Evolution articles within Nature Communications

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  • Article
    | Open Access

    Directed evolution is a powerful technique for generating improved biological systems through repeated rounds of mutagenesis and selection. Here the authors engineer the yeast retrotransposon Ty1 to enable the creation of large mutant libraries in vivoand use this system to generate improved variants of single enzymes and multigene pathways.

    • Nathan Crook
    • , Joseph Abatemarco
    •  & Hal S. Alper

  • Article
    | Open Access

    Viruses commonly exchange genetic material with their hosts, but not with species from other domains of life. Here, the authors find that the bacteriophage WO of Wolbachiacontains eukaryotic-like genes, implicating lateral genetic transfer between eukaryotes and viruses infecting bacteria.

    • Sarah R. Bordenstein
    •  & Seth R. Bordenstein

  • Article
    | Open Access

    Previous studies have disagreed over whether efficient or inefficient network structures should be more effective in promoting group performance. Here, Barkoczi and Galesic demonstrate that which structure is superior depends on the social learning strategy used by individuals in the network.

    • Daniel Barkoczi
    •  & Mirta Galesic

  • Article
    | Open Access

    Genes in the cytochrome P450 family have evolved a wide range of functions. Here, Liu et al. reconstruct the evolution of the P450 genes CYP98A8 and CYP98A9in the Brassicales, revealing a complex history of retrotransposition, tandem duplication and neofunctionalization, followed by subfunctionalization or gene loss in specific lineages.

    • Zhenhua Liu
    • , Raquel Tavares
    •  & Hugues Renault

  • Article
    | Open Access

    In many groups of organisms, speciation rates are higher when global temperatures are warmer. Here, Davis et al. find that marine crustaceans in the Anomura clade have higher speciation rates during cooler periods, whereas their freshwater relatives have the more typical relationship of higher speciation rates in warmer periods.

    • Katie E. Davis
    • , Jon Hill
    •  & Matthew A. Wills

  • Article
    | Open Access

    Colistin is an antibiotic used in the treatment of Pseudomonas aeruginosa infections in cystic fibrosis patients. Here, Jochumsen et al. reconstruct the pathways for the molecular evolution of colistin resistance in P. aeruginosaand show that the number of pathways is highly constrained by interactions among genes.

    • Nicholas Jochumsen
    • , Rasmus L. Marvig
    •  & Anders Folkesson

  • Article
    | Open Access

    Feralisation or the reintroduction of domestic animals into the wild population requires adaptation to survive. Here, the authors analyse the genetics of domestic chickens released into the wild and identify genomic regions that are selected for during feralisation.

    • M. Johnsson
    • , E. Gering
    •  & D. Wright

  • Article
    | Open Access

    Many of the theropod dinosaurs, the group including Tyrannosaurus rex, had bony ornamentation on their skulls. Here, Gates et al. show that such ornaments are associated with greater body size and accelerated body size evolution in theropods; however, these relationships are absent in the maniraptoriform dinosaurs, which had evolved pennaceous feathers.

    • Terry A. Gates
    • , Chris Organ
    •  & Lindsay E. Zanno

  • Article
    | Open Access

    Methods for ancestral sequence reconstruction are currently tested with computer simulations, since true biological phylogenies are unknown. Here, Randall et al.build an experimental phylogeny to benchmark the performance of alternate ancestral sequence reconstruction algorithms in inferring ancestral genotypes and phenotypes.

    • Ryan N. Randall
    • , Caelan E. Radford
    •  & Eric A. Gaucher

  • Article
    | Open Access

    Genetic linkage of ecologically relevant traits has been suggested to facilitate sympatric speciation. Here, Fruciano et al. show in sister species of cichlid fish the genetic non-independence of genomic regions responsible for differentiation in body size and pharyngeal jaw morphology, two characters associated with adaptive divergence in sympatry.

    • Carmelo Fruciano
    • , Paolo Franchini
    •  & Axel Meyer

  • Article
    | Open Access

    The acoustic properties of vocal signals generally depend on body size, but in some species males have traits that exaggerate the size conveyed by their vocal signals. Here, Charlton and Reby show that among terrestrial mammals, species with sexual selection for large male body size also have more exaggerated vocal signals for their size.

    • Benjamin D. Charlton
    •  & David Reby

  • Article
    | Open Access

    Morphological characters are generally thought to have higher rates of convergence than molecular characters. Here, Zou and Zhang provide empirical evidence for this assumption and devise a method to improve the accuracy of phylogenetic reconstruction through identifying and removing convergence-prone characters.

    • Zhengting Zou
    •  & Jianzhi Zhang

  • Article
    | Open Access

    The evolution of germ cell specification by maternal germ plasm has been proposed to accelerate vertebrate protein evolution by liberating selective constraints. Whittle and Extavour analyse global rates of protein evolution and find no support for this hypothesis in vertebrates or invertebrates.

    • Carrie A. Whittle
    •  & Cassandra G. Extavour

  • Article
    | Open Access

    Songbirds originated in Australia and have now diversified into approximately 5,000 species found across the world. Here, Moyle et al. combine phylogenomic and biogeographic analyses to show that songbird diversification was associated with the formation of islands providing a route out of Australia.

    • Robert G. Moyle
    • , Carl H. Oliveros
    •  & Brant C. Faircloth

  • Article
    | Open Access

    A recently emerged infectious cancer has caused the near extinction of the Tasmanian devil, but some populations persist. Here, Epstein et al. provide evidence for possible resistance via rapid evolution in two genomic regions that contain cancer-related immune response genes.

    • Brendan Epstein
    • , Menna Jones
    •  & Andrew Storfer

  • Article
    | Open Access

    Mutualisms in which ants protect plants in exchange for food and shelter have arisen independently multiple times. Here, Rubin and Moreau sequence the genomes of three mutualistic ant species and four of their non-mutualistic relatives and show that the transition to mutualism is associated with elevated evolutionary rates across the genome

    • Benjamin E. R. Rubin
    •  & Corrie S. Moreau

  • Article
    | Open Access

    Cells of the yeast Saccharomyces cerevisiaecan mate with other cells of opposite mating type. Here, the authors show that the combination of a pheromone and a pheromone-degrading enzyme allows yeast cells to monitor relative mate abundance within a population and adjust their commitment to sexual reproduction.

    • Alvaro Banderas
    • , Mihaly Koltai
    •  & Victor Sourjik

  • Article
    | Open Access

    Non-parental helpers contribute to offspring care in many species; however, the amount of care provided varies considerably across species. Here, Green et al. perform a phylogenetic comparative analysis of helping behavior in 36 cooperatively-breeding bird species and find that helper effort increases with relatedness to the recipient of care.

    • Jonathan P. Green
    • , Robert P. Freckleton
    •  & Ben J. Hatchwell

  • Article
    | Open Access

    Females tend to invest more than males in caring for offspring, which has been argued to be a consequence of the small initial difference in investment in eggs versus sperm. Here, Fromhage and Jennions formalize this argument mathematically in a model of the evolution of sex roles in parental care.

    • Lutz Fromhage
    •  & Michael D. Jennions

  • Article
    | Open Access

    In some species with internal fertilization, females can mate with multiple males and then manipulate which sperm fertilize the eggs. Here, Alonzo et al.find that by releasing ovarian fluid along with their eggs, female ocellated wrasse are able to influence paternity despite having external fertilization.

    • Suzanne H. Alonzo
    • , Kelly A. Stiver
    •  & Susan E. Marsh-Rollo

  • Article
    | Open Access

    Cooperation requires individuals to sacrifice individual rewards for group benefits. Here, Grimalda, Pondorfer and Tracer show in a foraging society of Papua New Guinea that social image building is a more powerful motivator of social cooperation than altruistic punishment.

    • Gianluca Grimalda
    • , Andreas Pondorfer
    •  & David P. Tracer

  • Article
    | Open Access

    Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.

    • Pedro Gómez
    • , Steve Paterson
    •  & Angus Buckling

  • Article
    | Open Access

    Species radiations can be driven by both adaptive and non-adaptive processes, but the relative importance of these drivers is unknown. Here, Nevado et al. show that multiple radiations in the New World lupins were associated with genome-wide accelerations in both coding and regulatory evolution, suggesting a strong influence of adaptive processes.

    • Bruno Nevado
    • , Guy W. Atchison
    •  & Dmitry A. Filatov

  • Article
    | Open Access

    Co-evolution of a new receptor-ligand pair will affect the downstream signal transduction network. Here, the authors use experimental evolution of yeast mating receptor Ste2 to show the effect of enhanced binding affinity and weakened interactions with the network's negative regulators on protein evolution.

    • Raphaël B. Di Roberto
    • , Belinda Chang
    •  & Sergio G. Peisajovich

  • Article
    | Open Access

    In honeybees, pheromones produced by the queen inhibit reproduction by workers and enforce a eusocial division of labour. Here, Duncan, Hyink and Dearden show that this inhibition is mediated by the Notch signalling pathway in the workers' ovaries.

    • Elizabeth J. Duncan
    • , Otto Hyink
    •  & Peter K. Dearden

  • Article
    | Open Access

    Male pheromones cis-vaccenyl acetate (cVA) and (Z)-7-Tricosene (7-T) mediate chemical mate-guarding in female D. melanogaster. Here, Laturney and Billeter show that females actively eject cVA from their reproductive tract post-copulation, and that cVA in concert with 7-T can reduce female attractiveness post-mating.

    • Meghan Laturney
    •  & Jean-Christophe Billeter

  • Article
    | Open Access

    Sharks’ dorsal fins are thought to assist propulsion and turns while pectoral fins are thought to oppose sharks’ negative buoyancy. Here, Payne and colleagues show that hammerhead sharks use an exaggerated dorsal fin to generate lift by swimming on their side.

    • Nicholas L. Payne
    • , Gil Iosilevskii
    •  & Yuuki Y. Watanabe

  • Article
    | Open Access

    Attine ants, including the leaf-cutting ants, cultivate fungi as their sole source of food. Here, Nygaard et al. use whole genome and transcriptome sequences from seven ant species and their fungal cultivars to reconstruct the reciprocal genetic changes underlying the evolution of the ant-fungus mutualism.

    • Sanne Nygaard
    • , Haofu Hu
    •  & Jacobus J. Boomsma

  • Review Article
    | Open Access

    Sex chromosome evolution begins when recombination between a homologous pair of chromosomes is halted. Here, Wright et al.review our current understanding of the causes and mechanisms of recombination suppression between incipient sex chromosomes and suggest future directions for the field.

    • Alison E. Wright
    • , Rebecca Dean
    •  & Judith E. Mank

  • Article
    | Open Access

    Unicellular social amoebae aggregate to form a multicellular life stage, making them a model system for the evolution of multicellularity. Here, Glöckner et al.use a comparative genomic and transcriptomic approach to determine the origin of the genes essential for multicellularity in the social amoebae.

    • Gernot Glöckner
    • , Hajara M. Lawal
    •  & Pauline Schaap

  • Article
    | Open Access

    The plumage of Cretaceous birds has previously been described only from compression fossils and isolated feathers in amber. Here, Xing et al.describe two 99 million year old bird wings found preserved in amber, enabling new insight into the evolution of feather arrangement, pigmentation, and structure.

    • Lida Xing
    • , Ryan C. McKellar
    •  & Xing Xu

  • Article
    | Open Access

    Social networks have important implications to a variety of ecological and evolutionary processes. Here, Ilany and Akçay develop a social network model and show that inheritance of social contacts leads to networks with properties observed in species such as sleepy lizards and spotted hyenas.

    • Amiyaal Ilany
    •  & Erol Akçay

  • Article
    | Open Access

    Sponges are early-diverging marine organisms that establish complex symbioses with microorganisms. Here, Thomas et al.analyse the microbial communities associated with 81 species of sponges from around the world, shedding light on the ecological and evolutionary drivers of these host-microbe associations.

    • Torsten Thomas
    • , Lucas Moitinho-Silva
    •  & Nicole S. Webster

  • Article
    | Open Access

    Transcription factors Distal-less(Dll) and spalt were co-opted during the evolution of butterfly eyespots. Here, Zhang and Reed use CRISPR/Cas9 genome editing to show that while spalt is a positive regulator of eyespots as predicted, Dll knockouts have positive effects on both eyespot size and number, thus suggesting that Dllis an eyespot repressor, not an activator as previously thought.

    • Linlin Zhang
    •  & Robert D. Reed

  • Article
    | Open Access

    Males help care for offspring in about 10% of mammal species. Here, West and Capellini perform phylogenetic comparative analyses on a sample of 529 mammal species and find that male care is associated with shorter lactation periods by females, larger litters of offspring, and more frequent breeding events.

    • Hannah E. R. West
    •  & Isabella Capellini

  • Article
    | Open Access

    Fruit flies gain valuable information about their environment by sensing chemicals. Here, Arguello et al. show strong signals of recent selection on the chemosensory system of the fruit fly Drosophila melanogaster, consistent with the adaptation of populations to their local chemical environment.

    • J. Roman Arguello
    • , Margarida Cardoso-Moreira
    •  & Richard Benton

  • Article
    | Open Access

    Cryptic genetic variants may not individually show discernible phenotypic effects, but collectively, these polymorphisms can lead to unexpected, genetically complex traits that might be relevant to evolution and disease. Here, the authors use large yeast populations to comprehensively dissect the genetic bases of 17 independent occurrences of a phenotype that arises due to combinations of epistatically interacting cryptic variants.

    • Matthew B. Taylor
    • , Joann Phan
    •  & Ian M. Ehrenreich

  • Article
    | Open Access

    Killer whales have evolved into specialized ecotypes based on hunting strategies and ecological niches. Here, Andrew Foote and colleagues sequenced the whole genome of individual killer whales representing 5 different ecotypes from North Pacific and Antarctic, and show expansion of small founder groups to adapt to specific ecological niches.

    • Andrew D. Foote
    • , Nagarjun Vijay
    •  & Jochen B.W. Wolf

  • Article
    | Open Access

    In vertebrate embryos, Wnt/β-catenin signaling induces an organizer area guiding the formation of body axes and inducing extra axes upon transplantation. Here, Kraus et al. show that Wnt ligands also induce an organizer in a sea anemone, indicating that the organizer dates back over 600 million years.

    • Yulia Kraus
    • , Andy Aman
    •  & Grigory Genikhovich

  • Article
    | Open Access

    Upstream open reading frames (uORFs) can repress gene expression. Here, Guo-Liang Chew and colleagues use bioinformatics approaches to show that conservation of uORF-mediated translational repression is mediated by sequence features in human, mouse and zebrafish genomes.

    • Guo-Liang Chew
    • , Andrea Pauli
    •  & Alexander F. Schier

  • Article
    | Open Access

    Mouse digit patterning is controlled by a Turing network of Bmp, Sox9, and Wnt. Here, Onimaru et al. show that fin patterning in the catshark, Scyliorhinus canicula, is controlled by the same network with a different spatial organization; thus, the Turing network is deeply conserved in limb development.

    • Koh Onimaru
    • , Luciano Marcon
    •  & James Sharpe

  • Article
    | Open Access

    Macroscopic organisms are rare in the fossil record until the Ediacaran Period, beginning 635 million years ago. Here, Zhu et al. report the discovery of 1.56-billion-year-old carbonaceous compression fossils that provide evidence of the evolution of macroscopic, multicellular eukaryotes long before the Ediacaran Period.

    • Shixing Zhu
    • , Maoyan Zhu
    •  & Huan Liu

  • Article
    | Open Access

    Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novogenome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation.

    • Morris Agaba
    • , Edson Ishengoma
    •  & Douglas R. Cavener

  • Article
    | Open Access

    Foraging is energetically demanding for animals like hawkmoths that feed while flying. Here, Haverkamp et al. show that Manduca sexta has an innate preference for feeding on species of Nicotianawhose flower corolla length best matches the length of their proboscis, which allowed more efficient foraging and yielded the highest caloric gain.

    • Alexander Haverkamp
    • , Julia Bing
    •  & Markus Knaden

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