Table of Contents

Volume 528 Number 7582 pp307-430

17 December 2015

About the cover

Male (left) and female Atlantic salmon under Northern lights in the River Alta, Norway, in a double-exposure taken with the same camera, in the same location and on the same night. Craig Primmer and colleagues use genome-wide association studies for age at maturity in Atlantic salmon to show that a single gene, VGLL3, strongly influences the variation in age at maturity, and therefore body size — a key trait in an important fished species. They find that the VGLL3 locus is an example of sex-dependent dominance, promoting earlier and later maturation in males and females, respectively. This mechanism provides a resolution for sexual conflict in this trait, for which selection favours different reproductive ages in the two sexes. Females benefit from being large (5–15 kg), and stay longer at sea feeding by maturing later, while males can have high fitness maturing at smaller sizes (1–3 kg). This discovery will have a substantial impact on population management of Atlantic salmon, where a decrease in the frequency of late maturation has been observed in many populations. Cover: Audun Rikardsen www.audunrikardsen.com

This Week

Editorials

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  • A seismic shift

    After 25 years of divisive debate, the governments of the world unite in Paris to fight global warming. But the hard work must start now.

  • Crop conundrum

    The EU should decide definitively whether gene-edited plants are covered by GM laws.

  • Science for peace

    The German research community can benefit from the influx of migrants.

World View

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Seven Days

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News in Focus

Feature

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  • The science myths that will not die

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    False beliefs and wishful thinking about the human experience are common. They are hurting people — and holding back science.

    • Megan Scudellari

comment

  • Chemistry: Why synthesize?

    Philip Ball ponders the many reasons that chemists make molecules, and weighs what is lost, and gained, when they don't.

Books and Arts

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Careers

Features

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naturejobs job listings and advertising features

Futures

  • Citadel

    How to survive the solstice.

    • John Gilbey

Specials

Outlook: Prostate cancer

Produced with support from: Ferring Pharmaceuticals and a grant from Astellas Pharma Global Development, Inc. and Medivation, Inc.

Outlook

research

Review

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  • Rarity in mass extinctions and the future of ecosystems

    • Pincelli M. Hull
    • Simon A. F. Darroch
    • Douglas H. Erwin

    The fossil record provides a nuanced view of ecosystem collapse over intervals of mass extinction, with abundant, biomineralizing and widespread species preferentially preserved; here the authors collate evidence for ‘mass rarity’ during these intervals, and suggest that the increasing rarity of modern species, rather than their outright extinction, may be a better metric for comparing the current biodiversity crisis to the ‘Big Five’ mass extinctions in the Earth’s history.

Articles

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  • Growth and splitting of neural sequences in songbird vocal development

    • Tatsuo S. Okubo
    • Emily L. Mackevicius
    • Hannah L. Payne
    • Galen F. Lynch
    • Michale S. Fee

    Neural sequences recorded from the vocal premotor area HVC in juvenile birds learning song ‘syllables’ show ‘prototype’ syllables forming early, with multiple new highly divergent neural sequences emerging from this precursor syllable as learning progresses.

  • Acute off-target effects of neural circuit manipulations

    • Timothy M. Otchy
    • Steffen B. E. Wolff
    • Juliana Y. Rhee
    • Cengiz Pehlevan
    • Risa Kawai
    • Alexandre Kempf
    • Sharon M. H. Gobes
    • Bence P. Ölveczky

    Transient manipulation of neural activity is widely used to probe the function of specific circuits, yet such targeted perturbations could also have indirect effects on downstream circuits that implement separate and independent functions; a study to test this reveals that transient perturbations of specific circuits in mammals and songbirds severely impair learned skills that recover spontaneously after permanent lesions of the same brain areas.

    See also
  • Functional overlap of the Arabidopsis leaf and root microbiota

    • Yang Bai
    • Daniel B. Müller
    • Girish Srinivas
    • Ruben Garrido-Oter
    • Eva Potthoff
    • Matthias Rott
    • Nina Dombrowski
    • Philipp C. Münch
    • Stijn Spaepen
    • Mitja Remus-Emsermann
    • Bruno Hüttel
    • Alice C. McHardy
    • Julia A. Vorholt
    • Paul Schulze-Lefert

    The microbiota of the rhizosphere (roots) and phyllosphere (leaves) of healthy plants consist of taxonomically structured bacterial communities; here the majority of species representing the main bacterial phyla from these two organs were isolated and genomes of about 400 representative bacteria were sequenced; the resources of cultured bacteria, corresponding genomes and a gnotobiotic plant system enabled an examination of the taxonomic overlap and functional specialization between the rhizosphere and phyllosphere bacterial microbiota.

    See also
  • Phosphorylation and linear ubiquitin direct A20 inhibition of inflammation

    • Ingrid E. Wertz
    • Kim Newton
    • Dhaya Seshasayee
    • Saritha Kusam
    • Cynthia Lam
    • Juan Zhang
    • Nataliya Popovych
    • Elizabeth Helgason
    • Allyn Schoeffler
    • Surinder Jeet
    • Nandhini Ramamoorthi
    • Lorna Kategaya
    • Robert J. Newman
    • Keisuke Horikawa
    • Debra Dugger
    • Wendy Sandoval
    • Susmith Mukund
    • Anuradha Zindal
    • Flavius Martin
    • Clifford Quan
    • Jeffrey Tom
    • Wayne J. Fairbrother
    • Michael Townsend
    • Søren Warming
    • Jason DeVoss
    • Jinfeng Liu
    • Erin Dueber
    • Patrick Caplazi
    • Wyne P. Lee
    • Christopher C. Goodnow
    • Mercedesz Balazs
    • Kebing Yu
    • Ganesh Kolumam
    • Vishva M. Dixit

    The authors define molecular mechanisms by which distinct domains of the ubiquitin editing enzyme A20 contribute to the regulation of inflammation and cell death.

Letters

Top
  • A large-scale dynamo and magnetoturbulence in rapidly rotating core-collapse supernovae

    • Philipp Mösta
    • Christian D. Ott
    • David Radice
    • Luke F. Roberts
    • Erik Schnetter
    • Roland Haas

    Global, three-dimensional simulations of rapidly rotating massive stars show that turbulence driven by magnetohydrodynamic instability is a promising mechanism for the formation of pulsars and magnetars, the latter potentially powering hyperenergetic and superluminous supernovae.

  • Multi-element logic gates for trapped-ion qubits

    • T. R. Tan
    • J. P. Gaebler
    • Y. Lin
    • Y. Wan
    • R. Bowler
    • D. Leibfried
    • D. J. Wineland

    Harnessing the entanglement of different ionic species could bring new flexibility in quantum computing, and now two groups independently demonstrate entanglement between different atomic species; Tan et al. achieve entanglement between different elements, whereas the related paper by Ballance et al. shows entanglement between different atomic isotopes, together demonstrating a first step towards mixed-species quantum logic.

    See also
    See also
  • Hybrid quantum logic and a test of Bell’s inequality using two different atomic isotopes

    • C. J. Ballance
    • V. M. Schäfer
    • J. P. Home
    • D. J. Szwer
    • S. C. Webster
    • D. T. C. Allcock
    • N. M. Linke
    • T. P. Harty
    • D. P. L. Aude Craik
    • D. N. Stacey
    • A. M. Steane
    • D. M. Lucas

    Harnessing the entanglement of different ionic species could bring new flexibility in quantum computing, and now two groups independently demonstrate entanglement between different atomic species; Ballance et al. achieve entanglement between different atomic isotopes, whereas the related paper by Tan et al. shows entanglement between different elements, together demonstrating a first step towards mixed-species quantum logic.

    See also
    See also
  • Radiative heat transfer in the extreme near field

    • Kyeongtae Kim
    • Bai Song
    • Víctor Fernández-Hurtado
    • Woochul Lee
    • Wonho Jeong
    • Longji Cui
    • Dakotah Thompson
    • Johannes Feist
    • M. T. Homer Reid
    • Francisco J. García-Vidal
    • Juan Carlos Cuevas
    • Edgar Meyhofer
    • Pramod Reddy

    Nanoscale radiative heat transfer between both dielectric and metal surfaces separated by gaps as small as two nanometres is characterized by large gap-dependent heat transfer enhancements that are accurately modelled by the theoretical framework of fluctuational electrodynamics and has important implications for technological design.

  • Spatial and temporal distribution of mass loss from the Greenland Ice Sheet since AD 1900

    • Kristian K. Kjeldsen
    • Niels J. Korsgaard
    • Anders A. Bjørk
    • Shfaqat A. Khan
    • Jason E. Box
    • Svend Funder
    • Nicolaj K. Larsen
    • Jonathan L. Bamber
    • William Colgan
    • Michiel van den Broeke
    • Marie-Louise Siggaard-Andersen
    • Christopher Nuth
    • Anders Schomacker
    • Camilla S. Andresen
    • Eske Willerslev
    • Kurt H. Kjær

    Aerial imagery from the 1980s is used to calculate ice mass loss around the entire Greenland Ice Sheet from 1900 to the present; during the twentieth century the Greenland Ice Sheet contributed at least 25.0 ± 9.4 millimetres of global-mean sea level rise.

    See also
  • Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

    • Nicola J. Barson
    • Tutku Aykanat
    • Kjetil Hindar
    • Matthew Baranski
    • Geir H. Bolstad
    • Peder Fiske
    • Céleste Jacq
    • Arne J. Jensen
    • Susan E. Johnston
    • Sten Karlsson
    • Matthew Kent
    • Thomas Moen
    • Eero Niemelä
    • Torfinn Nome
    • Tor F. Næsje
    • Panu Orell
    • Atso Romakkaniemi
    • Harald Sægrov
    • Kurt Urdal
    • Jaakko Erkinaro
    • Sigbjørn Lien
    • Craig R. Primmer

    Age at maturity in Atlantic salmon (Salmo salar) is governed to a substantial extent by a locus showing dominance reversal, providing a resolution for sexual conflict in this trait, for which selection favours different ages in the two sexes.

  • Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons

    • Alexandra Gennaris
    • Benjamin Ezraty
    • Camille Henry
    • Rym Agrebi
    • Alexandra Vergnes
    • Emmanuel Oheix
    • Julia Bos
    • Pauline Leverrier
    • Leon Espinosa
    • Joanna Szewczyk
    • Didier Vertommen
    • Olga Iranzo
    • Jean-François Collet
    • Frédéric Barras

    The identification of an enzymatic system repairing proteins containing oxidized methionine in the bacterial cell envelope, a compartment particularly susceptible to oxidative damage by host defence mechanisms.

  • Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

    • Derek A. Oldridge
    • Andrew C. Wood
    • Nina Weichert-Leahey
    • Ian Crimmins
    • Robyn Sussman
    • Cynthia Winter
    • Lee D. McDaniel
    • Maura Diamond
    • Lori S. Hart
    • Shizhen Zhu
    • Adam D. Durbin
    • Brian J. Abraham
    • Lars Anders
    • Lifeng Tian
    • Shile Zhang
    • Jun S. Wei
    • Javed Khan
    • Kelli Bramlett
    • Nazneen Rahman
    • Mario Capasso
    • Achille Iolascon
    • Daniela S. Gerhard
    • Jaime M. Guidry Auvil
    • Richard A. Young
    • Hakon Hakonarson
    • Sharon J. Diskin
    • A. Thomas Look
    • John M. Maris

    A causal variant is identified at the LMO1 oncogene locus that drives the genetic association of LMO1 with neuroblastoma susceptibility; the causal SNP disrupts a GATA transcription factor binding site within a tissue-specific super-enhancer element in the first intron of LMO1, thereby affecting LMO1 expression.

  • A mechanism for the suppression of homologous recombination in G1 cells

    • Alexandre Orthwein
    • Sylvie M. Noordermeer
    • Marcus D. Wilson
    • Sébastien Landry
    • Radoslav I. Enchev
    • Alana Sherker
    • Meagan Munro
    • Jordan Pinder
    • Jayme Salsman
    • Graham Dellaire
    • Bing Xia
    • Matthias Peter
    • Daniel Durocher

    A mechanism for the repression of homologous recombination in G1, the stage of the cell cycle preceding replication, is determined; the critical aspects are the interaction between BRCA1 and PALB2–BRCA2, and suppression of DNA-end resection.