Evolution articles within Nature Communications

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  • 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

    Here, the authors describe a pathogenic fungus from a 400-million-year-old fossil plant from the Devonian Rhynie Chert in Scotland. They use advanced imaging methods to determine that the fungus belongs to the sac fungi, the most diverse group of Fungi today.

    • Christine Strullu-Derrien
    • , Tomasz Goral
    •  & David L. Hawksworth

  • Article
    | Open Access

    A species’ response to anthropogenic climate change may depend on its adaptations to past climate changes. Here, the authors use whole-genome resequencing and genetic-environment association to identify genes important for local adaptation and project adaptation under future climate scenarios across bank vole populations in Britain.

    • Silvia Marková
    • , Hayley C. Lanier
    •  & Petr Kotlík

  • Article
    | Open Access

    Self-incompatibility in diploid Arabidopsis relatives is determined by a dominance relationship that is epigenetically regulated. Using transgenic methods, this study demonstrates that the dominance relationship between subgenomes of the allopolyploid species Arabidopsis kamchatica underlies it’s self-compatibility.

    • Chow-Lih Yew
    • , Takashi Tsuchimatsu
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    The modelling of human-like behaviours is one of the challenges in the field of Artificial Intelligence. Inspired by experimental studies of cultural evolution, the authors propose a reinforcement learning approach to generate agents capable of real-time  third-person imitation.

    • Avishkar Bhoopchand
    • , Bethanie Brownfield
    •  & Lei M. Zhang

  • Article
    | Open Access

    Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.

    • Lewis Stevens
    • , Isaac Martínez-Ugalde
    •  & Mark Blaxter

  • 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

    Even in the absence of apparent genetic and environmental differences, substantial behavioral individuality emerges. This study demonstrates that such seemingly stochastic variation in a clonal fish species translates into predictable differences in life-history measures and ultimately fitness.

    • Ulrike Scherer
    • , Sean M. Ehlman
    •  & Max Wolf

  • Article
    | Open Access

    E. coli maintains membrane lipid asymmetry by transferring glycerophospholipids from the outer membrane to the inner membrane; this requires outer membrane protein MlaA, periplasmic chaperone MlaC, and inner-membrane complex MlaBDEF. Here, the authors show that in some bacteria that lack MlaA and MlaC, MlaD forms a transenvelope bridge comprising a typical inner-membrane domain and, in addition, an outer-membrane domain.

    • Kyrie P. Grasekamp
    • , Basile Beaud Benyahia
    •  & Christophe Beloin

  • Article
    | Open Access

    The origin and early evolution of large scales in bony fishes and small scales in cartilaginous fishes are unclear. Here, the authors report a 425-million-year-old fish, Entelognathus, with a mosaic of scale and fin spine characters.

    • Xindong Cui
    • , Matt Friedman
    •  & Min Zhu

  • Article
    | Open Access

    Bdelloid rotifers can withstand a wide range of genotoxic stresses. Here the authors reveal that a DNA ligase of bacterial origin was acquired by horizontal gene transfer to confer high resistance to ionizing radiation in bdelloid rotifers and other organisms known for their extreme tolerance to stress.

    • Emilien Nicolas
    • , Paul Simion
    •  & Karine Van Doninck

  • Article
    | Open Access

    Global spatiotemporal patterns of plant diversification are unclear. Here, the authors use a genus-level phylogeny and global distribution data for 14,244 flowering plant genera, finding a negative correlation between spatial patterns of diversification and genus diversity.

    • Dimitar Dimitrov
    • , Xiaoting Xu
    •  & Zhiheng Wang

  • Article
    | Open Access

    The Mycobacterium tuberculosis complex (MTBC) includes several pathogens thought to have originated in East Africa from an ancestor closely related to Mycobacterium canettii. Here, the authors describe a clinical tuberculosis strain isolated in Ethiopia that has typical M. canettii features but is phylogenetically much closer to the MTBC clade, supporting that the emergence of MTBC pathogens is a recent evolutionary event.

    • Bazezew Yenew
    • , Arash Ghodousi
    •  & Daniela Maria Cirillo

  • Article
    | Open Access

    The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.

    • Tara A. Mahendrarajah
    • , Edmund R. R. Moody
    •  & Anja Spang

  • Article
    | Open Access

    Studies of the evolution of cooperation often assume information use that is inconsistent with empirical observations. Here, the authors’ research on general imitation dynamics reveals that cooperation is fostered by individuals using less personal information and more social information.

    • Xiaochen Wang
    • , Lei Zhou
    •  & Aming Li

  • Article
    | Open Access

    Scleractinian corals are important in both shallow and deep ecosystems. Here, the authors use global spatial distribution data with a phylogenetic approach to examine directionality and speed of colonization during depth diversification, finding an offshore-onshore pattern of evolution and that depth dispersion is associated with phenotypic innovations.

    • Ana N. Campoy
    • , Marcelo M. Rivadeneira
    •  & Chris Venditti

  • Article
    | Open Access

    Pneumococcal vaccination has been shown to promote emergence of non-vaccine S. pneumoniae serotypes. Here, the authors use data from Malawi to investigate whether vaccine introduction also results in changes in metabolic, virulence, and antimicrobial resistance profiles of circulating strains.

    • Uri Obolski
    • , Todd D. Swarthout
    •  & Robert S. Heyderman

  • Article
    | Open Access

    To control transposable elements, fruit flies rely on distinct genomic regions called piRNA clusters. Here, new piRNA clusters were identified across diverse Drosophila species, displaying a conserved and specialised role in the control of endogenous retroviruses in ovarian somatic cells.

    • Jasper van Lopik
    • , Azad Alizada
    •  & Benjamin Czech Nicholson

  • Article
    | Open Access

    Non-ammonia oxidising Thaumarachaeota lineages are common in acidic soils, but their evolution is unclear. Here, the authors assemble 15 genomes from deeply rooted Thaumarachaeota in topsoils and subsoils, investigating evolutionary divergence in the family Gagatemarchaeaceae.

    • Paul O. Sheridan
    • , Yiyu Meng
    •  & Cécile Gubry-Rangin

  • 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

    Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y.

    • Nan Hu
    • , Brian J. Sanderson
    •  & Matthew S. Olson

  • Article
    | Open Access

    Little is known about how the evolution of gut microbiota is impacted by their surrounding community. Here, the authors examine the evolutionary ecology of the human gut microbiome, modelling resource competition to show that local evolutionary history can impact the structure and function of host microbiota.

    • Benjamin H. Good
    •  & Layton B. Rosenfeld

  • Article
    | Open Access

    The contribution of adaptive radiation to species and phenotypic diversity within major clades is not clear. Here, the authors use morphological and phylogenetic data for 1226 species of frogs, finding that less than half of families resemble adaptive radiation, but that adaptive radiation contributed to 75% of diversity.

    • Gen Morinaga
    • , John J. Wiens
    •  & Daniel S. Moen

  • Article
    | Open Access

    The Marine Alveolates (MALVs) include important parasites of other protists/animals. Here, using new data from MALV-I, the psammosids, and a new group called the eleftherids, the authors show MALVs, and therefore parasitism in early dinoflagellates, evolved from two distinct free-living ancestors.

    • Corey C. Holt
    • , Elisabeth Hehenberger
    •  & Patrick J. Keeling

  • Article
    | Open Access

    Parental care in birds includes diverse behaviours but the variation in care from each parent across the breeding cycle and between species is unclear. Here, the authors study 1533 bird species, finding different patterns across breeding stages, and that species with strong sexual selection or paternity uncertainty tend to show female-biased care.

    • Daiping Wang
    • , Wenyuan Zhang
    •  & Xiang-Yi Li Richter

  • Article
    | Open Access

    Here, the authors report two fossil lampreys, jawless vertebrates, from the Middle-Late Jurassic fossil Lagerstätte Yanliao Biota of North China. These large lampreys have an extensively toothed feeding apparatus resembling the Southern Hemisphere pouched lamprey, suggesting an ancestral predatory habit and southern origin of living lampreys.

    • Feixiang Wu
    • , Philippe Janvier
    •  & Chi Zhang

  • Article
    | Open Access

    Kra-Dai language family exhibits great linguistic diversity and tremendous socio-cultural importance in East Asia. In this study, the authors found that Kra-Dai languages initially diverged ~4,000 years ago in Southern China coinciding with prehistoric demic and agricultural diffusions likely driven by climate change.

    • Yuxin Tao
    • , Yuancheng Wei
    •  & Menghan Zhang

  • Article
    | Open Access

    Animals differ remarkably in how parental care is distributed between the male and female parent. Here, the authors use evolutionary simulations to reveal that sex differences in care readily emerge in a characteristic manner that is not captured by current sex role theory.

    • Xiaoyan Long
    •  & Franz J. Weissing

  • Article
    | Open Access

    The evolution of the middle ear in early therians is unclear. Here, the authors report a reconstructed, detached middle ear in a eutherian mammal from the Early Cretaceous Jehol Biota, suggesting independent decoupling of hearing and chewing apparatuses.

    • Haibing Wang
    •  & Yuanqing Wang

  • Article
    | Open Access

    Studies on mutant invasion typically assume populations in isolation, rather than part of an ecological community. Here, the authors use computational models to investigate how enemy-victim interactions influence properties of mutant invasion, showing that selection is substantially weakened.

    • Dominik Wodarz
    •  & Natalia L. Komarova

  • Article
    | Open Access

    Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.

    • Ashley T. Sendell-Price
    • , Frank J. Tulenko
    •  & Manfred Schartl

  • Article
    | Open Access

    Marine food resources are commonly thought to have become marginal food or abandoned altogether with the spread of agriculture in Europe. Here, the authors use biomarkers in dental calculus to track widespread consumption of seaweed and aquatic plants through the Neolithic and into the Early Middle Ages.

    • Stephen Buckley
    • , Karen Hardy
    •  & Maria Eulalia Subirà

  • Article
    | Open Access

    West Nile virus is an animal pathogen that has spread rapidly in Europe in recent years, causing several human deaths. This study investigates the spatial and temporal dynamics of the virus circulation between Africa (its place of origin) and Europe.

    • Giulia Mencattelli
    • , Marie Henriette Dior Ndione
    •  & Giovanni Savini

  • Article
    | Open Access

    Photosynthesis is thought to be restricted to a few bacterial and eukaryotic phyla. Here, Li et al. provide evidence of photosynthetic abilities in uncultivated bacteria within the phylum Myxococcota, suggesting that some of these organisms may combine predatory and photosynthetic abilities.

    • Liuyang Li
    • , Danyue Huang
    •  & Yinzhao Wang

  • Article
    | Open Access

    The largest increase in marine biodiversity in Earth’s history took place nearly 500 million years ago during a geological period called the Ordovician. This event is well documented based on paleontological data, but its causes are debated. This study uses a numerical model to demonstrate that global climate cooling may have triggered biodiversification at that time.

    • Daniel Eliahou Ontiveros
    • , Gregory Beaugrand
    •  & Alexandre Pohl

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