@article{PingelMulchAlonsoetal.2016, author = {Pingel, Heiko and Mulch, Andreas and Alonso, Ricardo N. and Cottle, John and Hynek, Scott A. and Poletti, Jacob and Rohrmann, Alexander and Schmitt, Axel K. and Stockli, Daniel F. and Strecker, Manfred}, title = {Surface uplift and convective rainfall along the southern Central Andes (Angastaco Basin, NW Argentina)}, series = {Earth \& planetary science letters}, volume = {440}, journal = {Earth \& planetary science letters}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0012-821X}, doi = {10.1016/j.epsl.2016.02.009}, pages = {33 -- 42}, year = {2016}, abstract = {Stable-isotopic and sedimentary records from the orogenic Puna Plateau of NW Argentina and adjacent intermontane basins to the east furnish a unique late Cenozoic record of range uplift and ensuing paleoenvironmental change in the south-central Andes. Today, focused precipitation in this region occurs along the eastern, windward flanks of the Eastern Cordillera and Sierras Pampeanas ranges, while the orogen interior constitutes high-elevation regions with increasingly arid conditions in a westward direction. As in many mountain belts, such hydrologic and topographic gradients are commonly mirrored by a systematic relationship between the oxygen and hydrogen stable isotope ratios of meteoric water and elevation. The glass fraction of isotopically datable volcanic ash intercalated in sedimentary sequences constitutes an environmental proxy that retains a signal of the hydrogen-isotopic composition of ancient precipitation. This isotopic composition thus helps to elucidate the combined climatic and tectonic processes associated with topographic growth, which ultimately controls the spatial patterns of precipitation in mountain belts. However, between 25.5 and 27 degrees S present-day river-based hydrogen isotope lapse rates are very low, possibly due to deep-convective seasonal storms that dominate runoff. If not accounted for, the effects of such conditions on moisture availability in the past may lead to misinterpretations of proxy-records of rainfall. Here, we present hydrogen-isotope data of volcanic glass (delta Dg), extracted from 34 volcanic ash layers in different sedimentary basins of the Eastern Cordillera and the Sierras Pampeanas. Combined with previously published delta Dg records and our refined U-Pb and (U-Th)/He zircon geochronology on 17 tuff samples, we demonstrate hydrogen-isotope variations associated with paleoenvironmental change in the Angastaco Basin, which evolved from a contiguous foreland to a fault-bounded intermontane basin during the late Mio-Pliocene. We unravel the environmental impact of Mio-Pliocene topographic growth and associated orographic effects on long-term hydrogen-isotope records of rainfall in the south-central Andes, and potentially identify temporal variations in regional isotopic lapse rates that may also apply to other regions with similar topographic boundary conditions. (C) 2016 Elsevier B.V. All rights reserved.}, language = {en} } @article{PaijmansFickelCourtioletal.2016, author = {Paijmans, Johanna L. A. and Fickel, J{\"o}rns and Courtiol, Alexandre and Hofreiter, Michael and Foerster, Daniel W.}, title = {Impact of enrichment conditions on cross-species capture of fresh and degraded DNA}, series = {Molecular ecology resources}, volume = {16}, journal = {Molecular ecology resources}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12420}, pages = {42 -- 55}, year = {2016}, abstract = {Abstract By combining high-throughput sequencing with target enrichment ('hybridization capture'), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter - hybridization temperature - on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.}, language = {en} } @article{FoersterBullLenzetal.2018, author = {F{\"o}rster, Daniel W. and Bull, James K. and Lenz, Dorina and Autenrieth, Marijke and Paijmans, Johanna L. A. and Kraus, Robert H. S. and Nowak, Carsten and Bayerl, Helmut and K{\"u}hn, Ralph and Saveljev, Alexander P. and Sindicic, Magda and Hofreiter, Michael and Schmidt, Krzysztof and Fickel, J{\"o}rns}, title = {Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12924}, pages = {1356 -- 1373}, year = {2018}, abstract = {Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.}, language = {en} } @misc{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {972}, issn = {1866-8372}, doi = {10.25932/publishup-47444}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474441}, pages = {14}, year = {2020}, abstract = {Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.}, language = {en} } @article{vanKleunenDawsonEssletal.2015, author = {van Kleunen, Mark and Dawson, Wayne and Essl, Franz and Pergl, Jan and Winter, Marten and Weber, Ewald and Kreft, Holger and Weigelt, Patrick and Kartesz, John and Nishino, Misako and Antonova, Liubov A. and Barcelona, Julie F. and Cabezas, Francisco J. and Cardenas, Dairon and Cardenas-Toro, Juliana and Castano, Nicolas and Chacon, Eduardo and Chatelain, Cyrille and Ebel, Aleksandr L. and Figueiredo, Estrela and Fuentes, Nicol and Groom, Quentin J. and Henderson, Lesley and Inderjit, and Kupriyanov, Andrey and Masciadri, Silvana and Meerman, Jan and Morozova, Olga and Moser, Dietmar and Nickrent, Daniel L. and Patzelt, Annette and Pelser, Pieter B. and Baptiste, Maria P. and Poopath, Manop and Schulze, Maria and Seebens, Hanno and Shu, Wen-sheng and Thomas, Jacob and Velayos, Mauricio and Wieringa, Jan J. and Pysek, Petr}, title = {Global exchange and accumulation of non-native plants}, series = {Nature : the international weekly journal of science}, volume = {525}, journal = {Nature : the international weekly journal of science}, number = {7567}, publisher = {Nature Publ. Group}, address = {London}, issn = {0028-0836}, doi = {10.1038/nature14910}, pages = {100 -- +}, year = {2015}, abstract = {All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch(1,2) is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage(3). So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9\% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.}, language = {en} } @article{StraussSchirrmeisterGrosseetal.2017, author = {Strauss, Jens and Schirrmeister, Lutz and Grosse, Guido and Fortier, Daniel and Hugelius, Gustaf and Knoblauch, Christian and Romanovsky, Vladimir E. and Schadel, Christina and von Deimling, Thomas Schneider and Schuur, Edward A. G. and Shmelev, Denis and Ulrich, Mathias and Veremeeva, Alexandra}, title = {Deep Yedoma permafrost: A synthesis of depositional characteristics and carbon vulnerability}, series = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, volume = {172}, journal = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0012-8252}, doi = {10.1016/j.earscirev.2017.07.007}, pages = {75 -- 86}, year = {2017}, abstract = {Permafrost is a distinct feature of the terrestrial Arctic and is vulnerable to climate warming. Permafrost degrades in different ways, including deepening of a seasonally unfrozen surface and localized but rapid development of deep thaw features. Pleistocene ice-rich permafrost with syngenetic ice-wedges, termed Yedoma deposits, are widespread in Siberia, Alaska, and Yukon, Canada and may be especially prone to rapid-thaw processes. Freeze-locked organic matter in such deposits can be re-mobilized on short time-scales and contribute to a carbon-cycle climate feedback. Here we synthesize the characteristics and vulnerability of Yedoma deposits by synthesizing studies on the Yedoma origin and the associated organic carbon pool. We suggest that Yedoma deposits accumulated under periglacial weathering, transport, and deposition dynamics in non-glaciated regions during the late Pleistocene until the beginning of late glacial warming. The deposits formed due to a combination of aeolian, colluvial, nival, and alluvial deposition and simultaneous ground ice accumulation. We found up to 130 gigatons organic carbon in Yedoma, parts of which are well-preserved and available for fast decomposition after thaw. Based on incubation experiments, up to 10\% of the Yedoma carbon is considered especially decomposable and may be released upon thaw. The substantial amount of ground ice in Yedoma makes it highly vulnerable to disturbances such as thermokarst and thermo-erosion processes. Mobilization of permafrost carbon is expected to increase under future climate warming. Our synthesis results underline the need of accounting for Yedoma carbon stocks in next generation Earth-System-Models for a more complete representation of the permafrost-carbon feedback.}, language = {en} } @article{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {PLoS ONE}, volume = {15}, journal = {PLoS ONE}, number = {6}, publisher = {PLOS}, address = {San Francisco, California, US}, issn = {1932-6203}, doi = {10.1371/journal.pone.0234385}, pages = {12}, year = {2020}, abstract = {Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.}, language = {en} } @article{vanDrielGesztelyiBakerToeroeketal.2014, author = {van Driel-Gesztelyi, L. and Baker, Daniel N. and Toeroek, T. and Pariat, E. and Green, L. M. and Williams, D. R. and Carlyle, J. and Valori, G. and Demoulin, Pascal and Kliem, Bernhard and Long, D. M. and Matthews, S. A. and Malherbe, J. -M.}, title = {Coronal magnetic reconnection driven by CME expansion-the 2011 June 7 event}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, volume = {788}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0004-637X}, doi = {10.1088/0004-637X/788/1/85}, pages = {12}, year = {2014}, abstract = {Coronal mass ejections (CMEs) erupt and expand in a magnetically structured solar corona. Various indirect observational pieces of evidence have shown that the magnetic field of CMEs reconnects with surrounding magnetic fields, forming, e.g., dimming regions distant from the CME source regions. Analyzing Solar Dynamics Observatory (SDO) observations of the eruption from AR 11226 on 2011 June 7, we present the first direct evidence of coronal magnetic reconnection between the fields of two adjacent active regions during a CME. The observations are presented jointly with a data-constrained numerical simulation, demonstrating the formation/intensification of current sheets along a hyperbolic flux tube at the interface between the CME and the neighboring AR 11227. Reconnection resulted in the formation of new magnetic connections between the erupting magnetic structure from AR 11226 and the neighboring active region AR 11227 about 200 Mm from the eruption site. The onset of reconnection first becomes apparent in the SDO/AIA images when filament plasma, originally contained within the erupting flux rope, is redirected toward remote areas in AR 11227, tracing the change of large-scale magnetic connectivity. The location of the coronal reconnection region becomes bright and directly observable at SDO/AIA wavelengths, owing to the presence of down-flowing cool, dense (1010 cm(-3)) filament plasma in its vicinity. The high-density plasma around the reconnection region is heated to coronal temperatures, presumably by slow-mode shocks and Coulomb collisions. These results provide the first direct observational evidence that CMEs reconnect with surrounding magnetic structures, leading to a large-scale reconfiguration of the coronal magnetic field.}, language = {en} } @article{ValoriGreenDemoulinetal.2012, author = {Valori, Gherardo and Green, Lucie M. and Demoulin, Pascal and Vargas Dominguez, S. and van Driel-Gesztelyi, L. and Wallace, A. and Baker, Daniel N. and Fuhrmann, Marcel}, title = {Nonlinear force-free extrapolation of emerging flux with a global twist and serpentine fine structures}, series = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, volume = {278}, journal = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0038-0938}, doi = {10.1007/s11207-011-9865-8}, pages = {73 -- 97}, year = {2012}, abstract = {We study the flux emergence process in NOAA active region 11024, between 29 June and 7 July 2009, by means of multi-wavelength observations and nonlinear force-free extrapolation. The main aim is to extend previous investigations by combining, as much as possible, high spatial resolution observations to test our present understanding of small-scale (undulatory) flux emergence, whilst putting these small-scale events in the context of the global evolution of the active region. The combination of these techniques allows us to follow the whole process, from the first appearance of the bipolar axial field on the east limb, until the buoyancy instability could set in and raise the main body of the twisted flux tube through the photosphere, forming magnetic tongues and signatures of serpentine field, until the simplification of the magnetic structure into a main bipole by the time the active region reaches the west limb. At the crucial time of the main emergence phase high spatial resolution spectropolarimetric measurements of the photospheric field are employed to reconstruct the three-dimensional structure of the nonlinear force-free coronal field, which is then used to test the current understanding of flux emergence processes. In particular, knowledge of the coronal connectivity confirms the identity of the magnetic tongues as seen in their photospheric signatures, and it exemplifies how the twisted flux, which is emerging on small scales in the form of a sea-serpent, is subsequently rearranged by reconnection into the large-scale field of the active region. In this way, the multi-wavelength observations combined with a nonlinear force-free extrapolation provide a coherent picture of the emergence process of small-scale magnetic bipoles, which subsequently reconnect to form a large-scale structure in the corona.}, language = {en} } @article{KietzkeEgbeHoerholdetal.2006, author = {Kietzke, Thomas and Egbe, Daniel A. M. and H{\"o}rhold, Hans-Heinrich and Neher, Dieter}, title = {Comparative study of M3EH-PPV-based bilayer photovoltaic devices}, issn = {4018-4022}, doi = {10.1021/Ma0601991}, year = {2006}, abstract = {We have recently shown that efficient polymer solar cells can be fabricated by using a weakly soluble derivative of poly-p-vinylene (M3EH-PPV) as the electron donor. Here we present studies on bilayer devices using organic electron acceptors with varying LUMO levels and M3EH-PPV. It is found that the open-circuit voltage scales linearly with the LUMO level of the acceptor, reaching values as high as 1.5 V when cyano-substituted poly(p-phenyleneethynylene)-alt- poly(p-phenylenevinylene) copolymers are used. Further, we discovered that for an increasing number of triple bonds in the repeat unit of the acceptor polymer the device performance decreases with increasing thickness of the acceptor layer. Also, the quantum efficiency was smaller when using polymers with higher LUMO levels. Thus, further effort is needed to design optimum acceptor polymers for devices exhibiting large open-circuit voltage and high quantum efficiency}, language = {en} }