the deep ocean for certain periods during the Precambrian. The question mark denotes the uncertain (potentially oxic) deep ocean redox state during the Lomagundi interval.Transitions between ferruginous and euxinic states on a basin-to-global scale require a switch in the dominant redox chemistry. One mechanism to achieve this is via a shift in the relative rates at which iron and sulfate are delivered to the ocean, with higher iron inputs favoring the prevalence of ferruginous conditions (16, 17). As a result, observed shifts in the redox state of the ocean interior are interpreted as reflecting major state changes in the Earth system, such as an increase in atmospheric oxygen (16), periods with strongly elevated volcanism (2), sea-level changes that modify the extent of the global depositional shelf area (9), or intervals of enhanced Fe or S weathering due to continental breakup (3, 18). An alternative mechanism is that changes in nutrient supply and nutrient availability in the ocean can increase the export of organic matter from the surface to the subsurface ocean. More organic carbon export then leads to increased microbial respiration, stimulating the production of sulfide via sulfate reduction and essentially titrating ferrous iron from the water column as pyrite (18). As a result, switches between ferruginous and euxinic states have been linked to the relative supply or production of ferrous iron and free sulfide, causing transitions at the Fe:S ratio of 1:2, the stoichiometric ratio of pyrite (17, 19).Here, we present a theoretical analysis of redox shifts in anoxic biogeochemical systems of both the ocean interior and marine sediments. Both these systems display aqueous chemistries that can switch between ferrous-iron–dominated and free-sulfide–dominated states. In this analysis, we focus on the question of whether large shifts in the redox state also necessarily require large perturbations to boundary conditions.Paleoredox reconstructions often adopt an implicitly linear perspective in their interpretation of the rock record, whereby small changes in external inputs will only cause small shifts, while large shifts in redox chemistry—such as switches between ferruginous and euxinic deep waters—necessitate major changes in external inputs. Here, in contrast, we demonstrate not only that natural anoxic systems may be subject to critical thresholds—so-called “tipping points”—but that alternative stable states exist with a hysteresis barrier to reversibility. Our analysis reveals that the redox chemistry of anoxic systems shows nonlinear dynamics, characterized by both strong resilience (large changes in the supply of iron oxides or organic carbon must not necessarily induce a shift in redox chemistry) as well as dramatic shifts near the tipping points. As a result, large and abrupt redox changes may occur in response to small and gradual changes in external forcing, without any significant change in Fe or S input fluxes. The existence of redox tipping points in the ocean interior could have important implications for the interpretation of Earth’s evolution.