搜索结果：Ecology letters

Z. Tao, K. Zhang, R.M. Callaway, E. Siemann, Y. Liu, and W. Huang, "Native Plant Diversity Generates Microbial Legacies That Either Promote or Suppress Non-Natives, Depending on Drought History," Ecology Letters 27, no. 9 (2024): e14504, https://doi.org/10.1111/ele.14504. The above article, published online on 2 October 2024 in Wiley Online Library (http://onlinelibrary.wiley.com/), has been retracted by agreement between the journal Editor-in-Chief, Peter H. Thrall; and John Wiley & Sons Ltd. Concerns about the data were raised by one of the journal editors. Following publication, the editors identified unusual repetitive patterns in the data underlying the study. The editors concluded that the patterns, identified using common statistical analysis tools, were unlikely to have occurred by chance from a typical environmental data collection effort. When asked about the concerns, the authors shared some raw data but were unable to provide a satisfactory explanation to the editors for the patterns in the published data that the editors could not reconcile with the study's conclusions. When later presented with the possibility of retraction and a draft retraction statement, the authors disagreed strongly and provided a detailed rebuttal of the editors' assessment. They argued in part that the software tools the editors used to identify the duplication patterns had not been peer reviewed or otherwise validated. As part of an extensive investigation of the authors' rebuttal claims, the publisher consulted an anonymous and independent subject matter expert (SME), who confirmed the findings of the editors and noted that the repetitive patterns observed in the underlying data were inconsistent with the reliability required to support the article's conclusions. As a result of the post-publication review by the SME, the editors affirm that they have lost confidence in the results and conclusions. In line with the journal's editorial policies, the editors determined that unresolved concerns regarding data reliability warranted retraction. The authors disagree with the retraction.

Accurate prediction of community assembly is a central goal in ecology but is challenging because assembly is governed by numerous mechanisms. Few theoretical models explicitly incorporate or test multiple mechanisms at once. We empirically tested the predictive performance of a plant community assembly model built using all possible combinations of four 'mechanisms' (soil resource competition, dispersal and colonisation, spatiotemporal niche differentiation, population growth rates) and 11 underlying 'attributes' based on measured traits (e.g., fecundity, phenology). The full model accurately predicted out-of-sample biomass observations of five grasses sown in mixture along a soil nitrogen gradient (overall R2 = 0.65). Alternative model variants, parameterised using subsets of the mechanisms and their nested attributes, still retained high explanatory power if the model included at least three of the four mechanisms. Our results suggest that plant community composition is determined by simultaneous effects of multiple mechanisms, and simpler theories have much lower predictive abilities.

The storage effect is a general explanation for ecological coexistence, wherein different species specialise on different states of a fluctuating environment, for example, hot versus cold years. Despite the storage effect's prominence in theoretical ecology, we lack evidence on whether it maintains biodiversity in nature. Here, we examine five storage effect pathways in a community of 11 coral species from the Great Barrier Reef, using detailed size-structured demographic data collected over 5 years. We parameterize integral projection models, simulate coral communities, and quantify coexistence mechanisms through Modern Coexistence Theory. Fluctuations in survival and fecundity promote coexistence via the storage effect, but this stabilising mechanism is typically small compared to fitness differences. Despite exhibiting prerequisites for strong temporal niche partitioning, the storage effect cannot explain the coexistence of many species. Diversity maintenance likely requires large net contributions from other mechanisms, such as specialist natural enemies or spatial heterogeneity coupled with source-sink dynamics.

Bacteria exhibit extraordinary evolutionary and ecological diversity. They range from dominant, well-characterized phyla to rare lineages that are known only through environmental sequencing. This chapter reviews four key bacterial phyla, including Pseudomonadota, Bacillota, Actinomycetota, and Bacteroidota. These phyla are widely distributed, metabolically versatile, and play a central role in ecosystem functioning and human health. We discuss unique phyla within the PVC superphylum (Planctomycetota, Verrucomicrobiota, Chlamydiota) for their unusual cell biology, compartmentalization, and host associations. We also highlight hyperthermophilic phyla, such as Thermotogota, Aquificota, and Thermodesulfobacteriota, that thrive in geothermal ecosystems and drive sulfur and carbon cycling. We consider less-cultivated lineages, including Deinococcota, Acidobacteriota, Nitrospirota, Fusobacteriota, Fibrobacterota, Synergistota, Deferribacterota, and Chrysiogenota, in terms of their ecological niches, metabolic specializations, and roles in biogeochemical cycles, symbiosis, and disease. Collectively, these examples demonstrate the remarkable metabolic flexibility and ecological impact of bacteria, ranging from host-associated commensals and pathogens to free-living autotrophs in extreme environments. Despite advances in genomics and cultivation-independent methods, vast portions of bacterial diversity remain uncultured and poorly understood. Continued exploration of both dominant phyla and rare lineages promises to refine bacterial taxonomy, expand our understanding of microbial evolution, and reveal novel metabolic pathways with implications for ecology, medicine, and biotechnology.

The niche concept is central to ecology, evolution, and conservation biology. To assess resource dynamics in biological communities, the most widely used niche metrics are niche breadth and niche overlap. Colwell and Futuyma (1971) were the first to propose niche metrics that incorporated resource distinctness. In their framework, niche breadth and overlap are calculated using either a relative weighting factor d j or an absolute weighting factor δ j . Hanski (1978) later introduced an alternative weighting factor δ j ∗ , which accounts for both the quality and quantity of resource states in niche calculations. However, metrics based on d j , δ j and δ j ∗ have inherent mathematical and conceptual limitations. To overcome these issues, the present study introduces modified forms of these factors ( e d j , e δ j and e δ j ∗ ) and evaluates their performance using eight hypothetical and one empirical (ecological) resource matrix. The findings indicate that niche metrics incorporating the e d j factor represent the most coherent and biologically meaningful option.

Understanding the effects of climate change on ecological communities has been limited by a lack of general theory for how temperature affects competition. To fill this knowledge gap, we integrated Modern Coexistence Theory and the Metabolic Theory of Ecology by incorporating empirically derived temperature sensitivities into Modern Coexistence Theory's central model. We then simulated warming in consumer-resource systems and found that warming reduced both niche and fitness differences, making species more ecologically similar and competitive interactions more neutral. The greatest shifts in competition occurred when temperature sensitivities among species were highly asymmetrical. Effects of warming on competition via niche differences were comparable to those on fitness differences, suggesting that the emphasis on vital rates in global change research may overlook key biodiversity drivers. This general theory expands the domains of two prominent ecological theories and provides predictions for how warming may alter competition even in benign regions of species' thermal niches.

Tree species richness-productivity relationships (SPRs) at community level are generally positive but can weaken at individual levels due to increased competition. Using 12 years of growth data from a large forest biodiversity experiment, we examined effects of neighbourhood tree species richness, basal area, and niche differences on focal tree growth over time. As stands aged, the effect of greater neighbourhood basal area in more species-rich neighbourhoods on focal tree growth shifted from positive to negative, but this negative effect was offset by increasingly positive effects arising from greater niche differentiation between focal trees and their neighbours. Focal trees with acquisitive traits showed stronger growth responses to neighbourhood competition and niche difference; while the responses to neighbourhood richness were more positive in dry than in wet years. Our findings suggest that larger niche differences can balance increased competition in more species-rich forest stands, thus allowing these stands to maintain a greater total biomass than less diverse forest stands.

Animals must decode environmental information to make adaptive decisions. In passive dispersers, for whom only departure timing is under control, the mechanisms of take-off remain poorly understood. Using experimental evolution, we tested how niche breadth modulates passive dispersal in phytophagous mites by exposing specialist and generalist lineages to host-derived kairomones. Dispersal was highly context-dependent. Generalists exhibited higher baseline dispersal and increased take-off when detecting familiar target cues; however, they were inhibited by complex mixtures of unfamiliar cues (low signal-to-noise ratio). Conversely, specialists primarily tracked current host quality, departing significantly more frequently from unfamiliar plants, yet showing little modulation by target cue identity. These results demonstrate that divergent host specialisation in homogeneous versus heterogeneous environments fundamentally alters the way in which organisms integrate information from current and future habitats to drive dispersal. Niche breadth dictates the baseline propensity for informed departure, while olfactory context provides the final trigger for passive take-off.

Stability selection is the process by which species are lost from a community due to a structural susceptibility to extinction. Stability selection is non-adaptive because it does not lead to the evolution of traits that increase individual fitness. However, stability selection could still drive evolutionary change because the stability of populations is linked to heritable traits. Here we demonstrate both phenomena with a live predator-prey system. We show that the stability properties of a predator-prey pair vary with prey genetics, indicating the potential for differential extinction to influence the genotypic makeup of populations. Second, we show that the loss of unstable predator-prey pairs in subpopulations from the overall population can lead to trait evolution in the aggregate population, providing empirical support for the stability selection mechanism. Our results indicate that community-level processes such as predator-prey interactions can generate eco-evolutionary change at the population scale.

Stenopodidea represents one of the basal lineages within Pleocyemata, yet the male reproductive system (MRS) of this group remains poorly understood, with limited information available regarding its morphology and function. This study provides the first detailed description of the MRS in four stenopodidean shrimp species from two families: Stenopodidae (Stenopus hispidus, S. scutellatus, and S. spinosus) and Spongicolidae (Microprosthema semilaeve). We analyzed the anatomy, histology, and histochemistry of the testes and vas deferens (VD), as well as spermatozoal ultrastructure, and compared these findings with data from more derived pleocyematans to identify potentially ancestral reproductive traits. Our analyses revealed two principal types of secretion in the VD of Stenopus species and three in M. semilaeve, which together form the presumptive spermatophore. Some secretions occur in small amounts and are restricted to specific VD regions. The layers surrounding the spermatozoa are relatively simple, consisting primarily of a sperm cord enclosed by thin secretory layers, suggesting a plesiomorphic reproductive condition in Stenopodidea. Spermatozoa are elliptical and characterized by a large nucleus in direct contact with the cytoplasm, numerous peripheral vesicles, and a large vesicle containing concentric membrane whorls. This structure, previously described as a lamellar body, is reinterpreted here as a putative acrosome vesicle and differs markedly from acrosome vesicles described in other Pleocyemata. Taken together, the comparatively simple spermatophore architecture and distinctive spermatozoa ultrastructure highlight Stenopodidea as an important lineage for understanding the early evolution of reproductive traits in Pleocyemata.

Ocean acidification (OA) driven by increasing atmospheric CO2 is altering marine biodiversity. However, impacts of OA on ecosystem functioning at the community level, including calcification, primary production and nutrient uptake, remain largely unknown. Here, we conducted community transplant experiments at natural CO2 vents to assess how declining pH affects marine community species composition, biomass, and key ecosystem processes over time. Our results indicate that community shifts caused by declining pH lead to decreased biomass and calcification rates, while photosynthesis and nutrient uptake rates increased. By leveraging OA field model systems and in situ measurements of ecosystem functioning, this study provides critical insights into how OA-induced biodiversity loss reshapes the structure and functioning of temperate marine coastal ecosystems.

Collisions with anthropogenic structures kill billions of birds annually, yet risk factors remain poorly understood. Behavioural plasticity generally increases survival in changing environments, but its protective effects may be context-dependent. We assessed the link between behavioural innovation, a proxy for plasticity and collision incidence across 854 species and 259,873 lethal collision events involving buildings, communication towers and wind turbines. Overall, we found a significant positive residual correlation between innovation rate and collision incidence, independent of ecological covariates and phylogenetic relationships. However, this relationship was hazard-specific: innovativeness positively correlated with building collisions but showed no relationship with communication towers or wind turbines. Furthermore, collision risk was driven by food-related rather than technical innovations. Rather than demonstrating a universal mortality cost of cognitive capacity, our results suggest that opportunistic foraging behaviours may create ecological traps in structurally dense environments. Ultimately, behavioural plasticity can drive fitness consequences, but this risk is fundamentally context-dependent.

Quantifying biotic interactions at scale is critical to understanding ecosystem functions, such as plant-pollinator interactions. Here, we demonstrate how woody plant functional traits and vegetation structure gathered with remote sensing can aid in predicting plant-pollinator network indices from fine to broad spatial extents. We analysed 209 tropical plant-pollinator networks, where vegetation characteristics were generated using spectral and LiDAR data. We found that pollination network structures were correlated to plant traits reflective of drought-adaptive strategies and nutrient availability. Networks were predicted to be more nested and less specialised with increasing leaf nitrogen content. Further, relationships between leaf thickness, photosynthetic capacity, and water content indicate that networks may be more modular and less connected under arid, high-light conditions where plants invest in water-conserving tissues yet maintain high photosynthetic rates. Our findings reveal plant functional strategies as underlying environmental mechanisms that structure plant-pollinator networks, paving the way to predict interactions using remote sensing.

Soil fauna regulates litter decomposition and soil organic matter transformation, acting as both litter and microbial feeders. Whether these feeding modes shift along environmental gradients remains unclear. We tested if microbivory increases with decreasing litter quality and in colder climates, both factors limiting detritus digestion by fauna. Using stable isotope composition (δ13C, δ15N) of 7408 soil invertebrate samples from 228 forest sites across temperate to tropical biomes, we determined δ15N values are positively associated with litter C:N ratio and mean annual temperature, indicating a shift from detritivory toward microbivory under low litter quality with additional modulation by climate. In contrast, δ13C values showed no consistent association with litter C:N ratio or climate, reflecting context dependent microbial carbon routing. Our findings highlight litter quality as the primary driver of the detritivory-to-microbivory shift in soil fauna, with implications for predicting changes in climate and plant communities on carbon cycling in terrestrial ecosystems.

Reciprocal effects between plants and soil have been proposed as mechanisms that promote coexistence. However, recent theoretical and empirical works have questioned their role in stabilizing coexistence within multispecies communities. In these systems, soil-mediated indirect interactions may play a pivotal but often overlooked role. We investigate these indirect interactions using an experimental system of two competing shrub species grown in soil conditioned by a mediating third tree species. Tree-induced shifts in soil microbial communities, metabolites and nutrients boost growth in the weak competitor species while reducing germination in the dominant competitor. Simulations demonstrate that these shifts in plant performance are sufficient to stabilize coexistence, producing simulated spatial distributions consistent with those observed in natural communities. Our findings underscore the role of soil effects in driving indirect interactions that sustain coexistence in diverse plant communities, highlighting the importance of indirect but also positive and negative multitrophic interactions in maintaining biodiversity.

Cooperation in public goods is expected to evolve more rapidly in smaller groups than in larger groups because individuals receive a larger share of the benefits, reducing the benefits of freeloading. However, experimental evidence for this hypothesis remains limited to microorganisms, restricting our understanding of the evolution of cooperative traits. Here, we show that in the collectively defending larvae of Neodiprion sertifer, survival against predation is higher in cooperative groups, with benefits of cooperation more pronounced in small groups (5 larvae) than in large groups (20 larvae). Individuals also participate less in collective defence in larger groups, not because of higher life-history costs resulting from increased resource competition but because they adjust their contribution according to group size. These results provide novel empirical evidence that selection for cooperation in collective goods is group size-dependent, promoting cooperation in smaller groups, whereas the relative fitness of freeloaders is higher in larger groups.

Population recovery following environmental stress is known to depend on demographic structure, life-history and evolutionary dynamics. However, it is unclear how traits shaped by sexual selection affect population dynamics and recovery. We examined this by manipulating presence/absence of males expressing either a non-aggressive 'scrambler' phenotype or an aggressive and lethally armed 'fighter' phenotype in soil mite populations of different size. We experimentally altered the male phenotype in populations, subjected them to heat stress, and analysed their population dynamics and recovery. We show that populations with fighter males exhibited (i) reduced population size and stability, (ii) greater decline in response to heat stress in larger populations, (iii) higher rate of growth and (iv) incomplete population recovery. Such reduced population stability and recovery linked with armed and aggressive phenotypes underlines the importance of sexual selection in mediating population dynamics and resilience to environmental change with implications for managing natural populations.

The species-area relationship is a cornerstone of biodiversity theory and conservation. Yet, its temporal stability remains largely untested. Using nearly a century of disjunct vegetation-plot data from the Netherlands, we assess changes in the species-area relationship by constructing species-accumulation curves (SACs). We show that SACs have flattened significantly over time, indicating widespread biodiversity decline driven by habitat degradation and spatial homogenization, even within protected areas. Although grassland biodiversity has rebounded, forest biodiversity continues to decline, suggesting a greater extinction debt. These findings provide unprecedented evidence that biodiversity patterns captured by SACs shift over time. They also reveal a critical limitation of conservation strategies that rely solely on protected area expansion. As global biodiversity goals aim to halt biodiversity loss by 2030, our results emphasise the need for adaptive conservation strategies that integrate area-based protection with large-scale habitat restoration and improved ecosystem management.

The communities of unicellular microbes (bacteria, protists and yeasts) that underpin ecosystems are changing. In warmer conditions, protists tend to shrink, but the consequences of these changes in size are unclear. We show preliminary evidence that warming-mediated declines in cell size observed in protists also apply to bacteria and yeasts. Predicting the consequences of these warming-mediated size declines requires that the relationships between cell size and key functional traits are well-characterised. We show that the critical relationship between unicellular size and energy use-that is, metabolic scaling-has been systematically mis-estimated in the past. Projections of the effects of warming on unicellular respiration change from superlinear to sublinear once the metabolic scaling relationship is updated, with worrying consequences for the biological carbon pump and other ecosystem services. Other size-function scaling relationships (e.g., photosynthesis) are likely to have been similarly mis-estimated. Next, we show that theory on the relationships between size, temperature and demography is more ambivalent than previously recognised, leaving uncertainty as to how warming will alter the dynamics of unicellular populations. Finally, we identify pathways for improving our capacity to predict future changes in unicellular size, and decrease the uncertainty surrounding the consequences of these changes.