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Volume 496 Issue 7445, 18 April 2013

An African coelacanth and diver photographed by Laurent Ballesta in Sodwana Bay, South Africa. The African coelacanth (Latimeria chalumnae) attracted international attention when a specimen was netted off the South African coast in 1938, as coelacanths were thought to have gone extinct 70 million years ago. Now its genome has been sequenced. Phylogenomic analysis resolves the long-standing question of which lobe-finned fish is the closest living relative of the land vertebrates � it is the lungfish, and not the coelacanth. The protein-coding genes of the coelacanth are slowly evolving, which perhaps explains how similar todays coelacanth looks to its 300-million-year-old fossil ancestors. Examination of changes in genes and regulatory elements shows the importance of factors including brain and fin development, immunity and nitrogen excretion in the adaptation of vertebrates to land. Cover: Laurent Ballesta/Andromde Collection

Editorial

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  • The week in science: IVF Nobel laureate Bob Edwards dies, Thermo Fisher Scientific buys up Life Technologies for $13.6 billion, and Romania’s national research council resigns en masse.

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  • Decades after Thomas Lovejoy isolated fragments of the Brazilian rainforest in a grand experiment, researchers are building on his legacy around the world.

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Comment

  • Illegal logging threatens tropical forests and carbon stocks. Governments must work together to build an early warning system, say Jim Lynch and colleagues.

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    • Mark Maslin
    • Martin Sweeting
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  • The way Willi Hennig discovered evolutionary relationships should not be forgotten, say Quentin Wheeler, Leandro Assis and Olivier Rieppel.

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Books & Arts

  • John Carmody enjoys an exhibition that charts the trajectory of anaesthesia from its botanical beginnings.

    • John Carmody
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  • To mark UNESCO's World Book and Copyright Day on 23 April, Josie Glausiusz asks science editors at leading book publishers about trends and technology.

    • Josie Glausiusz
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Correspondence

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News & Views

  • The discovery of lipids on ceramic fragments from the Japanese Jōmon period provides the earliest evidence for the use of pottery for cooking and may prompt a rethink of some aspects of human innovation. See Letter p.351

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  • One of the most extreme starburst galaxies in the early Universe has been identified and characterized. This system shows the rapid formation of a massive galaxy when the Universe was only 6% of its current age. See Letter p.329

    • Desika Narayanan
    • Chris Carilli
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  • The relatedness of animals influences their behaviour, but how do they detect their kin? It seems that nasal sensory neurons differentiate between minute structural differences in urinary peptides that reflect genetic variation.

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  • A laser pulse can switch certain crystals from an insulating phase to a highly conducting phase. The ultrafast molecular motions that drive the transition have been directly observed using electron diffraction. See Letter p.343

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    • Eric Collet
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  • Human activity, such as agricultural fertilizer use, has increased the amount of nitrogen deposited onto forests from the atmosphere. The photosynthetic response to this in evergreen needleleaf forests has been quantified globally.

    • Beverly Law
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  • Predicting when the dynamics of a complex system will undergo a sudden transition is difficult. New experiments show that the spatial distribution of organisms can indicate when such tipping points are near. See Letter p.355

    • Stephen R. Carpenter
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Article

  • Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment.

    • Chris T. Amemiya
    • Jessica Alföldi
    • Kerstin Lindblad-Toh
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  • Here it is shown that ion flux through the TrkH–TrkA complex is upregulated by ATP and downregulated by ADP; solving the X-ray crystal structures of the tetrameric TrkA ring in the absence and presence of TrkH suggests a mechanism by which ATP-induced conformational changes in TrkA augment the activity of TrkH.

    • Yu Cao
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    • Ming Zhou
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  • This study reports the X-ray crystal structure of a Ktr K+ transporter; the structure of this KtrAB complex reveals how the dimeric membrane protein KtrB interacts with the cytosolic octameric KtrA regulatory protein.

    • Ricardo S. Vieira-Pires
    • Andras Szollosi
    • João H. Morais-Cabral
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Letter

  • Quantum mechanical calculations reveal a surprising strain-stiffening phenomenon in two crystalline solids, one of which is cementite, a precipitate found in carbon steels.

    • Chao Jiang
    • Srivilliputhur G. Srinivasan
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  • An analysis of the relative effects of transpiration and evaporation, which can be distinguished by how they affect isotope ratios in water, shows that transpiration is by far the largest water flux from Earth’s continents, representing 80 to 90 per cent of terrestrial evapotranspiration and using half of all solar energy absorbed by land surfaces.

    • Scott Jasechko
    • Zachary D. Sharp
    • Peter J. Fawcett
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  • Chemical analysis of food residues associated with Japanese Jōmon pottery, which dates from the Late Pleistocene epoch and is the oldest pottery so far investigated, shows that most deposits were derived from high-trophic-level aquatic food.

    • O. E. Craig
    • H. Saul
    • P. Jordan
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  • Early warning signals of systems collapse include increased recovery time after perturbations, and here spatially extended, connected yeast populations are used to identify a new warning indicator: recovery length after spatial disturbances.

    • Lei Dai
    • Kirill S. Korolev
    • Jeff Gore
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  • A study of compulsive drug-seeking behaviour in rats reveals that prolonged cocaine self-administration decreases prelimbic cortex activity resulting in increased compulsive drug-seeking actions; conversely, increasing activity in the prelimbic cortex decreases drug-seeking behaviour, a finding relevant to addiction treatment.

    • Billy T. Chen
    • Hau-Jie Yau
    • Antonello Bonci
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  • Genetically encoded probes for the non-peptidic morphogen retinoic acid allow the quantitative measurement of physiological RA concentration in vivo; the results support the source–sink diffusion model of morphogen dynamics proposed by Francis Crick in 1970.

    • Satoshi Shimozono
    • Tadahiro Iimura
    • Atsushi Miyawaki
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  • Hepatitis A virus particles released from cells can hijack and become wrapped in host-derived membranes by using proteins that facilitate the budding of many enveloped viruses, calling into question the traditional distinction between enveloped and non-enveloped viruses.

    • Zongdi Feng
    • Lucinda Hensley
    • Stanley M. Lemon
    Letter
  • Inhibition of kynurenine 3-monooxygenase (KMO) leads to amelioration of Huntington’s-disease-relevant phenotypes in yeast, fruitfly and mouse models; here the crystal structures of free and inhibitor-bound yeast KMO are presented, which could aid the development of targeted therapies for human neurodegenerative diseases.

    • Marta Amaral
    • Colin Levy
    • Nigel S. Scrutton
    Letter
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