Increasing risk of another Cape Town “Day Zero” drought in the 21st century

Three consecutive dry winters (2015–2017) in southwestern South Africa (SSA) resulted in the Cape Town “Day Zero” drought in early 2018. The contribution of anthropogenic global warming to this prolonged rainfall deficit has previously been evaluated through observations and climate models. However, model adequacy and insufficient horizontal resolution make it difficult to precisely quantify the changing likelihood of extreme droughts, given the small regional scale. Here, we use a high-resolution large ensemble to estimate the contribution of anthropogenic climate change to the probability of occurrence of multiyear SSA rainfall deficits in past and future decades. We find that anthropogenic climate change increased the likelihood of the 2015–2017 rainfall deficit by a factor of five to six. The probability of such an event will increase from 0.7 to 25% by the year 2100 under an intermediate-emission scenario (Shared Socioeconomic Pathway 2-4.5 [SSP2-4.5]) and to 80% under a high-emission scenario (SSP5-8.5). These results highlight the strong sensitivity of the drought risk in SSA to future anthropogenic emissions.

The Day Zero Cape Town drought was one of the worst water crises ever experienced in a metropolitan area (1, 2). Droughts are a regular occurrence in southwestern South Africa (SSA), having occurred during the late 1920s, early 1970s, and, more recently, during 2003–2004 (Fig. 1 A and B). However, the extended winter (April to September [AMJJAS]) 3-y rainfall deficit (Fig. 1 A and B; SI Appendix, Fig. S1) which drove the 2015–2017 Cape Town drought (2–8) was exceptional over the last century (4, 9). Storage in reservoirs supplying water to 3.7 million people in the Cape Town metropolitan area dropped to about 20% of capacity in May 2018. As a consequence, strict water-usage restrictions were implemented to delay water levels reaching 13.5%, the level at which much of the city’s municipal supply would have been disconnected (7), a scenario referred to as “Day Zero” by the municipal water authorities (7). Above-average winter rain over the rest of the 2018 austral winter allowed Cape Town to avoid the Day Zero scenario.Open in a separate windowFig. 1.(A) Mean 2015–2017 AMJJAS rainfall anomaly relative to 1921–1970. The dashed (continuous) line denotes negative anomalies beyond 1 (1.5) SD. (B) Time series of the observed (GPCC, blue; CRU, red) 3-y running mean AMJJAS WRI (Materials and Methods) from 1901 to 2017. The 2015–2017 mean is record-breaking over the period 1901–2017. (C–E) Mean 1921–1970 AMJJAS rainfall (millimeters per month) in observations (GPCC) (C), SPEAR_MED (D), and SPEAR_LO (E). The red lines encircle the area receiving at least 65% of the total annual rainfall during AMJJAS used to define WRI. (F) Monthly WRI in observations and models. Comparison of SPEAR_MED with SPEAR_LO shows how an enhanced resolution is key to capture finer-scale regional details of winter rainfall in the relatively small SSA Mediterranean region.While poor water-management practices and infrastructure deficiencies worsened the crisis (10, 11), the 2015–2017 rainfall deficit was the main driver of the drought (5). To facilitate the improvement of water-management practices and the infrastructure necessary to make the system more resilient, it is critical to first determine how likely a meteorological drought like the one in 2015–2017 might be in the coming decades. Increased aridity is expected in most of southern Africa (12–14) as a consequence of the Hadley Cell poleward expansion (4, 15–18) and southward shift of the Southern Hemisphere jet stream (19). Second, the risk of more extreme droughts should be quantified to understand the potential for emerging risks that could make a Day Zero event in Cape Town unavoidable.Previous work (5) has suggested that the Day Zero drought may have been made 1.4 to 6.4 times more likely over the last century due to +1 K of global warming, with the risk expected to scale linearly with one additional degree of warming. Such estimates make use of statistical models of the probability distribution’s tail (e.g., the generalized extreme value) applied to observations and previous-generation [i.e., as those participating to the Coupled Model Intercomparison Project Phase 3 (CMIP3) (20) and 5 (21)] climate models. CMIP3 and CMIP5 models have been shown to have a systematically biased position of the Southern Hemisphere jet stream toward the Equator, due to insufficient horizontal resolution (19). This produces a large uncertainty in model projections of jet-stream shifts (22, 23), thus hindering realistic projections of Southern Hemisphere climate change. Furthermore, for hydroclimatic variables, a statistical extrapolation of the probability distribution’s tail might have inherent limitations in providing precise estimates of the event probability of future extreme events, although its precision profits from the use of large ensembles (24, 25).Large ensembles of comprehensive climate models provide thousands of years of data that allow direct construction of the underlying probability distribution of hydroclimatic extremes without relying on a hypothesized statistical model of extremes (25, 26). South African winter rains have high interannual and decadal variability due to El Niño–Southern Oscillation (27), the Southern Annular Mode (28), and interdecadal variability (29). A multidecade to multicentury record may be required to detect the emergence of statistically significant trends in regional precipitation extremes. A large ensemble is, thus, a powerful method to isolate, at the decadal timescale, internal natural variability (e.g., SI Appendix, Fig. S2) from the forced signal (30–32).     

Optical vector field rotation and switching with near-unity transmission by fully developed chiral photonic crystals

State-of-the-art nanostructured chiral photonic crystals (CPCs), metamaterials, and metasurfaces have shown giant optical rotatory power but are generally passive and beset with large optical losses and with inadequate performance due to limited size/interaction length and narrow operation bandwidth. In this work, we demonstrate by detailed theoretical modeling and experiments that a fully developed CPC, one for which the number of unit cells N is high enough that it acquires the full potentials of an ideal (N → ∞) crystal, will overcome the aforementioned limitations, leading to a new generation of versatile high-performance polarization manipulation optics. Such high-N CPCs are realized by field-assisted self-assembly of cholesteric liquid crystals to unprecedented thicknesses not possible with any other means. Characterization studies show that high-N CPCs exhibit broad transmission maxima accompanied by giant rotatory power, thereby enabling large (>π) polarization rotation with near-unity transmission over a large operation bandwidth. Polarization rotation is demonstrated to be independent of input polarization orientation and applies equally well on continuous-wave or ultrafast (picosecond to femtosecond) pulsed lasers of simple or complex (radial, azimuthal) vector fields. Liquid crystal–based CPCs also allow very wide tuning of the operation spectral range and dynamic polarization switching and control possibilities by virtue of several stimuli-induced index or birefringence changing mechanisms.

Optical vector field (more commonly called polarization) rotators and switches are essential components of all modern optical and photonic systems for communications, ellipsometry, metrology, biological/chemical detection, and quantum processing/computing (1–10). There are, however, some inherent limitations. Wave plates made with birefringent crystals, for example, require strict alignment of the optic axis with respect to the polarization orientation of incident light and generally do not work with laser vector beams of complex polarization fields; Faraday rotators that do not have this requirement are generally too cumbersome and bulky due to their weak optical rotatory powers. One promising approach to circumvent these limitations is to employ chiral optical materials such as chiral photonic crystals and metasurfaces. Nevertheless, structural chirality, such as chiral metamaterials, metasurfaces, and photonic crystals that are capable of very large optical rotatory power (up to ∼100,000°/mm), are inevitably accompanied by large absorption losses (11–15). In metamaterials/surfaces, the intrinsic noncircular absorption and nanofabrication difficulty also add to the limitation of their practical scalability in the interaction length, resulting in small (<π) net polarization rotation angle, very small aperture, and narrow operating spectral bandwidth (11–13). Similar issues confront most chiral photonic crystals (CPCs) due to the limitations of molecular self-assembly or nanofabrication/processing technique and high transmission loss associated with operation near the Bragg reflection band (14, 15).Here, we show by theory and experimental corroborations that a fully developed liquid crystal–based CPC, one for which the number of unit cells N approaches that (N → ∞) of an ideal crystal, can circumvent all the aforementioned limitations and possess several advantageous characteristics impossible with conventional low-N thin counterparts. Such high-period–number chiral photonic crystals (HN-CPCs) are achieved by fabricating cholesteric liquid crystals (CLCs) to thicknesses several hundred times that of conventional ones using a refined field-assisted self-assembly (FASA) technique (16, 17; see SI Appendix, Note 1, for more details). Optical properties of CLCs as CPCs arise from complex “collective” responses from many unit cells. While thicker crystals obviously give rise to larger effects, the resulting properties as the crystal thickness or period number N evolves from low values to a very high value do not lend themselves to such simple linear extrapolation; as a function of N, pleasant surprises and new insights and possibilities abound. Our studies show that for N > 500, these CLCs exhibit simultaneously broad transmission maxima and large polarization rotation power in the off-Bragg-resonance spectral regime. Polarization rotation is independent of input polarization orientation and acts equally well on simple or complex vector fields (18–22) of continuous-wave (CW) or ultrafast pulsed laser beams. Liquid crystal–based CPCs also allow dynamic polarization switching and control by virtue of field–induced index/birefringence changing mechanisms at modest or ultrafast (picosecond to femtosecond) speeds (23–34).     

Air quality–related health damages of food

Agriculture is a major contributor to air pollution, the largest environmental risk factor for mortality in the United States and worldwide. It is largely unknown, however, how individual foods or entire diets affect human health via poor air quality. We show how food production negatively impacts human health by increasing atmospheric fine particulate matter (PM_2.5), and we identify ways to reduce these negative impacts of agriculture. We quantify the air quality–related health damages attributable to 95 agricultural commodities and 67 final food products, which encompass >99% of agricultural production in the United States. Agricultural production in the United States results in 17,900 annual air quality–related deaths, 15,900 of which are from food production. Of those, 80% are attributable to animal-based foods, both directly from animal production and indirectly from growing animal feed. On-farm interventions can reduce PM_2.5-related mortality by 50%, including improved livestock waste management and fertilizer application practices that reduce emissions of ammonia, a secondary PM_2.5 precursor, and improved crop and animal production practices that reduce primary PM_2.5 emissions from tillage, field burning, livestock dust, and machinery. Dietary shifts toward more plant-based foods that maintain protein intake and other nutritional needs could reduce agricultural air quality–related mortality by 68 to 83%. In sum, improved livestock and fertilization practices, and dietary shifts could greatly decrease the health impacts of agriculture caused by its contribution to reduced air quality.

The health and environmental consequences of feeding the increasingly large and affluent global population are becoming increasingly apparent. These consequences have spurred interest in identifying food production practices and diets that improve human health and reduce environmental harm. Recent work has demonstrated that many of the opportunities for food producers and consumers to improve nutritional outcomes also have environmental benefits, such as reducing greenhouse gas emissions, land and water use, and eutrophication (1–6). It is largely unknown, however, how individual foods and diets affect air quality, even though air pollution is the largest environmental mortality risk factor in the United States and globally (7, 8), and agriculture is itself known to be a major contributor to reduced air quality (8, 9). In the United States alone, atmospheric fine particulate matter (PM_2.5) from anthropogenic sources is responsible for about 100,000 premature deaths each year, one-fifth of which are linked to agriculture (10, 11).Here, we show how different foods affect human health by reducing air quality. We consider the emission of pollutants that contribute to atmospheric PM_2.5, the chronic exposure to which increases the incidence of premature mortality from cardiovascular disease, cancer, and stroke (12, 13). These pollutants include directly emitted PM_2.5 (primary PM_2.5) and PM_2.5 formed in the atmosphere (secondary PM_2.5) from the precursors ammonia (NH₃), nitrogen oxides (NO_x), sulfur dioxide (SO₂), and nonmethane volatile organic compounds (NMVOCs). From a spatially explicit inventory of emissions of primary PM_2.5 and secondary PM_2.5 precursors from agricultural supply chain activities for commodities in the contiguous United States (SI Appendix, Figs. S1 and S2) (14, 15) (Materials and Methods), we estimate increases in atmospheric concentrations of total (primary + secondary) PM_2.5 attributable to agricultural emissions; total PM_2.5 transport, chemistry, and removal; and exposure of populations to total PM_2.5 using an ensemble of three independent air quality models (16–19). We describe damages attributable to 95 agricultural commodities and 67 final food products (full list in SI Appendix, Table S1), which cover >99% of US agricultural production (20).     

From the Cover: Aquatic biodiversity enhances multiple nutritional benefits to humans

Humanity depends on biodiversity for health, well-being, and a stable environment. As biodiversity change accelerates, we are still discovering the full range of consequences for human health and well-being. Here, we test the hypothesis—derived from biodiversity–ecosystem functioning theory—that species richness and ecological functional diversity allow seafood diets to fulfill multiple nutritional requirements, a condition necessary for human health. We analyzed a newly synthesized dataset of 7,245 observations of nutrient and contaminant concentrations in 801 aquatic animal taxa and found that species with different ecological traits have distinct and complementary micronutrient profiles but little difference in protein content. The same complementarity mechanisms that generate positive biodiversity effects on ecosystem functioning in terrestrial ecosystems also operate in seafood assemblages, allowing more diverse diets to yield increased nutritional benefits independent of total biomass consumed. Notably, nutritional metrics that capture multiple micronutrients and fatty acids essential for human well-being depend more strongly on biodiversity than common ecological measures of function such as productivity, typically reported for grasslands and forests. Furthermore, we found that increasing species richness did not increase the amount of protein in seafood diets and also increased concentrations of toxic metal contaminants in the diet. Seafood-derived micronutrients and fatty acids are important for human health and are a pillar of global food and nutrition security. By drawing upon biodiversity–ecosystem functioning theory, we demonstrate that ecological concepts of biodiversity can deepen our understanding of nature’s benefits to people and unite sustainability goals for biodiversity and human well-being.

Species losses and range shifts because of climate change, harvesting, and other human activities are altering aquatic biodiversity locally and globally (1–5). In aquatic ecosystems, not only are some species severely depleted because of overfishing or habitat loss (3, 6–8), the ecosystem-level dimensions of biodiversity such as the total number of species and their functional diversity have also changed (9). Beyond the loss of particular species, changes in ecosystem-level dimensions of biodiversity threaten numerous ecosystem services to humans, which include the cultural, economic, or health benefits people derive from nature (10–13). In many regions, such as tropical coastal systems, the cumulative impacts of human activities are severe and associated with strong declines in taxonomic and ecological functional diversity (6) and coincide with regions with a high dependence of people upon wild-caught seafood for food and nutrition (14). In temperate regions, where some coastal communities depend on local wild seafood harvests to meet their nutritional needs (15, 16), species richness may be increasing as species recover from exploitation and warmer oceans allow species to expand their ranges into new territory (1, 2, 17).There is growing concern that biodiversity change leads to changes in human health and well-being (10, 13, 18). Specific and quantitative links between aquatic biodiversity and human health that distinguish contributions of species diversity from those of biomass, as predicted by biodiversity–ecosystem functioning theory, have not been established. At a time of unprecedented global change and increasing reliance on seafood to meet nutritional demands (19), there is an urgent need to understand how changing aquatic ecosystem structure may alter the provisioning of seafood-derived human nutrition.Seafood, consisting of wild-caught marine and freshwater finfish and invertebrates, provides an important source of protein and calories to humans. Additionally, unlike staple foods such as rice or other grains, seafood can address multiple dimensions of food and nutritional security simultaneously by providing essential micronutrients, such as vitamins, minerals, and polyunsaturated essential fatty acids critical to human health (19–22). Given the multiple attributes of seafood that are valuable to human health, it is possible that the diversity of an aquatic assemblage, distinct from the inclusion of any particularly nutritious species, could support human well-being consistent with a large body of evidence for biodiversity’s major contributions to ecological functions (11, 23–26). Dietary diversity is a basic tenet of a nutritious diet (27) and it is widely appreciated that diets composed of more food groups and more species are more nutritious (28–31). Ecological measures of dietary diversity (diet diversity, species richness, functional diversity, and Simpson’s index of evenness) have been associated with the nutritional value of diets in a range of contexts (27, 29, 32–38). These studies rely on relationships between species included in the diet (or other food intake measures) and nutritional adequacy of reported diets. However, a simple correlation between dietary diversity and a measure of dietary benefits provides only partial support for a claim that biodiversity benefits human well-being, consistent with the same ecological processes by which biodiversity supports numerous ecosystem functions and services (23, 26). We build upon this foundation of empirical relationships between diet diversity and diet quality by placing this question in the quantitative ecological theoretical framework that relates biodiversity to function (24, 25), thereby laying the groundwork for additional development of links between biodiversity science and our understanding of human well-being.Ecological theory predicts that biodiversity can be ecologically and economically important, apart from the importance of total biomass or the presence of particular species (23, 39). According to theory and over 500 explicit experimental tests (23, 40, 41), diversity in ecological communities and agricultural systems enhances ecosystem functioning by two mechanisms: 1) more diverse assemblages may outperform less diverse assemblages of the same density or biomass of individuals because more diverse assemblages will include more of the possible species and are therefore more likely to include high-performing species, assuming random processes of including species from the species pool (a selection effect), or 2) more diverse assemblages of a given density (or biomass) contain species with complementary functional traits, allowing them to function more efficiently (a complementarity effect) (25, 39). For aquatic animals, increased diversity enhances productivity of fish biomass (42) and also enhances temporal stability of biomass production and total yields (43, 44), providing economic and nutritional benefits to humans related to increased stability of harvests and production of biomass for consumption (43). However, when considering aquatic species from the perspective of human nutrition, functions other than biomass production become relevant because total seafood biomass consumption is not predictive of micronutrient benefits from seafood (45, 46).Here, we test a hypothesis central to ecological theory in the 21st century: whether biodiversity per se (species richness and ecological functional diversity), distinct from the identities and abundance of species, enhances human well-being (Fig. 1). We chose a measure of human well-being distinct from provision of protein, calories, or total yields—the micronutrient and essential fatty acid benefits of seafood. For increasing biodiversity per se (as opposed to increasing total seafood consumption) to enhance nutritional benefits as predicted by biodiversity–ecosystem functioning theory (25, 47), the amounts of various nutrients within edible tissues must differ among species, and furthermore, nutrient concentrations must trade off among species, such that species that have relatively high concentrations of some nutrients also have relatively low concentrations of others (25). Specifically, a “biodiversity effect” (sensu ref. 25) on nutritional benefits requires that concentrations of multiple nutrients are negatively correlated with each other, or uncorrelated, when compared among species, creating a complementary distribution of nutrients across species. In contrast, if nutrient concentrations in edible tissue are positively correlated for multiple nutrients across species such that, for example, a species containing high amounts of iron also has a high essential fatty acid concentration, thereby containing multiple nutrients in high concentrations simultaneously, seafood species or ecological functional diversity in the diet would not be important. In the case of positive correlations among nutrient concentrations, the ecosystem service of nutritional benefits would be enhanced by consuming more fish biomass or by selecting a few highly nutritious species, without considering species richness or ecological functional diversity.Open in a separate windowFig. 1.Aquatic biodiversity increases human well-being because edible species have distinct and complementary multinutrient profiles (A) and differ in mean micro- and macronutrient content (shown here relative to 10 and 25% thresholds of recommended dietary allowance, RDA, guidelines) for representative finfish (Abramis brama, Mullus surmuletus), mollusc (Mytilus galloprovincialis), and crustacean species (Nephrops norvegicus). Biodiversity–ecosystem functioning theory predicts that nutritional benefits, including the number of nutrient RDA targets met per 100 g portion (NT; i, iii) and minimum portion size (P_min; ii, iv) (B and E), are enhanced with increasing seafood species richness. Orange dots in B and E correspond to potential diets of high and low biodiversity levels. Seafood consumers with limited access to seafood each day may not reach RDA targets if diets are low in diversity (D–F versus A–C; gray shading indicates proportion of population that meets nutrient requirements). DHA: docosahexaenoic acid, EPA: eicosapentaenoic acid.We aimed to bridge two distinct theoretical frameworks—the biodiversity–ecosystem functioning theory and human nutrition science—by quantitatively testing for effects of aquatic species richness and ecological functional diversity (48, 49) in seafood diets on nutritional benefits via complementarity or selection effects. We used the public health measure of recommended dietary allowance (RDA) index to quantify nutritional benefits. RDAs are nutrient-based reference values that indicate the average daily dietary intake level that is sufficient to meet the nutrient requirement of nearly all (97 to 98%) healthy individuals in a particular life stage and gender group (50). Here, we used the RDA for females aged 19 to 50 y (SI Appendix, Tables S1 and S2; see SI Appendix, Table S1 for definitions of key terms). We measured nutritional value in terms of concentrations relative to RDAs, and we refer to these recommended amounts (or portions thereof) as “RDA targets” (SI Appendix, Tables S1 and S2 and Metrics). We quantified nutritional value in two ways: 1) the minimum amount of seafood tissue (in grams) required to meet given RDA targets (either for a single nutrient or the five micronutrients and fatty acids simultaneously; referred to as “minimum portion size required,” P_min [SI Appendix, Table S1, Eq. A1, and Metrics]) and 2) the number of nutrients that meet an RDA target in a single 100 g seafood portion (NT, SI Appendix, Table S1, Eq. A2). By considering nutritional value per unit biomass in both metrics, we avoided confounding diversity of seafood consumed with the total amount consumed (Metrics). We first tested two hypotheses: 1) seafood species richness increases NT because of complementarity in nutrient concentrations among species, and 2) seafood species richness increases the nutritional value of a 100 g edible portion of seafood, thereby lowering the minimum portion size, P_min, and improving the efficiency with which seafood consumers reach nutritional targets (Fig. 1). Following biodiversity–ecosystem functioning theory, we predicted that increased species richness is correlated with ecological functional diversity (51) in potential seafood diets and that ecological functional diversity is related to diversity in the concentration of essential elements and fatty acids that have nutritional value to human consumers, such that species and ecological functional diversity yields increased nutritional benefits. We also tested the hypothesis that seafood diversity increases total intake of heavy metal contaminants because some aquatic animals are known to bioaccumulate toxic metals in their tissues. For this reason, variation in bioaccumulation among species could lead to a biodiversity effect on contaminant intake that is detrimental to human health.In a global analysis of over 5,040 observations of nutrient concentrations in 547 aquatic species (SI Appendix, Fig. S1), we considered the provision of nutritional benefits to human consumers. To assess whether the relationships between biodiversity and human nutrition benefits depend on the geographic extent (global or local) over which seafood are harvested or accessed (11), we tested whether seafood species richness is associated with higher nutritional value at local scales (versus global scale) in traditional Indigenous seafood diets in North America (SI Appendix, Methods 1.4). Seafood is critical for Indigenous groups, who on average consume seafood at a rate that is 15 times higher than the global average per capita consumption rate (16). To test our hypotheses at the geographic scale of local consumer communities, we complemented our global analysis with additional analyses of 25 to 57 species in 14 geographically constrained groups of species consumed together as part of traditional Indigenous diets (SI Appendix, Methods 1.4).     

Crystal structure of a far-red–sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism

Cyanobacteriochromes (CBCRs) are small, linear tetrapyrrole (bilin)-binding photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. More spectrally diverse than canonical red/far-red–sensing phytochromes, CBCRs were thought to be restricted to sensing visible and near UV light until recently when several subfamilies with far-red–sensing representatives (frCBCRs) were discovered. Two of these frCBCRs subfamilies have been shown to incorporate bilin precursors with larger pi-conjugated chromophores, while the third frCBCR subfamily uses the same phycocyanobilin precursor found in the bulk of the known CBCRs. To elucidate the molecular basis of far-red light perception by this third frCBCR subfamily, we determined the crystal structure of the far-red–absorbing dark state of one such frCBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 which exhibits a reversible far-red/orange photocycle. Determined by room temperature serial crystallography and cryocrystallography, the refined 2.7-Å structure reveals an unusual all-Z,syn configuration of the phycocyanobilin (PCB) chromophore that is considerably less extended than those of previously characterized red-light sensors in the phytochrome superfamily. Based on structural and spectroscopic comparisons with other bilin-binding proteins together with site-directed mutagenesis data, our studies reveal protein–chromophore interactions that are critical for the atypical bathochromic shift. Based on these analyses, we propose that far-red absorption in Anacy_2551g3 is the result of the additive effect of two distinct red-shift mechanisms involving cationic bilin lactim tautomers stabilized by a constrained all-Z,syn conformation and specific interactions with a highly conserved anionic residue.

Cyanobacteria have developed elaborate, spectrally tuned photoreceptors and light-harvesting systems for adaptation and survival in a wide range of ecological niches (1–5). Many photoreceptor systems are modular components of much larger signaling proteins that integrate different sensor and effector modules into a single protein molecule to interface with diverse signal transduction pathways. Photoreceptors in the phytochrome superfamily utilize a specific lineage of GAF (cGMP phosphodiesterase, adenylyl cyclase and FhlA) domain that binds a thioether-linked linear tetrapyrrole (bilin) chromophore for light perception (6–11). Bilin-based photoreceptors play critical roles in plant development as well as in regulating cyanobacterial phototaxis, development, and light harvesting (2, 3, 12–17). Protein structural changes following the primary photochemical event then alter the downstream enzymatic activities and/or protein–protein interactions via an interdomain allosteric mechanism (18).Phytochromes possess a tripartite photosensory region consisting of three N-terminal domains (PAS, GAF, and PHY), known as the photosensory core module, in which the PAS and GAF domains are tethered via a “figure-eight knot” (14, 19, 20). In prototypical phytochromes, the bilin chromophore embedded in the GAF domain adopts a protonated 5-Z,syn, 10-Z,syn, 15-Z,anti configuration in the dark-adapted state. Light absorption triggers photoisomerization of the 15,16 double bond to generate a 15E,anti photoproduct, which typically absorbs far-red light (9, 14, 21). A long extension from the adjacent PHY domain is responsible for stabilizing the far-red–absorbing Pfr state (14, 20). In cyanobacteria, the phytochrome superfamily has diversified to yield a large family of more streamlined sensors, designated cyanobacteriochromes (CBCRs) (2, 4, 22–26). Unlike canonical phytochromes, CBCR photosensory modules consist of one or more GAF domains that are sufficient for covalent attachment of bilin and photoconversion. These small CBCR domains have also been used as light-sensing modules in a variety of synthetic biology applications (27–32). In contrast to canonical red/far-red phytochromes, CBCRs are able to sense light from near UV to far-red, utilizing a common phycocyanobilin (PCB) chromophore precursor (22–24, 26).The remarkable spectral diversity of CBCRs (SI Appendix, Fig. S1A) arises from extensive molecular evolution of the GAF domain scaffold. Many CBCRs leverage two thioether linkages to sense blue, violet, or near-UV light (8, 22, 23, 25, 33–35). Such “two-Cys” CBCRs possess an additional thioether linkage to the C10 methine bridge of the bilin that splits the chromophore in half, significantly shortening the conjugated π-system. Rupture of this covalent bond can occur upon 15Z/15E photoisomerization, which restores bilin conjugation across C10 to generate a photostate absorbing at wavelengths from teal to red (8, 33, 36, 37). Dual cysteine CBCRs have evolved multiple times, yielding a wide range of photocycles with (ultra)violet, blue, teal, green, orange, and red states (22).Red/green CBCRs such as AnPixJg2 and NpR6012g4 have red-absorbing dark states similar to phytochromes that photoconvert to green-absorbing lit states. In this CBCR subfamily, the molecular mechanism responsible for photoproduct tuning relies on trapping the 15E bilin in a twisted geometry that results in blue-shifted absorption (10, 11). In contrast, green/red CBCRs exhibit a reversed photocycle: the green-absorbing 15Z dark state photoconverts to yield a red-absorbing 15E photoproduct. This subfamily uses a protochromic mechanism first reported for the light-regulated histidine kinase RcaE (SI Appendix, Fig. S1B) in which photoconversion triggers a proton transfer to an uncharged chromophore inducing a spectral red shift (2, 38).Until recently, the light-sensing range of CBCRs appeared limited to the visible spectrum, thereby implicating phytochromes to be exclusively responsible for far-red sensing in cyanobacteria. Indeed, far-red–dependent remodeling of the photosynthetic apparatus in multiple cyanobacterial species is mediated by the red/far-red phytochrome RfpA (3, 39). The discovery of two lineages of CBCRs with far-red-absorbing dark states (frCBCRs) was thus surprising (40). Upon far-red light absorption, these frCBCRs convert to either an orange- or red-absorbing photoproduct state. These frCBCRs evolved from green/red CBCRs as part of a greater green/red (GGR) lineage and independent from evolution of other frCBCRs within the XRG (extended red/green) lineage (35, 40, 41). Owing to their small size and spectral overlap with the therapeutic window of optimum tissue penetrance (700 to 800 nm) (42–46), frCBCRs represent tantalizing scaffolds for development of FR-responsive optogenetic reagents for biomedical research and imaging applications (45, 47–50).To understand the molecular basis of far-red spectral tuning of the frCBCR family that evolved within GGR lineage, we determined the crystal structures of the FR-absorbing dark state of the representative FR/O CBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 at both ambient and cryogenic temperatures. These structures revealed an all-Z,syn configuration of its PCB chromophore that differs from those found in all known CBCRs and phytochromes. Based upon these crystallographic results, spectra of site-directed mutants of Anacy_2551g3 and related frCBCRs in the GGR lineage, and comparisons with other bilin-binding proteins, we identify key protein–chromophore interactions that support two tuning mechanisms simultaneously at work for far-red light detection in this family of frCBCRs.     

Human-relevant near-organ neuromodulation of the immune system via the splenic nerve

Neuromodulation of immune function by stimulating the autonomic connections to the spleen has been demonstrated in rodent models. Consequently, neuroimmune modulation has been proposed as a new therapeutic strategy for the treatment of inflammatory conditions. However, demonstration of the translation of these immunomodulatory mechanisms in anatomically and physiologically relevant models is still lacking. Additionally, translational models are required to identify stimulation parameters that can be transferred to clinical applications of bioelectronic medicines. Here, we performed neuroanatomical and functional comparison of the mouse, rat, pig, and human splenic nerve using in vivo and ex vivo preparations. The pig was identified as a more suitable model of the human splenic innervation. Using functional electrophysiology, we developed a clinically relevant marker of splenic nerve engagement through stimulation-dependent reversible reduction in local blood flow. Translation of immunomodulatory mechanisms were then assessed using pig splenocytes and two models of acute inflammation in anesthetized pigs. The pig splenic nerve was shown to locally release noradrenaline upon stimulation, which was able to modulate cytokine production by pig splenocytes. Splenic nerve stimulation was found to promote cardiovascular protection as well as cytokine modulation in a high- and a low-dose lipopolysaccharide model, respectively. Importantly, splenic nerve–induced cytokine modulation was reproduced by stimulating the efferent trunk of the cervical vagus nerve. This work demonstrates that immune responses can be modulated by stimulation of spleen-targeted autonomic nerves in translational species and identifies splenic nerve stimulation parameters and biomarkers that are directly applicable to humans due to anatomical and electrophysiological similarities.

The inflammatory status of the body is monitored and regulated through the neuroimmune axis, connecting the brain to the immune system via both humoral and neural pathways (1–3). In particular, the inflammatory reflex (3) controls systemic immune responses; detection of inflammatory stimuli in the periphery is communicated to the brain that activates outflow of neural signals to promote peripheral immune responses proportional to the threat. Studies in rodent models have identified the cholinergic anti-inflammatory pathway (CAIP) as the brain’s efferent response to infection and inflammation through peripheral neurotransmitters released in lymphoid organs, mainly the spleen (4, 5). Within this pathway, the peripheral connection between the vagus nerve (VN), the splenic nerve (SpN), and its terminal release of noradrenaline (NA) into the spleen have been identified as crucial components of this neural circuit (6–8) (SI Appendix, Fig. S1A).Importantly, the CAIP can be harnessed to promote immune control. Activation of the cervical VN by electrical stimulation (vagus nerve stimulation—VNS; SI Appendix, Fig. S1A) has been shown to be effective in reducing lipopolysaccharide (LPS)-induced levels of tumor necrosis factor alpha (TNF-α) (4, 6, 7) and in preclinical rodent models of chronic inflammatory diseases (9, 10). Murine models have generally been used to demonstrate biological proof of concepts of novel neuromodulation therapies in this and other contexts. However, the development of clinical bioelectronic medicines requires the accurate estimation and validation of stimulation parameters in a histologically, surgically, and anatomically relevant model to define device and therapy requirements. The translation of stimulation parameters from rodent to human is hampered by anatomical (e.g., size of nerves), histological (e.g., number of axons, connective tissue thickness, proportion of adipose tissue), and physiological (e.g., immunological) differences. Therefore, it is suggested that the use of large animal models, human tissues, and in silico modeling are more appropriate for the optimization and scaling of human-relevant parameters (11, 12).Although early clinical feasibility studies have provided preliminary evidence of immunomodulatory effects of VNS in patients (13, 14), clear demonstration of the translation of the splenic anti-inflammatory pathway in clinically relevant species is currently lacking in the literature. The VN has a functionally and anatomically complex composition. In animals and humans, the VN contains both afferent and efferent axons of varying size (large, medium, and small) and degree of myelination (heavily myelinated, lightly myelinated, and unmyelinated axons) innervating multiple organs and muscles (15). As a consequence, currently used VNS results in activation of off-target circuits (SI Appendix, Fig. S1A) that can cause dysphonia, coughing, hoarseness, pain, and dyspnea (16–18); in some patients, these can be managed and can also improve over time (18). Further, it remains unclear which axons (efferent versus afferent, myelinated versus unmyelinated) within the VN relay immunomodulatory signals to peripheral organs (19, 20). As a result, it is difficult to optimize the stimulation parameters necessary to activate axons within the VN which carry signals to the spleen. Typically, clinical parameters are selected based on the individual patient’s tolerance of off-target effects (13, 21) without direct evidence of activation of the anti-inflammatory pathway because of a lack of an organ-specific biomarker. Since the SpN directly transmits neural signals to the spleen and is the fundamental nodal circuit in mediating the anti-inflammatory response (22), SpN stimulation (SpNS) may represent an alternative modality providing the opportunity for near-organ modulation of the immune system (SI Appendix, Fig. S1 B and C). Proof of concept experiments in rodents have shown that immune responses can indeed be modulated by stimulation of the SpN with comparable cytokine suppressive effects to VNS (7, 8, 23).Here, we anatomically, histologically, and functionally compared the mouse, rat, pig, and human SpN, demonstrating the superiority of the pig as a translational model of the human SpN. We then performed functional in vivo pig electrophysiological studies to identify organ-specific physiological biomarkers that can be used to assess nerve engagement and to refine stimulation parameters. Finally, we assessed the large animal translation of the spleen-dependent anti-inflammatory pathway in the pig using in vitro splenocyte preparations together with two in vivo models of acute inflammation.     

Inhibition of 3-phosphoinositide–dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts

Cellular senescence is defined as a stable, persistent arrest of cell proliferation. Here, we examine whether senescent cells can lose senescence hallmarks and reenter a reversible state of cell-cycle arrest (quiescence). We constructed a molecular regulatory network of cellular senescence based on previous experimental evidence. To infer the regulatory logic of the network, we performed phosphoprotein array experiments with normal human dermal fibroblasts and used the data to optimize the regulatory relationships between molecules with an evolutionary algorithm. From ensemble analysis of network models, we identified 3-phosphoinositide–dependent protein kinase 1 (PDK1) as a promising target for inhibitors to convert the senescent state to the quiescent state. We showed that inhibition of PDK1 in senescent human dermal fibroblasts eradicates senescence hallmarks and restores entry into the cell cycle by suppressing both nuclear factor κB and mTOR signaling, resulting in restored skin regeneration capacity. Our findings provide insight into a potential therapeutic strategy to treat age-related diseases associated with the accumulation of senescent cells.

Cellular senescence is defined as a stable, persistent exit from the cell cycle in response to stresses such as telomere shortening, oxidative stress, oncogene activation, and DNA damage (1, 2). A benefit of cellular senescence is prevention of tumorigenesis by blocking proliferation of damaged cells that may undergo malignant transformation (2, 3). However, senescent cells accumulate in tissues during aging and secrete proinflammatory cytokines, which can contribute to aging and age-related diseases, including cancer (2, 3). In studies with animal models, elimination of senescent cells prevents, alleviates, or reverses symptoms of aging (4, 5) and various age-related diseases (6, 7), such as osteoarthritis and atherosclerosis.Cell-cycle arrest alone is not cellular senescence; cellular senescence requires additional signals that convert transient cell-cycle arrest into persistent exit from the cell cycle so that the cells fail to proliferate in response to growth signals, a process called geroconversion (8, 9). Terminally differentiated, nonmitotic cells can also undergo senescence; thus, cell-cycle exit is only one aspect of the senescent phenotype. Cellular senescence is a complex biological mechanism regulated by various signaling pathways (10, 11). Signaling pathways that mediate cellular senescence can be divided into three major categories. The first category includes the pathways that cause cell-cycle arrest in response to DNA damage, such as p53/p21^CIP1 and p16^INK4a/pRb pathways (11–14). The second category consists of the pathways mediating cell growth and energy metabolism, such as PI3K/AKT/mTOR and SIRT1/AMPK pathways (15–18). Activation of mTOR in cells arrested by persistent DNA damage represents a second stimulus that can convert transiently arrested cells into senescent cells that exhibit hypertrophy and an expanded lysosomal compartment (19). The last category consists of the pathways mediating the senescence-associated secretory phenotype (SASP) (3, 10, 20). The SASP is a characteristic feature of senescent cells and reflects their secretion of proinflammatory cytokines and chemokines. These cytokines and chemokines maintain cellular senescence through positive autoregulatory feedbacks, affect nonsenescent nearby cells, and promote aging and age-related diseases, including cancer (3, 21). Nuclear factor κB (NF-κB) activity is important for SASP, and suppression of NF-κB prevents age-related diseases and delays aging in mice (22, 23).Spontaneous reversion from senescence to proliferation is extremely rare, but the reversion through manipulations is not. Some studies reported that senescent cells can reenter the cell cycle (24). The current understanding of senescence is as a dynamic multistep process that is reversible under some conditions (25). About 70 to 90% of cells with low p16^INK4a levels in replicative senescence, which is senescence related to the finite number of divisions a cell can perform before telomeres become too short, resume proliferation following p53 inactivation (26). Inactivation of p53 also enables cells to escape from therapy-induced senescence, caused by the chemotherapeutic agent Adriamycin (27). Cells with oncogene-induced senescence can also escape from the senescent state. For instance, about 50% of mouse embryo fibroblasts with high Ras levels reenter the cell cycle upon inactivation of all three Rb family members (28), and about 70% of the fibroblasts reenter upon activation of H3K9 demethylases (29).Here, we applied a systems biology approach to identify mechanisms underlying cell-cycle arrest, cell growth, and the SASP with the goal of finding inhibitable targets to convert the senescent state to the quiescent state. We studied normal human dermal fibroblasts (NHDFs), which can be experimentally induced into the senescent state (8). We constructed a molecular signaling network of cellular senescence using information in the literature and network databases to identify the relevant molecules, experimental data from time series of phosphorylated proteins in NHDFs to define the input–output relationships that reflect cellular states upon each input condition, and an evolutionary algorithm to determine the regulatory logic of the network (SI Appendix, Fig. S1 A–C). By analyzing the regulatory signaling network, we predicted that PDK1 was an inhibitor target that can convert senescent fibroblasts to quiescent fibroblasts (SI Appendix, Fig. S1D). To validate this prediction, we conducted experiments with NHDFs exposed to PDK1 inhibitors (SI Appendix, Fig. S1E), which eliminated hallmarks of cellular senescence, restored the proliferation of the cells in response to growth factors, and restored skin regeneration capacity in two-dimensional (2D) culture and a three-dimensional (3D) skin equivalent model. Our findings provide insight into a potential therapeutic strategy to treat aging and age-related diseases.     

From the Cover: An ecophysiological explanation for manganese enrichment in rock varnish

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese—over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant—a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

Rock varnish (also called desert varnish) is a thin, dark coating found on exposed surfaces of rocks in arid environments that is composed primarily of clay minerals and manganese and iron oxides (1–3). It has long been recognized as a geochemical puzzle (4–6) and has received considerable scientific and popular interest due to its widespread occurrence (7), association with archaeological petroglyphs (8–10), use in age dating (11–17), potential as a paleoclimate proxy (16, 18–20), and comparisons to rock coatings on Mars (21–24). However, many interpretations and applications of varnish hinge on understanding the mechanism of its formation, which remains unknown.The most perplexing aspect of varnish is its extremely high enrichment in manganese. Varnish characteristically contains 10–30 wt% MnO—two to three orders of magnitude higher manganese content than typical underlying rocks or the surrounding dust from which much of the mass comprising varnish originates (2, 3, 25). Other major elements including iron, silicon, aluminum, magnesium, sodium, and titanium, although abundant, are not enriched.Diverse microorganisms are known to be associated with varnish, but whether or not they play a role in its origin has been fiercely debated (26). Numerous processes, both abiotic (e.g., dust deposition, water leaching, photochemical manganese oxidation) and biological (e.g., microbial mediation of binding and cementation, microbial manganese oxidation), have been proposed to contribute (summarized in SI Appendix, Text), but since varnish grows very slowly—at most tens of microns over a thousand years (27)—empirical demonstration has not been attainable. While many of these processes may be relevant to varnish formation, none of them satisfactorily explains the highly and selectively enriched manganese content in varnish.In this paper, we stepped back from the various paradigms that have been previously proposed and considered varnish formation from a holistic perspective. Synthesizing results from physical, chemical, and biological analyses, we reevaluated the relationship between varnish microflora and their environment and developed a hypothesis linking specific manganese accumulation to environmental adaptations of major members of the varnish microbial community.     

Robust folding of a de novo designed ideal protein even with most of the core mutated to valine

Protein design provides a stringent test for our understanding of protein folding. We previously described principles for designing ideal protein structures stabilized by consistent local and nonlocal interactions, based on a set of rules relating local backbone structures to tertiary packing motifs. The principles have made possible the design of protein structures having various topologies with high thermal stability. Whereas nonlocal interactions such as tight hydrophobic core packing have traditionally been considered to be crucial for protein folding and stability, the rules proposed by our previous studies suggest the importance of local backbone structures to protein folding. In this study, we investigated the robustness of folding of de novo designed proteins to the reduction of the hydrophobic core, by extensive mutation of large hydrophobic residues (Leu, Ile) to smaller ones (Val) for one of the designs. Surprisingly, even after 10 Leu and Ile residues were mutated to Val, this mutant with the core mostly filled with Val was found to not be in a molten globule state and fold into the same backbone structure as the original design, with high stability. These results indicate the importance of local backbone structures to the folding ability and high thermal stability of designed proteins and suggest a method for engineering thermally stabilized natural proteins.

The de novo design of protein structures, starting from pioneering work (1, 2), has been achieved in tandem with our understanding of how amino acid sequences determine folded structures (3–16). A breakthrough in protein design methodology was a finding of principles for encoding funnel-shaped energy landscapes into amino acid sequences (7, 10, 17, 18). Based on studies of protein folding, it had been suggested that naturally occurring proteins have evolved to have funnel-shaped energy landscapes toward their folded structures (19–23). However, complicated structures of naturally occurring proteins with nonideal features for folding—for example, kinked α-helices, bulged β-strands, long or strained loops, and buried polar groups—make it difficult to understand how the funnels are encoded in amino acid sequences. By focusing on protein structures without such nonideal features, we proposed principles for designing ideal protein structures stabilized by completely consistent local and nonlocal interactions (24), based on a set of rules relating local backbone structures to preferred tertiary motifs (7, 10). These design rules describe the relation of the lengths or torsion patterns of two secondary structure elements and the connecting loop to favorable packing geometries (SI Appendix, Fig. S1A). The design principles enable to encode strongly funneled energy landscapes into amino acid sequences, by the stabilization of folded structures (positive design) and by the destabilization of nonnative conformations (negative design) due to the restriction of folding conformational space by the rules (SI Appendix, Fig. S1C). In the design procedure, backbone structures for a target topology are generated based on a blueprint (SI Appendix, Fig. S1B), in which either the lengths or backbone torsion patterns of the secondary structures and loops are determined using the rules so that the tertiary motifs present in the target topology are favored, and then amino acid sequences stabilizing the generated backbone structures are designed. The designed amino acid sequences stabilize their folded structures both with nonlocal interactions such as hydrophobic core packing and with local interactions favoring the secondary structures and loops specified in the blueprint, which destabilize a myriad of nonnative topologies through local backbone strain captured by the rules, thereby resulting in funnel-shaped energy landscapes (SI Appendix, Fig. S1C). The principles have enabled the de novo design of ideal protein structures for various topologies with atomic-level accuracy (Fig. 1) (6, 7, 10, 13).Open in a separate windowFig. 1.In silico energy landscapes and far-UV circular dichroism (CD) spectra for 10 de novo designed ideal proteins. (A–E) Five designs by Koga et al. in 2012 (7). (F–I) Four designs by Lin et al. in 2015 (10). (J) Top7 by Kuhlman et al. in 2003 (6). (Top) Design models. (Middle) Energy landscapes obtained from Rosetta ab initio structure prediction simulations (41). Red points represent the lowest energy structures obtained in independent Monte Carlo structure prediction trajectories starting from an extended chain for each sequence; the y axis is the Rosetta all-atom energy; the x axis is the Cα root-mean-square deviation (RMSD) to the design model. Green points represent the lowest energy structures obtained in trajectories starting from the design model. (Bottom) The far-UV CD spectra during thermal denaturation with the melting temperature T_m, which is obtained by fitting to the denaturation curves shown in SI Appendix, Fig. S2.Interestingly, the de novo designs exhibit prominent characteristics in terms of thermal stability when compared with naturally occurring proteins. The circular dichroism (CD) measurements up to 170 °C conducted in this study revealed the melting temperature (T_m), which was above 100 °C for most of the designs (Fig. 1) (6, 7, 10). Therefore, the designs have great potential for use as scaffolds to engineer proteins with specific functions of interest. Indeed, miniprotein structures (∼40 residues) designed de novo according to the rules were applied as scaffolds for creating protein binders specific for influenza hemagglutinin and botulinum neurotoxin, displaying high thermal stability (>70 °C) despite the small size (25).The rules in the principles described above emphasize the importance of local backbone structures not the details of amino acid side chains to protein folding, which is also supported by studies using simple calculations with the hydrophobic-polar lattice model or the snake-cube model (26, 27). On the other hand, it is known that hydrophobic interactions are the dominant driving force for folding (28, 29) and the cores of naturally occurring proteins are tightly packed with hydrophobic amino acid residues (30, 31) like a jigsaw puzzle. Indeed, in our design principles, protein cores were designed to be tightly packed and as “fat” as possible with larger hydrophobic residues so that energy landscapes were sculpted to be deeply funneled into a target topology by lowering its energy (SI Appendix, Fig. S1C).Which factor, the local backbone structures encoded by the rules or the tight core packing with fat hydrophobic residues, contributes more to the generation of funnels in the designs? Here, we studied the contribution of hydrophobic core packing to folding ability and thermal stability by investigating the robustness of folding against the reduction of packing, using the design with the highest thermal stability among our nine de novo designs (Fig. 1, except Top7), Rsmn2x2_5_6 (10). We started to study single-residue mutants from Leu or Ile to Val that prune one carbon atom from the aliphatic side chain, which lose the tight packing like a jigsaw puzzle and decrease the hydrophobicity, and then, we combined the mutations. Consequently, we found that a mutant with 10 residue substitutions of Leu or Ile with Val still has the folding ability and high thermal stability despite its reduced and loosened hydrophobic core packing. This result suggests the importance of the local backbone structures for the folding ability and stability of the de novo designs.     

Paleo-ENSO influence on African environments and early modern humans

In this study, we synthesize terrestrial and marine proxy records, spanning the past 620 ky, to decipher pan-African climate variability and its drivers and potential linkages to hominin evolution. We find a tight correlation between moisture availability across Africa to El Niño Southern Ocean oscillation (ENSO) variability, a manifestation of the Walker Circulation, that was most likely driven by changes in Earth’s eccentricity. Our results demonstrate that low-latitude insolation was a prominent driver of pan-African climate change during the Middle to Late Pleistocene. We argue that these low-latitude climate processes governed the dispersion and evolution of vegetation as well as mammals in eastern and western Africa by increasing resource-rich and stable ecotonal settings thought to have been important to early modern humans.

The role of climatically driven environmental change in triggering key stages of hominin evolution over the last 6 My has long been recognized (1–3). More recently, environmental changes across Africa have been implicated in major shifts in the population structure of hominins over the last half of a million years—the key demographic context for the emergence of Homo sapiens (4–8). However, evaluating the impact of environmental changes and their possible effects on hominin evolution and demography is difficult, as high-resolution climate archives are temporally and spatially sparse (9–11). Further problems are introduced by the fact that available proxy studies usually detail climate variability of only one study site or region (3, 12, 13), which makes it difficult to study its consequences for evolutionary processes across large spatial scales. Here, we provide a pan-African view on climate change during the Middle to Late Pleistocene in order to construct a framework for understanding hominin evolution within this timeframe. To achieve this, we have combined 11 terrestrial lacustrine and marine sedimentary archives (Fig. 1 and SI Appendix, Tables S1 and S2; see details on site selection criteria in the SI Appendix) detailing wet–dry variability of eastern and western Africa during the last 620 ky—the time interval of the emergence of H. sapiens in Africa and its subsequent out-of-Africa dispersal (Fig. 1 and SI Appendix, Table S1).Open in a separate windowFig. 1.Suite of study sites and the global WC. (A) Location map of marine and terrestrial proxy records used for the reconstruction of African climate. Note that the black dots associated with marine sites (small gray dots) are referred to their respective hinterland region. SAH = Ocean Drilling Program (ODP) Site 659; LIB = ODP663; BOS = Lake Bosumtwi; CON = ODP Site 1075; NAM1 = GeoB1028-5; NAM2 = ODP Site 1082; LOM = MD96-2048; MAL = Lake Malawi; MAG = Lake Magadi; CHB = Paleolake Chew Bahir; and MED = ODP Site 967. The full list of references and coordinates for all sites is provided in SI Appendix, Table S1. Blue dots mark marine sites used for the reconstruction of the WC (SI Appendix, Table S2). (B) SST anomalies and resulting changes in tropical heating and convection (related to WC) under El Niño conditions (positive ENSO phase). (C) SST anomalies and resulting changes in tropical heating and convection (related to WC) under La Niña conditions (negative ENSO phase). For more details on the effect of El Niño/La Niña on African precipitation, see SI Appendix. Blue areas = cooling relative to normal conditions; red areas = warming relative to normal conditions; and black arrows indicate transport direction.Today, the climate of tropical Africa is governed by convection, with the seasonal migration of the tropical rain belt dictating the pattern of precipitation (9). Changes in seasonal positioning of the rain belt relate to insolation variability, with rainfall occurring in northern/southern Africa during boreal/austral summer (14). In addition, observational data suggest that the African climate is highly sensitive to changes in the Walker circulation (WC), which is manifested via the El Niño Southern Oscillation (ENSO) (15, 16; see SI Appendix for more details). ENSO originates from sea surface temperature (SST) anomalies in the equatorial Pacific Ocean, and these changes impact the atmospheric WC, which in turn alters the location and strength of tropical convection cells (Fig. 1) (17). Through this coupled ocean–atmosphere system, ENSO events are propagated around the globe by Kelvin and Rossby waves (16), eventually reaching the African continent (see SI Appendix for more details). Here, changes in ENSO state alter the east–west trending moisture gradient across Africa (18–20). This leads to opposing dry and humid conditions between eastern and western Africa so that, during La Niña, eastern Africa experiences drier conditions than western Africa and vice versa during El Niño events. For instance, during El Niño years, eastern Africa experiences positive precipitation anomalies of up to 60% (or 200 mm per year) relative to the yearly precipitation budget during non–El Niño years, while western Africa experiences a 20 to 40% precipitation reduction (21, 22). Besides these modern driving mechanisms, spatiotemporal precipitation changes in Africa on much longer time scales have also been attributed to changes in Atlantic meridional overturning circulation, global atmospheric CO₂ concentrations (pCO₂), and/or the waning and waxing of global ice sheets (23–26). However, the interplay of these various driving mechanisms on orbital time scales and their pan-African impact on precipitation remains ambiguous.     

Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM

The radial spoke (RS) heads of motile cilia and flagella contact projections of the central pair (CP) apparatus to coordinate motility, but the morphology is distinct for protozoa and metazoa. Here we show the murine RS head is compositionally distinct from that of Chlamydomonas. Our reconstituted murine RS head core complex consists of Rsph1, Rsph3b, Rsph4a, and Rsph9, lacking Rsph6a and Rsph10b, whose orthologs exist in the protozoan RS head. We resolve its cryo-electron microscopy (cryo-EM) structure at 3.2-Å resolution. Our atomic model further reveals a twofold symmetric brake pad-shaped structure, in which Rsph4a and Rsph9 form a compact body extended laterally with two long arms of twisted Rsph1 β-sheets and potentially connected dorsally via Rsph3b to the RS stalk. Furthermore, our modeling suggests that the core complex contacts the periodic CP projections either rigidly through its tooth-shaped Rsph4a regions or elastically through both arms for optimized RS–CP interactions and mechanosignal transduction.

The majority of motile cilia and flagella are composed of nine dynein arm-containing peripheral doublet microtubules (DMTs) surrounding a central pair (CP) of MTs (the “9+2” axoneme). The radial spoke (RS) is a T-shaped protein complex with an orthogonal head pointing toward the CP and a stalk anchored on each A-tubule of the DMTs (1–5). It acts as the mechanochemical transducer between the CP and axonemal dynein arms to regulate flagellar/ciliary motility (6–11). The flagella of Chlamydomonas reinhardtii, a widely used model organism, contain two full-size RSs (RS1 and RS2) in each 96-nm repeat unit of the axoneme. In contrast, motile cilia/flagella of Tetrahymena thermophila and metazoa possess triplet RSs (RS1 to RS3) (2–4, 11). The Chlamydomonas RS is composed of at least 23 subunit proteins (RSP1 to RSP23) (2, 12, 13). Seventeen of them have mammalian homologs (14). Mutations leading to the loss of the entire RS or RS head result in immotile flagella in Chlamydomonas (6–8) but in rotatory ciliary beat in mammals, causing primary ciliary dyskinesia (PCD), a genetic syndrome characterized by recurrent respiratory infections, situs inversus, infertility, and hydrocephalus (4, 15–21).The most striking morphological differences in the RS lie in the RS head, the key structural domain that mediates the mechanosignaling by directly contacting projections of the CP (9–11). The heads of RS1 and RS2 consist of two structurally identical, rotationally symmetric halves that differ largely from that of RS3 (3, 4). Furthermore, their morphologies differ dramatically between protozoa and metazoa. In Chlamydomonas and Tetrahymena, for instance, the heads of RS1 and RS2 are rich in lateral branches that also form a connection between the two heads (2, 4). In contrast, in sea urchin (Strongylocentrotus purpuratus) and human, the heads of RS1 and RS2 resemble a pair of ice skate blades with many fewer interfaces toward the CP (3, 4). Despite the importance of the RS and RS head in cilia/flagella motility, the structural details of the RS and the RS–CP interactions remain poorly understood, especially in mammals.The RS heads have probably been remodeled to comply with both structural and functional alterations of the axoneme during evolution. How the morphological changes occurred, however, remains unclear. The Chlamydomonas RS head is composed of RSP1, -4, -6, -9, and -10 and part (the C terminus) of the stalk component, RSP3. Each of the symmetrical halves of the head contains one copy of these components (2, 10, 22). All the head components have mammalian orthologs (Rsph1, -4a, -6a, -9, -10b, and -3b) (11, 14). In sharp contrast to the markedly reduced surface area of metazoan RS heads, the peptides of human RSPH4A, -6A, and -10B are longer than their Chlamydomonas orthologs by 1.5-, 1.3-, and 4-fold, respectively (11). Only RSPH1 (309 amino acids [aa]) is shorter than RSP1 (814 aa) (11). The lengths of mouse RS head proteins are also similarly changed as their human counterparts (SI Appendix, Fig. S1A). Furthermore, while murine Rsph4a is essential for the head formation of RS1 to RS3 in motile multicilia of the trachea, ependyma, and oviduct (15), Rsph6a is specifically expressed in sperm for their normal flagellar formation (23). RSP4/Rsph4a and RSP6/Rsph6a are paralogs: RSP4 and RSP6 share 48% sequence identity (24), whereas murine Rsph4a is 63% identical to Rsph6a (SI Appendix, Fig. S1B). Sea urchin and Ciona, however, have only one ortholog (11, 25). These results suggest that, unlike the protozoan RS heads, the metazoan ones may not simultaneously contain Rsph4a and Rsph6a. The general shapes of the RS structure in axonemes have been determined by conventional electron microscopy (EM) (26–28) and cryo-electron tomography (cryo-ET) (2–5). Recently, a 15-Å-resolution RS structure of Chlamydomonas was resolved by cryo-EM single-particle analysis (29). The resolutions, however, do not suffice for the delineation of the locations of individual RS subunits.In the present study, by biochemical and structural analyses, we show the murine RS head is both compositionally and morphologically distinct from that of Chlamydomonas. Our study suggests that the RS head has experienced profound remodeling to probably comply with both structural and functional alterations of the axoneme during evolution for coordinated ciliary or flagellar motility.     

Legume–microbiome interactions unlock mineral nutrients in regrowing tropical forests

Legume trees form an abundant and functionally important component of tropical forests worldwide with N₂-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N₂-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N₂-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N₂–fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N₂-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N₂-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N₂-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.

The legume family is the most diverse angiosperm family in the Neotropics (1–3), with dinitrogen (N₂)-fixing legume trees growing fast and supplying tropical forests with substantial quantities of nitrogen (N) during succession (4). This N₂-fixing strategy requires that trees can access scarce sources of inorganic nutrients, including bioavailable forms of phosphorus (P) for metabolites and growth and molybdenum (Mo) for nitrogenase functioning (5–7) (the enzyme that catalyzes conversion of atmospheric N₂ to bioavailable N).However, in highly weathered tropical soils, in addition to their pools in organic matter (8, 9), large amounts of P and Mo are often occluded in an inorganic form in insoluble iron (Fe) and aluminum (Al)-bearing minerals (10, 11) and thus not available for immediate biological uptake. For example, both P and Mo are scarce in the oxisols and inceptisols that have developed from Mo-poor basalt bedrock in Panamanian tropical forests (7, 12) (SI Appendix, Table S1) and that contain P-adsorbing kaolinite, goethite, and hematite secondary minerals (SI Appendix, Fig. S1). Our own observations from these Panamanian forests show significant differences in the chemistry of soils beneath N₂ fixing versus nonfixing trees, with significantly lower concentrations of nitric acid–extractable P, Fe, and Al and lower pH below N₂-fixing trees (SI Appendix, Table S2). Moreover, a strong association between extracted P and Fe plus Al, but not between P and soil organic carbon, implies that soil P is significantly influenced by mineral dynamics within these tropical soils (SI Appendix, Fig. S2, P < 0.001 for Fe and Al and P > 0.10 for carbon, Pearson test).These patterns raise the biogeochemical hypothesis that N₂-fixing legume trees may strategically employ specific mechanisms to enhance mineral weathering (5, 13, 14), resulting in improved access to occluded inorganic mineral nutrients, enhanced N₂-fixation, and enhanced carbon sequestration by forest biomass during succession. Here, we address this hypothesis by investigating 1) whether N₂-fixing trees induce locally elevated rates of silicate mineral (olivine) weathering (compared to nonfixing trees), causing the depletion of elements critical to N₂-fixation; 2) whether the altered soil beneath N₂-fixing trees is linked to compositional and functional differences in the microbiomes and metagenomes associated with soil minerals; and 3) whether the presence of N₂-fixers affects biogeochemical nutrient cycling in rooting zone soils beneath neighboring non-N₂–fixing forest trees.     

“You” speaks to me: Effects of generic-you in creating resonance between people and ideas

Creating resonance between people and ideas is a central goal of communication. Historically, attempts to understand the factors that promote resonance have focused on altering the content of a message. Here we identify an additional route to evoking resonance that is embedded in the structure of language: the generic use of the word “you” (e.g., “You can’t understand someone until you’ve walked a mile in their shoes”). Using crowd-sourced data from the Amazon Kindle application, we demonstrate that passages that people highlighted—collectively, over a quarter of a million times—were substantially more likely to contain generic-you compared to yoked passages that they did not highlight. We also demonstrate in four experiments (n = 1,900) that ideas expressed with generic-you increased resonance. These findings illustrate how a subtle shift in language establishes a powerful sense of connection between people and ideas.

Consider the feeling evoked by watching a gripping scene in a film, hearing a moving song, or coming across a quotation that seems to be written just for you. Experiencing resonance, a sense of connection, is a pervasive human experience. Prior research examining the processes that promote this experience suggests that altering a message to evoke emotion (1–7), highlighting its applicability to a person’s life (2, 6, 8–10), or appealing to a person’s beliefs (4, 8, 11) can all contribute to an idea’s resonance. Here we examine an additional route to cultivating this experience, which is grounded in a message’s form rather than its content: the use of a linguistic device that frames an idea as applying broadly.The ability to frame an idea as general rather than specific is a universal feature of language (12–15). One frequently used device is the generic usage of the pronoun “you” (15–17). Although “you” is often used to refer to a specific person or persons (e.g., “How did you get to work today?”), in many languages, it can also be used to refer to people in general (e.g., “You avoid rush hour if you can.”). This general use of “you” is comparable to the more formal “one,” but is used much more frequently (18).Research indicates that people often use “you” in this way to generalize from their own experiences. For example, a person reflecting on getting fired from their job might say, “It makes you feel betrayed” (18). Here, we propose that using “you” to refer to people in general has additional social implications, affecting whether an idea evokes resonance.Two features of the general usage of “you” (hereafter, “generic-you”) motivate this hypothesis. First, generic-you conveys that ideas are generalizable. Rather than expressing information that applies to a particular situation (e.g., “Leo broke your heart”), generic-you expresses information that is timeless and applies across contexts (e.g., “Eventually, you recover from heartbreak”; 18–23). Second, generic-you is expressed with the same word ("you") that is used in nongeneric contexts to refer to the addressee. Thus, even when “you” is used generically, the association to its specific meaning may further pull in the addressee, heightening resonance. Together, these features suggest that generic-you should promote the resonance of an idea. We tested this hypothesis across five preregistered studies (24–28), using a combination of crowd-sourced data and online experimental paradigms. Data, code, and materials are publicly available via the Open Science Framework (https://osf.io/6J2ZC/) (29). Study 1 used publicly available data from the Amazon Kindle application. Studies 2–5 were approved by the University of Michigan Health Sciences and Behavioral Sciences institutional review board (IRB) under HUM00172473 and deemed exempt from ongoing IRB review. All participants who participated in studies 2–5 provided informed consent via a checkbox presented through the online survey platform, Qualtrics.     

Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells

Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein–protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor (Kd=120 nM,MW=734 Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein–protein interaction involved in actin filament processing and cell migration.

Metastasis is a complex multistep process (1, 2) employing, among others, mechanisms governing actin cytoskeleton dynamics involving integrin signaling and actin regulatory proteins (3–5). So far, all approved antimetastatic drugs antagonize integrins (6) or inhibit downstream kinases (7, 8) (SI Appendix, Fig. S1). In the metastatic setting however, these drugs appear to have only limited success (9–13) and 5-y survival is not increasing satisfactorily (14, 15), making new approaches in antimetastatic drug development essential to meet this urgent medical need.The enabled/vasodilator stimulated phosphoprotein protein family (Ena/VASP) acts as a crucial hub in cell migration by linking actin filaments to invadopodia and focal adhesions (16–22). Due to their role in the transformation of benign lesions into invasive and metastatic cancer, Ena/VASP proteins are discussed as part of the invasive signature and as a marker of breast carcinogenesis (23–25). At the advanced tumor stage, the protein family is overexpressed (26–28), which has been shown to increase migration speed in vivo (29) and to potentiate invasiveness (30). Yet, no sufficiently potent probes to interfere with Ena/VASP in vivo have been reported.The three vertebrate Ena/VASP family members, enabled homolog (ENAH), VASP, and Ena-VASP-like (EVL), share a tripartite structural organization in which two Ena/VASP homology domains (EVH1 and EVH2) are separated by a more divergent proline-rich central part. Interactions of the EVH2 domain are involved in the elongation and protection of barbed-end actin filaments from capping proteins and tetramerization (31, 32). EVH1 folds into a structured globular domain that interacts with proteins at focal adhesions (33), the leading edge (34, 35), and invadopodia (36, 37) by recognizing the motif [F/W/L/Y]PxϕP (35, 38) (ϕ hydrophobic, x any; SI Appendix, Fig. S3) in poly-L-proline type II helix (PPII) conformation.In the course of our research into small molecules as potential inhibitors of protein–protein interactions (39) we recently in silico designed and stereo-selectively synthesized scaffolds, coined ProMs, which mimic pairs of prolines in PPII conformation (40). The modular combination of different ProMs thereby allowed us to generate nonpeptidic secondary-structure mimetics that fulfill the steric requirements of the addressed proline-rich motif-recognizing domain (41–47). For the EVH1 domain, our proof-of-concept study yielded a canonically binding, nontoxic, cell-membrane-permeable, 706-Da inhibitor 1 (Fig. 1A) composed of two different ProM scaffolds and 2-chloro-(L)-phenylalanine (2-Cl-Phe) (40). While the synthetic inhibitor 1 represents the compound with the highest reported affinity toward Ena/VASP EVH1 domains, a further improvement was required for in vivo experiments. Here we report successful structure-based optimization of inhibitor 1 based on 22 high-resolution crystal structures of ENAH EVH1 in complex with different inhibitors (SI Appendix, Tables S1–S6), including the well-resolved C-terminal binding epitope TEDEL of ActA from Listeria monocytogenes (48). Newly identified interaction sites adjacent to the C terminus of 1 were addressed by in silico designed and stereo-selectively synthesized modifications of the ProM-1 scaffold (Fig. 1A). While drastically increasing the affinity against a rather flat protein surface we conserved structural simplicity, low molecular weight, nontoxicity, and cell-membrane permeability. Potent compounds against Ena/VASP were shown to also act in vivo, i.e., by inhibiting cancer cell extravasation in zebrafish at only 1 μM, thereby paving the way for future preclinical studies.Open in a separate windowFig. 1.(A) Structure of the first-generation Ena/VASP EVH1 inhibitor 1. All compositions share the N-acetylated 2-chloro-phenylalanine unit (blue) attached to a central ProM-2 scaffold (red). Esterification of the C terminus renders the inhibitors cell-membrane permeable (40). (B) General (modular) architecture of nonpeptidic, conformationally preorganized inhibitors used in this study. Structural variation (pink) was achieved by replacing the C-terminal ProM-1 unit (green) by ProM-9, ProM-13, ProM-12, ProM-15, or ProM-17 (Table 1).     

Thermal niches of planktonic foraminifera are static throughout glacial–interglacial climate change

Abiotic niche lability reduces extinction risk by allowing species to adapt to changing environmental conditions in situ. In contrast, species with static niches must keep pace with the velocity of climate change as they track suitable habitat. The rate and frequency of niche lability have been studied on human timescales (months to decades) and geological timescales (millions of years), but lability on intermediate timescales (millennia) remains largely uninvestigated. Here, we quantified abiotic niche lability at 8-ka resolution across the last 700 ka of glacial–interglacial climate fluctuations, using the exceptionally well-known fossil record of planktonic foraminifera coupled with Atmosphere–Ocean Global Climate Model reconstructions of paleoclimate. We tracked foraminiferal niches through time along the univariate axis of mean annual temperature, measured both at the sea surface and at species’ depth habitats. Species’ temperature preferences were uncoupled from the global temperature regime, undermining a hypothesis of local adaptation to changing environmental conditions. Furthermore, intraspecific niches were equally similar through time, regardless of climate change magnitude on short timescales (8 ka) and across contrasts of glacial and interglacial extremes. Evolutionary trait models fitted to time series of occupied temperature values supported widespread niche stasis above randomly wandering or directional change. Ecotype explained little variation in species-level differences in niche lability after accounting for evolutionary relatedness. Together, these results suggest that warming and ocean acidification over the next hundreds to thousands of years could redistribute and reduce populations of foraminifera and other calcifying plankton, which are primary components of marine food webs and biogeochemical cycles.

Abiotic niche dynamics determine patterns of community composition over space and regulate trajectories of diversity over time (1). Both niche lability (2, 3) and conservatism (1, 4) have been proposed to spur speciation, and abiotic niche lability has been associated with ecological invasions (5–7) and with reduced risk of extinction during times of climate change (8). Thus, a deeper understanding of species’ propensity for niche stasis versus lability could improve predictions of biodiversity restructuring in response to anthropogenic climate change (9).Stasis in species’ abiotic niches through time has been documented in empirical research, but most such studies have been limited to ecological niche modeling on decadal scales (reviewed in ref. 10) or paleoecological examination on 10⁶ to 10⁷ y scales (5, 11, 12). Since empirical rates of niche change are scarce and difficult to acquire, many studies merely assume that niche evolution occurs at a constant rate along branches of a phylogeny (2, 3, 6, 7). Niche dynamics at intermediate timescales of centuries to millennia are particularly poorly documented (10), and studies at this meso scale have been restricted to terrestrial systems (e.g., refs. 13–15) or to comparisons between the present day and the single historical time step of the Last Glacial Maximum, ∼21 ka (16–20). Quantifying the rate and relative frequency of niche change in marine species over timescales of 10² to 10⁵ years is important, however, because species will adapt or go extinct in response to anthropogenic ocean changes over this timescale (21).Here, we investigated climatic niche lability from the rich sedimentary archive of global planktonic foraminifera across the last 700 ka of glacial–interglacial cycles at 8-ka resolution. Planktonic foraminifera (Protista) construct “shells” (tests) of calcite, thereby sequestering carbon and recording an isotopic signature of past ocean conditions. Tests readily accumulate over large expanses of the seafloor. Consequently, the fossil record of foraminifera—arguably “the best fossil record on Earth” (22)—affords an exceptionally high-resolution view into past species distributions. This detailed record fuels studies of biostratigraphy, paleoclimatology, and paleoecology (20, 22–25). Moreover, the complete species diversity of planktonic foraminifera has been described for the Plio–Pleistocene, with good agreement between morphological and molecular phylogenies (22, 25–27). Although some have speculated that foraminifera competitively exclude each other (24), recent work found that planktonic foraminifera species seldom restrict each other’s distributions (28). Presumably, therefore, species occupy the full envelope of existing environmental conditions within their tolerance limits, and geographic distributions are determined almost entirely by physical ocean conditions.We developed five analyses to investigate the degree of abiotic niche lability in foraminifera. All methods examined the univariate niche axis of temperature, which is the single most important explanatory variable in regard to geographic distributions of foraminifera (20, 29–32) and is a climate-related stressor and extinction driver for diverse marine fauna across timescales (33, 34). The adaptive potential of thermal niches has been taken as a key determinant of global community structure and genetic connectance in plankton (35). Primary productivity and other environmental variables, however, may also structure abiotic niches of plankton (36). Our suite of analyses quantified whether and by how much planktonic foraminiferal niches shifted along a temperature axis. First, we correlated time series of species’ thermal optima with global temperature to determine whether species tracked suitable habitat or experienced environmental fluctuations in situ. We then quantified species’ niche dissimilarity between pairs of time bins—either tracking niches across bin boundaries or contrasting niches at climatic extremes of glacial maxima and interglacial thermal peaks. To characterize niche change we applied trait evolution models to time series of temperatures at occupied sites. Lastly, we explored variation in intraspecific niche lability among ecotypes while accounting for phylogenetic relatedness. SI Appendix, Table S1 lists the response variable and sample size for each analysis.