Ecology articles within Nature Communications

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  • 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

    Parental care can take many forms but how this diversity arises is not well understood. Here, the authors compile data for over 1300 amphibian species and show that different forms of care evolve at different rates, prolonged care can be easily reduced, and biparental care is evolutionarily unstable.

    • Andrew I. Furness
    •  & Isabella Capellini

  • Article
    | Open Access

    The capacity to predict zoonotic disease outbreaks is hampered by data availability and complex relationships between humans, wildlife, and the environment. Here the authors present a modelling framework that identifies potential high-risk locations for Ebola outbreaks under various climatic, demographic, and land use scenarios.

    • David W. Redding
    • , Peter M. Atkinson
    •  & Kate E. Jones

  • Article
    | Open Access

    The defaunation of vertebrates may disrupt forest functioning through the loss of plant-animal interactions, but impacts on forests remain unquantified. Here the authors show that seed dispersal is a key interaction and defaunation of primates and birds negatively impacts forest regeneration.

    • Charlie J. Gardner
    • , Jake E. Bicknell
    •  & Zoe G. Davies

  • Article
    | Open Access

    Little is known about the long-term dynamics of mesopelagic fish despite their large contribution to total fish biomass. Here, the authors analyze the Santa Barbara Basin otolith record and suggest that mesopelagic fish populations were large but fluctuated with surface climate over the last ~2000 years.

    • William A. Jones
    •  & David M. Checkley Jr.

  • Article
    | Open Access

    Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.

    • Zheng-Shuang Hua
    • , Yu-Lin Wang
    •  & Wen-Jun Li

  • Article
    | Open Access

    Deep learning has the potential to identify ecological relationships between environment and complex phenotypes that are difficult to quantify. Here, the authors use deep learning to analyse associations among elevation, climate and phenotype across ~2000 moth species in Taiwan.

    • Shipher Wu
    • , Chun-Min Chang
    •  & Sheng-Feng Shen

  • Article
    | Open Access

    The Paleocene-Eocene Thermal Maximum (c. 55 million years ago) was a period associated with massive carbon injection into the atmosphere, yet discrepancies in carbon isotope proxy records have led to substantial uncertainties in the source, scale, and timing of carbon emissions. Here, the authors propose that membrane lipids of marine planktonic archaea can reliably record the carbon isotope excursion and surface ocean warming, giving a new constraint for the source and size of the PETM carbon emissions.

    • Felix J. Elling
    • , Julia Gottschalk
    •  & Ann Pearson

  • Article
    | Open Access

    Policies aiming to preserve vegetated coastal ecosystems (VCE) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here the authors assessed organic carbon storage in VCE across Australian and the potential annual CO2 emission benefits of VCE conservation and find that Australia contributes substantially the carbon stored in VCE globally.

    • Oscar Serrano
    • , Catherine E. Lovelock
    •  & Carlos M. Duarte

  • Article
    | Open Access

    Compared to motherhood, the molecular changes associated with fatherhood are less understood. Here, the authors investigate gene expression changes associated with paternal care in male stickleback fish, and compare them with patterns in territorial aggression.

    • Syed Abbas Bukhari
    • , Michael C. Saul
    •  & Alison M. Bell

  • Article
    | Open Access

    Predictions of coral reef dynamics under climate change are hindered by lack of long-term records. Here the authors couple historical and re-survey data from the Great Barrier Reef to show major phase-shifts in the coral and non-coral community over the last 90 years.

    • Maoz Fine
    • , Ove Hoegh-Guldberg
    •  & Sophie Dove

  • Article
    | Open Access

    An important question in ecology is how much species at higher trophic levels affect lower levels through top-down cascades. Here the authors show through analyses of pelagic size spectra that such cascades are strong in freshwater systems and can also arise in nutrient rich marine systems.

    • Axel G. Rossberg
    • , Ursula Gaedke
    •  & Pavel Kratina

  • Article
    | Open Access

    Drought is intensifying due to climate change, impacting forests globally. Here, the authors track nearly 2 million trees through severe drought and show that tree height is the greatest predictor of mortality risk, suggesting that the tallest trees may be the most vulnerable.

    • Atticus E. L. Stovall
    • , Herman Shugart
    •  & Xi Yang

  • 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

  • Article
    | Open Access

    Here, Shah et al. perform a meta-analysis and show that people who live or work in agricultural land in Southeast Asia are on average 1.7 times more likely to be infected with a pathogen than controls, suggesting that agricultural land-use increases infectious disease risk.

    • Hiral A. Shah
    • , Paul Huxley
    •  & Kris A. Murray

  • Article
    | Open Access

    Predator-prey coevolution is expected to hasten evolutionary rates, but this is difficult to test in long-lived species. Here, the authors report consequences of experimental coevolution between bacterial predators and prey, including accelerated molecular evolution and parallel genomic and phenotypic adaptation.

    • Ramith R. Nair
    • , Marie Vasse
    •  & Gregory J. Velicer

  • Article
    | Open Access

    Alkaline lakes have some of the highest productivity rates in freshwater ecosystems. Here the authors report amplicon, metagenome, and proteome sequencing from microbial mat communities of four alkaline lakes in Canada, and compare these lakes to central Asian soda lakes, revealing a shared core microbiome despite the geographical distance.

    • Jackie K. Zorz
    • , Christine Sharp
    •  & Marc Strous

  • Article
    | Open Access

    The fish Astyanax mexicanus has divergent cave and river-dwelling eco-morphotypes. Here, Hyacinthe et al. show that cave and river fish communicate sonically, but that the sounds produced and the responses elicited in the two morphs depend differently on the social and behavioral context.

    • Carole Hyacinthe
    • , Joël Attia
    •  & Sylvie Rétaux

  • Article
    | Open Access

    There was extensive degradation during the warm middle Holocene and permafrost area was reduced substantially. Here the authors synthesize data across the Tibetan permafrost region and find that paleoclimate is more important than modern climate in shaping current permafrost carbon distribution, and its importance increases with soil depth.

    • Jinzhi Ding
    • , Tao Wang
    •  & Lin Zhao

  • Article
    | Open Access

    Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.

    • Keara L. Grady
    • , Jackson W. Sorensen
    •  & Ashley Shade

  • Article
    | Open Access

    A single species of electric eel, Electrophorus electricus, has been described. Here, de Santana et al. show that there are three major lineages of Electrophorus distributed across Greater Amazonia and describe two new species, one with a much stronger electric discharge than was previously known.

    • C. David de Santana
    • , William G. R. Crampton
    •  & Wolmar B. Wosiacki

  • Article
    | Open Access

    Predicted responses to climate change may be informed by evolutionary history. Here, the authors reconstruct the phylogeny of lacertid lizards and investigate how the evolution of this clade has varied with paleoclimates and how closely adapted extant species are to modern climates.

    • Joan Garcia-Porta
    • , Iker Irisarri
    •  & Katharina C. Wollenberg Valero

  • Article
    | Open Access

    Understanding mechanisms of soil organic matter (SOM) decomposition and stabilisation improves soil-climate feedback predictions. Here the authors show that roots in boreal forest promote organic nitrogen economy and provide a framework on how roots affect decomposition and stabilisation of SOM.

    • Bartosz Adamczyk
    • , Outi-Maaria Sietiö
    •  & Jussi Heinonsalo

  • Article
    | Open Access

    Linear controllability theories have stimulated research on control of complex networks. Here the authors investigate the concordance between linear and nonlinear approaches in ranking the importance of nodes in nonlinear networks, and conclude that linear controllability may not be applicable.

    • Junjie Jiang
    •  & Ying-Cheng Lai

  • Article
    | Open Access

    Here, Llewellyn and colleagues present evidence of meiotic sex in Trypanosoma cruzi, the causative agent of Chagas disease. These findings have implications for the epidemiology of the disease in endemic regions and challenge existing ideas that the parasites are strictly clonal.

    • Philipp Schwabl
    • , Hideo Imamura
    •  & Martin S. Llewellyn

  • Article
    | Open Access

    Investigating malaria transmission at three sites in Uganda, the authors identify super-spreaders and show that super-spreading is more prominent at low-intensity transmission, and that seasonality and environmental stochasticity have a greater influence on super-spreading.

    • Laura Cooper
    • , Su Yun Kang
    •  & David L. Smith

  • Article
    | Open Access

    Large brains are expected to be beneficial in variable environments by enabling flexible behavioral responses. Here, the authors show that relative brain size in birds is bimodally distributed in colder, seasonal environments, suggesting that both large and small brains can be adaptive solutions to harsh conditions.

    • Trevor S. Fristoe
    •  & Carlos A. Botero

  • Article
    | Open Access

    The sensitivity of soil organic carbon (SOC) in subsoil (below 0.3 m) to climate change is poorly constrained. Here, the authors map global subsoil (0.3–1 m soil layer) SOC turnover times and find that temperature and in general climate effects are secondary to effects due to soil properties at both local and global scales—this now needs to be regarded for diagnosing subsoil SOC dynamics.

    • Zhongkui Luo
    • , Guocheng Wang
    •  & Enli Wang

  • Article
    | Open Access

    How the water use efficiency of trees changes with atmospheric CO2 variations has mostly been studied on short time scales. Here, a newly compiled data set covering 1915 to 1995 shows how rates of change in water use efficiency vary with location and rainfall over the global tropics on a decadal scale.

    • Mark A. Adams
    • , Thomas N. Buckley
    •  & Tarryn L. Turnbull

  • Article
    | Open Access

    Conservation planning rarely considers the uncertainty in management outcomes. Here, the authors develop a value of information approach to quantify uncertainty of threat management success and show that it can improve efficiency of interventions across a large sample of threatened species.

    • Sam Nicol
    • , James Brazill-Boast
    •  & Iadine Chadès

  • Article
    | Open Access

    It is thought that fungi protect themselves from predators by the production of toxic compounds. Here, Xu et al. show that a wide range of animal predators avoid feeding on Fusarium fungi, and this depends on fungal production of a bis-naphthopyrone pigment that is not toxic to the predators.

    • Yang Xu
    • , Maria Vinas
    •  & Petr Karlovsky

  • Article
    | Open Access

    Ocean acidification is expected to have a negative impact on calcifying organisms, however, our understanding of the acclimation potential of corals in their natural habit is currently limited. Here, the authors find that scleractinian corals living in high pCO2 conditions cannot fully adapt the chemistry of their internal calcifying fluid compared to corals growing in ambient conditions.

    • M. Wall
    • , J. Fietzke
    •  & A. Paytan

  • Review Article
    | Open Access

    Subseafloor microbial activities are central to global biogeochemical cycles, affecting Earth’s surface oxidation, ocean chemistry, and climate. Here the authors review present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to fill those gaps.

    • Steven D’Hondt
    • , Robert Pockalny
    •  & Arthur J. Spivack

  • Article
    | Open Access

    The global ecological predictors of soil priming remain unclear. Here the authors conducted a global survey of soils from 86 global locations using an isotopic approach and find that in more mesic sites with high SOC concentrations, soil priming effects are more likely to be negative.

    • Felipe Bastida
    • , Carlos García
    •  & Manuel Delgado-Baquerizo

  • Article
    | Open Access

    Corals occasionally split their spawning over two consecutive months rather than utilising a single annual event. Here, the authors model coral larval dispersal to show that split spawning may increase the reliability of larval supply to reefs, with implications for recovery from disturbances.

    • Karlo Hock
    • , Christopher Doropoulos
    •  & Peter J. Mumby

  • Article
    | Open Access

    The U.S. Endangered Species Act (ESA) requires that federal agencies consult with the U.S. Fish and Wildlife Service (FWS) or National Marine Fisheries Service (NMFS) to ensure federal actions do not jeopardize the existence of listed species. Here, the authors analyze recorded from 2000–2017 and investigate the role of NMFS in the consultations.

    • Michael J. Evans
    • , Jacob W. Malcom
    •  & Ya-Wei Li

  • Article
    | Open Access

    Theory suggests that neutral genetic diversity is determined by census population size, but this is not observed empirically. Here, the authors show that in butterflies, neutral genetic diversity correlates with both body size and chromosome number, suggesting that linked selection is also an important factor.

    • Alexander Mackintosh
    • , Dominik R. Laetsch
    •  & Konrad Lohse

  • Article
    | Open Access

    Global average, geographical distribution and temporal variations of the 13C isotopic signature of enteric fermentation emissions are not well understood. Here the authors established a global dataset and show a larger emission increase between the two periods (2002–2006 and 2008–2012) than previous studies.

    • Jinfeng Chang
    • , Shushi Peng
    •  & Philippe Bousquet

  • Article
    | Open Access

    Stomata enable gas exchange for photosynthesis but close to promote survival during drought. Here, Henry et al. provide evidence for a safety-efficiency trade-off whereby plants with greater stomatal conductance under well-watered conditions are more sensitive to stomatal closure during dehydration.

    • Christian Henry
    • , Grace P. John
    •  & Lawren Sack

  • Article
    | Open Access

    Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

    • Melody S. Clark
    • , Leyre Villota Nieva
    •  & Lloyd S. Peck

  • Article
    | Open Access

    The empirical consequences of human explorative strategies are not fully understood. Here the authors find that during undisturbed conditions, more-explorative vessels gained no performance advantage while during a major disturbance event, explorers benefited significantly from less-impacted revenues and were also more likely to continue fishing.

    • Shay O’Farrell
    • , James N. Sanchirico
    •  & Andrew Strelcheck

  • Article
    | Open Access

    Seagrass meadows are important but one of the most threatened ecosystems globally. Here the authors analyse data about extent and density of seagrasses in Europe from 1869 to 2016, and find evidence of recent trend reversal for declining European seagrass meadows.

    • Carmen B. de los Santos
    • , Dorte Krause-Jensen
    •  & Rui Santos

  • Article
    | Open Access

    It is unclear whether species’ responses to climate change tend to be adaptive or sufficient to keep up with climate change. Here, Radchuk et al. perform a meta-analysis showing that in birds phenology has advanced adaptively in some species, though not all the way to the new optima.

    • Viktoriia Radchuk
    • , Thomas Reed
    •  & Stephanie Kramer-Schadt

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