Ecology articles within Nature Communications

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  • Article
    | Open Access

    Anthropogenic stressors affect many aspects of marine organismal health. Here, the authors expose surgeonfish to temperature and pesticide stressors and show that the stressors, separately and in combination, have adverse effects on thyroid signaling, which disrupts several sensory systems and important predation defenses.

    • Marc Besson
    • , William E. Feeney
    •  & David Lecchini

  • Article
    | Open Access

    Non-traditional stable isotopes, such as of calcium, have potential to expand our understanding of ancient diets. Here, Martin et al. use stable calcium isotopes recovered from fossil tooth enamel to compare the dietary ecology of hominins and other primates in the Turkana Basin 2-4 million years ago.

    • Jeremy E. Martin
    • , Théo Tacail
    •  & Vincent Balter

  • Article
    | Open Access

    Differential abundance analysis of microbiome data continues to be challenging due to data complexity. The authors propose a method which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples.

    • Huang Lin
    •  & Shyamal Das Peddada

  • Article
    | Open Access

    The global biodiversity decline might conceal complex local and group-specific trends. Here the authors report a quantitative synthesis of longterm biodiversity trends across Europe, showing how, despite overall increase in biodiversity metric and stability in abundance, trends differ between regions, ecosystem types, and taxa.

    • Francesca Pilotto
    • , Ingolf Kühn
    •  & Peter Haase

  • Article
    | Open Access

    Little is known about gene expression of organisms in the deep sea, partially owing to constraints on sampling these organisms in situ. Here the authors circumvent this problem, fixing tissue of a deep-sea mussel at 1,688 m in depth, and later analyzing transcriptomes to reveal gene expression patterns showing tidal oscillations.

    • Audrey M. Mat
    • , Jozée Sarrazin
    •  & Marjolaine Matabos

  • Article
    | Open Access

    The authors of this study compile data on spatial and temporal dynamics of surface water bodies across China, covering a time span from 1989 – 2016. The study describes hot-spot areas with strongly decreasing trends in surface water area and terrestrial water storage in North China and discusses implications of water resources and security in China.

    • Xinxin Wang
    • , Xiangming Xiao
    •  & Bo Li

  • Article
    | Open Access

    Roads are widespread and can impact ecological communities. Cooke et al. use data for 75 bird species across Great Britain to show that common species are disproportionately abundant near roads, whereas rarer, smaller-bodied and migrant species are more likely to be negatively associated with roads.

    • Sophia C. Cooke
    • , Andrew Balmford
    •  & Alison Johnston

  • Article
    | Open Access

    The dynamics of ecological communities depends on interactions between species as well as those between species and their environment, however the effects of the latter are poorly understood. Here, Yeakel et al. reveal how species that modify their environment (ecosystem engineers) impact community dynamics and the risk of extinction.

    • Justin D. Yeakel
    • , Mathias M. Pires
    •  & Thilo Gross

  • Article
    | Open Access

    Different aspects of biodiversity may not necessarily converge in their response to climate change. Here, the authors investigate 25-year shifts in taxonomic, functional and phylogenetic diversity of tropical forests along a spatial climate gradient in West Africa, showing that drier forests are less stable than wetter forests.

    • Jesús Aguirre-Gutiérrez
    • , Yadvinder Malhi
    •  & Imma Oliveras

  • Article
    | Open Access

    Here, the authors present a theoretical framework based on community ecology and network science to investigate the efficacy of fecal microbiota transplantation in conditions associated with a disrupted gut microbiota, using the recurrent Clostridioides difficile infection as a prototype disease.

    • Yandong Xiao
    • , Marco Tulio Angulo
    •  & Yang-Yu Liu

  • Article
    | Open Access

    Massive stores of carbon and nutrients in permafrost could be released by global warming. Here the authors show that though warming across the Tibetan alpine permafrost region accelerates nitrogen liberation, contrary to expectations the elevated nutrients do not alleviate plant nitrogen limitation.

    • Dan Kou
    • , Guibiao Yang
    •  & Yuanhe Yang

  • Article
    | Open Access

    There is mixed evidence for how temperature affects diversification rates. Here, authors use a supermatrix of nearly 20,000 rosid species, comprising almost a quarter of flowering plants, to show that tropical groups are older and speciated twice as slowly as their counterparts from cooler climates.

    • Miao Sun
    • , Ryan A. Folk
    •  & Robert P. Guralnick

  • Article
    | Open Access

    Phenotypic robustness to environmental variation is seemingly at odds with evolvability. Here, the authors analyze carotenoid use and accommodation in feather development across a recent avian range expansion and show that cooption of a stress-buffering mechanism can reconcile robustness and evolvability.

    • Ahva L. Potticary
    • , Erin S. Morrison
    •  & Alexander V. Badyaev

  • Article
    | Open Access

    Understanding why certain alien species become naturalized can shed light on biological invasion patterns. In this global analysis on thousands of taxa, van Kleunen and colleagues show that plant species of economic use are more likely to become naturalized, and that this underlies geographic patterns and phylogenetic signals in naturalization

    • Mark van Kleunen
    • , Xinyi Xu
    •  & Trevor S. Fristoe

  • Article
    | Open Access

    Terrestrial carbon uptake as high inter-annual variability which can be used to help understand future responses to climate change. Here the authors’ modeling reveals a large portion of this variability is driven by human land use changes and management, and not captured by other models.

    • Chao Yue
    • , Philippe Ciais
    •  & Alexander A. Nassikas

  • Article
    | Open Access

    Habitat complexity influences the sensory ecology of predator-prey interactions. Here, the authors show that habitat complexity also affects the use of different decision-making paradigms, namely habit- and plan-based action selection. Simulations across habitat types show that only savanna-like terrestrial habitats favor planning during visually-guided predator evasion, while aquatic and simple terrestrial habitats do not.

    • Ugurcan Mugan
    •  & Malcolm A. MacIver

  • Article
    | Open Access

    It is unclear whether rapid global change will lead to unexpected trait combinations. In this global meta-analysis on vascular plants, Cui et al. show that, although within-species responses do not always follow the leaf economic spectrum, the slopes of interspecific trait relationships are robust to rapid environmental change.

    • Erqian Cui
    • , Ensheng Weng
    •  & Jianyang Xia

  • Article
    | Open Access

    The ecological niche of host-associated microbes is defined by both abiotic and biotic dimensions. Here the authors analyse published data on fungal and oomycete pathogens of plants, demonstrating that specialization can evolve independently on abiotic and biotic axes and that interactions with host plants reduce thermal niche breadth.

    • Thomas M. Chaloner
    • , Sarah J. Gurr
    •  & Daniel P. Bebber

  • Article
    | Open Access

    Fire is an important component of many African ecosystems, but prediction of fire activity is challenging. Here, the authors use a statistical framework to assess the seasonal environmental drivers of African fire, which allow for a better prediction of fire activity.

    • Yan Yu
    • , Jiafu Mao
    •  & Yaoping Wang

  • Article
    | Open Access

    Safeguarding protected areas from invasive species is recognised as a global conservation objective. Here, Liu et al. analyse the occurrence of terrestrial alien animal invaders in protected areas and potential drivers globally, suggesting an impending risk for uninvaded protected areas in absence of preventive actions.

    • Xuan Liu
    • , Tim M. Blackburn
    •  & Yiming Li

  • Article
    | Open Access

    Understanding why many species ranges are contracting while others are stable or expanding is important to inform conservation in an increasingly human-modified world. Here, Pacifici and colleagues investigate changes in the ranges of 204 mammals, showing that human factors mostly explain range contractions while life history explains both contraction and expansion.

    • Michela Pacifici
    • , Carlo Rondinini
    •  & Moreno Di Marco

  • Article
    | Open Access

    The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.

    • Frederik V. Seersholm
    • , Daniel J. Werndly
    •  & Michael Bunce

  • Article
    | Open Access

    Seasonal influenza epidemics vary in timing and size, but the causes of the variation remain unclear. Here, the authors analyse a 15-year city-level data set, and find that fluctuations in climatic factors do not predict onset timing, and that while antigenic change does not have a consistent effect on epidemic size, the timing of onset and heterosubtypic competition do.

    • Edward K. S. Lam
    • , Dylan H. Morris
    •  & Colin A. Russell

  • Article
    | Open Access

    Parasitic interactions are difficult to document in the fossil record. Here, Zhang et al. analyze a large population of a Cambrian brachiopod and show it was frequently encrusted by tubes aligned to its feeding currents and that encrustation was associated with reduced biomass, suggesting a fitness cost.

    • Zhifei Zhang
    • , Luke C. Strotz
    •  & Glenn A. Brock

  • Article
    | Open Access

    Biology can profoundly influence the planet’s climate, but over Earth’s long history these effects are poorly constrained. Here the authors show that on early Earth, the evolution of microbes producing and consuming methane likely controlled warming and glacial events, and thus Earth’s habitability

    • Boris Sauterey
    • , Benjamin Charnay
    •  & Régis Ferrière

  • Article
    | Open Access

    Environmental change and species diversity could jointly affect the stability of animal communities. Here the authors use citizen science data on bats, birds, and butterflies along urbanization and agricultural intensification gradients in France to show that both environmental change and diversity loss destabilise communities, but in different ways.

    • Théophile Olivier
    • , Elisa Thébault
    •  & Colin Fontaine

  • Article
    | Open Access

    In animal groups, the degree of alignment of individuals could have different benefits and costs for individuals depending on their reliance on private or social information. Here the authors show that in shoals of three-spined sticklebacks, some individuals reach resources faster when groups are disordered, a state which favours reliance on privately acquired information, while other individuals reach resources faster when groups are ordered, allowing them to exploit social information more effectively.

    • Hannah E. A. MacGregor
    • , James E. Herbert-Read
    •  & Christos C. Ioannou

  • Article
    | Open Access

    Both geography and ecology can drive the origins of new species. Siqueira et al. show how geological changes in the structure of Miocene reefs and the concurrent evolution of new feeding strategies combine to explain why coral reefs contain such a diversity of fish species.

    • Alexandre C. Siqueira
    • , Renato A. Morais
    •  & Peter F. Cowman

  • Article
    | Open Access

    Mutualism is typically portrayed as a destabilizing process in community ecology. Here, via a random matrix model that considers species density, the author shows that mutualistic interactions can, in fact, enhance population density at equilibrium and increase community resilience to perturbation.

    • Lewi Stone

  • Article
    | Open Access

    Associations with mycorrhizal fungi can affect the outcome of plant competition in complex ways. Here the authors use a decade-long field survey and two hyphal exclusion experiments to reveal a critical role of underground fungal networks in facilitating seedling growth and fitness of ectomycorrhizal plants but not arbuscular mycorrhizal plants.

    • Minxia Liang
    • , David Johnson
    •  & Xubing Liu

  • Article
    | Open Access

    Extracting causality from time series on natural populations is challenging. Here the authors apply empirical dynamical modeling to 25 years of fish survey data from North Sea fisheries to quantify causal effects of age structure, abundance, and environment on population spatial variability, finding both common and species-specific patterns.

    • Jheng-Yu Wang
    • , Ting-Chun Kuo
    •  & Chih-hao Hsieh

  • Article
    | Open Access

    The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.

    • Nina A. Kamennaya
    • , Kalotina Geraki
    •  & Mikhail V. Zubkov

  • Article
    | Open Access

    It is crucial yet challenging to identify cause-consequence relation in complex dynamical systems where direct causal links can mix with indirect ones. Leng et al. propose a data-driven model-independent method to distinguish direct from indirect causality and test its applicability to real-world data.

    • Siyang Leng
    • , Huanfei Ma
    •  & Luonan Chen

  • Article
    | Open Access

    Here, Pasolli et al. perform a large-scale genome-wide comparative analysis of publicly available and newly sequenced food and human metagenomes to investigate the prevalence and diversity of lactic acid bacteria (LAB), indicating food as a major source of LAB species in the human gut.

    • Edoardo Pasolli
    • , Francesca De Filippis
    •  & Danilo Ercolini

  • Article
    | Open Access

    The drivers of genetic diversity (GD) are poorly understood at the global scale. Here the authors show, for terrestrial mammals, that within-species GD covaries with phylogenetic diversity and is higher in locations with more stable past climates. They also interpolate GD for data-poor locations such as the tropics.

    • Spyros Theodoridis
    • , Damien A. Fordham
    •  & David Nogues-Bravo

  • Article
    | Open Access

    Sensory drive theory posits that selection on sexual signals should depend on the environmental background. Here, Hulse et al. analyze the spatial statistics of body patterning in 10 darter fish species and find a correlation with habitat spatial statistics only for males, consistent with sexual selection via sensory drive.

    • Samuel V. Hulse
    • , Julien P. Renoult
    •  & Tamra C. Mendelson

  • Article
    | Open Access

    Density-dependence is rarely accounted for in plant-plant facilitation studies. Here the authors develop a framework that incorporates density-dependence in the stress-gradient hypothesis, and test it first through modeling and then empirically on Arabidopsis thaliana along salt stress gradients.

    • Ruichang Zhang
    •  & Katja Tielbörger

  • Article
    | Open Access

    Warming is expected to increase C sink capacity in high-latitude ecosystems, but plant-herbivore interactions could moderate or offset this effect. Here, Silfver and colleagues test individual and interactive effects of warming and insect herbivory in a field experiment in Subarctic forest, showing that even low intensity insect herbivory strongly reduces C sink potential.

    • Tarja Silfver
    • , Lauri Heiskanen
    •  & Juha Mikola

  • Article
    | Open Access

    Lake fisheries are vulnerable to environmental changes. Here, Kao et al. develop a Bayesian networks model to analyze time-series data from 31 major fisheries lake across five continents, showing that fish catches can respond either positively or negatively to climate and land-use changes.

    • Yu-Chun Kao
    • , Mark W. Rogers
    •  & Joelle D. Young

  • Article
    | Open Access

    Snow algae bloom along the coast of Antarctica and are likely to be biogeochemically important. Here, the authors produced the first map of such blooms, show that they are driven by warmer temperatures and proximity to birds and mammals, and are likely to increase given projected climate changes.

    • Andrew Gray
    • , Monika Krolikowski
    •  & Matthew P. Davey

  • Article
    | Open Access

    Key events in human evolution are thought to have occurred between 3 and 2.5 Ma, but the fossil record of this period is sparse. Here, Alemseged et al. report a new fossil site from this period, Mille-Logya, Ethiopia, and characterize the geology, basin evolution and fauna, including specimens of Homo.

    • Zeresenay Alemseged
    • , Jonathan G. Wynn
    •  & Joseph Mohan

  • Article
    | Open Access

    The causes of the Upper Pleistocene megafauna extinction in Australia and New Guinea are debated, but fossil data are lacking for much of this region. Here, Hocknull and colleagues report a new, diverse megafauna assemblage from north-eastern Australia that persisted until ~40,000 years ago.

    • Scott A. Hocknull
    • , Richard Lewis
    •  & Rochelle A. Lawrence

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