Molecular ecology articles within Nature Communications

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  • Article
    | Open Access

    Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

    • Senne Heeren
    • , Ilse Maes
    •  & Frederik Van den Broeck

  • Perspective
    | Open Access

    Endangered polar ecosystems play critical roles in the Earth’s climate system and comprise many different habitats with unique organisms. Here, the authors propose a community road map to use multi-omics data from polar organisms for conservation, ecosystem services and societal gain.

    • M. S. Clark
    • , J. I. Hoffman
    •  & T. Mock

  • Article
    | Open Access

    This study found that cnidarian animals including corals, anemones and jellyfish share a common mechanism to regulate their association with symbiotic algae. Despite evolving independently, these animals all use the same carbon-nitrogen negative feedback loop for algae control, shedding light on the repeated evolution of these marine symbiotic relationships.

    • Guoxin Cui
    • , Jianing Mi
    •  & Manuel Aranda

  • Article
    | Open Access

    The chronology and mode of parallel evolution remain unclear. Here, the authors compare mid-Holocene and contemporary bottlenose dolphin adaptations between pelagic and coastal ecosystems with paleogenomics, finding rapid adaptation to newly emerged habitat from standing genetic variation.

    • Marie Louis
    • , Petra Korlević
    •  & Andrew D. Foote

  • Article
    | Open Access

    Disentangling how evolutionary history and environmental adaptation shape metabolic phenotypes is an open problem, especially for microbes whose phenotypes cannot be determined directly and are inferred from genomic information. Here, Ramon & Stelling propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and link genotype and environment to phenotype for 245 bacterial species.

    • Charlotte Ramon
    •  & Jörg Stelling

  • Article
    | Open Access

    This study investigates the average genome size of planktonic prokaryotes across tropical and polar oceans and down to the hadal realm. Using hundreds of metagenomes of marine microorganisms, genome size was found to be highest in the perennially cold polar ocean, suggesting that environmental factors influence genome size selection and the ecological strategies of marine microbes.

    • David K. Ngugi
    • , Silvia G. Acinas
    •  & Carlos M. Duarte

  • Article
    | Open Access

    Rearrangements in the genome are important for local adaptation and speciation but are often difficult to identify reliably. Here the authors show that rearrangements underlie large chromosome regions that separate differentially migratory willow warblers.

    • Max Lundberg
    • , Alexander Mackintosh
    •  & Staffan Bensch

  • Article
    | Open Access

    Planktonic foraminifera are key to understanding paleoclimate and plankton evolution, but their origins are unclear. Here, the authors use a molecular clock to suggest that benthic foraminifera dispersed in plankton and renew planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction.

    • Raphaël Morard
    • , Christiane Hassenrück
    •  & Michal Kucera

  • 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 timing and ecological dynamics of extinction in the late Pleistocene are not well understood. Here, the authors use sediment ancient DNA from permafrost cores to reconstruct the paleoecology of the central Yukon, finding a substantial turnover in ecosystem composition between 13,500-10,000 years BP and persistence of some species past their supposed extinctions.’

    • Tyler J. Murchie
    • , Alistair J. Monteath
    •  & Hendrik N. Poinar

  • Article
    | Open Access

    Legacies of past plant communities are likely to influence plant-soil interactions. Here, the authors report a reciprocal transplant experiment showing that soil microbial legacies shaped by previous plants persist for soil fungi and root endophytes but can be reversed by a next generation of plants for soil bacteria.

    • S. Emilia Hannula
    • , Robin Heinen
    •  & T. Martijn Bezemer

  • Article
    | Open Access

    Modular, rather than integrated systems are classically thought to allow functional diversity to evolve rapidly. A study of cichlid fish shows integration between divergent jaw systems at the phylogenetic, population, and genetic scales, suggesting integration can and does facilitate rapid, coordinated trait evolution.

    • Andrew J. Conith
    •  & R. Craig Albertson

  • Article
    | Open Access

    Biodiversity-ecosystem functioning relationships may vary with climate. Here, the authors study relationships of plant and soil microbial diversity with soil nutrient multifunctionality in 130 dryland sites in China, finding a shift towards greater importance of soil microbial diversity in arid conditions.

    • Weigang Hu
    • , Jinzhi Ran
    •  & Jianming Deng

  • Article
    | Open Access

    Standing genetic variation allows natural populations to evolve rapidly. Genome sequences of a resurrected Daphnia population show that genetic variation carried by only five founding individuals from the regional genotype pool is enough to fuel rapid evolution in response to strong selection pressures with no evidence of genetic erosion.

    • Anurag Chaturvedi
    • , Jiarui Zhou
    •  & Luc De Meester

  • Article
    | Open Access

    The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that mediates interactions between bacteria and their invertebrate hosts. Here, the authors catalogue eCIS loci from 1,249 prokaryotic genomes, showing enrichment in non-pathogenic environmental microbes, and identifying eCIS-associated toxins that inhibit the growth of bacteria and/or yeast.

    • Alexander Martin Geller
    • , Inbal Pollin
    •  & Asaf Levy

  • Article
    | Open Access

    Here, Griffiths et al. show infection of 80–100% of sampled vampire bats in Peru with a newly discovered betaherpesvirus (DrBHV) that exhibits specificity within neotropical bats and evidence for superinfection. These data suggest that DrBHV could be a candidate for virally vectored vaccines that spread autonomously through a bat population.

    • Megan E. Griffiths
    • , Laura M. Bergner
    •  & Daniel G. Streicker

  • Article
    | Open Access

    Classical epidemiological approaches have been limited in their ability to formally test hypotheses. Here, Dellicour et al. illustrate how phylodynamic and phylogeographic analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.

    • Simon Dellicour
    • , Sebastian Lequime
    •  & Philippe Lemey

  • Article
    | Open Access

    Biomonitoring via environmental DNA (eDNA) is an important conservation tool for freshwater ecosystems, but this is complicated by eDNA movement downstream. Here, Carraro et al. develop and test an approach to reconstruct high-resolution spatial biodiversity patterns from freshwater eDNA.

    • Luca Carraro
    • , Elvira Mächler
    •  & Florian Altermatt

  • Article
    | Open Access

    The relationship between the coral animal and symbiotic algae is essential to coral health, and researchers are turning to Exaiptasia, a model cnidarian system, to study this relationship mechanistically. Here the authors find that endosymbiotic algae become limited by nitrogen at high population densities and provide the host with high levels of fixed carbon.

    • Tingting Xiang
    • , Erik Lehnert
    •  & Arthur R. Grossman

  • Article
    | Open Access

    Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.

    • G. Sallé
    • , S. R. Doyle
    •  & J. A. Cotton

  • Article
    | Open Access

    Cotton bollworm is an important agricultural pest with widespread resistance to insecticides. Here Wang et al. identifies CYP6AEs from cotton bollworm involved in detoxifying plant toxins and chemical insecticides through the CRISPR-Cas9-based reverse genetics approach in conjunction with in vitro metabolism.

    • Huidong Wang
    • , Yu Shi
    •  & Yidong Wu

  • Article
    | Open Access

    A central problem in biodiversity estimation from genetic markers is the ability of algorithms to retain ‘true’ species while discarding artefacts. Here, the authors present a new post-clusturing curation algorithm using OTU co-occurrences to estimate plant biodiversity from soil samples.

    • Tobias Guldberg Frøslev
    • , Rasmus Kjøller
    •  & Anders Johannes Hansen

  • Article
    | Open Access

    The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.

    • Joost A. M. Raeymaekers
    • , Anurag Chaturvedi
    •  & Filip A. M. Volckaert

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