Ecological genetics articles within Nature Communications

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  • Article
    | Open Access

    Extinction of megafauna is a defining trend of the last 50,000 years. Here, the authors use genomic data to infer population histories of 139 extant megafauna, suggesting that their population decline is better explained by Homo sapiens expansion than by climate change.

    • Juraj Bergman
    • , Rasmus Ø. Pedersen
    •  & Jens-Christian Svenning

  • Article
    | Open Access

    Ecogeographic rules link spatial patterns in phenotype and environment, potentially reflecting adaptation. This study identifies nine genes associated with body mass variation in song sparrow populations, supporting Bergmann’s Rule and highlighting the role of natural selection in local adaptation.

    • Katherine Carbeck
    • , Peter Arcese
    •  & Jennifer Walsh

  • Article
    | Open Access

    Biodiversity often increases the functioning and productivity of ecosystems or communities. This work shows that such a positive diversity effect, namely overyielding in mixtures of two divergent Arabidopsis thaliana genotypes, can be genetically mapped and resolved to a single gene.

    • Samuel E. Wuest
    • , Lukas Schulz
    •  & Pascal A. Niklaus

  • Comment
    | Open Access

    The Tara Pacific program and expedition focused on coral reefs across the Pacific Ocean and used a coordinated sampling effort to address questions at multiple scales using a common suite of samples. Here, we highlight some of the Tara Pacific achievements, discussing the benefits of long-duration sea expeditions for investigating a wide array of research questions within a selected ecosystem.

    • Serge Planes
    •  & Denis Allemand

  • Article
    | Open Access

    The interplay of migration and adaptation was key in shaping species’ responses to Quaternary climate change. Illustrating this, Luqman et al. show that adaptive responses in a plant species emerged from climate-induced range shifts due to heterogenous sieving of adaptive alleles across space and time.

    • Hirzi Luqman
    • , Daniel Wegmann
    •  & Alex Widmer

  • Article
    | Open Access

    A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes.

    • Emily E. Wroblewski
    • , Lisbeth A. Guethlein
    •  & Peter Parham

  • Article
    | Open Access

    The genetic basis of spider major ampullate (Ma) gland silk production remains unknown. Hu et al. unveil a molecular atlas of this gland for the golden orb-weaving spider combining genome assembly and multiomics, revealing the single-cell spatial architecture of silk production in the Ma gland.

    • Wenbo Hu
    • , Anqiang Jia
    •  & Yi Wang

  • Article
    | Open Access

    Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.

    • Zefu Wang
    • , Minghui Kang
    •  & Jianquan Liu

  • Article
    | Open Access

    Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.

    • Kevin Nota
    • , Jonatan Klaminder
    •  & Laura Parducci

  • 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 long-term effectiveness of assisted gene flow of trees could be jeopardised by rapid climate change. Here the authors analyse a large dataset of relocated black spruce populations in Canada, finding that local adaptation to climate of origin improved NPP responses, but only for up to ~15 years after planting.

    • Martin P. Girardin
    • , Nathalie Isabel
    •  & Patrick Lenz

  • Article
    | Open Access

    Metagenome approaches can unravel relationships between environment, community composition, and ecological functions. Here, the authors show that bacterial communities sampled from rainwater pools can be clustered into few classes with distinct functional capacities and genetic repertoires, the assembly of which is likely driven by local conditions.

    • Alberto Pascual-García
    •  & Thomas Bell

  • Article
    | Open Access

    Ecological niche breadth may help explain spatial distribution patterns in animals. In this study on European bats, Alberdi et al. combine DNA metabarcoding and species distribution modelling to show that dietary niche breadth is related to hunting flexibility and broad-scale spatial patterns in species distribution.

    • Antton Alberdi
    • , Orly Razgour
    •  & M. Thomas P. Gilbert

  • Article
    | Open Access

    Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.

    • Stéphanie Manel
    • , Pierre-Edouard Guerin
    •  & Loïc Pellissier

  • Article
    | Open Access

    Reductions in seawater pH are affecting marine ecosystems globally. Here, the authors describe phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the mussel Mytilus galloprovincialis, and suggest that standing variation within natural populations plays an important role in bolstering species’ adaptive capacity to global change.

    • M. C. Bitter
    • , L. Kapsenberg
    •  & C. A. Pfister

  • Article
    | Open Access

    Examples of overdominance are usually explained by deleterious effects in homozygotes. Here, Kellenberger et al. describe a case of overdominance in the floral color of the Alpine orchid Gymnadenia rhellicani apparently maintained by pollinator preferences without deleterious effects in homozygotes.

    • Roman T. Kellenberger
    • , Kelsey J. R. P. Byers
    •  & Philipp M. Schlüter

  • Article
    | Open Access

    Genetic variation from coexisting species influences interspecific interactions in a community. Here, the authors develop a framework for identifying quantitative trait loci (QTLs) underlying community dynamics and validate the tool using data from co-culturing of two bacterial species.

    • Libo Jiang
    • , Xiaoqing He
    •  & Rongling Wu

  • Article
    | Open Access

    Host-parasite coevolution can lead to arms races favouring novel immunogenetic alleles or the maintenance of diversity in a balanced polymorphism. Here, Lighten et al. combine data on MHC diversity across three guppy species and simulations to show that polymorphisms of immunogenetic supertypes may persist even as alleles within supertypes are involved in an arms race.

    • Jackie Lighten
    • , Alexander S. T. Papadopulos
    •  & Cock van Oosterhout

  • Article
    | Open Access

    Population structure of the model plantArabidopsis thaliana is shaped by glacial refugia and recent admixture. Here the authors show that genetically distinct groups of A. thalianahave spread east-west across Europe since the most recent ice age, likely as a result of human activity.

    • Cheng-Ruei Lee
    • , Hannes Svardal
    •  & Magnus Nordborg

  • Article
    | Open Access

    Accurate determination of population size for highly-mobile marine animals is often prohibitively difficult. Here, Bravingtonet al.estimate the abundance of southern bluefin tuna using a method based on the number of parent-offspring pairs detected genetically in samples from the catch.

    • Mark V. Bravington
    • , Peter M. Grewe
    •  & Campbell R. Davies

  • Article
    | Open Access

    Delimiting populations is crucial for conserving threatened species. Using genome-wide data from the whole of Antarctica, Cristofari et al.show that Emperor penguins are organised into a single global population that have shared demography since the late Quarternary.

    • Robin Cristofari
    • , Giorgio Bertorelle
    •  & Emiliano Trucchi

  • Article
    | Open Access

    The role of wild elk in the spread and persistence of bovine brucellosis in the Great Yellowstone area is unclear. Here, Kamath et al. analyse the genomic sequences of 245 Brucella abortusisolates from elk, bison and cattle, supporting the idea that elk is an important reservoir and source of livestock infections.

    • Pauline L. Kamath
    • , Jeffrey T. Foster
    •  & Paul C. Cross

  • Article
    | Open Access

    Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.

    • Maud Fagny
    • , Etienne Patin
    •  & Lluis Quintana-Murci

  • Article
    | Open Access

    Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.

    • Marius Roesti
    • , Benjamin Kueng
    •  & Daniel Berner

  • Article
    | Open Access

    Age-related macular degeneration (AMD) is a major cause of blindness worldwide. Here, the authors carry out a two-stage genome-wide association study for AMD and identify three new AMD risk loci, highlighting the shared and distinct genetic basis of the disease in East Asians and Europeans.

    • Ching-Yu Cheng
    • , Kenji Yamashiro
    •  & Chiea Chuen Khor

  • Article
    | Open Access

    The genetic basis of sex chromosome pseudoautosomal regions (PAR) in organisms with female heterogamety is largely unknown. Smeds et al.provide the first molecular characterization of the PAR in birds with differentiated sex chromosomes and show a potential recombination hotspot and no evidence for strong sexual antagonism in this region.

    • Linnéa Smeds
    • , Takeshi Kawakami
    •  & Hans Ellegren

  • Article
    | Open Access

    Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.

    • W. Wang
    • , G. Haberer
    •  & J Messing

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