@article{BanksNishiyamaHasebeetal.2011,
  author    = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  title     = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants},
  series = {Science},
  volume    = {332},
  journal   = {Science},
  number    = {6032},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.1203810},
  pages     = {960 -- 963},
  year      = {2011},
  abstract  = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  language  = {en}
}
@article{JohnMutti2005,
  author    = {John, Cedric Michael and Mutti, Maria},
  title     = {Relative control of paleoceanography, climate, and eustasy over heterozoan carbonates : a perspective from slope sediments of the Marion Plateau (ODP LEG 194)},
  issn      = {1527-1404},
  year      = {2005},
  abstract  = {In this paper we explore the relative control of paleoceanography, eustasy, and water temperature over the evolution of a carbonate slope system deposited on the Marion Plateau (Northeastern Australia). Growth of several carbonate platforms started in the early Miocene on this plateau, and although they occurred in low-latitude subtropical waters they are composed mainly of heterozoan organisms. We investigated an upper to distal slope transect drilled during ODP Leg 194 and located close to the Northern Marion Platform. We reconstructed mass accumulation rates of carbonate as well as the evolution in the ratios of carbon and oxygen stable isotopes. Power spectrum analysis of the carbon isotope record revealed the existence of cycles with main frequencies centered around 409 Kyr and 1800 Kyr. We interpret the 409 Kyr cycle as being paced by changes in the eccentricity of the Earth orbit, and we suggest that the 1800 Kyr cycle could be linked to long-term eustatic changes. Finally, on the basis of the timing of changes in mass accumulation rates of carbonate we infer that the strength and direction of oceanic currents affected sedimentation on the Marion Plateau by shifting depocenters of slope sedimentation, a process probably further modulated by sea-level changes. We argue that the evolution and demise of the heterozoan carbonate systems present on the Marion Plateau were controlled mainly by the evolution of strong benthic currents, and that eustasy and water temperature alone did not account for the drowning of the platforms in the mid Miocene},
  language  = {en}
}
@article{JohnAdatteMutti2006,
  author    = {John, Cedric Michael and Adatte, Thierry and Mutti, Maria},
  title     = {Regional trends in clay mineral fluxes to the Queensland margin and ties to middle Miocene global cooling},
  issn      = {0031-0182},
  doi       = {10.1016/j.palaeo.2005.09.010},
  year      = {2006},
  abstract  = {Three ODP sites located on the Marion Plateau, Northeast Australian margin, were investigated for clay mineral and bulk mineralogy changes through the early to middle Miocene. Kaolinite to smectite (K/S) ratios, as well as mass accumulation rates of clays, point to a marked decrease in accumulation of smectite associated with an increase in accumulation of kaolinite starting at similar to 15.6 Ma, followed by a, second increase in accumulation of kaolinite at similar to 13.2 Ma. Both of these increases are correlative to an increase in the calcite to detritus ratio. Comparison of our record with published precipitation proxies from continental Queensland indicates that increases in kaolinite did not correspond to more intense tropical-humid conditions, but instead to periods of greater aridity. Three mechanisms are explored to explain the temporal trends in clad, on the Marion Plateau: sea-level changes, changes in oceanic currents, and denudation of the Australian continent followed by reworking and eolian transport of clays. Though low mass accumulation rates of kaolinite are compatible with a possible contribution of eolian material after 14 Ma, when Australia became more arid, the lateral distribution of kaolinite along slope indicates mainly fluvial input for all clays and thus rules out this mechanism as well as oceanic current transport as the main controls behind clay accumulation on the plateau. We propose a model explaining the good correlation between long-term sea-level fall, decrease in smectite accumulation, increase in kaolinite accumulation and increase in carbonate input to the distal slope locations. We hypothesize that during low sea level and thus periods of drier continental climate in Queensland, early Miocene kaolinite-rich lacustrine deposits were being reworked, and that the progradation of the heterozoan carbonate platforms towards the basin center favored input of carbonate to the distal slope sites. The major find of our study is that increase kaolinite fluxes on the Queensland margin during the early and middle Miocene did not reflect the establishment of a tropical climate, and this stresses that care must be taken when reconstructing Australian climate based on deep-sea clay records alone.},
  language  = {en}
}
@phdthesis{John2003,
  author    = {John, C{\´e}dric Micha{\"e}l},
  title     = {Miocene climate as recorded on slope carbonates : examples from Malta (Central Mediterranean) and Northeastern Australia (Marion Plateau, ODP LEG 194)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000820},
  school      = {Universit{\"a}t Potsdam},
  year      = {2003},
  abstract  = {Im Rahmen dieser Doktorarbeit wurden die Hangkarbonate von zwei mioz{\"a}nen heterozoischen Karbonatsystemen n{\"a}her untersucht: die Malta Inselgruppe (zentrales Mittelmeer) und das Marion Plateau (Nordost Australien, ODP Leg 194). Die Auswirkungen der mittelmioz{\"a}nen Abk{\"u}hlung (Mi3), die auf 13.6 Ma datiert wird und starken Einfluß auf die Sauerstoffisotopenkurve hatte, in den oben genannten Flachwassersystemen stellten das Ziel dieser Arbeit dar. Dieses Abk{\"u}hlungsereignis beeinflußte außerdem sehr stark die ozeanographischen und klimatischen Muster, die im weiteren Verlauf zum modernen Eishausklima f{\"u}hrten. So steht insbesondere die Vereisung von Ostantarktika mit diesem Ereignis in Verbindung. Diese Arbeit untersucht den Einfluß dieses Ereignisses auf Flachwassersysteme, um vorliegende Untersuchungen in Tiefwassersystemen zu erg{\"a}nzen und so zum globalen Verst{\"a}ndnis des mioz{\"a}nen Klimawechsels beizutragen. Die Profile auf der Maltainselgruppe wurden mit Hilfe von Kohlenstoff- und Sauerstoffisotopen Auswertungen im Gesamtgestein, Gesamtgesteinmineralogie, Tonmineralanalyse und organischer Geochemie untersucht. Durch einen Wechsel von karbonatischeren zu tonigeren Sedimenten beeinflußte das mittelmioz{\"a}ne Abk{\"u}hlungsereignis die Sedimentation in diesem Gebiet sehr stark. Weiterhin wurde beobachtet, daß jede Phase der antarktischen Vereisung, nicht nur das mittelmioz{\"a}ne Hauptereignis, zu einem erh{\"o}hten terrigenen Eintrag in den Hangsedimenten der Maltainselgruppe f{\"u}hrte. Akkumulationsraten zeigen, daß dieser erh{\"o}hte terrigene Eintrag den einzelnen Vereisungsperioden zusammenh{\"a}ngt und die karbonatischen Sedimente durch tonreiche Sedimente \“verunreinigt\” wurden. Das daraufhin entwickelte Modell erkl{\"a}rt diesen erh{\"o}hten terrigenen Eintrag mit einer nordw{\"a}rtigen Verlagerung der innertropischen Konvergenzzone durch die Bildung von kalten, dichten Luftmassen, die zu verst{\"a}rkten Niederschl{\"a}gen in Nordafrika f{\"u}hrten. Diese verst{\"a}rkten Niederschl{\"a}ge (oder verst{\"a}rkter afrikanischer Monsun) beeinflußten die kontinentale Verwitterung und den Eintrag, mit der Folge, daß verst{\"a}rkt terrigene Sedimente im Bereich der Hangsedimente der Maltainselgruppe abgelagert wurden. Die tonreichen Intervalle weisen {\"A}hnlichkeiten zu sapropelischen Ablagerungen auf, was mit Hilfe der Spektral analyse des Karbonatgehalts und der geochemischen Analyse des organischen Materials gezeigt wurde. Auf dem Marion Plateau wurden die Sauerstoff- und Kohlenstoffisotopenkurven anhand von Foraminiferen der Gattung Cibicidoides spp. rekonstruiert. Der Karbonatgehalt wurde mit Hilfe einer chemischen Methode (Coulometer) ermittelt. Genauso wie die Sedimente der Maltainselgruppe beeinflußte das mittelmioz{\"a}ne Abk{\"u}hlungsereignis (Mi3) auch die Sedimente auf dem Marion Plateau. So kam es bei 13,8 Ma, in etwa zur Zeit der Vereisung von Ostantarktika, zu einem Abfall der Karbonatakkumulationsraten. Weiterhin traten {\"A}nderungen in der Zusammensetzung der Sedimente auf, so nehmen neritische Karbonatfragmente ab, der planktische Foraminiferengehalt nimmt zu und es wurden verst{\"a}rkt Quarz und Glaukonit abgelagert. Ein {\"u}berraschendes Ergebnis ist die Tatsache, daß der große N12-N14 Meeresspiegelabfall um 11,5 Ma die Akkumulationsraten der Karbonate auf dem Hang nicht beeinflußte. Dieses Ergebnis ist umso erstaunlicher, da Karbonatplattformen normalerweise sehr sensitiv auf Meeresspiegel{\"a}nderungen reagieren. Der Grund, warum sich die Karbonatakkumulationsraten schon um 13,6 Ma (Mi3) und nicht erst um 11,5 Ma (N12-N14) verringerten, liegt in der Tatsache, daß die ozeanischen Str{\"o}mungen die Karbonatsedimentation auf dem Hang des Marion Plateau schon im Mioz{\"a}n kontrollierten. Das mittelmioz{\"a}ne Ereignis (Mi3) erh{\"o}hte die St{\"a}rke diese Str{\"o}mungen und als eine Ursache wurde die Karbonatakkumulation auf den H{\"a}ngen reduziert. Die Amplitude des N12-N14 Meeresspiegelabfalls liegt bei 90 m unter der Ber{\"u}cksichtigung der Sauerstoffisotopendaten aus der Tiefsee und Berechnungen des Meeresspiegels anhand des \“coastal onlaps\”, die w{\"a}hrend Leg 194 gemacht wurden. Die Isotopendaten dieser Arbeit weisen hingegen auf einen verringerten Meeresspiegelabfall von 70 m hin. Als allgemeine Schlußfolgerung kann gesagt werden, daß der mittelmioz{\"a}ne Klimaumschwung die Karbonatsysteme zumindest an den beiden untersuchten Lokalit{\"a}ten beeinflußt hat. Allerdings waren die Auswirkungen sehr von den unterschiedlichen lokalen Gegebenheiten abh{\"a}ngig. Insbesondere wirkten sich die Anwesenheit einer Landmasse (Malta) und die Abwesenheit einer Barriere vor den Einfl{\"u}ssen des offenen Ozeans (Marion Plateau) stark auf die Ablagerung der Karbonate aus.},
  language  = {en}
}
@article{JohnKarnerMutti2004,
  author    = {John, Cedric Michael and Karner, G. D. and Mutti, Maria},
  title     = {delta O-18 and Marion Plateau backstripping : Combining two approaches to constrain late middle Miocene eustatic amplitude},
  issn      = {0091-7613},
  year      = {2004},
  abstract  = {delta(18)O(benthic), values from Leg 194 Ocean Drilling Program Sites 1192 and 1195, (drilled on the Marion Plateau) were combined with deep-sea values to reconstruct the magnitude range of the late middle Miocene sea-level fall (13.6-11.4 Ma). In parallel, an estimate for the late middle Miocene sea-level fall was calculated from the stratigraphic relationship identified during Leg 194 and the structural relief of carbonate platforms that form the Marion Plateau. Corrections for thermal subsidence induced by Late Cretaceous rifting, flexural sediment loading, and sediment compaction were taken into account. The response of the lithosphere to sediment loading was considered for a range of effective elastic thicknesses (10 < T-e < 40 km). By overlapping the sea-level range of both the deep-sea isotopes and the results from the backstripping analysis, we demonstrate that the amplitude of the late middle Miocene sea-level fall was 45-68 m (56.5 +/- 11.5 m). Including an estimate for sea-level variation using the delta(18)O(benthic) results from the subtropical Marion Plateau, the range of sea-level fall is tightly constrained between 45 and 55 in (50.0 +/- 5.0 m). This result is the first precise quantitative estimate for the amplitude of the late middle Miocene eustatic fall that sidesteps the errors inherent in using benthic foraminifera assemblages to predict paleo-water depth. The estimate also includes an error analysis for the flexural response of the lithosphere to both water and sediment loads. Our result implies that the extent of ice buildup in the Miocene was larger than previously estimated, and conversely that the amount of cooling associated with this event was less important},
  language  = {en}
}