Ecological modelling articles within Nature Communications

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  • Article
    | Open Access

    Human-driven movements and extinctions of species have made plant communities across biomes more homogenous. Here the authors quantify plant vascular species and phylogenetic homogenization across the globe, finding that non-native species naturalisations have been a major driver.

    • Barnabas H. Daru
    • , T. Jonathan Davies
    •  & Charles C. Davis

  • Article
    | Open Access

    The ongoing disproportionate increases in temperature and precipitation in the Alaska may alter the latitudinal gradients in greenup and snowmelt timings as well as carbon dynamics. With a broad range of datasets and model results, the authors show that the carbon response to early greenup or delayed snowmelt varies greatly depending upon local climatic limits.

    • JiHyun Kim
    • , Yeonjoo Kim
    •  & Crystal L. Schaaf

  • Article
    | Open Access

    Root-mycorrhizal interactions could help explain the heterogeneity of plant responses to CO2 fertilisation and nutrient availability. Here the authors combine tree-ring and metagenomic data to reveal that tree growth responses to increasing CO2 along a soil nutrient gradient depend on the nitrogen foraging traits of ectomycorrhizal fungi.

    • Peter T. Pellitier
    • , Inés Ibáñez
    •  & Kirk Acharya

  • Article
    | Open Access

    The fraction of leaf nitrogen allocated to RuBisCO indicates differing nitrogen use strategies of plants and varies considerably. Here the authors show that this variation is largely driven by leaf thickness and phosphorus content with light intensity, atmospheric dryness and soil pH also having considerable influence.

    • Xiangzhong Luo
    • , Trevor F. Keenan
    •  & Yao Zhang

  • Article
    | Open Access

    Change in ecological communities can be driven by extrinsic forces, but the degree to which intrinsic population dynamics drive turnover has remained unclear. Here the authors use metacommunity modelling to show that biodiversity change previously attributed to external drivers can be explained based on intrinsic ecosystem dynamics.

    • Jacob D. O’Sullivan
    • , J. Christopher D. Terry
    •  & Axel G. Rossberg

  • Article
    | Open Access

    Microbiomes designed with predictable functions could enable broad applications in health, agriculture and bioprocessing. Here the authors use a model-guided approach to design diverse synthetic human gut communities for production of the health-relevant metabolite butyrate.

    • Ryan L. Clark
    • , Bryce M. Connors
    •  & Ophelia S. Venturelli

  • Article
    | Open Access

    Anthropogenic losses of animal pollinators threaten ecosystem functioning. Here the authors report a global analysis showing geographically varied yet widespread declines of pollinator diversity and abundance with land use intensification, particularly in tropical biomes.

    • Joseph Millard
    • , Charlotte L. Outhwaite
    •  & Tim Newbold

  • Article
    | Open Access

    Advanced ecological modelling reveals how Sahul (Australia and New Guinea) was first peopled, suggesting the most probable routes and surprisingly rapid early settlement of this continent by anatomically modern humans starting 50,000 to 75,000 years ago.

    • Corey J. A. Bradshaw
    • , Kasih Norman
    •  & Frédérik Saltré

  • Article
    | Open Access

    Whether invasive species must first establish in conditions within their native climatic niche before spreading remains largely untested. This study presents the Niche Margin Index for estimating climatic niche-matching of alien mammal species to a particular site, which could be used to help predict the success of invasions.

    • Olivier Broennimann
    • , Blaise Petitpierre
    •  & Antoine Guisan

  • Article
    | Open Access

    Climate change is a threat to global biodiversity, but the potential effects on freshwater fishes have not been well studied. Here the authors model future flow and water temperature extremes and predict that increases in water temperature in particular will pose serious threats to freshwater fishes

    • Valerio Barbarossa
    • , Joyce Bosmans
    •  & Aafke M. Schipper

  • Article
    | Open Access

    Food web responses to species losses have the potential to cascade to ecosystem services. Here the authors apply ecological network robustness modelling to ecosystem services in salt marsh ecosystems, finding that species with supporting roles are critical to robustness of both food webs and ecosystem services.

    • Aislyn A. Keyes
    • , John P. McLaughlin
    •  & Laura E. Dee

  • Article
    | Open Access

    The effects of climate on vector-borne disease systems are highly context-dependent. Here, the authors incorporate laboratory-measured physiological traits of the mosquito Aedes aegypti into climate-driven mechanistic models to predict number, timing, and duration of outbreaks in Ecuador and Kenya.

    • Jamie M. Caldwell
    • , A. Desiree LaBeaud
    •  & Erin A. Mordecai

  • Article
    | Open Access

    Ticks are an important vector of disease in China, posing threats to humans, livestock and wild animals. Here, Zhao et al. compile a database of the distributions of the 124 tick species known in China and 103 tick-borne pathogens and predict the additional suitable habitats for the predominant vector species.

    • Guo-Ping Zhao
    • , Yi-Xing Wang
    •  & Li-Qun Fang

  • Article
    | Open Access

    Soil organic matter (SOM) is a huge sink of carbon, but the varied flux dynamics are challenging to predict. Here, the authors present a new model with the complexities of SOM cycling, including parameters for substrate accessibility, microbe diversity, and enzymatic substrate depolymerization.

    • Julien Sainte-Marie
    • , Matthieu Barrandon
    •  & Delphine Derrien

  • Article
    | Open Access

    Cloud cover and scarcity of ground-based validation hinder remote sensing of forest dynamics in the Amazon basin. Here, the authors analyse imagery from a high-frequency geostationary satellite sensor to study monthly NDVI patterns in the Amazon forest, finding support for spatially extensive seasonality.

    • Hirofumi Hashimoto
    • , Weile Wang
    •  & Ramakrishna R. Nemani

  • Article
    | Open Access

    Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.

    • Sarah P. Hammarlund
    • , Tomáš Gedeon
    •  & William R. Harcombe

  • Article
    | Open Access

    Mapping and quantifying degree of forest modification is critical to conserve and manage forests. Here the authors propose a new quantitative metric for landscape integrity and apply it to a global forest map, showing that less than half of the world’s forest cover has high integrity, most of which is outside nationally designed protected areas.

    • H. S. Grantham
    • , A. Duncan
    •  & J. E. M. Watson

  • Article
    | Open Access

    Whether or not diversity begets stability in ecological networks could depend on the spatial dispersal dynamics of species. Here the authors use mathematical models based on Turing pattern formation to show that trophic interactions combined with dispersal can destabilize complex ecosystems.

    • Joseph W. Baron
    •  & Tobias Galla

  • Article
    | Open Access

    Warming in the high latitudes is expected to stimulate soil organic matter decomposition which leads to enhanced carbon emissions. Here, the authors show that short-term experiments do not capture the complexity of vegetation dynamics in the Arctic and might thus not provide a full picture of long term processes.

    • Nicholas J. Bouskill
    • , William J. Riley
    •  & Robert F. Grant

  • Perspective
    | Open Access

    Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.

    • Emily J. Zakem
    • , Martin F. Polz
    •  & Michael J. Follows

  • Comment
    | Open Access

    Decision makers must have sufficient confidence in models if they are to influence their decisions. We propose three screening questions to critically evaluate models with respect to their purpose, organization, and evidence. They enable a more transparent, robust, and secure use of model outputs.

    • Volker Grimm
    • , Alice S. A. Johnston
    •  & P. Thorbek

  • Article
    | Open Access

    Mechanisms and consequences of the acclimation of soil respiration to warming are unclear. Here, the authors combine soil respiration, metagenomics, and functional gene results from a 7-year grassland warming experiment to a microbial-enzyme decomposition model, showing functional gene information to lower uncertainty and improve fit.

    • Xue Guo
    • , Qun Gao
    •  & Jizhong Zhou

  • Article
    | Open Access

    The ecological niche of a given microbe is difficult to define, but can be approximated from the range of biochemical reactions encoded by its genome. Here the authors use these genomic data and analyze them using manifold learning, which generates a diffusion map of the metabolic niche space of over 2500 bacteria.

    • Ashkaan K. Fahimipour
    •  & Thilo Gross

  • Article
    | Open Access

    Satellites provide clear evidence of greening trends in the Arctic, but high-resolution pan-Arctic quantification of these trends is lacking. Here the authors analyse high-resolution Landsat data to show widespread greening in the Arctic, and find that greening trends are linked to summer warming overall but not always locally.

    • Logan T. Berner
    • , Richard Massey
    •  & Scott J. Goetz

  • Article
    | Open Access

    Microbes interact in different ways than macro-organisms, but their interactions can still form the basis for broader macroecological patterns like the Species Abundance Distribution. Here, the author shows that thre general ecological patterns can be found in microbes, within and across biome types.

    • Jacopo Grilli

  • Article
    | Open Access

    Ecosystem Based Management measures developed to prevent overfishing could be particularly important under climate change. Here the authors combine climate and fish stock modelling to show that EBM cap implementation reduces climate-driven fishery declines under RCP 4.5 and 8.5 before midcentury. However, there are thermal tipping points beyond which potential collapses are predicted.

    • K. K. Holsman
    • , A. C. Haynie
    •  & A. E. Punt

  • Article
    | Open Access

    Rarely are the outcomes of mathematical (probability) models of wildlife disease detection used to inform policy or management changes. Here the authors develop a proactive hunting surveillance program that shortened the time required to establish freedom from chronic wasting disease at the population level in reindeer.

    • Atle Mysterud
    • , Petter Hopp
    •  & Hildegunn Viljugrein

  • Article
    | Open Access

    Plant-pollinator interactions are not fixed but instead can change seasonally and across years. Here, the authors provide a holistic perspective on how plants and pollinators first enter, then comprise, and ultimately leave interaction networks over time.

    • Bernat Bramon Mora
    • , Eura Shin
    •  & Daniel B. Stouffer

  • 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

    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

    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

    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

    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

    Numerous marine ecosystem models are used to project animal biomass over time but integrating them can be challenging. Here the authors develop a test for statistical significance in multi-model ensemble trends, and thus relate future biomass trends to current patterns of ecological and socioeconomic status.

    • Daniel G. Boyce
    • , Heike K. Lotze
    •  & Boris Worm

  • Article
    | Open Access

    Aside from their pollination function, pollinators consume and are consumed by other members of ecological communities; these relationships could explain the controversial effects of pollinators on ecological networks. Here the authors show that when mutualists such as pollinators are introduced into food webs, they increase ecosystem biodiversity, stability, and function.

    • Kayla R. S. Hale
    • , Fernanda S. Valdovinos
    •  & Neo D. Martinez

  • Article
    | Open Access

    Europe hosts isolated remnants of the steppe belt that once covered much of Eurasia. Here the authors combine genomic data and ecological niche modelling on three plant and three insect species to show evolution independent of the zonal steppe and high conservation value of these extrazonal steppes.

    • Philipp Kirschner
    • , Eliška Záveská
    •  & Peter Schönswetter

  • Article
    | Open Access

    Measurement of species abundance is fundamental in ecology, yet challenging at large spatial scales. Here, the authors show estimates of abundance of 1248 woody plant species over the East Asian islands that highlight macroevolutionary processes of biodiversity and the status of the national red listing.

    • Keiichi Fukaya
    • , Buntarou Kusumoto
    •  & Yasuhiro Kubota

  • Article
    | Open Access

    Species loss from ecological networks can impair network stability and ecosystem function. Here the authors simulate animal extinctions in interaction networks between plants and avian frugivores, showing that frugivore extinctions have comparatively weak effects on network structure, but strongly reduce seed-dispersal distance.

    • Isabel Donoso
    • , Marjorie C. Sorensen
    •  & Matthias Schleuning

  • Article
    | Open Access

    Little is known about how the speed of ecosystem collapse depends on ecosystem size. Here, Cooper, Willcock et al. analyse empirical data and models finding that although regime shift duration increases with ecosystem size, this relationship saturates and even large ecosystems can collapse in a few decades.

    • Gregory S. Cooper
    • , Simon Willcock
    •  & John A. Dearing

  • Article
    | Open Access

    Understanding to what extent geographic patterns in threatened species diversity are driven by environmental features or human activities could aid conservation. Here, Howard et al. investigate broad scale patterns in species richness of threatened vertebrates and test the role of environmental and anthropogenic drivers.

    • Christine Howard
    • , Curtis H. Flather
    •  & Philip A. Stephens

  • Article
    | Open Access

    It is unclear whether bird migration patterns are restricted to interglacial periods or are maintained during glacial maxima. Somveille et al. apply a global migration simulation model to climate reconstruction to show that the prevalence of this phenomenon has likely been largely maintained up to 50,000 years ago.

    • Marius Somveille
    • , Martin Wikelski
    •  & Walter Jetz

  • Article
    | Open Access

    The contribution of symbiotic dinitrogen fixation to the forest carbon sink could change throughout forest succession. Here the authors model nitrogen cycling and light competition between trees based on data from Panamanian forest plots, showing that fixation contributes substantially to the carbon sink in early successional stages.

    • Jennifer H. Levy-Varon
    • , Sarah A. Batterman
    •  & Lars O. Hedin

  • Article
    | Open Access

    Prior studies have examined fixed traits that correlate with plant invasiveness. Here the authors use a database of population matrices to compare demographic traits of invasive species in their native and invaded ranges, finding that demographic amplification is an important predictor of invasiveness.

    • Kim Jelbert
    • , Danielle Buss
    •  & Dave Hodgson

  • Article
    | Open Access

    Greenhouse gas mitigation can involve land-use changes that alter the habitat available for wildlife. Here, Ohashi et al. perform an integrated assessment showing that climate mitigation can be beneficial for global biodiversity but may entail local biodiversity losses where land-based mitigation is implemented.

    • Haruka Ohashi
    • , Tomoko Hasegawa
    •  & Tetsuya Matsui

  • Article
    | Open Access

    Improving estimates of forest biomass based on remote sensing data is important to assess global carbon cycling. Here the authors develop an approach to use forest gap models to simulate lidar waveforms and compare the outputs with ICESAT-1 GLAS profiles, showing improved estimates across the Amazon basin.

    • Edna Rödig
    • , Nikolai Knapp
    •  & Andreas Huth

  • Article
    | Open Access

    Individual-based models are widely used to simulate complex systems of interacting agents. Here the authors provide a mathematical framework that automates the analysis of any model in a wide class, facilitating a deeper understanding of the scientific questions these models are used to address.

    • Stephen J. Cornell
    • , Yevhen F. Suprunenko
    •  & Otso Ovaskainen

  • Article
    | Open Access

    Mismatches between the pace of climate change and plant responses may lead to delayed upslope shifts or extinction of mountain species. Here the authors investigate 135 alpine plant species, finding that extinction debts are more common among cold-adapted plants and colonization credits among warm-adapted plants.

    • Sabine B. Rumpf
    • , Karl Hülber
    •  & Stefan Dullinger

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