Ecological modelling articles within Nature Communications

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  • Article
    | Open Access

    This study shows that a multitrophic community model jointly recapitulates diel rhythms in abundances of Prochlorococcus picocyanobacteria, as well as viral infection, viral abundances and grazer abundances. Model-data integration implies that grazing predominantly controls Prochlorococcus abundances in surface waters of the North Pacific Subtropical Gyre, despite high viral densities.

    • Stephen J. Beckett
    • , David Demory
    •  & Joshua S. Weitz

  • Article
    | Open Access

    Soil priming could release large amounts of soil C into the atmosphere. Here the authors show that experimental warming boosts soil priming and CO2 emissions in grasslands potentially due to microbial changes. Model accuracy could be improved by incorporating these mechanisms.

    • Xuanyu Tao
    • , Zhifeng Yang
    •  & Jizhong Zhou

  • Article
    | Open Access

    West Nile Virus is emerging as an important pathogen in Europe, likely driven by recent climate and land-use changes. Here, the authors estimate the extent of the climate change-driven impact by modelling the change in West Nile Virus ecological suitability across the continent in the absence of climate change.

    • Diana Erazo
    • , Luke Grant
    •  & Simon Dellicour

  • Article
    | Open Access

    Live poultry markets in rural areas can be hotspots for transmission of pathogens, but the effects of markets on selection of viral virulence are not known. This study demonstrates through mathematical modelling that high turnover rate and persistence of viral particles can select for highly virulent pathogens in markets.

    • Justin K. Sheen
    • , Fidisoa Rasambainarivo
    •  & C. Jessica E. Metcalf

  • Article
    | Open Access

    Using a global synthesis of size spectra data from pelagic food webs, this study finds that size structure is not driven by temperature as often suggested, but by the nutrient status of the system. This means that modest phytoplankton declines projected for key fishing grounds at mid-latitudes will amplify into substantial reductions in the supportable biomass of fish.

    • Angus Atkinson
    • , Axel G. Rossberg
    •  & Constantin Frangoulis

  • Article
    | Open Access

    Forest responses can have major effects on tree architecture and community structure near the edges of forest fragments. Here, using terrestrial LiDAR scanning data from long-term forest plots, the authors find a net negative effect of fragmentation on Amazonian Forest aboveground biomass.

    • Matheus Henrique Nunes
    • , Marcel Caritá Vaz
    •  & Eduardo Eiji Maeda

  • Article
    | Open Access

    The microbiome is thought to be important for its host’s wellbeing, but it varies much among individuals. We offer a solution to this conundrum, showing that factors like the form of microbes’ contribution to hosts’ fitness and host population size may be preventing natural selection from operating effectively.

    • Itay Daybog
    •  & Oren Kolodny

  • Article
    | Open Access

    Ecosystems must be able to bounce back from perturbations to persist without species extinctions. This study uses theoretical modelling to show the importance of reactivity—how species respond in the short term to perturbations—for assessing the health of complex ecosystems, revealing that it can be a better predictor of extinction risk than stability.

    • Yuguang Yang
    • , Katharine Z. Coyte
    •  & Aming Li

  • Article
    | Open Access

    Channel networks are key to coastal wetland functioning. Here, the authors show how vegetation enhances network branching, and hypothesize that this may enhance the storm surge buffering capacity of wetlands and their resilience under sea-level rise.

    • Roeland C. van de Vijsel
    • , Jim van Belzen
    •  & Johan van de Koppel

  • Article
    | Open Access

    European rivers have over a million barriers hindering aquatic species migration and altering freshwater habitats. This study quantifies the spatial extent of upstream fish habitat alteration caused by physical blockage and shows that impoundments have altered 10% or 200,000 km of free-flowing river habitat in Europe.

    • Piotr Parasiewicz
    • , Kamila Belka
    •  & Wiesław Wiśniewolski

  • Article
    | Open Access

    Colonizer establishment produces fundamental building blocks that shape the structure of assembling pollination networks. In this model, while colonizers leverage indirect competition to establish, adaptive foraging by pollinators maintains species coexistence which produces nested networks.

    • Sabine Dritz
    • , Rebecca A. Nelson
    •  & Fernanda S. Valdovinos

  • Article
    | Open Access

    Protected areas are vital for conserving biodiversity, but their effectiveness is often unknown. A study on 638 species in Finland’s protected and unprotected sites finds mixed impacts; only a subset of species benefit from protection, mainly experiencing slower declines within protected areas.

    • Andrea Santangeli
    • , Benjamin Weigel
    •  & Marjo Saastamoinen

  • Article
    | Open Access

    Cooperative disease defense is part of group-level collective behavior. Here, the authors explore individual decisions, finding that garden ants increase grooming highly infectious individuals when they perceive a high pathogen load and suppress grooming after having been groomed by nestmates.

    • Barbara Casillas-Pérez
    • , Katarína Boďová
    •  & Sylvia Cremer

  • Article
    | Open Access

    Isolating the relationships between biodiversity and ecosystem functioning in natural ecosystems is challenging. Here, the authors apply a causal inference approach to observational data from grasslands and find a negative effect of biodiversity on productivity driven by non-native and rare species.

    • Laura E. Dee
    • , Paul J. Ferraro
    •  & Michel Loreau

  • Article
    | Open Access

    Antibiotics impact the gut microbiota in complex ways. Here, employing ecological models of resource competition, Newton et al. elucidate species coexistence patterns under resource competition and species-specific death rates, providing a model to predict microbiota dynamics under deleterious perturbations.

    • Daniel P. Newton
    • , Po-Yi Ho
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    The contribution of animal ecosystem engineers to coastal geomorphological processes is often neglected. Here, the authors combine observational, experimental and modelling work to demonstrate that ecosystem engineering by mussels is a much stronger driver of salt marsh accretion rates than expected.

    • Sinéad M. Crotty
    • , Daniele Pinton
    •  & Christine Angelini

  • Article
    | Open Access

    Desert-dwelling species are adapted to high temperatures, but further warming may push them beyond their physiological limits. Here, the authors integrate biophysical models and species distributions to project physiological impacts of climate change on desert birds globally and identify potential refugia.

    • Liang Ma
    • , Shannon R. Conradie
    •  & David S. Wilcove

  • Article
    | Open Access

    This study uses a compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by different dispersal models. Multi-generation dispersal models reveal implicit links among siblings from a common ancestor (coalescent connectivity) that could improve spatial conservation planning.

    • Térence Legrand
    • , Anne Chenuil
    •  & Vincent Rossi

  • Article
    | Open Access

    It is currently unknown how climate and land use changes could affect the endemic area of Lassa virus, a zoonotic pathogen responsible for Lassa fever. Here, the authors show that by 2070, new regions in Africa will likely become ecologically suitable for Lassa virus, drastically increasing the population living in conditions favourable for virus circulation.

    • Raphaëlle Klitting
    • , Liana E. Kafetzopoulou
    •  & Simon Dellicour

  • Article
    | Open Access

    Leaf functional traits are increasingly used as proxies for plant functions. Here, the authors show that leaf water affects other leaf traits and is a better predictor of whole-leaf photosynthesis and leaf area than leaf nitrogen or phosphorus content.

    • Zhiqiang Wang
    • , Heng Huang
    •  & Ian J. Wright

  • Article
    | Open Access

    At a time when protecting the environment is urgent, dealing with inherent uncertainties in the responses of biodiversity to disturbances is essential. This study promotes a promising tool to assess the vulnerability of species assemblages to guide protection efforts even if species response and disturbance regimes are poorly documented.

    • Arnaud Auber
    • , Conor Waldock
    •  & David Mouillot

  • Article
    | Open Access

    Coronaviruses may spill over from bats to humans. This study uses epidemiological data, species distribution models, and probabilistic risk assessment to map overlap among people and SARSr-CoV bat hosts and estimate how many people are infected with bat-origin SARSr-CoVs in Southeast Asia annually.

    • Cecilia A. Sánchez
    • , Hongying Li
    •  & Peter Daszak

  • Article
    | Open Access

    Shrub encroachment trends are widespread yet complex. Here the authors demonstrate that not considering dispersal and fire leads to overestimating shrub expansion in Arctic tundra and therefore its role as carbon sink.

    • Yanlan Liu
    • , William J. Riley
    •  & Margaret S. Torn

  • Article
    | Open Access

    Postfire sagebrush seeding treatments are widely applied across the western USA but evidence for the success of this restoration approach has been variable. Examining >1500 wildfires, this study shows that positive treatment effects were only detected after considering systematic differences between treated and untreated sites due to effects of selection biases in restoration.

    • Allison B. Simler-Williamson
    •  & Matthew J. Germino

  • Article
    | Open Access

    Lianas are an important component of tropical forests. Here the authors compare liana and tree functional trait distributions from across the tropics and use a liana-tree competition model to show that a key hydraulic trait influences liana viability and its response to future climate conditions.

    • Alyssa M. Willson
    • , Anna T. Trugman
    •  & David Medvigy

  • Article
    | Open Access

    It is unclear how far the impact of deforestation can spread. Here the authors analyse freshwater eDNA data along two rivers in the Amazon forest, and find that low levels of deforestation are linked to substantial reductions of fish and mammalian diversity downstream.

    • Isabel Cantera
    • , Opale Coutant
    •  & Sébastien Brosse

  • Article
    | Open Access

    The positive relationship between species diversity and functional diversity has been shown to vary. Here, the authors use theoretical models and data from Galápagos land snail communities to show how eco-evolutionary processes can force species to evolve narrower trait breadths in more species-rich communities to avoid competition, creating a negative relationship.

    • György Barabás
    • , Christine Parent
    •  & Frederik De Laender

  • Article
    | Open Access

    This study uses multispecies modelling to show that the management of a coral predator, the crown-of-thorns starfish, could help corals recover following bleaching events. They show that management was most effective when heat stress severity for corals was low to moderate, when corals had lower heat sensitivity and when the recruitment rate of starfish was high.

    • Jacob G. D. Rogers
    •  & Éva E. Plagányi

  • Article
    | Open Access

    Organisms can alter their physiological response to warming. Here, the authors show that the ability to raise metabolic rate following exposure to warming is inverse to body size and provide a mathematical model which estimates that metabolic plasticity could amplify energy flux through ecosystems in response to warming.

    • Rebecca L. Kordas
    • , Samraat Pawar
    •  & Eoin J. O’Gorman

  • Article
    | Open Access

    Global evaporation is a key climatic process that remains highly uncertain. Here, the authors shed light on this process with a novel hybrid model that integrates a deep learning representation of ecosystem stress within a physics-based framework.

    • Akash Koppa
    • , Dominik Rains
    •  & Diego G. Miralles

  • Article
    | Open Access

    Invertebrate-derived eDNA (iDNA) is an emerging tool for taxonomic and spatial biodiversity monitoring. Here, the authors use metabarcoding of leech-derived iDNA to estimate vertebrate occupancy over an entire protected area, the Ailaoshan Nature Reserve, China.

    • Yinqiu Ji
    • , Christopher C. M. Baker
    •  & Douglas W. Yu

  • Article
    | Open Access

    The apparent temperature sensitivity of atmospheric CO2 growth rate has increased markedly over the past six decades, however, the increase remains unexplained. Here we show that tropical extreme droughts amplified the interannual variability in atmospheric CO2 growth rate and drove the sensitivity change.

    • Xiangzhong Luo
    •  & Trevor F. Keenan

  • Article
    | Open Access

    Population density can influence the dynamics of emerging infections, but the specific effects at a local (within-city) level are not well understood. Here, the authors investigate the influence of population density on dynamics of dengue outbreaks in Rio de Janeiro and propose that this variable holds the key to how space should be aggregated.

    • Victoria Romeo-Aznar
    • , Laís Picinini Freitas
    •  & Mercedes Pascual

  • Article
    | Open Access

    Even evergreen tropical forests can have seasonal dynamics, which may be sensitive to disturbance. Here, the authors combine high-resolution remote sensing observations and microclimate data to show that forest fragmentation impacts canopy phenology dynamics in the Amazon forest.

    • Matheus Henrique Nunes
    • , José Luís Campana Camargo
    •  & Eduardo Eiji Maeda

  • Article
    | Open Access

    Bacteria often live in densely packed, spatially-structured communities; however, much of our understanding of their behavior stems from studies in liquid culture. Here, Monaco et al. show how spatial structure and quorum sensing modulate a cooperative behavior in colonies of Pseudomonas aeruginosa.

    • Hilary Monaco
    • , Kevin S. Liu
    •  & Joao B. Xavier

  • Article
    | Open Access

    The influence of human pressure within the matrix surrounding habitat fragments remains poorly understood. This study measures the relationship between habitat fragmentation, matrix condition and the change in extinction risk of 4,426 terrestrial mammals, finding that fragmentation and matrix condition are stronger predictors of risk than habitat loss and habitat amount.

    • Juan Pablo Ramírez-Delgado
    • , Moreno Di Marco
    •  & Oscar Venter

  • Article
    | Open Access

    Outbreaks of Crown-of-Thorn Starfish (CoTS) have caused coral cover declines across the Indo-Pacific. Here the authors analyse long-term CoTS, coral reef fish monitoring, and fisheries catch data from the Great Barrier Reef to demonstrate removal of predatory fish as a contributor to CoTS outbreaks.

    • Frederieke J. Kroon
    • , Diego R. Barneche
    •  & Michael J. Emslie

  • 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

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