Evolution articles within Nature Communications

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  • Article
    | Open Access

    Sequence composition is thought to be a major factor governing the functionality of horizontally transferred genes. In contrast, Porse et al. show that phylogenetic origin, and the type of resistance mechanism, are major factors affecting the functionality of horizontally transferred antibiotic resistance genes.

    • Andreas Porse
    • , Thea S. Schou
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

    • Alissa Mittnik
    • , Chuan-Chao Wang
    •  & Johannes Krause

  • Article
    | Open Access

    Three alternatives have been proposed for the ecological state of the ancestral snake: fossorial (burrowing), aquatic, or terrestrial. Here, the authors use an integrative geometric morphometric approach that suggests evolution from terrestrial to fossorial in the most recent common ancestor of extant snakes.

    • Filipe O. Da Silva
    • , Anne-Claire Fabre
    •  & Nicolas Di-Poï

  • Article
    | Open Access

    Phenotypic plasticity has been suggested to facilitate survival in new environments and subsequent adaptation. Here, the authors reanalyze transcriptomic data from experimental evolution studies in combination with computational metabolic network analysis and show that genetic adaptation tends to reverse plastic changes in order to recover fitness.

    • Wei-Chin Ho
    •  & Jianzhi Zhang

  • Article
    | Open Access

    Wolbachia causes cytoplasmic incompatibility (CI) between mosquitoes infected with different strains, but the genetic basis of observed CI diversity is unknown. Here, Bonneau et al. sequence Wolbachia from over 100 Culex pipiens lines and show that crossing types match variations of the toxin-antitoxin cidA-cidB genes.

    • Manon Bonneau
    • , Celestine Atyame
    •  & Mylène Weill

  • Article
    | Open Access

    The cellular mechanisms underlying autophagy are conserved; however it is unclear how they evolved in higher organisms. Here the authors identify two oxidation-sensitive cysteine residues in the autophagy receptor SQSTM1/p62 in vertebrates which allow activation of pro-survival autophagy in stress conditions.

    • Bernadette Carroll
    • , Elsje G. Otten
    •  & Viktor I. Korolchuk

  • Article
    | Open Access

    A number of paravian dinosaurs have been described from the Jurassic Yanliao biota, but these have tended to be morphologically similar to Archaeopteryx. Here, Hu. describe the new paravian dinosaur, Caihong juji gen. et sp. nov., which possesses a suite of unusual skeletal and feather characteristics.

    • Dongyu Hu
    • , Julia A. Clarke
    •  & Xing Xu

  • Article
    | Open Access

    The phylogeny of beetles, which represent ~25% of known extant animal species, has been a challenge to resolve. Here, Zhang et al. infer a time-calibrated phylogeny for Coleoptera based on 95 protein-coding genes in 373 species and suggest an association between the hyperdiversification of beetles and the rise of angiosperms.

    • Shao-Qian Zhang
    • , Li-Heng Che
    •  & Peng Zhang

  • Article
    | Open Access

    How RNA building blocks have formed on an early Earth by a continuous process is still a mystery awaiting its solution. Here, the authors report that fluctuations of physical parameters like temperature and pH could have been enough to facilitate nucleoside formation from simple starting materials.

    • Sidney Becker
    • , Christina Schneider
    •  & Thomas Carell

  • Article
    | Open Access

    New antibiotics with reduced potential for resistance are urgently needed. Here, the authors use a multidisciplinary approach to characterize substrate discrimination in macrolide resistance kinases and present a strategy for the prediction of mutations that expand the substrate range of antibiotic-inactivating enzymes.

    • Andrew C. Pawlowski
    • , Peter J. Stogios
    •  & Gerard D. Wright

  • Article
    | Open Access

    Physical structure is known to contribute to the appearance of bird plumage through structural color and specular reflection. Here, McCoy, Feo, and colleagues demonstrate how a third mechanism, structural absorption, leads to low reflectance and super black color in birds of paradise feathers.

    • Dakota E. McCoy
    • , Teresa Feo
    •  & Richard O. Prum

  • Article
    | Open Access

    Substantial evidence now supports the idea that the ancestral bat was a small, night flying predator capable of laryngeal echolocation. Here, the authors confirm this hypothesis using phylogenetic comparative analyses and further suggest an underlying tradeoff between echolocation and vision in both ancient and modern species and an association between sensory specialization and diet.

    • Jeneni Thiagavel
    • , Clément Cechetto
    •  & John M. Ratcliffe

  • Article
    | Open Access

    Studies of honest signaling have found an inconsistent relationship between carotenoid coloration and individual quality. Here, Weaver et al. compare dietary and biochemically converted carotenoid coloration using meta-analyses and show that converted carotenoids drive relationships with quality measures.

    • Ryan J. Weaver
    • , Eduardo S. A. Santos
    •  & Geoffrey E. Hill

  • Article
    | Open Access

    Cross-cultural interactions can cause cultural change, a process known as acculturation. Here, Erten et al. develop a model of cultural change under immigration, considering individuals’ orientations towards acculturation, and find that willingness to interact cross-culturally and resident cultural conservatism favour cultural coexistence.

    • E. Yagmur Erten
    • , Pieter van den Berg
    •  & Franz J. Weissing

  • Article
    | Open Access

    The ‘pace of life’ depends on both metabolic rate and life history traits; however, whether these evolve similarly in response to the environment is not clear. Here, Auer et al. show parallel evolution of metabolic rate and a suite of life history traits in response to predator environment in Trinidadian guppies.

    • Sonya K. Auer
    • , Cynthia A. Dick
    •  & David N. Reznick

  • Article
    | Open Access

    Eukaryotes often silence transposable elements (TEs) via DNA methylation. Here, the authors show that evolution of VANC, an Arabidopsis anti-silencing factor, and its target motifs allows sequence-specific demethylation, suggesting a way TEs can proliferate while minimizing damage to the host genome.

    • Aoi Hosaka
    • , Raku Saito
    •  & Tetsuji Kakutani

  • Article
    | Open Access

    Sexual recombination and mutation rate may play different roles in adaptive evolution depending on the fitness landscape. Here, Peabody et al. examine how the two factors affect the rate of adaptation of an E. coli strain capable of sexual recombination, under different conditions during experimental evolution.

    • George L. Peabody V
    • , Hao Li
    •  & Katy C. Kao

  • Article
    | Open Access

    The oldest known penguin fossils date to approximately 62 million years ago. Here, Mayr et al. describe Kumimanu biceae, an extinct penguin from approximately 55–60 million years ago, which represents an independent origin of giant size soon after the evolutionary transition from flight to diving.

    • Gerald Mayr
    • , R. Paul Scofield
    •  & Alan J. D. Tennyson

  • Article
    | Open Access

    African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.

    • Ananyo Choudhury
    • , Michèle Ramsay
    •  & Michael S. Pepper

  • Article
    | Open Access

    Sexual selection on males is thought to favour male-biased gene expression. Here, Veltsos et al. experimentally evolve Drosophila pseudoobscura under different mating systems and, contrary to expectation, most often find masculinization of the transcriptome under monogamy rather than under elevated polyandry.

    • Paris Veltsos
    • , Yongxiang Fang
    •  & Michael G. Ritchie

  • Article
    | Open Access

    The double-strand breaks generated by CRISPR-Cas systems are the target of multiple DNA repair pathways. Here the authors find incompatibility between NHEJ and type II-A CRISPR-Cas systems due to Csn2 mediated inhibition of end-joining.

    • Aude Bernheim
    • , Alicia Calvo-Villamañán
    •  & David Bikard

  • Article
    | Open Access

    Plants produce large numbers of structurally diverse metabolites through multistep pathways that often use the same precursors. Here the authors utilize the pathway leading to the production of acylated sucroses in the tomato plant to illustrate how metabolite diversity can arise through biochemical pathway evolution.

    • Pengxiang Fan
    • , Abigail M. Miller
    •  & Robert L. Last

  • Article
    | Open Access

    Fossils of ticks are rare, and little is known about their ancient hosts. Here, Peñalver and colleagues describe ticks in Cretaceous amber, including representatives of the new family Deinocrotonidae, which are associated with a dinosaur feather and nest biota.

    • Enrique Peñalver
    • , Antonio Arillo
    •  & Ricardo Pérez-de la Fuente

  • Article
    | Open Access

    Selection for recombination requires genetic diversity and negative linkage disequilibrium, which can be produced by coevolutionary arms races. Here the authors propose a qualitatively different scenario that can favour recombination in seasonal environments through the ‘genomic storage effect’.

    • Davorka Gulisija
    •  & Joshua B. Plotkin

  • Article
    | Open Access

    Live birth may be a precursor for parent-offspring associations and subsequent sociality, but the ubiquity of live birth in mammals and parental care in birds precludes testing the relationship in those clades. Here the authors show that live birth, but not egg attendance, is associated with the evolution of social grouping in squamate reptiles.

    • Ben Halliwell
    • , Tobias Uller
    •  & Geoffrey M. While

  • Article
    | Open Access

    Developmental processes often involve nonlinearities, but the consequences for translating genotype to phenotype are not well characterized. Here, Green et al. vary Fgf8 signaling across allelic series of mice and show that phenotypic robustness in craniofacial shape is explained by a nonlinear effect of Fgf8 expression.

    • Rebecca M. Green
    • , Jennifer L. Fish
    •  & Benedikt Hallgrímsson

  • Article
    | Open Access

    Storytelling entails costs in terms of time and effort, yet it is a ubiquitous feature of human society. Here, Smith et al. show benefits of storytelling in Agta hunter-gatherer communities, as storytellers have higher reproductive success and storytelling is associated with higher cooperation in the group.

    • Daniel Smith
    • , Philip Schlaepfer
    •  & Andrea Bamberg Migliano

  • Article
    | Open Access

    Terrestrial vertebrates branched from the lobe-finned fish in the Late Devonian. Here, Lu et al. describe the new lobe-finned fish Ptyctolepis brachynotus dating from the Early Devonian, which preserves a novel combination of cranial characters and suggests revision of evolutionary relationships among bony fish.

    • Jing Lu
    • , Sam Giles
    •  & Min Zhu

  • Article
    | Open Access

    Heterogeneous complex networks tend to be a more realistic representation of social networks than homogenous ones. Here Kleineberg investigates the role of network heterogeneity in the emergence of cooperation in social dilemmas and shows that it can sometimes hinder it.

    • Kaj-Kolja Kleineberg

  • Article
    | Open Access

    Animal sexual signals should be conspicuous to mates but not to enemies. Here, the authors show that call site properties can set limits on the attractiveness of male frogs' advertisement call, but that males may balance sexual success over predation risk by digging deeper puddles.

    • Wouter Halfwerk
    • , Judith A. H. Smit
    •  & Michael J. Ryan

  • Article
    | Open Access

    Evolution of resistance is a common cause of cancer treatment failure and tumor progression. Here, the authors present a method for integrating evolutionary principles based on adaptive therapy into abiraterone therapy for metastatic castrate-resistant prostate cancer and show the positive results of an interim analysis of a trial cohort.

    • Jingsong Zhang
    • , Jessica J. Cunningham
    •  & Robert A. Gatenby

  • Article
    | Open Access

    Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.

    • Kazuki Ichikawa
    • , Shingo Tomioka
    •  & Shinich Morishita

  • Article
    | Open Access

    Bivalve molluscs have evolved various characteristics to adapt to benthic filter-feeding. Here, Li et al investigate the genome, transcriptomes and proteomes of scallop Chlamys farreri, revealing evidences of molecular adaptations to semi-sessile life and neurotoxins.

    • Yuli Li
    • , Xiaoqing Sun
    •  & Zhenmin Bao

  • Article
    | Open Access

    An E. coli strain able to use CO2 fixation for sugar synthesis was previously generated by experimental evolution of an engineered strain. Here, Herz et al. show that specific mutations in five genes, encoding carbon metabolism enzymes or key regulators, are sufficient to enable robust growth of the strain.

    • Elad Herz
    • , Niv Antonovsky
    •  & Ron Milo

  • Article
    | Open Access

    The evolution of new sex chromosomes potentially generates reproductive isolation. Here, Bracewell et al. combine crossing experiments with population and functional genomics to characterize neo-sex chromosome evolution and incipient speciation in the mountain pine beetle, Dendroctonus ponderosae.

    • Ryan R. Bracewell
    • , Barbara J. Bentz
    •  & Jeffrey M. Good

  • Article
    | Open Access

    Africanized honey bees (AHB) are notoriously aggressive, but in Puerto Rico they have a ‘gentle’ phenotype. Here, Avalos et al. show that there has been a soft selective sweep at several loci in the Puerto Rican AHB population and suggest a role in the rapid evolution of gentle behaviour.

    • Arian Avalos
    • , Hailin Pan
    •  & Guojie Zhang

  • Article
    | Open Access

    The canonical scenario of sex chromosome evolution is through the differentiation of ancestral pairs of autosomes. Here, Fraïsse and colleagues use a comparative genomic analysis that shows the deep conservation of the Z chromosome in Lepidoptera and supports a non-canonical origin of the W chromosome.

    • Christelle Fraïsse
    • , Marion A. L. Picard
    •  & Beatriz Vicoso

  • Article
    | Open Access

    Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

    • Yoav Kallus
    • , John H. Miller
    •  & Eric Libby

  • Article
    | Open Access

    Human infections with Campylobacter fetus are often assumed to be derived from livestock. Here, Iraola et al. provide evidence that healthy humans may act as carriers and dispersers, and C. fetus may have originated in humans as an intestinal pathobiont and then adapted as a livestock pathogen.

    • Gregorio Iraola
    • , Samuel C. Forster
    •  & Trevor D. Lawley

  • Article
    | Open Access

    Wing pattern mimicry in the butterfly Papilio polytes is controlled by a single Mendelian locus, the mimicry supergene doublesex. Here, Zhang and colleagues reconstruct the complex evolutionary history of the doublesex supergene and mimicry in the Papilio polytes species group.

    • Wei Zhang
    • , Erica Westerman
    •  & Marcus R. Kronforst

  • Article
    | Open Access

    Breeding has increased crop productivity, but whether it has also changed phenotypic plasticity is unclear. Here, the authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability.

    • Joseph L. Gage
    • , Diego Jarquin
    •  & Natalia de Leon

  • 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

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