Evolution articles within Nature Communications

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  • Article
    | Open Access

    Syphilis is caused by the bacterium Treponema pallidum subspecies pallidum (TPA), and incidence has risen recently in many countries. Here, Beale et al. provide whole-genome TPA sequences from 73 clinical samples and show how antimicrobial resistance emerged independently in circulating lineages.

    • Mathew A. Beale
    • , Michael Marks
    •  & Nicholas R. Thomson

  • Article
    | Open Access

    The homology of digits across amniotes is debated. Here, the authors compare the developmental transcriptomes of digits across five divergent amniotes and show high evolutionary dynamism in expression profiles, with conservation of a distinct developmental identity only in the anterior-most digit.

    • Thomas A. Stewart
    • , Cong Liang
    •  & Günter P. Wagner

  • Article
    | Open Access

    Quantifying the effects of noise in gene expression is difficult since noise and mean expression are coupled. Here the authors determine fitness landscapes in mean-noise expression space to uncouple these two parameters and show that changes in noise and mean expression are similarly detrimental to fitness.

    • Jörn M. Schmiedel
    • , Lucas B. Carey
    •  & Ben Lehner

  • Article
    | Open Access

    Mutators are expected to re-evolve low mutation rates to reduce deleterious load, but empirical evidence is mixed. Here, the authors show that load can vary across mutators and genetic backgrounds, which their simulations suggest can substantially alter antimutator dynamics.

    • Alejandro Couce
    •  & Olivier Tenaillon

  • Article
    | Open Access

    The Atlantic salmon has suffered widespread population declines over the last century. Here, Lehnert et al. reconstruct changes in effective population size of 172 populations based on genomic linkage information revealing mostly temperature-associated population declines with over 60% of populations in decline since 1975.

    • S. J. Lehnert
    • , T. Kess
    •  & I. R. Bradbury

  • Article
    | Open Access

    Hypsodonty is a durable pattern of dentition seen in mammals with abrasive diets. Here, Melo and colleagues describe new fossils of the stem-mammal Menadon besairiei from the Late Triassic, which show the convergent evolution of hypsodonty before mammals.

    • Tomaz P. Melo
    • , Ana Maria Ribeiro
    •  & Marina Bento Soares

  • Article
    | Open Access

    Sensory drive theory predicts that vocal signalling coevolves with auditory sensitivity, but empirical evidence is limited. Here, Charlton et al. show that vocal characteristics and hearing have coevolved in forest mammals, due to constraints imposed by the local signalling environment.

    • Benjamin D. Charlton
    • , Megan A. Owen
    •  & Ronald R. Swaisgood

  • Article
    | Open Access

    The role of gene expression noise in the evolution of drug resistance in mammalian cells is unclear. Here, by uncoupling noise from mean expression of a drug resistance gene in CHO cells the authors show that noisy expression aids adaptation to high drug levels, but delays it at low drug levels.

    • Kevin S. Farquhar
    • , Daniel A. Charlebois
    •  & Gábor Balázsi

  • Article
    | Open Access

    Flight loss has occurred numerous times in bird evolution. Here, the authors examine convergent sites in the exonic and intronic sequences of 48 bird genomes, finding amino-acid changes in two genes, ATGL and ACOT7, with potential implications for a change in metabolism rather than anatomy.

    • Shengkai Pan
    • , Yi Lin
    •  & Xiangjiang Zhan

  • Article
    | Open Access

    H3K9me3 and H3K27me3 chromatin silencing marks are usually deposited by different SET-domain proteins. Here the authors show that the Enhancer-of-zeste-like protein Ezl1, from the unicellular eukaryote Paramecium tetraurelia, catalyzes methylation of histone H3 in vitro and in vivo with an apparent specificity toward K9 and K27, and controls the repression of transposable elements.

    • Andrea Frapporti
    • , Caridad Miró Pina
    •  & Sandra Duharcourt

  • Article
    | Open Access

    It is expected that plasmids are costly and therefore that selection is required to maintain them within bacterial populations. Here, Wein et al. show that plasmid stability can emerge even in the absence of positive selection and that loss may be determined by transcription-replication conflict.

    • Tanita Wein
    • , Nils F. Hülter
    •  & Tal Dagan

  • Article
    | Open Access

    Little is known about the internal anatomy of early eyes. Here, Scholtz and colleagues show the internal eye structures from fossils of two genera of trilobites, which support an ancestral apposition eye with crystalline cones in Trilobita and a close affinity with Mandibulata.

    • Gerhard Scholtz
    • , Andreas Staude
    •  & Jason A. Dunlop

  • Article
    | Open Access

    In asexual populations selection at different genomic loci can interfere with each other. Here, using a biophysical model of molecular evolution the authors show that interference results in long-term degradation of molecular function, an effect that strongly depends on genome size.

    • Torsten Held
    • , Daniel Klemmer
    •  & Michael Lässig

  • Review Article
    | Open Access

    The reciprocal interaction between genetic and cultural evolution is well recognised in humans. Here, Whitehead and colleagues review the growing body of evidence that culture is also a major driver of both neutral and adaptive genetic evolution in non-human animals.

    • Hal Whitehead
    • , Kevin N. Laland
    •  & Andrew Whiten

  • Article
    | Open Access

    Different classes of human evolved regulatory elements are located in non-coding regions of the genome. The authors connect the expansion of the cortical surface and connectivity with human evolved elements and show that their target genes are involved in neurodevelopmental disease susceptibility.

    • Hyejung Won
    • , Jerry Huang
    •  & Daniel H. Geschwind

  • Article
    | Open Access

    Dog breeds differ in evolutionary age and admixture with wolves, enabling comparison across domestication stages. Here, Hansen Wheat et al. show that correlations among behaviours are decoupled in modern breeds compared to ancient breeds and suggest this reflects a recent shift in selection pressure.

    • Christina Hansen Wheat
    • , John L. Fitzpatrick
    •  & Hans Temrin

  • Article
    | Open Access

    Although the centromere-specific histone CENP-A usually assembles on specific genomic sequences, centromeric DNA is not conserved. Here the authors characterize the genome and centromeres of related fission yeasts and provide evidence that Schizosaccharomyces centromere DNA possesses intrinsic conserved properties that promote assembly of CENP-A chromatin.

    • Pin Tong
    • , Alison L. Pidoux
    •  & Robin C. Allshire

  • Article
    | Open Access

    Domesticated maize and some varieties of wild teosinte grow in close proximity in parts of Mexico but rarely cross-fertilize. Here the authors show that a pistil-expressed pectin methylesterase, encoded by a gene within the Teosinte crossing barrier1-s haplotype, prevents fertilization of these teosintes by incompatible pollen.

    • Yongxian Lu
    • , Samuel A. Hokin
    •  & Mathew M. S. Evans

  • Article
    | Open Access

    Helicobacter pylori, a bacterial pathogen that infects human stomachs, has high genetic diversity across hosts. Here, Ailloud et al. reveal genetic structuring of H. pylori populations among different stomach regions of individual hosts and find signals of genetic associations with stomach region.

    • Florent Ailloud
    • , Xavier Didelot
    •  & Sebastian Suerbaum

  • Article
    | Open Access

    Chemical imaging and spectroscopy have previously been used to identify eumelanin residue in fossils and infer dark coloration. Here, Manning and colleagues develop an approach to identify pheomelanin (red pigment) residues and ascertain their distribution in fossils.

    • Phillip L. Manning
    • , Nicholas P. Edwards
    •  & Roy A. Wogelius

  • Article
    | Open Access

    Host phylogeny and diet are major explanatory factors of animal gut microbiome diversity, but our understanding of these associations is limited by a focus on captive animals and a narrow taxonomic scope. Here, the authors isolate evolutionary and ecological drivers of gut microbiomes from wild mammals, birds, reptiles, amphibians, and fish.

    • Nicholas D. Youngblut
    • , Georg H. Reischer
    •  & Andreas H. Farnleitner

  • Article
    | Open Access

    The heat-sensitive ion channel TRPV1 is essential to temperature sensing in mammals and other animals. Here the authors find that the platypus form of TRPV1 does not desensitize, identify the mechanism underlying this property, and show that knock-in of this form of the receptor in mice leads to deficits in heat sensitivity.

    • Lei Luo
    • , Yunfei Wang
    •  & Ren Lai

  • Article
    | Open Access

    Our understanding of the origin of jaws is hampered by the poor fossil preservation of pharyngeal morphology. Here, Dearden et al. provide insight into the skull conditions of early jawed vertebrates through three-dimensional computed tomography imaging of a 415 million year old stem-chondrichthyan.

    • Richard P. Dearden
    • , Christopher Stockey
    •  & Martin D. Brazeau

  • Article
    | Open Access

    What drives changes in morphological diversity? Here, Arbour et al. analyse skull 3D shape evolution across the bat radiation using µCT scan data, finding two phases of skull shape diversification, early adaptive shifts related to echolocation, and more recent shifts related to diet transitions.

    • Jessica H. Arbour
    • , Abigail A. Curtis
    •  & Sharlene E. Santana

  • Article
    | Open Access

    Sexual selection has the potential to either increase or decrease absolute fitness. Here, Cally et al. perform a meta-analysis of 65 experimental evolution studies and find that sexual selection on males tends to increase fitness, especially in females evolving under stressful conditions.

    • Justin G. Cally
    • , Devi Stuart-Fox
    •  & Luke Holman

  • Article
    | Open Access

    The pygmy hog (Porcula salvania), now highly endangered and restricted in a small region at the southern foothills of the Himalaya, is the only suid species in mainland Eurasia that outlived the expansion of wild boar (Sus scrofa). Here, the authors analyze genomes of pygmy hog and related suid species, and identify signals of introgression among these species.

    • Langqing Liu
    • , Mirte Bosse
    •  & Ole Madsen

  • Article
    | Open Access

    Protein phosphorylation has various regulatory functions. Here, the authors map 241 phosphorylation hotspot regions across 40 eukaryotic species, showing that they are enriched at interfaces and near catalytic residues, and enable the discovery of functionally important phospho-sites.

    • Marta J. Strumillo
    • , Michaela Oplová
    •  & Pedro Beltrao

  • Article
    | Open Access

    The archaeological record provides large ensembles of radiocarbon dates which can be used to infer long-term changes in human demography. Here, the authors analyse the radiocarbon record of the Iberian peninsula, finding support for a bottleneck during the Last Glacial-Interglacial transition

    • Javier Fernández-López de Pablo
    • , Mario Gutiérrez-Roig
    •  & Sergi Lozano

  • Article
    | Open Access

    What factors explain variation in the pace and trajectory of evolutionary divergence between lineages? Here, the authors show that a proxy measure for sexual selection intensity predicts both the rate and direction of plumage colour evolution in a diverse radiation of New World passerine birds.

    • Christopher R. Cooney
    • , Zoë K. Varley
    •  & Gavin H. Thomas

  • Article
    | Open Access

    Queen pheromones are used by eusocial insects to regulate all aspects of colony life. Here, Holman et al. compare the effects of queen pheromone on gene expression and splicing in four eusocial insect species, giving insight into the mechanism and evolution of division of reproductive labour.

    • Luke Holman
    • , Heikki Helanterä
    •  & Alexander S. Mikheyev

  • Article
    | Open Access

    The mechanisms that accommodate variable external dependencies in evolution are not clear. Here, the authors show that switches between external and internal metabolic controls of carotenoid-producing networks in birds are linked to shifts in evolutionary rates, with internalization of control resulting in bursts of evolutionary diversification.

    • Alexander V. Badyaev
    • , Alexander B. Posner
    •  & Dawn M. Higginson

  • Article
    | Open Access

    Many abiotic and biotic factors shape the macroevolution of phenotype, but these factors are rarely disentangled across large radiations. Here, Miller et al. investigate plumage evolution across woodpeckers, finding influences of habitat and climate, but also convergence apparently driven by mimicry

    • Eliot T. Miller
    • , Gavin M. Leighton
    •  & Russell A. Ligon

  • Article
    | Open Access

    Information on protein sequence variability and conservation can be leveraged to identify functionally important regions. Here, the authors develop new conservation measures that exploit taxonomy distances and LIST, a tool for predicting deleteriousness of human variants.

    • Nawar Malhis
    • , Steven J. M. Jones
    •  & Jörg Gsponer

  • Article
    | Open Access

    Females are choosy about their mates, which should erode genetic diversity but in practice does not. Here, selection and genomic resequencing of Drosophila supports the hypothesis that this paradox can be explained by sexually selected traits reflecting genetic variation in condition.

    • Robert J. Dugand
    • , Joseph L. Tomkins
    •  & W. Jason Kennington

  • Article
    | Open Access

    The early evolution of the deuterostomes is not well resolved. Here, Topper and colleagues investigate the early Cambrian metazoan Yanjiahella biscarpa, concluding that it is a stem echinoderm, is among the oldest known deuterstomes, and supports an ancestral enteropneust body plan in hemichordates.

    • Timothy P. Topper
    • , Junfeng Guo
    •  & Zhifei Zhang

  • Article
    | Open Access

    Although male genital shape is known to evolve rapidly in response to sexual selection, relatively little is known about the evolution of female genital shape. Here, the authors show that across onthophagine dung beetles, female genital shape has diverged much more rapidly than male genital shape.

    • Leigh W. Simmons
    •  & John L. Fitzpatrick

  • Article
    | Open Access

    Sociality explains substantial variation in ageing across species, but less is known about this relationship within species. Here, the authors show that female dominant Seychelles warblers with helpers at the nest have higher late-life survival and lower telomere attrition and the probability of having helpers increases with age.

    • Martijn Hammers
    • , Sjouke A. Kingma
    •  & David S. Richardson

  • Article
    | Open Access

    Central Anatolia harbored some of the earliest farming societies outside the Fertile Crescent of the Near East. Here, the authors report and analyze genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers, and suggest high genetic continuity between the hunter-gatherers and early farmers of Anatolia.

    • Michal Feldman
    • , Eva Fernández-Domínguez
    •  & Johannes Krause

  • Article
    | Open Access

    While the role of effective population size (Ne) in explaining variation in genetic diversity has received much attention, the role of spontaneous mutation rate is largely ignored. Here, Xu et al. show that giant duckweed has a high Ne yet low genetic diversity, likely due to its low mutation rate.

    • Shuqing Xu
    • , Jessica Stapley
    •  & Meret Huber

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