Volume 528 Issue 7582, 17 December 2015

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

Editorial

World View

Research Highlights

Social Selection

Seven Days

News

News Feature

Comment

Books & Arts

Correspondence

Correction

News & Views

  • News & Views |

    Pollution from atmospheric nitrogen deposition is a major threat to biodiversity. The 160-year-old Park Grass experiment has uniquely documented this threat and demonstrated how nitrogen reductions lead to recovery. See Letter p.401

    • David Tilman
    •  & Forest Isbell

    Special:

  • News & Views |

    Control of quantum particles has been extended to enable different types of ion to be entangled — correlated in a non-classical way. This opens up opportunities for the development of new quantum technologies. See Letters p.380 & p.384

    • Tobias Schaetz
  • News & Views |

    Large-scale cultivation and genome sequencing of the bacteria that inhabit the leaves and roots of Arabidopsis plants have paved the way for probing how microbial communities assemble and function. See Article p.364

    • Gwyn A. Beattie
  • News & Views |

    Aerial photographs, remote-sensing observations and geological evidence together provide a reconstruction of mass loss from the Greenland Ice Sheet since 1900 — a great resource for climate scientists. See Letter p.396

    • Beata M. Csatho
  • News & Views |

    The discovery that the gene SRY on the mammalian Y chromosome drives testis development marked a turning point in the decades-long quest to understand the genetic underpinnings and evolution of sex determination.

    • Jennifer A. Marshall Graves

Review Article

  • Review Article |

    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.

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

Article

  • Article |

    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.

    • Tatsuo S. Okubo
    • , Emily L. Mackevicius
    • , Hannah L. Payne
    • , Galen F. Lynch
    •  & Michale S. Fee
  • Article |

    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.

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

    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.

    • 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
  • Article |

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

    • 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

Letter

  • Letter |

    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.

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

    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.

    • T. R. Tan
    • , J. P. Gaebler
    • , Y. Lin
    • , Y. Wan
    • , R. Bowler
    • , D. Leibfried
    •  & D. J. Wineland
  • Letter |

    Web summaryHarnessing 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.

    • 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
  • Letter |

    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.

    • 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
  • Letter |

    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.

    • 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
  • Letter |

    Data from the long-running Park Grass Experiment is used to show that grassland biodiversity is recovering since UK atmospheric nitrogen levels started to decline 25 years ago in all but the most acidic soils.

    • J. Storkey
    • , A. J. Macdonald
    • , P. R. Poulton
    • , T. Scott
    • , I. H. Köhler
    • , H. Schnyder
    • , K. W. T. Goulding
    •  & M. J. Crawley
  • Letter |

    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.

    • 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
  • Letter |

    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.

    • 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
  • Letter |

    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.

    • 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
  • Letter |

    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.

    • 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

Feature

  • Feature |

    The 2015 Nature Awards for Mentoring in Science recognize Chinese scientists who have invested in the next generation.

    • Ed Gerstner

    Collection:

Futures

  • Futures |

    How to survive the solstice.

    • John Gilbey

Outlook

  • Outlook |

    Prostate cancer is one of the most common cancers in men — most will develop the disease if they live long enough. But it is not always deadly, and the number of cases often depends on how hard doctors look for it. By Richard Hodson, infographic by Mohamed Ashour.

    • Richard Hodson
  • Outlook |

    The standard blood test for prostate cancer led to a spike in diagnoses of the disease. But the technique's results are often misleading — and conflicting studies have not helped to forge a consensus.

    • Emily Sohn
  • Outlook |

    Work to determine which prostate cancers are truly dangerous may finally be coming to fruition.

    • Sarah Deweerdt
  • Outlook |

    Surveillance is becoming a watchword for men with less-aggressive prostate cancer. If and when the disease progresses, new and newly-timed therapies are at hand.

    • Meredith Wadman
  • Outlook |

    Strategies to destroy treatment-defying tumours in men with prostate cancer are beginning to make a difference.

    • Neil Savage
  • Outlook |

    Inflammation is an underlying cause of many cancers — and prostate cancer might turn out to be one of their number.

    • Kirsten Weir
  • Outlook |

    In 2004, surgeon Declan Murphy was not convinced that using a robot to remove a cancer-riddled prostate was a significant improvement on keyhole, or laparoscopic, surgery. Eight-hundred robotic procedures later, he has not only changed his mind, but is now director of Robotic Surgery at the Peter MacCallum Cancer Centre in Melbourne, Australia.

    • Bianca Nogrady
  • Outlook |

    Combination therapies that activate the immune system in complementary ways could help more men with prostate cancer to contain their disease long term.

    • Katherine Bourzac
  • Outlook |

    Despite advances in detection and therapy, much about this common malignancy remains unknown. Here are some of the most important unresolved issues.

    • Richard Hodson

Nature Index

  • Nature Index |

    The benefits of economics and history converge with the demands of population growth and sustainability issues in China's most productive research and technology centres.

    • Peng Tian
  • Nature Index |

    The ambition driving China's astonishing progress in the output of high-quality science is particularly strong in some cities, whose growth far outstrips expectation.

    • Sarah O'Meara
  • Nature Index |

    Amid fierce international competitiveness, governments at all levels are responding by orchestrating collaborations between industry and academic institutions.

    • David Cyranoski
  • Nature Index |

    The diverse histories of China's cities strongly influence their collaboration patterns.

    • Hepeng Jia
  • Nature Index |

    A description of the terminology and methodology used in this supplement, and a guide to the functionality available free online at natureindex.com .

  • Nature Index |

    China's leading institutions for high-quality science, ordered by weighted fractional count (WFC) for 2014. Also shown are the total number of articles, and the change in WFC from 2013. Articles are from the 68 journals that comprise the Nature Index (see 'How to use the index', S190 ).

Collections

  • Nature Outlook |

    Prostate cancer

    Most men, if they live long enough, will get prostate cancer. Thanks to screening, many cancers are now caught early. But some men have life-changing treatment for tumours that may never have threatened their health. New biomarker approaches promise more accurate prognoses, whereas treatment advances offer hope for metastatic cancers that so far have been beyond our control.

  • Nature Index |

    Nature Index 2015 China

    The 2015 Nature Index supplement dedicated to China reveals that the country’s output of high-quality science continues to grow — a trend that shows no signs of slowing. With data from three sequential years (2012–2014), the Nature Index has become a powerful tool to explore emerging trends in research. In Nature Index 2015 Chinathe data highlight the contribution of particular Chinese cities to the country’s scientific ascension.

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