A simulation study comparing supertree and combined analysis methods using SMIDGen

Background  

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.     

Assay and Electrophoresis of Superoxide Dismutase from Red Spruce (Picea rubens Sarg.), Loblolly Pine (Pinus taeda L.), and Scotch Pine (Pinus sylvestris L.) : A Method for Biomonitoring

This paper reports a method for extracting the antioxidant enzyme superoxide dismutase (SOD) from the needles of red spruce (Picea rubens Sarg.), loblolly pine (Pinus taeda L.), and scotch pine (Pinus sylvestris L.) with high efficiency and free from interfering compounds. The extraction employs phosphate buffer with polyvinylpolypyrrolidone and Triton X-100 followed by dialysis overnight. The isozymes of SOD in each species were separated electrophoretically and tested for their sensitivity to KCN and H₂O₂. An isozyme resistant to these inhibitors was found in the spruce but not the pine needles. The isozymes from the spruce needles were examined for individual responses to aging and H₂O₂ inhibition. Four of the five CuZn isozymes in spruce were found to have increased significantly but equally by October of their first year and two of those four isozymes were found to be more sensitive to H₂O₂. The response of the SOD isozymes in loblolly pine seedlings to O₃ was also examined and the isozymes were found to be induced equally. Because the SOD activity in the young pine needles was too low to electrophorese, the SOD activity from the pines in the O₃ experiment had to be partially purified using CHCl₃ and ethanol, then concentrated.     

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

Several methods have been developed for simultaneous estimation of alignment and tree, of which POY is the most popular. In a 2007 paper published in Systematic Biology, Ogden and Rosenberg reported on a simulation study in which they compared POY to estimating the alignment using ClustalW and then analyzing the resultant alignment using maximum parsimony. They found that ClustalW+MP outperformed POY with respect to alignment and phylogenetic tree accuracy, and they concluded that simultaneous estimation techniques are not competitive with two-phase techniques. Our paper presents a simulation study in which we focus on the NP-hard optimization problem that POY addresses: minimizing treelength. Our study considers the impact of the gap penalty and suggests that the poor performance observed for POY by Ogden and Rosenberg is due to the simple gap penalties they used to score alignment/tree pairs. Our study suggests that optimizing under an affine gap penalty might produce alignments that are better than ClustalW alignments, and competitive with those produced by the best current alignment methods. We also show that optimizing under this affine gap penalty produces trees whose topological accuracy is better than ClustalW+MP, and competitive with the current best two-phase methods.     

Communication inGalago crassicaudatus

The olfactory, visual and, auditory communicative behaviors of a colony of feralGalago crassicaudatus (four males ad three females) observed over a two year period are documented. The enclosure was constructed to simulate a natural environment, but all stimulus possibilities available in the wild were not present and several new ones were introduced. It is not known how many of such differences may have affected the animals' behavior, however not all behaviors observed in the wild appear in the lab. The characteristics of several calls are described in detail and illustrated with sonagrams. These include an agonistic call, a sexual call, a possible alarm or mobbing call, a possible territorial or spacing call and a “low grunting sound” which appears in contexts of sexual and territorial calls. Compared to “higher” primates these galagos exhibit a small number of vocalizations. The communicative system appears directly correlated to social organization.     

Phylogenetic networks: modeling, reconstructibility, and accuracy

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.     

Identification of Markers for Newly Formed ��-Cells in the Perinatal Period: A Time of Recognized ��-Cell Immaturity

Markers of β-cell maturity would be useful in staging the differentiation of stem/progenitor cells to β-cells whether in vivo or in vitro. We previously identified markers for newly formed β-cells in regenerating rat pancreases after 90% partial pancreatectomy. To test the generality of these markers of newly formed β-cells, we examined their expression during the perinatal period, a time of recognized β-cell immaturity. We show by semiquantitative RT-PCR and immunostaining over the time course from embryonic day 18/20 to birth, 1 day, 2 days, 3 days, 7 days, and adult that MMP-2, CK-19, and SPD are truly markers of new and immature β-cells and that their expression transiently peaks in the perinatal period and is not entirely synchronous. The shared expression of these markers among fetal, newborn, and newly regenerated β-cells, but not adult, strongly supports their use as potential markers for new β-cells in the assessment of both the maturity of stem cell–derived insulin-producing cells and the presence of newly formed islets (neogenesis) in the adult pancreas. (J Histochem Cytochem 58:369–376, 2010)