The free-living SAR11 clade is a globally abundant group of oceanic Alphaproteobacteria, with small genome sizes and rich genomic A+T content. However, the taxonomy of SAR11 has become controversial recently. Some researchers argue that the position of SAR11 is a sister group to Rickettsiales. Other researchers advocate that SAR11 is located within free-living lineages of Alphaproteobacteria. Here, we use the natural vector representation method to identify the evolutionary origin of the SAR11 clade. This alignment-free method does not depend on any model assumptions. With this approach, the correspondence between proteome sequences and their natural vectors is one-to-one. After fixing a set of proteins, each bacterium is represented by a set of vectors. The Hausdorff distance is then used to compute the dissimilarity distance between two bacteria. The phylogenetic tree can be reconstructed based on these distances. Using our method, we systematically analyze four data sets of alphaproteobacterial proteomes in order to reconstruct the phylogeny of Alphaproteobacteria. From this we can see that the phylogenetic position of the SAR11 group is within a group of other free-living lineages of Alphaproteobacteria.

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For the physical vacuum free boundary problem with the sound speed being C^1/2-Holder continuous near vacuum boundaries of the one-dimensional compressible Euler equations with damping, the global existence of the smooth solution is proved, which is shown to converge to the Barenblatt self-similar solution for the porous media equation with the same total mass when the initial datum is a small perturbation of the Barenblatt solution. The pointwise convergence with a rate of density, the convergence rate of velocity in the supremum norm, and the precise expanding rate of the physical vacuum boundaries are also given. The proof is based on a construction of higher-order weighted functionals with both space and time weights capturing the behavior of solutions both near vacuum states and in large time, an introduction of a new ansatz, higher-order nonlinear energy estimates, and elliptic estimates.

InthispaperwedevelopaconservativelocaldiscontinuousGalerkin(LDG) method for the Schro ̈ dinger-Korteweg-de Vries (Sch-KdV) system, which arises in var- ious physical contexts as a model for the interaction of long and short nonlinear waves. Conservative quantities in the discrete version of the number of plasmons, energy of the oscillations and the number of particles are proved for the LDG scheme of the Sch-KdV system. Semi-implicit time discretization is adopted to relax the time step constraint from the high order spatial derivatives. Numerical results for accuracy tests of stationary traveling soliton, and the collision of solitons are shown. Numerical ex- periments illustrate the accuracy and capability of the method.

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