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The origin of regular spatial patterns in ecological systems has long fascinated researchers. Turing’s activator–inhibitor principle is considered the central paradigm to explain such patterns. According to this principle, local activation combined with long-range inhibition of growth and survival is an essential prerequisite for pattern formation. Here, we show that the physical principle of phase separation, solely based on density-dependent movement by organisms, represents an alternative class of self-organized pattern formation in ecology. Using experiments with self-organizing mussel beds, we derive an empirical relation between the speed of animal movement and local animal density. By incorporating this relation in a partial differential equation, we demonstrate that this model corresponds mathematically to the well-known Cahn–Hilliard equation for phase separation in physics. Finally, we show that the predicted patterns match those found both in field observations and in our experiments. Our results reveal a principle for ecological self-organization, where phase separation rather than activation and inhibition processes drives spatial pattern formation.

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to reproductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young., This meta-analysis was financed by the grant of the Polish National Science Centre (Narodowe Centrum Nauki) (no. 2017/27/B/NZ8/00465) awarded to Lucyna Hałupka.

There is a vivid debate on the relative importance of local and regional factors in shaping microbial communities, and on whether microbial organisms show a biogeographic signature in their distribution. Taking a metacommunity approach, spatial factors can become important either through dispersal limitation (compare large spatial scales) or mass effects (in case of strongly connected systems). We here analyze two datasets on bacterial communities [characterized by community fingerprinting through denaturing gradient gel electrophoresis (DGGE)] in meso- to eutrophic shallow lakes to investigate the importance of spatial factors at three contrasting scales. Variation partitioning on datasets of both the bacterial communities of 11 shallow lakes that are part of a strongly interconnected and densely packed pond system 2,500 km) shows a strong impact of local environmental factors on bacterial community composition, with a marginal impact of spatial distance. Our results indicate that dispersal is not strongly limiting even at large spatial scales, and that mass effects do not have a strong impact on bacterial communities even in physically connected systems. We suggest that the fast population growth rates of bacteria facilitate efficient species sorting along environmental gradients in bacterial communities over a very broad range of dispersal rates.

Biotic interactions that hierarchically organize ecosystems by driving ecological and evolutionary processes across spatial scales are ubiquitous in our biosphere. Biotic interactions have been extensively studied at local and global scales, but how long-distance, cross-ecosystem interactions at intermediate landscape scales influence the structure, function, and resilience of ecological systems remains poorly understood. We used remote sensing, modeling, and field data to test the hypothesis that the long-distance impact of an invasive species dramatically affects one of the largest tidal flat ecosystems in East Asia. We found that the invasion of exotic cordgrass Spartina alterniflora can produce long-distance effects on native species up to 10 km away, driving decadal coastal ecosystem transitions. The invasive cordgrass at low elevations facilitated the expansion of the native reed Phragmites australis at high elevations, leading to the massive loss and reduced resilience of the iconic Suaeda salsa “Red Beach” marshes at intermediate elevations, largely as a consequence of reduced soil salinity across the landscape. Our results illustrate the complex role that long-distance interactions can play in shaping landscape structure and ecosystem resilience and in bridging the gap between local and global biotic interactions.

Significance Pteropods are abundant aragonitic calcifiers, contributing up to 89% of total pelagic calcification. Because of their delicate shells, they are considered “canaries in the coalmine” to indicate impacts of ocean acidification. Their sensitivity to high CO2 levels and limited fossil record has led to the widely held view that pteropods only became abundant after the PETM. Based on phylogenomic analyses, we show that all major pteropod groups have Cretaceous origins and, hence, they must have survived past perturbations in the Earth’s carbon cycle. Although this suggests that pelagic aragonitic calcifiers have been more resilient to past ocean acidification than currently thought, it is unlikely that pteropods have experienced global change of the current magnitude and speed during their evolutionary history., Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification. Their aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in the Earth’s carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset (2,654 genes) incorporating new data for 21 pteropod species and revised fossil evidence. In agreement with traditional taxonomy, we recovered molecular support for a division between “sea butterflies” (Thecosomata; mucus-web feeders) and “sea angels” (Gymnosomata; active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled, and unshelled groups, diverged in the mid- to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene–Eocene Thermal Maximum (PETM), the closest analog to modern-day ocean acidification and warming. Our findings indicate that planktonic aragonitic calcifiers have shown resilience to perturbations in the Earth’s carbon cycle over evolutionary timescales.

Significance Maternal effect senescence, the decline in offspring quality with increasing maternal age, is common in animals despite its negative impact on fitness. To understand how maternal effect senescence might evolve, we built matrix population models to calculate selection gradients on survival and fertility as functions of maternal age. We estimated the model’s parameters with data from an aquatic invertebrate. The strength of selection eventually declines with age and maternal age, implying that maternal effect senescence could be favored by selection and evolve in the same way as senescence. Our framework can be applied to investigate maternal effect senescence in organisms with diverse life histories and unifies the demographic approaches to age-related and maternal effect senescence., Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate, Brachionus manjavacas (Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness for B. manjavacas and that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.

Significance All plants and animals are associated with communities of viruses and microbes that interact via a suite of metabolites. These components play critical roles in the success of these assemblages; however, the role of individual components (i.e., bacteria, viruses, metabolites) and how these govern ecological interactions between macroorganisms is not understood. This study investigates the role of holobiont components in coral–turf algal interactions. The data demonstrate that an emergent microbiome and metabolome form at the interface between coral and turf algae in competitive interactions. Machine learning analyses show that this emergent community predicts the outcome of these interactions. These results provide insight into rules of community assembly in microbiomes and the roles of holobiont components in mediating ecological interactions., Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral–turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

Diverse forms of cultivation have evolved across the tree of life. Efficient farming requires that the farmer deciphers and actively promotes conditions that increase crop yield. For plant cultivation, this can include evaluating tradeoffs among light, nutrients, and protection against herbivores. It is not understood if, or how, nonhuman farmers evaluate local conditions to increase payoffs. Here, we address this question using an obligate farming mutualism between the ant Philidris nagasau and epiphytic plants in the genus Squamellaria that are cultivated for their nesting sites and floral rewards. We focused on the ants' active fertilization of their crops and their protection against herbivory. We found that ants benefited from cultivating plants in full sun, receiving 7.5-fold more floral food rewards compared to shade-cultivated plants. The higher reward levels correlated with higher levels of crop protection provided by the ants. However, while high-light planting yielded the greatest immediate food rewards, sun-grown crops contained less nitrogen compared to shade-grown crops. This was due to lower nitrogen input from ants feeding on floral rewards instead of insect protein gained from predation. Despite this tradeoff, farming ants optimize crop yield by selectively planting their crops in full sun. Ancestral state reconstructions across this ant-plant clade show that a full-sun farming strategy has existed for millions of years, suggesting that nonhuman farmers have evolved the means to evaluate and balance conflicting crop needs to their own benefit.

Significance Global change threatens the genetic diversity of economically important and foundational ecosystem-building species such as corals. We tested whether cryopreserved coral sperm could be used to transfer genetic diversity among genetically isolated populations of the critically endangered Caribbean elkhorn coral, Acropora palmata. Here we report successful assisted gene flow (AGF) in corals using cryopreserved sperm, yielding the largest living wildlife population ever created from cryopreserved cells. Furthermore, we produced direct evidence that genetically distinct populations of Caribbean coral can interbreed. Thus, we demonstrated that sperm cryopreservation can enable efficient, large-scale AGF in corals. This form of assisted genetic migration can enhance genetic diversity and help critically endangered species adapt to local environments in the face of rapid global change., Assisted gene flow (AGF) is a conservation intervention to accelerate species adaptation to climate change by importing genetic diversity into at-risk populations. Corals exemplify both the need for AGF and its technical challenges; corals have declined in abundance, suffered pervasive reproductive failures, and struggled to adapt to climate change, yet mature corals cannot be easily moved for breeding, and coral gametes lose viability within hours. Here, we report the successful demonstration of AGF in corals using cryopreserved sperm that was frozen for 2 to 10 y. We fertilized Acropora palmata eggs from the western Caribbean (Curaçao) with cryopreserved sperm from genetically distinct populations in the eastern and central Caribbean (Florida and Puerto Rico, respectively). We then confirmed interpopulation parentage in the Curaçao–Florida offspring using 19,696 single-nucleotide polymorphism markers. Thus, we provide evidence of reproductive compatibility of a Caribbean coral across a recognized barrier to gene flow. The 6-mo survival of AGF offspring was 42%, the highest ever achieved in this species, yielding the largest wildlife population ever raised from cryopreserved material. By breeding a critically endangered coral across its range without moving adults, we show that AGF using cryopreservation is a viable conservation tool to increase genetic diversity in threatened marine populations.

Significance Survey data show a large-scale decline in insects. This global decline is often linked to human actions in intensive agricultural areas. To investigate whether this decline has a causal relationship with neonicotinoid insecticides, we performed an outdoor experiment with representative surface water concentrations of the neonicotinoid thiacloprid. We exposed naturally formed aquatic communities to increasing neonicotinoid concentrations and monitored insect emergence during a 3-mo period. We show that increasing neonicotinoid concentrations strongly decreased the abundance and biomass of five major insect orders that together comprised >99% of the 55,574 collected insects as well as the diversity of the most species-rich freshwater family, thus showing a causal relation between insect decline and neonicotinoids., There is an ongoing unprecedented loss in insects, both in terms of richness and biomass. The usage of pesticides, especially neonicotinoid insecticides, has been widely suggested to be a contributor to this decline. However, the risks of neonicotinoids to natural insect populations have remained largely unknown due to a lack of field-realistic experiments. Here, we used an outdoor experiment to determine effects of field-realistic concentrations of the commonly applied neonicotinoid thiacloprid on the emergence of naturally assembled aquatic insect populations. Following application, all major orders of emerging aquatic insects (Coleoptera, Diptera, Ephemeroptera, Odonata, and Trichoptera) declined strongly in both abundance and biomass. At the highest concentration (10 µg/L), emergence of most orders was nearly absent. Diversity of the most species-rich family, Chironomidae, decreased by 50% at more commonly observed concentrations (1 µg/L) and was generally reduced to a single species at the highest concentration. Our experimental findings thereby showcase a causal link of neonicotinoids and the ongoing insect decline. Given the urgency of the insect decline, our results highlight the need to reconsider the mass usage of neonicotinoids to preserve freshwater insects as well as the life and services depending on them.

Eens et al.(1) question (i) whether our data are sufficient to state that low-frequency songs are sexually selected and (ii) whether anthropogenic noise really affects male–female communication, as males may just get closer to make their songs more audible.

Significance Although viruses are well-characterized regulators of eukaryotic algae, little is known about those infecting unicellular predators in oceans. We report the largest marine virus genome yet discovered, found in a wild predatory choanoflagellate sorted away from other Pacific microbes and pursued using integration of cultivation-independent and laboratory methods. The giant virus encodes nearly 900 proteins, many unlike known proteins, others related to cellular metabolism and organic matter degradation, and 3 type-1 rhodopsins. The viral rhodopsin that is most abundant in ocean metagenomes, and also present in an algal virus, pumps protons when illuminated, akin to cellular rhodopsins that generate a proton-motive force. Giant viruses likely provision multiple host species with photoheterotrophic capacities, including predatory unicellular relatives of animals., Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae. Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions., This work was supported by Agence Nationale de la Recherche ANR-2010-JCJC-1608 and ANR-14-CE19-0014 (to D.P.); Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI project, ANR-10-INBS-08); and by King Abdullah University of Science and Technology BAS/1/1062-01-01 (to H.H.). The Institute of Plant Sciences Paris-Saclay benefits from the support of the LabEx Saclay Plant Sciences (ANR-10-LABX-0040-SPS). M.A.-T. was supported by a Humboldt-Capes fellowship.

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.

Significance Urban, Westernized populations suffer extensively from noncommunicable diseases such as allergies. However, the overlapping effects of living environment and lifestyle are difficult to separate. Intriguingly, also our fellow animals, dogs, suffer from analogous diseases. Therefore, we suggest that pet dogs, sharing their environment and lifestyle with humans but having a comparatively simple life, provide a valuable model for understanding origins of noncommunicable diseases. We show that living environment and lifestyle concurrently, but still independently, shape both the skin microbiota and the risk of allergic disease in dogs. Urbanized lifestyle, featuring restricted animal contacts and small family size, is allergy promoting both in rural and urban dogs. Hence, both environment and lifestyle seem to influence the microbiota and, probably consequently, immune tolerance., A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations.

Significance Coral reef taxa produce a diverse array of molecules, some of which are important pharmaceuticals. To better understand how molecular diversity is generated on coral reefs, tandem mass spectrometry datasets of coral metabolomes were analyzed using a novel approach called meta-mass shift chemical (MeMSChem) profiling. MeMSChem profiling uses the mass differences between molecules in molecular networks to determine how molecules are related. Interestingly, the same molecules gain and lose chemical groups in different ways depending on the taxa it came from, offering a partial explanation for high molecular diversity on coral reefs., Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.g., H2, CH2, COCH2). MeMSChem profiling was used to analyze a publicly available metabolomic dataset of coral, algal, and fungal mat holobionts (i.e., the host and its associated microbes and viruses) sampled from some of Earth’s most remote and pristine coral reefs. Each type of holobiont had distinct mass shift profiles, even when the analysis was restricted to molecules found in all samples. This result suggests that holobionts modify the same molecules in different ways and offers insights into the generation of molecular diversity. Three genera of stony corals had distinct patterns of molecular relatedness despite their high degree of taxonomic relatedness. MeMSChem profiles also partially differentiated between individuals, suggesting that every coral reef holobiont is a potential source of novel chemical diversity.

The structure of the competitive network is an important driver of biodiversity and coexistence in natural communities. In addition to determining which species survive, the nature and intensity of competitive interactions within the network also affect the growth, productivity, and abundances of those individuals that persist. As such, the competitive network structure may likewise play an important role in determining community-level functioning by capturing the net costs of competition. Here, using an experimental system comprising 18 wood decay basidiomycete fungi, we test this possibility by quantifying the links among competitive network structure, species diversity, and community function. We show that species diversity alone has negligible impacts on community functioning, but that diversity interacts with two key properties of the competitive network—competitive intransitivity and average competitive ability—to ultimately shape biomass production, respiration, and carbon use efficiency. Most notably, highly intransitive communities comprising weak competitors exhibited a positive diversity–function relationship, whereas weakly intransitive communities comprising strong competitors exhibited a negative relationship. These findings demonstrate that competitive network structure can be an important determinant of community-level functioning, capturing a gradient from weakly to strongly competitive communities. Our research suggests that the competitive network may therefore act as a unifying link between diversity and function, providing key insight as to how and when losses in biodiversity will impact ecosystem function.

Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of principle. We run regressions of trait observations for leaf mass per area, stem-specific density, and seed mass from a global database against multiple environmental drivers, making use of findings of global trait convergence. This analysis explained up to 52% of the global variation of traits. Global trait maps, generated by coupling the regression equations to gridded soil and climate maps, showed up to orders of magnitude variation in trait values. Subsequently, nine vegetation types were characterized by the trait combinations that they possess using Gaussian mixture density functions. The trait maps were input to these functions to determine global occurrence probabilities for each vegetation type. We prepared vegetation maps, assuming that the most probable (and thus, most suited) vegetation type at each location will be realized. This fully traits-based vegetation map predicted 42% of the observed vegetation distribution correctly. Our results indicate that a major proportion of the predictive ability of DGVMs with respect to vegetation distribution can be attained by three traits alone if traits like stem-specific density and seed mass are included. We envision that our traits-based approach, our observation-driven trait maps, and our vegetation maps may inspire a new generation of powerful traits-based DGVMs.

Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change.

Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.

The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, non-parametric, and parametric analyses, and rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation (PAR); but the individual responses of each lineage differ to these environmental variables. The models estimate global biogeographic patterns and seasonal variability of cell abundance with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans, and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9±0.1 x1027 and 7.0±0.3 x1026 cells, respectively. Using projections of sea-surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 28 and 14% for Prochlorococcus and Synechococcus, respectively. The changes are geographically uneven but include an increase in areas, where both lineages are currently abundant, an expansion towards higher latitudes, and for Synechococcus, mid-latitude regions with declining abundances. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes even just considering projected future climate conditions. Due to the high abundances and contributions to primary production of Prochlorococcus and Synechococcus, these changes may have large impacts on ocean ecosystems and biogeochemical cycles. Fil: Flombaum, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera; Argentina. University of California. Department of a Earth System Science; Estados Unidos. Instituto Franco-Argentino sobre Estudios del Clima y sus Impactos; Argentina Fil: Gallegos, José L.. University of California. Department of a Earth System Science; Estados Unidos Fil: Gordillo, Rodolfo A.. University of California. Department of a Earth System Science; Estados Unidos Fil: Rincon, José. University of California. Department of a Earth System Science; Estados Unidos Fil: Zabala, Lina L.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera; Argentina. Instituto Franco-Argentino sobre Estudios del Clima y sus Impactos; Argentina Fil: Jiao, Nianzhi. Xiamen University. State Key Lab for Marine Environmental Sciences. Institute of Microbes and Ecosphere; República de China Fil: Karl, David M.. University of Hawaii. Center for Microbial Oceanography: Research and Education; Estados Unidos Fil: Li, William K. W.. Bedford Institute of Oceanography. Fisheries and Oceans Canada; Canadá Fil: Lomas, Michael W.. Bigelow Laboratory for Ocean Sciences; Estados Unidos Fil: Veneziano, Daniele. Massachusetts Institute of Technology. Department of Civil and Environmental Engineering; Estados Unidos Fil: Vera, Carolina Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera; Argentina. Instituto Franco-Argentino sobre Estudios del Clima y sus Impactos; Argentina Fil: Vrugt, Jasper A.. University of California. Department of a Earth System Science; Estados Unidos. University of California. Departament of Civil Engineering; Estados Unidos Fil: Martiny, Adam C.. University of California. Department of a Earth System Science; Estados Unidos. University of California. Ecology and Evolutionary Biology; Estados Unidos

Ecosystems can show sudden and persistent changes in state despite only incremental changes in drivers. Such critical transitions are difficult to predict, because the state of the system often shows little change before the transition. Early-warning indicators (EWIs) are hypothesized to signal the loss of system resilience and have been shown to precede critical transitions in theoretical models, paleo-climate time series, and in laboratory as well as whole lake experiments. The generalizability of EWIs for detecting critical transitions in empirical time series of natural aquatic ecosystems remains largely untested, however. Here we assessed four commonly used EWIs on long-term datasets of five freshwater ecosystems that have experienced sudden, persistent transitions and for which the relevant ecological mechanisms and drivers are well understood. These case studies were categorized by three mechanisms that can generate critical transitions between alternative states: competition, trophic cascade, and intraguild predation. Although EWIs could be detected in most of the case studies, agreement among the four indicators was low. In some cases, EWIs were detected considerably ahead of the transition. Nonetheless, our results show that at present, EWIs do not provide reliable and consistent signals of impending critical transitions despite using some of the best routinely monitored freshwater ecosystems. Our analysis strongly suggests that a priori knowledge of the underlying mechanisms driving ecosystem transitions is necessary to identify relevant state variables for successfully monitoring EWIs.

Size-selective mortality inevitably leads to a decrease in population density and exerts a direct negative effect on targeted size classes. But density and population size structure are also shaped by food-dependent processes, such as individual growth, maturation, and reproduction. Mortality relaxes competition and thereby alters the dynamic interplay among these processes. As shown by the recently developed size-structured theory, which can account for food-dependent individual performance, this altered interplay can lead to overcompensatory responses in size class–specific biomass, with increasing mortality. We experimentally tested this theory by subjecting laboratory fish populations to a range of size-selective mortality rates. Overall, the results were in agreement with theoretical predictions. Biomass of the juvenile size class increased above control levels at intermediate adult mortality rates and thereafter declined at high mortality rates. Juvenile biomass also increased when juveniles themselves were subjected to intermediate mortality rates. Biomass in other size classes decreased with mortality. Such biomass overcompensation can have wide-ranging implications for communities and food webs, including a high sensitivity of top predators to irreversible catastrophic collapses, the establishment of alternative stable community states, and the promotion of coexistence and biodiversity.

The past was a world of giants, with abundant whales in the sea and large animals roaming the land. However, that world came to an end following massive late-Quaternary megafauna extinctions on land and widespread population reductions in great whale populations over the past few centuries. These losses are likely to have had important consequences for broad-scale nutrient cycling, because recent literature suggests that large animals disproportionately drive nutrient movement. We estimate that the capacity of animals to move nutrients away from concentration patches has decreased to about 8% of the preextinction value on land and about 5% of historic values in oceans. For phosphorus (P), a key nutrient, upward movement in the ocean by marine mammals is about 23% of its former capacity (previously about 340 million kg of P per year). Movements by seabirds and anadromous fish provide important transfer of nutrients from the sea to land, totalling ∼150 million kg of P per year globally in the past, a transfer that has declined to less than 4% of this value as a result of the decimation of seabird colonies and anadromous fish populations. We propose that in the past, marine mammals, seabirds, anadromous fish, and terrestrial animals likely formed an interlinked system recycling nutrients from the ocean depths to the continental interiors, with marine mammals moving nutrients from the deep sea to surface waters, seabirds and anadromous fish moving nutrients from the ocean to land, and large animals moving nutrients away from hotspots into the continental interior.

Trophic cascades have been a central paradigm in explaining the structure of ecological communities but have been demonstrated mainly through comparative studies or experimental manipulations. In contrast, evidence for shifts in trophic cascades caused by intrinsically driven population dynamics is meager. By using empirical data of a cannibalistic fish population covering a 10-year period and a size-structured population model, we show the occurrence of a dynamic trophic cascade in a lake ecosystem, in which the community over time alternates between two different configurations. The intrinsically driven change in the size structure of the fish population from a dominance of stunted individuals to a dominance of gigantic cannibals among adult individuals is the driving force behind distinct abundance switches observed in zooplankton and phytoplankton. The presence of the phase with gigantic cannibals depends critically on the energy they extract from their victims, allowing strong reproduction for a number of years.

Catastrophic population collapses such as observed in many exploited fish populations have been argued to result from depensatory growth mechanisms (i.e., reduced reproductive success at low population densities, also known as Allee effect). Empirical support for depensation from population-level data is, however, hard to obtain and inconclusive. Using a size-structured, individual-based model we show that catastrophic population collapses may nonetheless be an intrinsic property of many communities, because of two general aspects of individual life history: size- and food-dependent individual growth and individual mortality decreasing with body size. Positive density dependence, characteristic for depensatory growth mechanisms and catastrophic behavior, results as a direct and robust consequence of the interplay between these individual life-history traits, which are commonly found in many species.

Many species expanded their geographic ranges from core “refugium” populations when the global climate warmed after the Pleistocene. The bottlenecks that occur during such range expansions diminish genetic variation in marginal populations, rendering them less responsive to selection. Here, we show that range expansion also strongly depletes inbreeding depression. We compared inbreeding depression among 20 populations across the expanded range of a common European plant, and found that marginal populations had greatly reduced inbreeding depression. Similar patterns were also revealed by multilocus computer simulations. Low inbreeding depression is predicted to ease conditions for the evolution of self-fertilization, and selfing is known to be particularly frequent in marginal populations. Therefore, our findings expose a remarkable aspect of evolution at range margins, where a history of expansion can reverse the direction of selection on the mating system, providing a parsimonious explanation for the high incidence of selfing in marginal populations.

Recent studies have reported that independent adaptive radiations can lead to identical ecomorphs. Our phylogenetic analyses of nuclear and mitochondrial DNA sequences here indicate that a major radiation of ranid frogs on Madagascar produced morphological, physiological, and developmental characters that are remarkably similar to those that independently evolved on the Indian subcontinent. We demonstrate further that, in several cases, adult and larval stages each evolved sets of characters which are not only convergent between independent lineages, but also allowed both developmental stages to invade the same adaptive zone. It is likely that such covariations are produced by similar selective pressures on independent larval and adult characters rather than by genetic or functional linkage. We briefly discuss why larval/adult covariations might constitute an important evolutionary phenomenon in species for which more than one developmental stage potentially has access to multiple environmental conditions.