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  • Springer Nature  (34)
  • Oxford University Press  (18)
  • Geological Society of America (GSA)
  • Springer Science + Business Media
  • 1
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    Coincidence of a high-fluence blazar outburst with a PeV-energy neutrino event (2016)
    Springer Nature
    Details
    Publication Date: 2016-08-03
    Description: Nature Physics 12, 807 (2016). doi:10.1038/nphys3715 Authors: M. Kadler, F. Krauß, K. Mannheim, R. Ojha, C. Müller, R. Schulz, G. Anton, W. Baumgartner, T. Beuchert, S. Buson, B. Carpenter, T. Eberl, P. G. Edwards, D. Eisenacher Glawion, D. Elsässer, N. Gehrels, C. Gräfe, S. Gulyaev, H. Hase, S. Horiuchi, C. W. James, A. Kappes, A. Kappes, U. Katz, A. Kreikenbohm, M. Kreter, I. Kreykenbohm, M. Langejahn, K. Leiter, E. Litzinger, F. Longo, J. E. J. Lovell, J. McEnery, T. Natusch, C. Phillips, C. Plötz, J. Quick, E. Ros, F. W. Stecker, T. Steinbring, J. Stevens, D. J. Thompson, J. Trüstedt, A. K. Tzioumis, S. Weston, J. Wilms & J. A. Zensus
    Print ISSN: 1745-2473
    Electronic ISSN: 1745-2481
    Topics: Physics
    Published by Springer Nature
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  • 2
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    Evolution Along the Mutation Gradient in the Dynamic Mitochondrial Genome of Salamanders (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-20
    Description: Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Sequestration and subduction of deep-sea carbonate in the global ocean since the Early Cretaceous (2018)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2018
    Description: 〈span〉〈div〉Abstract〈/div〉Deep-sea carbonate represents Earth’s largest carbon sink and one of the least-known components of the long-term carbon cycle that is intimately linked to climate. By coupling the deep-sea carbonate sedimentation history to a global tectonic model, we quantify this component within the framework of a continuously evolving seafloor. A long-term increase in marine carbonate carbon flux since the mid-Cretaceous is dominated by a post-50 Ma doubling of carbonate accumulation to ∼310 Mt C/yr at present-day. This increase was caused largely by the immense growth in deep-sea carbonate carbon storage, post-dating the end of the Early Eocene Climate Optimum. We suggest that a combination of a retreat of epicontinental seas, underpinned by long-term deepening of the seafloor, the inception of major Himalayan river systems, and the weathering of the Deccan Traps drove enhanced delivery of Ca〈sup〉2+〈/sup〉 and HCO〈sub〉3〈/sub〉〈sup〉–〈/sup〉 into the oceans and atmospheric CO〈sub〉2〈/sub〉 drawdown in the 15 m.y. prior to the onset of glaciation at ca. 35 Ma. Relatively stagnant mid-ocean ridge, rift- and subduction-related degassing during this period support our contention that continental silicate weathering, rather than a major decrease in CO〈sub〉2〈/sub〉 degassing, may have triggered an increase in marine carbonate accumulation and long-term Eocene global cooling. Our results provide new constraints for global carbon cycle models, and may improve our understanding of carbonate subduction-related metamorphism, mineralization and isotopic signatures of degassing.〈/span〉
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 4
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    Sequestration and subduction of deep-sea carbonate in the global ocean since the Early Cretaceous (2018)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2018
    Description: 〈span〉Deep-sea carbonate represents Earth’s largest carbon sink and one of the least-known components of the long-term carbon cycle that is intimately linked to climate. By coupling the deep-sea carbonate sedimentation history to a global tectonic model, we quantify this component within the framework of a continuously evolving seafloor. A long-term increase in marine carbonate carbon flux since the mid-Cretaceous is dominated by a post-50 Ma doubling of carbonate accumulation to ~310 Mt C/yr at present-day. This increase was caused largely by the immense growth in deep-sea carbonate carbon storage, post-dating the end of the Early Eocene Climate Optimum. We suggest that a combination of a retreat of epicontinental seas, underpinned by long-term deepening of the seafloor, the inception of major Himalayan river systems, and the weathering of the Deccan Traps drove enhanced delivery of Ca〈sup〉2+〈/sup〉 and HCO〈sub〉3〈/sub〉〈sup〉–〈/sup〉 into the oceans and atmospheric CO〈sub〉2〈/sub〉 drawdown in the 15 m.y. prior to the onset of glaciation at ca. 35 Ma. Relatively stagnant mid-ocean ridge, rift- and subduction-related degassing during this period support our contention that continental silicate weathering, rather than a major decrease in CO〈sub〉2〈/sub〉 degassing, may have triggered an increase in marine carbonate accumulation and long-term Eocene global cooling. Our results provide new constraints for global carbon cycle models, and may improve our understanding of carbonate subduction-related metamorphism, mineralization and isotopic signatures of degassing.〈/span〉
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 5
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    A new fungal large subunit ribosomal RNA primer for high-throughput sequencing surveys (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-31
    Description: The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable region of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Together, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Mantle dynamics of continentwide Cenozoic subsidence and tilting of Australia (2011)
    Geological Society of America (GSA)
    Details
    Publication Date: 2011-10-01
    Description: Australia is distinctive because it experienced first-order, broad-scale vertical motions during the Cenozoic. Here, we use plate-tectonic reconstructions and a model of mantle convection to quantitatively link the large-scale flooding history of the continent to mantle convection since 50 Ma. Subduction-driven geodynamic models show that Australia undergoes a 200 m northeast downward tilt as it approaches and overrides subducted slabs between Melanesia and the proto–Tonga-Kermadec subduction systems. However, the model only produces the observed continentwide subsidence, with 300 m of northeast downward tilt since the Eocene, if we assume that Australia has moved northward away from a relatively hot mantle anomaly. The models suggest that Australia's paleoshoreline evolution can only be reproduced if the continent moved northward, away from a large buoyant anomaly. This results in continentwide subsidence of ∼200 m. The additional progressive, continentwide tilting down to the northeast can be attributed to the horizontal motion of the continent toward subducted slabs sinking below Melanesia.
    Print ISSN: 1941-8264
    Electronic ISSN: 1947-4253
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 7
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    Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-19
    Description: Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis , the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders’ high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade’s base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    REPLY: Early to middle Miocene monsoon climate in Australia (2012)
    Geological Society of America (GSA)
    Details
    Publication Date: 2012-06-01
    Description: Travouillon et al. (2012) challenge our interpretation of proxy records (Herold et al., 2011), citing five points for rainforest at Riversleigh and across northern and central Australia in the early to middle Miocene; points that we refute here. (1) Cenogram/body mass distribution patterns Travouillon et al. (2009) were equivocal in assigning some fauna sites to open forest or rainforest using cenograms alone, but using cenograms and body mass distribution (BMD) in combination, they interpreted the majority of the Riversleigh sites as rainforest. Yet, their Discriminant Function Analysis (DFA) of the same faunas identified a mix of open forest (2/6) and rainforest sites (4/6) for the early Miocene, and all five middle Miocene sites as open forest. Thus their own data imply a mosaic of habitats in space and time in the Riversleigh area of northern Australia.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 9
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    Nanoscale spin reversal by non-local angular momentum transfer following ultrafast laser excitation in ferrimagnetic GdFeCo (2013)
    Springer Nature
    Details
    Publication Date: 2013-03-21
    Description: Nature Materials 12, 293 (2013). doi:10.1038/nmat3597 Authors: C. E. Graves, A. H. Reid, T. Wang, B. Wu, S. de Jong, K. Vahaplar, I. Radu, D. P. Bernstein, M. Messerschmidt, L. Müller, R. Coffee, M. Bionta, S. W. Epp, R. Hartmann, N. Kimmel, G. Hauser, A. Hartmann, P. Holl, H. Gorke, J. H. Mentink, A. Tsukamoto, A. Fognini, J. J. Turner, W. F. Schlotter, D. Rolles, H. Soltau, L. Strüder, Y. Acremann, A. V. Kimel, A. Kirilyuk, Th. Rasing, J. Stöhr, A. O. Scherz & H. A. Dürr Ultrafast laser techniques have revealed extraordinary spin dynamics in magnetic materials that equilibrium descriptions of magnetism cannot explain. Particularly important for future applications is understanding non-equilibrium spin dynamics following laser excitation on the nanoscale, yet the limited spatial resolution of optical laser techniques has impeded such nanoscale studies. Here we present ultrafast diffraction experiments with an X-ray laser that probes the nanoscale spin dynamics following optical laser excitation in the ferrimagnetic alloy GdFeCo, which exhibits macroscopic all-optical switching. Our study reveals that GdFeCo displays nanoscale chemical and magnetic inhomogeneities that affect the spin dynamics. In particular, we observe Gd spin reversal in Gd-rich nanoregions within the first picosecond driven by the non-local transfer of angular momentum from larger adjacent Fe-rich nanoregions. These results suggest that a magnetic material’s microstructure can be engineered to control transient laser-excited spins, potentially allowing faster (~ 1 ps) spin reversal than in present technologies.
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 10
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    Slow DNA Loss in the Gigantic Genomes of Salamanders (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-29
    Description: Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ~1–30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes—the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis , Danio rerio , Gallus gallus , Homo sapiens , and Xenopus tropicalis . Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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