Consensus Clusters in Robinson-Foulds Reticulation Networks

Inference of phylogenetic networks - the evolutionary histories of species involving speciation as well as reticulation events - has proved to be an extremely challenging problem even for smaller datasets easily tackled by supertree inference methods. An effective way to boost the scalability of distance-based supertree methods originates from the Pareto (for clusters) property, which is a highly desirable property for phylogenetic consensus methods. In particular, one can employ strict consensus merger algorithms to boost the scalability and accuracy of supertree methods satisfying Pareto; cf. SuperFine. In this work, we establish a Pareto-like property for phylogenetic networks. Then we consider the recently introduced RF-Net method that heuristically solves the so-called RF-Network problem and which was demonstrated to be an efficient and effective tool for the inference of hybridization and reassortment networks. As our main result, we provide a constructive proof (entailing an explicit refinement algorithm) that the Pareto property applies to the RF-Network problem when the solution space is restricted to the popular class of tree-child networks. This result implies that strict consensus merger strategies, similar to SuperFine, can be directly applied to boost both accuracy and scalability of RF-Net significantly. Finally, we further investigate the optimum solutions to the RF-Network problem; in particular, we describe structural properties of all optimum (tree-child) RF-networks in relation to strict consensus clusters of the input trees

Bestimmung des Knochenalters: Vergleich einer konventionellen Röntgenmethode mit einer neuentwickelten Ultraschallmethode

Das objektive Kriterium für die biologische Gesamtreife und Entwicklung eines Menschen ist nicht sein kalendarisches Alter, sondern sein Knochenalter. Aus diesem Grund besitzt die Knochenaltersbestimmung in der Diagnostik von Wachstums- und Entwicklungsstörungen besondere klinische Relevanz. In der Methodik der radiologischen Skelettaltersbestimmung haben sich nur Methoden etablieren können, welche für die Altersbestimmung Radiogramme der Hand nutzen. Das Handskelett wird aufgrund seiner Vielzahl sekundärer Ossifikationszentren als repräsentativer Teil des Skelettsystems angesehen. Zu den am weitesten verbreiteten Methoden der Knochenaltersbestimmung zählt die Atlasmethode von Greulich & Pyle, die auf der subjektiven Beurteilung des Radiogramms durch den Untersucher basiert. In der Fachliteratur lassen si h aufgrund dieser Subjektivität oft widersprüchliche Angaben über die Interbeurteiler-Variabilität der Methode finden. Au h der Einfluss vom Grad der Qualifizierung eines Untersuchers sowie seiner Erfahrung im Umgang mit der Methode werden kontrovers diskutiert. Ziele dieser Studie waren deshalb die erneute Begutachtung der widersprüchlichen Literaturangaben über die Interbeurteiler-Variabilität der Greulich & Pyle-Methode und die Evaluierung der Tauglichkeit einer neuentwickelten sonographischen Methode zur Knochenaltersbestimmung im Vergleich zur Standardmethode von Greulich & Pyle.

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

<p>Abstract</p> <p>Background</p> <p>Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest gene duplications, duplications and losses, or deep coalescence (incomplete lineage sorting) events needed to reconcile a gene tree and a species tree. While a gene tree parsimony approach can be informative about genome evolution and phylogenetics, error in gene trees can profoundly bias the results.</p> <p>Results</p> <p>We introduce efficient algorithms that rapidly search local Subtree Prune and Regraft (SPR) or Tree Bisection and Reconnection (TBR) neighborhoods of a given gene tree to identify a topology that implies the fewest duplications, duplication and losses, or deep coalescence events. These algorithms improve on the current solutions by a factor of <it>n </it>for searching SPR neighborhoods and <it>n</it>²for searching TBR neighborhoods, where <it>n </it>is the number of taxa in the given gene tree. They provide a fast error correction protocol for ameliorating the effects of gene tree error by allowing small rearrangements in the topology to improve the reconciliation cost. We also demonstrate a simple protocol to use the gene rearrangement algorithm to improve gene tree parsimony phylogenetic analyses.</p> <p>Conclusions</p> <p>The new gene tree rearrangement algorithms provide a fast method to address gene tree error. They do not make assumptions about the underlying processes of genome evolution, and they are amenable to analyses of large-scale genomic data sets. These algorithms are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing more credible estimates of reconciliation cost.</p

Evapotranspiration of Rewetted and Drained Fen Soils With Grass – Long Term Lysimeter Studies

In the context of reducing greenhouse gas (GHG) emissions to combat climate change, rewetting of peatlands is of particular importance. High groundwater levels covering organic matter in the soil prevent its oxidation to CO2. The amount of water needed to allow the rewetting of peatlands can be determined in lysimeter studies. The evapotranspiration in fens depends essentially on the groundwater table, the vegetation (transpirational active biomass) and the saturation deficit of the atmosphere. After rewetting, these factors can lead to an evapotranspiration of 1000 l m-2 a-1 and even 2000 l m-2 a-1 in dry years depending on the vegetation. In a long term experiment over 20 years, the lysimeters planted with Phragmites australis showed the highest evapotranspiration rates, followed by those covered with Carex species. Evaluation of these results for a large, flooded, rewetted fen area in the Havelländisches Luch in the federal state of Brandenburg, Germany, with Phragmites confirmed the high values of evapotranspiration measured at the groundwater lysimeter station of ZALF in Paulinenau

Nutrient Balances of Rewetted Fens – Groundwater Lysimeter Results

With the raising of groundwater levels to protect fens and the climate, there may be a risk of nutrients, such as nitrogen or potassium, leaching into the groundwater. Great amounts of nutrients, which are accumulated largely by peat forming plants like Phragmites australis and Carex spec., are conveyed into rewetted fens through high amounts of introduced water. Nitrogen leaching into the groundwater is very low even at the beginning of flooding and there is no sudden, pronounced leaching. Only a portion of potassium is taken up by plants whereas the rest might be found in the groundwater. Increasing nutrient inputs must be expected as soon as more contaminated water is added contributing to the regeneration of groundwater and increasing the pollution with nutrients at once