@misc{AlterMeyerPostetal.2015, author = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael}, title = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {965}, issn = {1866-8372}, doi = {10.25932/publishup-43892}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438920}, pages = {1510 -- 1522}, year = {2015}, abstract = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.}, language = {en} } @misc{MeyerPalkopoulouBalekaetal.2017, author = {Meyer, Matthias and Palkopoulou, Eleftheria and Baleka, Sina Isabelle and Stiller, Mathias and Penkman, Kirsty E. H. and Alt, Kurt W. and Ishida, Yasuko and Mania, Dietrich and Mallick, Swapan and Meijer, Tom and Meller, Harald and Nagel, Sarah and Nickel, Birgit and Ostritz, Sven and Rohland, Nadin and Schauer, Karol and Sch{\"u}ler, Tim and Roca, Alfred L. and Reich, David and Shapiro, Beth and Hofreiter, Michael}, title = {Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {790}, issn = {1866-8372}, doi = {10.25932/publishup-44013}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-440139}, pages = {14}, year = {2017}, abstract = {The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.}, language = {en} } @misc{GaertnerSteinfathAndorfetal.2009, author = {G{\"a}rtner, Tanja and Steinfath, Matthias and Andorf, Sandra and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Improved heterosis prediction by combining information on DNA- and metabolic markers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45132}, year = {2009}, abstract = {Background: Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance or epistasis based models are commonly used explanations. Conclusion/Significance: The heterosis level is clearly a function of the combination of the parents used for offspring production. This results in a major challenge for plant breeders, as usually several thousand combinations of parents have to be tested for identifying the best combinations. Thus, any approach to reliably predict heterosis levels based on properties of the parental lines would be highly beneficial for plant breeding. Methodology/Principal Findings: Recently, genetic data have been used to predict heterosis. Here we show that a combination of parental genetic and metabolic markers, identified via feature selection and minimum-description-length based regression methods, significantly improves the prediction of biomass heterosis in resulting offspring. These findings will help furthering our understanding of the molecular basis of heterosis, revealing, for instance, the presence of nonlinear genotype-phenotype relationships. In addition, we describe a possible approach for accelerated selection in plant breeding.}, language = {en} } @misc{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1324}, issn = {1866-8372}, doi = {10.25932/publishup-43111}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431115}, pages = {9}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @misc{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1330}, issn = {1866-8372}, doi = {10.25932/publishup-43127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431272}, pages = {11}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @misc{PaijmansBarlowFoersteretal.2019, author = {Paijmans, Johanna L. A. and Barlow, Axel and F{\"o}rster, Daniel W. and Henneberger, Kirstin and Meyer, Matthias and Nickel, Birgit and Nagel, Doris and Wors{\o}e Havm{\o}ller, Rasmus and Baryshnikov, Gennady F. and Joger, Ulrich and Rosendahl, Wilfried and Hofreiter, Michael}, title = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {505}, issn = {1866-8372}, doi = {10.25932/publishup-42255}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-422555}, pages = {12}, year = {2019}, abstract = {Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.}, language = {en} } @misc{YoungUedaGuehretal.2018, author = {Young, Linda and Ueda, Kiyoshi and G{\"u}hr, Markus and Bucksbaum, Philip H. and Simon, Marc and Mukamel, Shaul and Rohringer, Nina and Prince, Kevin C. and Masciovecchio, Claudio and Meyer, Michael and Rudenko, Artem and Rolles, Daniel and Bostedt, Christoph and Fuchs, Matthias and Reis, David A. and Santra, Robin and Kapteyn, Henry and Murnane, Margaret and Ibrahim, Heide and L{\´e}gar{\´e}, Fran{\c{c}}ois and Vrakking, Marc and Isinger, Marcus and Kroon, David and Gisselbrecht, Mathieu and L'Huillier, Anne and W{\"o}rner, Hans Jakob and Leone, Stephen R.}, title = {Roadmap of ultrafast x-ray atomic and molecular physics}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {668}, issn = {1866-8372}, doi = {10.25932/publishup-42423}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-424238}, pages = {46}, year = {2018}, abstract = {X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (1020 W cm-2) of x-rays at wavelengths down to ~1 {\AA}ngstrom, and HHG provides unprecedented time resolution (~50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ~280 eV (44 {\AA}ngstroms) and the bond length in methane of ~1 {\AA}ngstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and {\AA}ngstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at {\AA}ngstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since its discovery roughly 30 years ago, showcasing experiments in AMO physics and other applications. Here we capture the perspectives of 17 leading groups and organize the contributions into four categories: ultrafast molecular dynamics, multidimensional x-ray spectroscopies; high-intensity x-ray phenomena; attosecond x-ray science.}, language = {en} } @misc{MerksSwinarskiMeyeretal.2018, author = {Merks, Anne Margarete and Swinarski, Marie and Meyer, Alexander Matthias and M{\"u}ller, Nicola Victoria and {\"O}zcan, Ismail and Donat, Stefan and Burger, Alexa and Gilbert, Stephen and Mosimann, Christian and Abdelilah-Seyfried, Salim and Pan{\´a}kov{\´a}, Daniela}, title = {Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {849}, issn = {1866-8372}, doi = {10.25932/publishup-42702}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427026}, pages = {17}, year = {2018}, abstract = {Development of a multiple-chambered heart from the linear heart tube is inherently linked to cardiac looping. Although many molecular factors regulating the process of cardiac chamber ballooning have been identified, the cellular mechanisms underlying the chamber formation remain unclear. Here, we demonstrate that cardiac chambers remodel by cell neighbour exchange of cardiomyocytes guided by the planar cell polarity (PCP) pathway triggered by two non-canonical Wnt ligands, Wnt5b and Wnt11. We find that PCP signalling coordinates the localisation of actomyosin activity, and thus the efficiency of cell neighbour exchange. On a tissue-scale, PCP signalling planar-polarises tissue tension by restricting the actomyosin contractility to the apical membranes of outflow tract cells. The tissue-scale polarisation of actomyosin contractility is required for cardiac looping that occurs concurrently with chamber ballooning. Taken together, our data reveal that instructive PCP signals couple cardiac chamber expansion with cardiac looping through the organ-scale polarisation of actomyosin-based tissue tension.}, language = {en} }