Evolutionary developmental biology

  • Article
    | Open Access

    The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.

    • Shalu Jhanwar
    • , Jonas Malkmus
    •  & Rolf Zeller
  • Article
    | Open Access

    The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.

    • Jonas Malkmus
    • , Laurène Ramos Martins
    •  & Rolf Zeller
  • Article
    | Open Access

    Modular, rather than integrated systems are classically thought to allow functional diversity to evolve rapidly. A study of cichlid fish shows integration between divergent jaw systems at the phylogenetic, population, and genetic scales, suggesting integration can and does facilitate rapid, coordinated trait evolution.

    • Andrew J. Conith
    •  & R. Craig Albertson
  • Article
    | Open Access

    The common ancestor of all living arthropods had biramous postantennal appendages, with an endopodite and exopodite branching off the limb base. This study uses microtomographic imaging of the Cambrian arthropod Leanchoilia to reveal a previously undetected exite at the base of most appendages, suggesting a deeper origin for exites in arthropod phylogeny.

    • Yu Liu
    • , Gregory D. Edgecombe
    •  & Xianguang Hou
  • Article
    | Open Access

    Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

    • Joana P. Bernardes
    • , Uwe John
    •  & Lutz Becks
  • Article
    | Open Access

    The authors show in Nematostella that the more orally expressed β-catenin targets repress the more aborally expressed β-catenin targets, thus patterning the oral-aboral axis. This likely represents the common mechanism of β-catenin-dependent axial patterning shared by Cnidaria and Bilateria.

    • Tatiana Lebedeva
    • , Andrew J. Aman
    •  & Grigory Genikhovich
  • Article
    | Open Access

    In addition to major innovations in their locomotor system, early birds evolved highly derived skulls. Here, Wang et al. three dimensionally reconstruct the skull of a new enantiornithine bird from the Early Cretaceous that illustrates the early avialan transitions in skull morphology and function.

    • Min Wang
    • , Thomas A. Stidham
    •  & Zhonghe Zhou
  • Article
    | Open Access

    Here, the authors show that the Hox genes Antennapedia (Antp) and Ultrabithorax (Ubx) control flight appendage morphology in Drosophila. This role is dependent on a particular spatial expression profile and dosage, which was also found in evolutionary distant four-winged insect species.

    • Rachel Paul
    • , Guillaume Giraud
    •  & Samir Merabet
  • Article
    | Open Access

    The evolution of metamorphic species may be constrained by different ecologies of the larval and adult stages. Here, Bardua et al. show that in frogs, adult ecology is more important than larval ecology for skull evolution, but species that don’t feed as tadpoles evolve faster than those that do.

    • Carla Bardua
    • , Anne-Claire Fabre
    •  & Anjali Goswami
  • Article
    | Open Access

    The Cambrian is known as a period of rapid animal diversification, but the development of these animals is not well characterized. Here, Steiner et al. describe a new assemblage of Cambrian eggs, embryos and early postembryonic stages from Mongolia that provides insight into ancient bilaterian development and evolution.

    • Michael Steiner
    • , Ben Yang
    •  & Philip Donoghue
  • Article
    | Open Access

    Sex chromosome gene content and expression is unusual. Here the authors use single cell RNA-Seq on Drosophila larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, while genes on the single Y chromosome become maximally active in primary spermatocytes.

    • Sharvani Mahadevaraju
    • , Justin M. Fear
    •  & Brian Oliver
  • Article
    | Open Access

    Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

    • Shingo Miyauchi
    • , Enikő Kiss
    •  & Francis M. Martin
  • Article
    | Open Access

    Clonal ascidians are able to undergo whole body regeneration (WBR), where entire new bodies can be regenerated from blood vessel fragments. Here, the authors provide evidence in Botrylloides diegensis supporting pou3 and vasa expressing blood-borne cells isolated with anti-IA6 antibody as candidate stem cells responsible for WBR.

    • Susannah H. Kassmer
    • , Adam D. Langenbacher
    •  & Anthony W. De Tomaso
  • Article
    | Open Access

    Spiralians have ciliary bands, used for locomotion and feeding, but defining molecular features of these structures are unknown. Here, the authors report a gene, Lophotrochin, that contains a protein domain only found in spiralians, and specifically expressed in diverse ciliary bands across the group, which provides a molecular signature for these structures.

    • Longjun Wu
    • , Laurel S. Hiebert
    •  & J. David Lambert
  • Article
    | Open Access

    Phenotypic robustness to environmental variation is seemingly at odds with evolvability. Here, the authors analyze carotenoid use and accommodation in feather development across a recent avian range expansion and show that cooption of a stress-buffering mechanism can reconcile robustness and evolvability.

    • Ahva L. Potticary
    • , Erin S. Morrison
    •  & Alexander V. Badyaev
  • Article
    | Open Access

    The teleost Astyanax mexicanus has sighted morphs living in surface rivers and various blind morphs living in caves. Here, the authors suggest that loss of eyes in cave morphs is linked to mutations in the cystathionine ß-synthase a (cbsa) gene, which cause eye degeneration by disrupting function of the optic circulatory system.

    • Li Ma
    • , Aniket V. Gore
    •  & William R. Jeffery
  • Article
    | Open Access

    Genomic studies of paleopteran insects, such as mayflies, are needed to reconstruct early insect evolution. Here, Almudi and colleagues present the genome of the mayfly Cloeon dipterum and use transcriptomics to characterize its adaptations to distinct habitats and the origin of insect wings.

    • Isabel Almudi
    • , Joel Vizueta
    •  & Fernando Casares
  • Article
    | Open Access

    Developmental duration is a key life-history trait. Cooney et al. compile data on 3096 bird species to quantify the degree to which phylogenetic history, body size and ecological variables like predation risk or breeding phenology influence variation in developmental duration.

    • Christopher R. Cooney
    • , Catherine Sheard
    •  & Alison E. Wright
  • Article
    | Open Access

    How traits specific to modern humans have evolved is difficult to study. Here, Gokhman et al. compare measured and reconstructed DNA methylation maps of present-day humans, archaic humans and chimpanzees and find that genes that affect vocal tract and facial anatomy show methylation changes between archaic and modern humans.

    • David Gokhman
    • , Malka Nissim-Rafinia
    •  & Liran Carmel
  • Article
    | Open Access

    A transposon insertion in the regulatory region of maize Tb1 gene leads to increased apical dominance and a reduction of tillering. Here, the authors showed that a duplicated rice Tb1 orthologue, OsTb2, has gained a regulatory effect on tillering opposite that of OsTb1 during artificial selection only in upland japonica rice.

    • Jun Lyu
    • , Liyu Huang
    •  & Fengyi Hu
  • Article
    | Open Access

    Tradeoffs are central to life history theory and evolutionary biology, yet almost nothing is known about their mechanistic basis. Here the authors characterize one such mechanism and find a transposable element insertion is associated with the switch between alternative life history strategies.

    • Alyssa Woronik
    • , Kalle Tunström
    •  & Christopher W. Wheat
  • Article
    | Open Access

    The cerebellum is critical in sensory-motor control and is structurally diverse across vertebrates. Here, the authors investigate the evolutionary relationship between locomotory mode and cerebellum architecture across squamates by integrating study of gene expression, cell distribution, and 3D morphology.

    • Simone Macrì
    • , Yoland Savriama
    •  & Nicolas Di-Poï
  • Article
    | Open Access

    Vertebrate telencephalon formation requires Foxg-Fgf8 cross-regulation, but while ascidians express Foxg in the neural plate, they lack a telencephalon. Here the authors show that Foxg loss does not affect ascidian brain formation, indicating that telencephalon evolution required recruitment of Fgf downstream of Foxg.

    • Boqi Liu
    •  & Yutaka Satou
  • Article
    | Open Access

    An understanding of the ancestral state of the neural crest (NC) gene regulatory network (GRN) gives insight into vertebrate evolution. Here, the authors use transcriptomic and chromatin accessibility analyses of the lamprey NC, as well as cross-species enhancer assays, to identify GRN elements conserved throughout vertebrates.

    • Dorit Hockman
    • , Vanessa Chong-Morrison
    •  & Tatjana Sauka-Spengler
  • Article
    | Open Access

    Numerous tissues are derived from the lateral plate mesoderm (LPM) but how this is specified is unclear. Here, the authors identify a pan-LPM reporter activity found in the zebrafish draculin (drl) gene that also shows transgenic activity in LPM-corresponding territories of several chordates, including chicken, axolotl, lamprey, Ciona, and amphioxus.

    • Karin D. Prummel
    • , Christopher Hess
    •  & Christian Mosimann
  • 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

    Mechanisms coupling Hox genes to neural crest are largely unknown. Here, the authors use cross species regulatory comparisons between the Hox2 genes of jawed vertebrates and lamprey, a jawless vertebrate, finding a conserved ancestral mechanism for Hox2 neural crest regulation.

    • Hugo J. Parker
    • , Bony De Kumar
    •  & Robb Krumlauf
  • Article
    | Open Access

    Neural architecture may be shaped by selection, but is likely also constrained by development. Here, Keesey and colleagues find an inverse relationship between allocation towards visual and olfactory sensory systems across the genus Drosophila, which may reflect a developmental trade-off.

    • Ian W. Keesey
    • , Veit Grabe
    •  & Bill S. Hansson
  • Article
    | Open Access

    Hydra regenerate various body parts on amputation by activation of the appropriate organiser, but how head formation is controlled is unclear. Here, the authors identify the transcription factor Sp5 as restricting head formation, by being activated by beta-catenin and then acting as a repressor of Wnt3.

    • Matthias C. Vogg
    • , Leonardo Beccari
    •  & Brigitte Galliot
  • Article
    | Open Access

    The evolutionary mechanisms leading to the development of sperm are poorly understood. Here, the authors infer that neofunctionalisation and expression changes of the orthologue of DUO1 in algal ancestors of land plants were key events for sperm differentiation and sexual reproduction in this lineage.

    • Asuka Higo
    • , Tomokazu Kawashima
    •  & Takashi Araki
  • Article
    | Open Access

    Certain genotypes define developmental plasticity and discrete morphologies, but a mechanism as to how this arises is unclear. Here, the authors show that dosage-specific sulfotransferase (SEUD-1) expression specifies which mouthparts are expressed in the nematode Pristionchus pacificus, dependent on the environment.

    • Linh T. Bui
    • , Nicholas A. Ivers
    •  & Erik J. Ragsdale
  • Article
    | Open Access

    The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier.

    • Toshiya Ando
    • , Takeshi Matsuda
    •  & Teruyuki Niimi
  • Article
    | Open Access

    The Mll3/4 histone methyltransferases can act as tumour suppressors in humans. Here, the authors identify three orthologs of mammalian MLL3/4 in the planarian Schmidtea mediterranea and show that knockdown causes outgrowths in regenerating animals, suggesting that the tumour suppressive function of these genes is deeply conserved.

    • Yuliana Mihaylova
    • , Prasad Abnave
    •  & A. Aziz Aboobaker
  • Article
    | Open Access

    In humans, caspase-5 is an LPS sensor that can induce gasdermin D cleavage and pyroptosis. Here, the authors show that zebrafish caspy2 is a functional homolog as it also senses cytosolic LPS to activate the noncanonical inflammasome and to protect against bacterial infection, but it does so via pyrin death domain interactions.

    • Dahai Yang
    • , Xin Zheng
    •  & Qin Liu
  • Article
    | Open Access

    Hox genes regulate anterior–posterior axis formation but their role in cnidarians is unclear. Here, the authors disrupt Hox genes NvAx1 and NvAx6 in the starlet sea anemone, Nematostella vectensis, showing antagonist function in patterning the oral–aboral axis and a link to Wnt signaling.

    • Timothy Q. DuBuc
    • , Thomas B. Stephenson
    •  & Mark Q. Martindale
  • Article
    | Open Access

    The AID/APOBEC cytidine deaminase family are nucleic acid editors, important for antigen receptor expression and thought to have evolved along with vertebrate adaptive immunity. Here the authors show this family may have evolved prior to adaptive immunity as members with cytidine deaminase activity are present and functional in invertebrate sea urchins and brachiopods.

    • Mei-Chen Liu
    • , Wen-Yun Liao
    •  & Sebastian D. Fugmann
  • Article
    | Open Access

    Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.

    • Jordi Paps
    •  & Peter W. H. Holland
  • Article
    | Open Access

    The red-shouldered soapberry bug, Jadera haematoloma, is a potential model system for developmental plasticity. Here, the authors show that the reaction norm for wing polyphenism has evolved in a recently derived ecotype and identify insulin signaling as a candidate pathway underlying this adaptive change.

    • Meghan M. Fawcett
    • , Mary C. Parks
    •  & David R. Angelini
  • Article
    | Open Access

    The arthropod head is complex and its evolution has been difficult to reconstruct. Here, Park et al. describe new specimens of the Cambrian stem-group euarthropod Kerygmachela that preserve evidence of primitive compound eyes and a unipartite brain, providing insight into the structure of the early arthropod head.

    • Tae-Yoon S. Park
    • , Ji-Hoon Kihm
    •  & Jakob Vinther
  • Article
    | Open Access

    Fossil juvenile Mesozoic birds are exceedingly rare and can provide important insight into the early evolution of avian development. Here, Knoll et al. describe one of the smallest known Mesozoic avians, which indicates a clade-wide asynchronous pattern of osteogenesis and great variation in basal bird hatchling size and skeletal maturation tempo.

    • Fabien Knoll
    • , Luis M. Chiappe
    •  & Jose Luis Sanz
  • 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

    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