@article{MartinezGonzalezPastorYabarLaggetal.2016, author = {Martinez Gonzalez, M. J. and Pastor Yabar, A. and Lagg, A. and Asensio Ramos, A. and Collados Vera, M. and Solanki, S. K. and Balthasar, H. and Berkefeld, T. and Denker, Carsten and Doerr, H. P. and Feller, A. and Franz, M. and Gonz{\´a}lez Manrique, Sergio Javier and Hofmann, A. and Kneer, F. and Kuckein, Christoph and Louis, R. and von der L{\"u}he, O. and Nicklas, H. and Orozco, D. and Rezaei, R. and Schlichenmaier, R. and Schmidt, D. and Schmidt, W. and Sigwarth, M. and Sobotka, M. and Soltau, D. and Staude, J. and Strassmeier, Klaus G. and Verma, Meetu and Waldman, T. and Volkmer, R.}, title = {Inference of magnetic fields in the very quiet Sun}, series = {Journal of geophysical research : Earth surface}, volume = {596}, journal = {Journal of geophysical research : Earth surface}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201628449}, pages = {11}, year = {2016}, abstract = {Context. Over the past 20 yr, the quietest areas of the solar surface have revealed a weak but extremely dynamic magnetism occurring at small scales (<500 km), which may provide an important contribution to the dynamics and energetics of the outer layers of the atmosphere. Understanding this magnetism requires the inference of physical quantities from high-sensitivity spectro-polarimetric data with high spatio-temporal resolution. Aims. We present high-precision spectro-polarimetric data with high spatial resolution (0.4") of the very quiet Sun at 1.56 mu m obtained with the GREGOR telescope to shed some light on this complex magnetism. Methods. We used inversion techniques in two main approaches. First, we assumed that the observed profiles can be reproduced with a constant magnetic field atmosphere embedded in a field-free medium. Second, we assumed that the resolution element has a substructure with either two constant magnetic atmospheres or a single magnetic atmosphere with gradients of the physical quantities along the optical depth, both coexisting with a global stray-light component. Results. Half of our observed quiet-Sun region is better explained by magnetic substructure within the resolution element. However, we cannot distinguish whether this substructure comes from gradients of the physical parameters along the line of sight or from horizontal gradients (across the surface). In these pixels, a model with two magnetic components is preferred, and we find two distinct magnetic field populations. The population with the larger filling factor has very weak (similar to 150 G) horizontal fields similar to those obtained in previous works. We demonstrate that the field vector of this population is not constrained by the observations, given the spatial resolution and polarimetric accuracy of our data. The topology of the other component with the smaller filling factor is constrained by the observations for field strengths above 250 G: we infer hG fields with inclinations and azimuth values compatible with an isotropic distribution. The filling factors are typically below 30\%. We also find that the flux of the two polarities is not balanced. From the other half of the observed quiet-Sun area similar to 50\% are two-lobed Stokes V profiles, meaning that 23\% of the field of view can be adequately explained with a single constant magnetic field embedded in a non-magnetic atmosphere. The magnetic field vector and filling factor are reliable inferred in only 50\% based on the regular profiles. Therefore, 12\% of the field of view harbour hG fields with filling factors typically below 30\%. At our present spatial resolution, 70\% of the pixels apparently are non-magnetised.}, language = {en} } @article{VermaDenkerBalthasaretal.2016, author = {Verma, Meetu and Denker, Carsten and Balthasar, H. and Kuckein, Christoph and Gonz{\´a}lez Manrique, Sergio Javier and Sobotka, M. and Gonzalez, N. Bello and Hoch, S. and Diercke, Andrea and Kummerow, Philipp and Berkefeld, T. and Collados Vera, M. and Feller, A. and Hofmann, A. and Kneer, F. and Lagg, A. and L{\"o}hner-B{\"o}ttcher, J. and Nicklas, H. and Pastor Yabar, A. and Schlichenmaier, R. and Schmidt, D. and Schmidt, W. and Schubert, M. and Sigwarth, M. and Solanki, S. K. and Soltau, D. and Staude, J. and Strassmeier, Klaus G. and Volkmer, R. and von der L{\"u}he, O. and Waldmann, T.}, title = {Horizontal flow fields in and around a small active region The transition period between flux emergence and decay}, series = {Polymers}, volume = {596}, journal = {Polymers}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201628380}, pages = {12}, year = {2016}, abstract = {Context. The solar magnetic field is responsible for all aspects of solar activity. Thus, emergence of magnetic flux at the surface is the first manifestation of the ensuing solar activity. Aims. Combining high-resolution and synoptic observations aims to provide a comprehensive description of flux emergence at photospheric level and of the growth process that eventually leads to a mature active region. Methods. The small active region NOAA 12118 emerged on 2014 July 17 and was observed one day later with the 1.5-m GREGOR solar telescope on 2014 July 18. High-resolution time-series of blue continuum and G-band images acquired in the blue imaging channel (BIC) of the GREGOR Fabry-Perot Interferometer (GFPI) were complemented by synoptic line-of-sight magnetograms and continuum images obtained with the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). Horizontal proper motions and horizontal plasma velocities were computed with local correlation tracking (LCT) and the differential affine velocity estimator (DAVE), respectively. Morphological image processing was employed to measure the photometric and magnetic area, magnetic flux, and the separation profile of the emerging flux region during its evolution. Results. The computed growth rates for photometric area, magnetic area, and magnetic flux are about twice as high as the respective decay rates. The space-time diagram using HMI magnetograms of five days provides a comprehensive view of growth and decay. It traces a leaf-like structure, which is determined by the initial separation of the two polarities, a rapid expansion phase, a time when the spread stalls, and a period when the region slowly shrinks again. The separation rate of 0.26 km s(-1) is highest in the initial stage, and it decreases when the separation comes to a halt. Horizontal plasma velocities computed at four evolutionary stages indicate a changing pattern of inflows. In LCT maps we find persistent flow patterns such as outward motions in the outer part of the two major pores, a diverging feature near the trailing pore marking the site of upwelling plasma and flux emergence, and low velocities in the interior of dark pores. We detected many elongated rapidly expanding granules between the two major polarities, with dimensions twice as large as the normal granules.}, language = {en} } @article{GonzalezManriqueKuckeinPastorYabaretal.2016, author = {Gonzalez Manrique, Sergio Javier and Kuckein, Christoph and Pastor Yabar, A. and Collados Vera, M. and Denker, Carsten and Fischer, C. E. and G{\"o}m{\"o}ry, P. and Diercke, Andrea and Gonzalez, N. Bello and Schlichenmaier, R. and Balthasar, H. and Berkefeld, T. and Feller, A. and Hoch, S. and Hofmann, A. and Kneer, F. and Lagg, A. and Nicklas, H. and Orozco Suarez, D. and Schmidt, D. and Schmidt, W. and Sigwarth, M. and Sobotka, M. and Solanki, S. K. and Soltau, D. and Staude, J. and Strassmeier, Klaus G. and Verma, Meetu and Volkmer, R. and von der L{\"u}he, O. and Waldmann, T.}, title = {Fitting peculiar spectral profiles in He I 10830 angstrom absorption features}, series = {Astronomische Nachrichten = Astronomical notes}, volume = {337}, journal = {Astronomische Nachrichten = Astronomical notes}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0004-6337}, doi = {10.1002/asna.201512433}, pages = {1057 -- 1063}, year = {2016}, abstract = {The new generation of solar instruments provides better spectral, spatial, and temporal resolution for a better understanding of the physical processes that take place on the Sun. Multiple-component profiles are more commonly observed with these instruments. Particularly, the He i 10830 triplet presents such peculiar spectral profiles, which give information on the velocity and magnetic fine structure of the upper chromosphere. The purpose of this investigation is to describe a technique to efficiently fit the two blended components of the He i 10830 triplet, which are commonly observed when two atmospheric components are located within the same resolution element. The observations used in this study were taken on 2015 April 17 with the very fast spectroscopic mode of the GREGOR Infrared Spectrograph (GRIS) attached to the 1.5-m GREGOR solar telescope, located at the Observatorio del Teide, Tenerife, Spain. We apply a double-Lorentzian fitting technique using Levenberg-Marquardt least-squares minimization. This technique is very simple and much faster than inversion codes. Line-of-sight Doppler velocities can be inferred for a whole map of pixels within just a few minutes. Our results show sub-and supersonic downflow velocities of up to 32 km s(-1) for the fast component in the vicinity of footpoints of filamentary structures. The slow component presents velocities close to rest. (C) 2016 WILEY-VCH Verlag GmbH\& Co. KGaA, Weinheim}, language = {en} } @article{VermaDenkerBoehmetal.2016, author = {Verma, Meetu and Denker, Carsten and B{\"o}hm, F. and Balthasar, H. and Fischer, C. E. and Kuckein, Christoph and Gonzalez, N. Bello and Berkefeld, T. and Collados Vera, M. and Diercke, Andrea and Feller, A. and Gonzalez Manrique, Sergio Javier and Hofmann, A. and Lagg, A. and Nicklas, H. and Orozco Suarez, D. and Pator Yabar, A. and Rezaei, R. and Schlichenmaier, R. and Schmidt, D. and Schmidt, W. and Sigwarth, M. and Sobotka, M. and Solanki, S. K. and Soltau, D. and Staude, J. and Strassmeier, Klaus G. and Volkmer, R. and von der L{\"u}he, O. and Waldmann, T.}, title = {Flow and magnetic field properties in the trailing sunspots of active region NOAA 12396}, series = {Astronomische Nachrichten = Astronomical notes}, volume = {337}, journal = {Astronomische Nachrichten = Astronomical notes}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0004-6337}, doi = {10.1002/asna.201612447}, pages = {1090 -- 1098}, year = {2016}, abstract = {Improved measurements of the photospheric and chromospheric three-dimensional magnetic and flow fields are crucial for a precise determination of the origin and evolution of active regions. We present an illustrative sample of multi-instrument data acquired during a two-week coordinated observing campaign in August 2015 involving, among others, the GREGOR solar telescope (imaging and near-infrared spectroscopy) and the space missions Solar Dynamics Observatory (SDO) and Interface Region Imaging Spectrograph (IRIS). The observations focused on the trailing part of active region NOAA 12396 with complex polarity inversion lines and strong intrusions of opposite polarity flux. The GREGOR Infrared Spectrograph (GRIS) provided Stokes IQUV spectral profiles in the photospheric Si i.1082.7 nm line, the chromospheric He I lambda 1083.0 nm triplet, and the photospheric Ca I lambda 1083.9 nm line. Carefully calibrated GRIS scans of the active region provided maps of Doppler velocity and magnetic field at different atmospheric heights. We compare quick-look maps with those obtained with the " Stokes Inversions based on Response functions" (SIR) code, which furnishes deeper insight into the magnetic properties of the region. We find supporting evidence that newly emerging flux and intruding opposite polarity flux are hampering the formation of penumbrae, i.e., a penumbra fully surrounding a sunspot is only expected after cessation of flux emergence in proximity to the sunspots. (C) 2016 WILEY-VCH Verlag GmbH\& Co.KGaA, Weinheim}, language = {en} } @article{DenkerKuckeinVermaetal.2018, author = {Denker, Carsten and Kuckein, Christoph and Verma, Meetu and Manrique Gonzalez, Sergio Javier Gonzalez and Diercke, Andrea and Enke, Harry and Klar, Jochen and Balthasar, Horst and Louis, Rohan E. and Dineva, Ekaterina Ivanova}, title = {High-cadence Imaging and Imaging Spectroscopy at the GREGOR Solar Telescope-A Collaborative Research Environment for High-resolution Solar Physics}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, volume = {236}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0067-0049}, doi = {10.3847/1538-4365/aab773}, pages = {12}, year = {2018}, abstract = {In high-resolution solar physics, the volume and complexity of photometric, spectroscopic, and polarimetric ground-based data significantly increased in the last decade, reaching data acquisition rates of terabytes per hour. This is driven by the desire to capture fast processes on the Sun and the necessity for short exposure times "freezing" the atmospheric seeing, thus enabling ex post facto image restoration. Consequently, large-format and high-cadence detectors are nowadays used in solar observations to facilitate image restoration. Based on our experience during the "early science" phase with the 1.5 m GREGOR solar telescope (2014-2015) and the subsequent transition to routine observations in 2016, we describe data collection and data management tailored toward image restoration and imaging spectroscopy. We outline our approaches regarding data processing, analysis, and archiving for two of GREGOR's post-focus instruments (see http://gregor.aip.de), i.e., the GREGOR Fabry-P{\´e}rot Interferometer (GFPI) and the newly installed High-Resolution Fast Imager (HiFI). The heterogeneous and complex nature of multidimensional data arising from high-resolution solar observations provides an intriguing but also a challenging example for "big data" in astronomy. The big data challenge has two aspects: (1) establishing a workflow for publishing the data for the whole community and beyond and (2) creating a collaborative research environment (CRE), where computationally intense data and postprocessing tools are colocated and collaborative work is enabled for scientists of multiple institutes. This requires either collaboration with a data center or frameworks and databases capable of dealing with huge data sets based on virtual observatory (VO) and other community standards and procedures.}, language = {en} } @article{DenkerDinevaBalthasaretal.2018, author = {Denker, Carsten and Dineva, Ekaterina Ivanova and Balthasar, Horst and Verma, Meetu and Kuckein, Christoph and Diercke, Andrea and Manrique Gonzalez, Sergio Javier Gonzalez}, title = {Image Quality in High-resolution and High-cadence Solar Imaging}, series = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, volume = {293}, journal = {Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0038-0938}, doi = {10.1007/s11207-018-1261-1}, pages = {24}, year = {2018}, abstract = {Broad-band imaging and even imaging with a moderate bandpass (about 1 nm) provides a photon-rich environment, where frame selection (lucky imaging) becomes a helpful tool in image restoration, allowing us to perform a cost-benefit analysis on how to design observing sequences for imaging with high spatial resolution in combination with real-time correction provided by an adaptive optics (AO) system. This study presents high-cadence (160 Hz) G-band and blue continuum image sequences obtained with the High-resolution Fast Imager (HiFI) at the 1.5-meter GREGOR solar telescope, where the speckle-masking technique is used to restore images with nearly diffraction-limited resolution. The HiFI employs two synchronized large-format and high-cadence sCMOS detectors. The median filter gradient similarity (MFGS) image-quality metric is applied, among others, to AO-corrected image sequences of a pore and a small sunspot observed on 2017 June 4 and 5. A small region of interest, which was selected for fast-imaging performance, covered these contrastrich features and their neighborhood, which were part of Active Region NOAA 12661. Modifications of theMFGS algorithm uncover the field-and structure-dependency of this imagequality metric. However, MFGS still remains a good choice for determining image quality without a priori knowledge, which is an important characteristic when classifying the huge number of high-resolution images contained in data archives. In addition, this investigation demonstrates that a fast cadence and millisecond exposure times are still insufficient to reach the coherence time of daytime seeing. Nonetheless, the analysis shows that data acquisition rates exceeding 50 Hz are required to capture a substantial fraction of the best seeing moments, significantly boosting the performance of post-facto image restoration.}, language = {en} } @article{GonzalezManriqueKuckeinColladosetal.2018, author = {Gonzalez Manrique, Sergio Javier and Kuckein, Christoph and Collados, M. and Denker, Carsten and Solanki, S. K. and Gomory, P. and Verma, Meetu and Balthasar, H. and Lagg, A. and Diercke, Andrea}, title = {Temporal evolution of arch filaments as seen in He I 10 830 angstrom}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {617}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201832684}, pages = {11}, year = {2018}, abstract = {Aims. We study the evolution of an arch filament system (AFS) and of its individual arch filaments to learn about the processes occurring in them. Methods. We observed the AFS at the GREGOR solar telescope on Tenerife at high cadence with the very fast spectroscopic mode of the GREGOR Infrared Spectrograph (GRIS) in the He I 10 830 angstrom spectral range. The He I triplet profiles were fitted with analytic functions to infer line-of-sight (LOS) velocities to follow plasma motions within the AFS. Results. We tracked the temporal evolution of an individual arch filament over its entire lifetime, as seen in the He I 10 830 angstrom triplet. The arch filament expanded in height and extended in length from 13 ' to 21 '. The lifetime of this arch filament is about 30 min. About 11 min after the arch filament is seen in He I, the loop top starts to rise with an average Doppler velocity of 6 km s(-1). Only two minutes later, plasma drains down with supersonic velocities towards the footpoints reaching a peak velocity of up to 40 km s(-1) in the chromosphere. The temporal evolution of He I 10 830 angstrom profiles near the leading pore showed almost ubiquitous dual red components of the He I triplet, indicating strong downflows, along with material nearly at rest within the same resolution element during the whole observing time.}, language = {en} } @article{WutkeSandovalCastellanosBeneckeetal.2018, author = {Wutke, Saskia and Sandoval-Castellanos, Edson and Benecke, Norbert and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez, Javier and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Malaspinas, Anna-Sapfo and Morales-Muniz, Arturo and Orlando, Ludovic and Reissmann, Monika and Trinks, Alexandra and Ludwig, Arne}, title = {Decline of genetic diversity in ancient domestic stallions in Europe}, series = {Science Advances}, volume = {4}, journal = {Science Advances}, number = {4}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aap9691}, pages = {7}, year = {2018}, abstract = {Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.}, language = {en} } @article{VermaDenkerBalthasaretal.2018, author = {Verma, Meetu and Denker, Carsten and Balthasar, H. and Kuckein, Christoph and Rezaei, R. and Sobotka, Michal and Deng, N. and Wang, Haimin and Tritschler, A. and Collados, M. and Diercke, Andrea and Gonz{\´a}lez Manrique, Sergio Javier}, title = {High-resolution imaging and near-infrared spectroscopy of penumbral decay}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {614}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201731801}, pages = {14}, year = {2018}, abstract = {Aims. Combining high-resolution spectropolarimetric and imaging data is key to understanding the decay process of sunspots as it allows us to scrutinize the velocity and magnetic fields of sunspots and their surroundings. Methods. Active region NOAA 12597 was observed on 2016 September 24 with the 1.5-meter GREGOR solar telescope using high-spatial-resolution imaging as well as imaging spectroscopy and near-infrared (NIR) spectropolarimetry. Horizontal proper motions were estimated with local correlation tracking, whereas line-of-sight (LOS) velocities were computed with spectral line fitting methods. The magnetic field properties were inferred with the "Stokes Inversions based on Response functions" (SIR) code for the Si I and Ca I NIR lines. Results. At the time of the GREGOR observations, the leading sunspot had two light bridges indicating the onset of its decay. One of the light bridges disappeared, and an elongated, dark umbral core at its edge appeared in a decaying penumbral sector facing the newly emerging flux. The flow and magnetic field properties of this penumbral sector exhibited weak Evershed flow, moat flow, and horizontal magnetic field. The penumbral gap adjacent to the elongated umbral core and the penumbra in that penumbral sector displayed LOS velocities similar to granulation. The separating polarities of a new flux system interacted with the leading and central part of the already established active region. As a consequence, the leading spot rotated 55 degrees clockwise over 12 h. Conclusions. In the high-resolution observations of a decaying sunspot, the penumbral filaments facing the flux emergence site contained a darkened area resembling an umbral core filled with umbral dots. This umbral core had velocity and magnetic field properties similar to the sunspot umbra. This implies that the horizontal magnetic fields in the decaying penumbra became vertical as observed in flare-induced rapid penumbral decay, but on a very different time-scale.}, language = {en} } @article{DenglerWagnerDembiczetal.2018, author = {Dengler, J{\"u}rgen and Wagner, Viktoria and Dembicz, Iwona and Garcia-Mijangos, Itziar and Naqinezhad, Alireza and Boch, Steffen and Chiarucci, Alessandro and Conradi, Timo and Filibeck, Goffredo and Guarino, Riccardo and Janisova, Monika and Steinbauer, Manuel J. and Acic, Svetlana and Acosta, Alicia T. R. and Akasaka, Munemitsu and Allers, Marc-Andre and Apostolova, Iva and Axmanova, Irena and Bakan, Branko and Baranova, Alina and Bardy-Durchhalter, Manfred and Bartha, Sandor and Baumann, Esther and Becker, Thomas and Becker, Ute and Belonovskaya, Elena and Bengtsson, Karin and Benito Alonso, Jose Luis and Berastegi, Asun and Bergamini, Ariel and Bonini, Ilaria and Bruun, Hans Henrik and Budzhak, Vasyl and Bueno, Alvaro and Antonio Campos, Juan and Cancellieri, Laura and Carboni, Marta and Chocarro, Cristina and Conti, Luisa and Czarniecka-Wiera, Marta and De Frenne, Pieter and Deak, Balazs and Didukh, Yakiv P. and Diekmann, Martin and Dolnik, Christian and Dupre, Cecilia and Ecker, Klaus and Ermakov, Nikolai and Erschbamer, Brigitta and Escudero, Adrian and Etayo, Javier and Fajmonova, Zuzana and Felde, Vivian A. and Fernandez Calzado, Maria Rosa and Finckh, Manfred and Fotiadis, Georgios and Fracchiolla, Mariano and Ganeva, Anna and Garcia-Magro, Daniel and Gavilan, Rosario G. and Germany, Markus and Giladi, Itamar and Gillet, Francois and Giusso del Galdo, Gian Pietro and Gonzalez, Jose M. and Grytnes, John-Arvid and Hajek, Michal and Hajkova, Petra and Helm, Aveliina and Herrera, Mercedes and Hettenbergerova, Eva and Hobohm, Carsten and Huellbusch, Elisabeth M. and Ingerpuu, Nele and Jandt, Ute and Jeltsch, Florian and Jensen, Kai and Jentsch, Anke and Jeschke, Michael and Jimenez-Alfaro, Borja and Kacki, Zygmunt and Kakinuma, Kaoru and Kapfer, Jutta and Kavgaci, Ali and Kelemen, Andras and Kiehl, Kathrin and Koyama, Asuka and Koyanagi, Tomoyo F. and Kozub, Lukasz and Kuzemko, Anna and Kyrkjeeide, Magni Olsen and Landi, Sara and Langer, Nancy and Lastrucci, Lorenzo and Lazzaro, Lorenzo and Lelli, Chiara and Leps, Jan and Loebel, Swantje and Luzuriaga, Arantzazu L. and Maccherini, Simona and Magnes, Martin and Malicki, Marek and Marceno, Corrado and Mardari, Constantin and Mauchamp, Leslie and May, Felix and Michelsen, Ottar and Mesa, Joaquin Molero and Molnar, Zsolt and Moysiyenko, Ivan Y. and Nakaga, Yuko K. and Natcheva, Rayna and Noroozi, Jalil and Pakeman, Robin J. and Palpurina, Salza and Partel, Meelis and Paetsch, Ricarda and Pauli, Harald and Pedashenko, Hristo and Peet, Robert K. and Pielech, Remigiusz and Pipenbaher, Natasa and Pirini, Chrisoula and Pleskova, Zuzana and Polyakova, Mariya A. and Prentice, Honor C. and Reinecke, Jennifer and Reitalu, Triin and Pilar Rodriguez-Rojo, Maria and Rolecek, Jan and Ronkin, Vladimir and Rosati, Leonardo and Rosen, Ejvind and Ruprecht, Eszter and Rusina, Solvita and Sabovljevic, Marko and Maria Sanchez, Ana and Savchenko, Galina and Schuhmacher, Oliver and Skornik, Sonja and Sperandii, Marta Gaia and Staniaszek-Kik, Monika and Stevanovic-Dajic, Zora and Stock, Marin and Suchrow, Sigrid and Sutcliffe, Laura M. E. and Swacha, Grzegorz and Sykes, Martin and Szabo, Anna and Talebi, Amir and Tanase, Catalin and Terzi, Massimo and Tolgyesi, Csaba and Torca, Marta and Torok, Peter and Tothmeresz, Bela and Tsarevskaya, Nadezda and Tsiripidis, Ioannis and Tzonev, Rossen and Ushimaru, Atushi and Valko, Orsolya and van der Maarel, Eddy and Vanneste, Thomas and Vashenyak, Iuliia and Vassilev, Kiril and Viciani, Daniele and Villar, Luis and Virtanen, Risto and Kosic, Ivana Vitasovic and Wang, Yun and Weiser, Frank and Went, Julia and Wesche, Karsten and White, Hannah and Winkler, Manuela and Zaniewski, Piotr T. and Zhang, Hui and Ziv, Yaron and Znamenskiy, Sergey and Biurrun, Idoia}, title = {GrassPlot - a database of multi-scale plant diversity in Palaearctic grasslands}, series = {Phytocoenologia}, volume = {48}, journal = {Phytocoenologia}, number = {3}, publisher = {Cramer}, address = {Stuttgart}, issn = {0340-269X}, doi = {10.1127/phyto/2018/0267}, pages = {331 -- 347}, year = {2018}, abstract = {GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). GrassPlot collects plot records (releves) from grasslands and other open habitats of the Palaearctic biogeographic realm. It focuses on precisely delimited plots of eight standard grain sizes (0.0001; 0.001;... 1,000 m(2)) and on nested-plot series with at least four different grain sizes. The usage of GrassPlot is regulated through Bylaws that intend to balance the interests of data contributors and data users. The current version (v. 1.00) contains data for approximately 170,000 plots of different sizes and 2,800 nested-plot series. The key components are richness data and metadata. However, most included datasets also encompass compositional data. About 14,000 plots have near-complete records of terricolous bryophytes and lichens in addition to vascular plants. At present, GrassPlot contains data from 36 countries throughout the Palaearctic, spread across elevational gradients and major grassland types. GrassPlot with its multi-scale and multi-taxon focus complements the larger international vegetationplot databases, such as the European Vegetation Archive (EVA) and the global database " sPlot". Its main aim is to facilitate studies on the scale-and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. GrassPlot is a dynamic database and will expand through new data collection coordinated by the elected Governing Board. We invite researchers with suitable data to join GrassPlot. Researchers with project ideas addressable with GrassPlot data are welcome to submit proposals to the Governing Board.}, language = {en} } @phdthesis{GonzalezManrique2017, author = {Gonz{\´a}lez Manrique, Sergio Javier}, title = {High-Resolution Observations of Emerging Flux Regions}, school = {Universit{\"a}t Potsdam}, pages = {104}, year = {2017}, language = {en} } @misc{BarlowHartmannGonzalezetal.2020, author = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Consensify}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1033}, issn = {1866-8372}, doi = {10.25932/publishup-47252}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472521}, pages = {24}, year = {2020}, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, language = {en} } @article{BarlowHartmannGonzalezetal.2020, author = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Consensify}, series = {Genes / Molecular Diversity Preservation International}, volume = {11}, journal = {Genes / Molecular Diversity Preservation International}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes11010050}, pages = {22}, year = {2020}, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, language = {en} } @article{AlbertiGonzalezPaijmansetal.2018, author = {Alberti, Federica and Gonzalez, Javier and Paijmans, Johanna L. A. and Basler, Nikolas and Preick, Michaela and Henneberger, Kirstin and Trinks, Alexandra and Rabeder, Gernot and Conard, Nicholas J. and Muenzel, Susanne C. and Joger, Ulrich and Fritsch, Guido and Hildebrandt, Thomas and Hofreiter, Michael and Barlow, Axel}, title = {Optimized DNA sampling of ancient bones using Computed Tomography scans}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12911}, pages = {1196 -- 1208}, year = {2018}, abstract = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99\% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.}, language = {en} } @article{Gonzalez2014, author = {Gonzalez, Javier}, title = {Phylogenetic position of the most endangered Chilean bird: the Masafuera Rayadito (Aphrastura masafuerae; Furnariidae)}, series = {Tropical conservation science}, volume = {7}, journal = {Tropical conservation science}, number = {4}, publisher = {Mongabay.com}, address = {Menlo Park}, issn = {1940-0829}, pages = {677 -- 689}, year = {2014}, abstract = {Masafuera Rayadito (Aphrastura masafuerae; Furnariidae) is a Critically Endangered species endemic to Alejandro Selkirk Island (Juan Fernandez Archipelago, Chile). Categorized as probably extinct in 1980, later estimates, ranging from 140 (in 2002) to 500 individuals (in 2006-2007), showed a fluctuating population size of the species. The grazing of goats and cattle has increased habitat loss for the species. Other threats are lack of nesting sites, introduced species such as feral cats and rats (Rattus rattus and R. norvegicus), and increased populations of natural predators like the Masafuera Hawk. In order to increase the availability of nesting sites, 81 nest boxes were installed in different habitats in 2006, with evidence of use during subsequent breeding seasons. Despite conservation concerns, however, no genetic studies are yet available for this furnariid. This study reports for the first time the levels of genetic divergence of the species, based on nucleotide sequences of the mitochondrial DNA (cytochrome oxidase subunit 1 gene; COI). Aphrastura masafuerae is closely related to a widespread species of furnariid distributed mainly in Chile on the mainland, the Thorn-tailed Rayadito (A. spinicauda). The Masafuera Rayadito diverged from its mainland sister species probably during the Pleistocene 0.57 +/- 0.19 Myr ago. Consistent with mitochondrial and nuclear molecular clocks, the estimated time of the split between A. masafuerae and A. spinicauda is in perfect agreement with the geological origin of the Juan Fernandez Archipelago, which is of volcanic origin. In order to assess genetic variability within the population of this fragile bird, further studies using a multi-locus genetic approach at the population level are necessary.}, language = {en} } @article{WutkeBeneckeSandovalCastellanosetal.2016, author = {Wutke, Saskia and Benecke, Norbert and Sandoval-Castellanos, Edson and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez Soto, Javier Esteban and Hallsson, Jon Hallsteinn and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Ruttkay, Matej and Trinks, Alexandra and Ludwig, Arne}, title = {Spotted phenotypes in horses lost attractiveness in the Middle Ages}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep38548}, pages = {9}, year = {2016}, abstract = {Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.}, language = {en} } @misc{WutkeAnderssonBeneckeetal.2016, author = {Wutke, Saskia and Andersson, Leif and Benecke, Norbert and Sandoval-Castellanos, Edson and Gonzalez, Javier and Hallsson, Jon Hallsteinn and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Munoz-Rodriguez, Mariana B. and Ruttkay, Matej and Trinks, Alexandra and Hofreiter, Michael and Ludwig, Arne}, title = {The origin of ambling horses}, series = {Current biology}, volume = {26}, journal = {Current biology}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2016.07.001}, pages = {R697 -- R699}, year = {2016}, abstract = {Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called 'gaited' horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th-11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.}, language = {en} } @article{BalthasarGoemoeryGonzalezManriqueetal.2016, author = {Balthasar, H. and G{\"o}m{\"o}ry, P. and Gonz{\´a}lez Manrique, Sergio Javier and Kuckein, Christoph and Kavka, J. and Kucera, A. and Schwartz, P. and Vaskova, R. and Berkefeld, T. and Collados Vera, M. and Denker, Carsten and Feller, A. and Hofmann, A. and Lagg, A. and Nicklas, H. and Suarez, D. and Pastor Yabar, A. and Rezaei, R. and Schlichenmaier, R. and Schmidt, D. and Schmidt, W. and Sigwarth, M. and Sobotka, M. and Solanki, S. K. and Soltau, D. and Staude, J. and Strassmeier, Klaus G. and Volkmer, R. and von der L{\"u}he, O. and Waldmann, T.}, title = {Spectropolarimetric observations of an arch filament system with the GREGOR solar telescope}, series = {Astronomische Nachrichten = Astronomical notes}, volume = {337}, journal = {Astronomische Nachrichten = Astronomical notes}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0004-6337}, doi = {10.1002/asna.201612432}, pages = {1050 -- 1056}, year = {2016}, abstract = {Arch filament systems occur in active sunspot groups, where a fibril structure connects areas of opposite magnetic polarity, in contrast to active region filaments that follow the polarity inversion line. We used the GREGOR Infrared Spectrograph (GRIS) to obtain the full Stokes vector in the spectral lines SiI lambda 1082.7 nm, He I lambda 1083.0 nm, and Ca I lambda 1083.9 nm. We focus on the near-infrared calcium line to investigate the photospheric magnetic field and velocities, and use the line core intensities and velocities of the helium line to study the chromospheric plasma. The individual fibrils of the arch filament system connect the sunspot with patches of magnetic polarity opposite to that of the spot. These patches do not necessarily coincide with pores, where the magnetic field is strongest. Instead, areas are preferred not far from the polarity inversion line. These areas exhibit photospheric downflows of moderate velocity, but significantly higher downflows of up to 30 km s(-1) in the chromospheric helium line. Our findings can be explained with new emerging flux where the matter flows downward along the field lines of rising flux tubes, in agreement with earlier results. (C) 2016 WILEY-VCH Verlag GmbH\& Co. KGaA, Weinheim}, language = {en} } @article{DenkerHeibelRendteletal.2016, author = {Denker, Carsten and Heibel, C. and Rendtel, J. and Arlt, K. and Balthasar, H. and Diercke, Andrea and Gonzalez Manrique, Sergio Javier and Hofmann, A. and Kuckein, Christoph and {\"O}nel, H. and Valliappan, Senthamizh Pavai and Staude, J. and Verma, Meetu}, title = {Solar physics at the Einstein Tower}, series = {Astronomische Nachrichten = Astronomical notes}, volume = {337}, journal = {Astronomische Nachrichten = Astronomical notes}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0004-6337}, doi = {10.1002/asna.201612442}, pages = {1105 -- 1113}, year = {2016}, language = {en} } @article{KuckeinDierckeGonzalezManriqueetal.2017, author = {Kuckein, Christoph and Diercke, Andrea and Gonz{\´a}lez Manrique, Sergio Javier and Verma, Meetu and Loehner-Boettcher, Johannes and Socas-Navarro, H. and Balthasar, Horst and Sobotka, M. and Denker, Carsten}, title = {Ca II 8542 angstrom brightenings induced by a solar microflare}, series = {Astronomy and astrophysics : an international weekly journal}, volume = {608}, journal = {Astronomy and astrophysics : an international weekly journal}, publisher = {EDP Sciences}, address = {Les Ulis}, issn = {1432-0746}, doi = {10.1051/0004-6361/201731319}, pages = {13}, year = {2017}, abstract = {Aims. We study small-scale brightenings in Ca II 8542 angstrom line-core images to determine their nature and effect on localized heating and mass transfer in active regions. Methods. High-resolution two-dimensional spectroscopic observations of a solar active region in the near-infrared Ca II 8542 angstrom line were acquired with the GREGOR Fabry-Perot Interferometer attached to the 1.5-m GREGOR telescope. Inversions of the spectra were carried out using the NICOLE code to infer temperatures and line-of-sight (LOS) velocities. Response functions of the Ca II line were computed for temperature and LOS velocity variations. Filtergrams of the Atmospheric Imaging Assembly (AIA) and magnetograms of the Helioseismic and Magnetic Imager (HMI) were coaligned to match the ground-based observations and to follow the Ca II brightenings along all available layers of the atmosphere. Results. We identified three brightenings of sizes up to 2 ' x 2 ' that appeared in the Ca II 8542 angstrom line-core images. Their lifetimes were at least 1.5 min. We found evidence that the brightenings belonged to the footpoints of a microflare (MF). The properties of the observed brightenings disqualified the scenarios of Ellerman bombs or Interface Region Imaging Spectrograph (IRIS) bombs. However, this MF shared some common properties with flaring active-region fibrils or flaring arch filaments (FAFs): (1) FAFs and MFs are both apparent in chromospheric and coronal layers according to the AIA channels; and (2) both show flaring arches with lifetimes of about 3.0-3.5 min and lengths of similar to 20 ' next to the brightenings. The inversions revealed heating by 600 K at the footpoint location in the ambient chromosphere during the impulsive phase. Connecting the footpoints, a dark filamentary structure appeared in the Ca II line-core images. Before the start of the MF, the spectra of this structure already indicated average blueshifts, meaning upward motions of the plasma along the LOS. During the impulsive phase, these velocities increased up to -2.2 km s(-1). The structure did not disappear during the observations. Downflows dominated at the footpoints. However, in the upper photosphere, slight upflows occurred during the impulsive phase. Hence, bidirectional flows are present in the footpoints of the MF.}, language = {en} }