Extended Newick: it is time for a standard representation of phylogenetic networks

Background  

Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).     

Environmental assessment of energy-driven biorefineries: the case of the coffee cut-stems (CCS) in Colombia

The International Journal of Life Cycle Assessment - Coffee cut-stems (CCS) are typically left in the field after coffee harvesting as fertilizer or used partially for cooking and drying of coffee...     

Mitochondria: The hands of the clock?

The output of the master clock to control peripheral circadian functions and temporal organization in metazoans is unknown. We recently reported a periodic dip of lipidperoxidation (PDL) at 03 h in humans by monitoring the serum levels of malondialdehyde (MDA), a marker of lipidperoxidation, over a 24-hour period and suggested that PDL may represent a redox signal of the master clock. Mitochondria are considered to be the major source of lipidperoxidation in most tissues. Their activity is known to be disrupted in many malignant tissues. To test the possible role of mitochondrial activity on the induction of the PDL, we monitored the daily MDA levels in the serum of 16 cancer patients, suffering from different kinds of malignant tumors, and compared them with those found in the healthy humans of our previous study. Discriminant analysis revealed a significant difference between both groups only at 03 h ( p = 0.000001), thus indicating the critical relevance of this time point for differences between both groups. In the light of the emerging role of the mitochondrion in cell signaling, we suggest that the signal transduction from the master clock may be related to central and peripheral mitochondrial activity and its ROS (reactive oxygen species) generation. This notion could involve nitric oxide, as a known potent regulator of mitochondrial function and as an essential part of the mitochondrial signaling pathway. The PDL could additionally be useful as a circadian phase marker in chronobiology research.     

The New Face of Debt-Peonage in the Bolivian Amazon: Social Networks and Bargaining Instruments

The debt-peonage system is an agreement between patrons and laborers in different economic activities worldwide. A common feature is social exploitation of laborers that generate profits to the patrons. In recent literature it has been argued that debt-peonage can be an economically sound arrangement that secures the needs of actors. The paper evaluates to what extent traditionally strong debt-peonage in forest-dwelling communities in the Bolivian Amazon, has developed in a way that better secures the needs and economic interest of multiple actors. Case studies in sixteen communities yielded qualitative information on debt relations between peasants, traders and former patrons. Debt-peonage changed from a mechanism to provide and keep workforce indebted to new social relationships, equitable commercial links, opportunity to access work capital and production chain diversification. This rapid shift was caused by important changes in land and forest regulations.     

On Nakhleh's Metric for Reduced Phylogenetic Networks

We prove that Nakhleh's metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phylogenetic networks.