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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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In this paper, a homotopy continuation method for the computation of nonnegative Z-/H-eigenpairs of a nonnegative tensor is presented. We show that the homotopy continuation method is guaranteed to compute a nonnegative eigenpair. Additionally, using degree analysis, we show that the number of positive Z-eigenpairs of an irreducible nonnegative tensor is odd. A novel homotopy continuation method is proposed to compute an odd number of positive Z-eigenpairs, and some numerical results are presented.

A two species interacting system motivated by the density functional theory for triblock copolymers contains long range interaction that affects the two species differently. In a two species periodic assembly of discs, the two species appear alternately on a lattice. The minimal two species periodic assembly is the one with the least energy per lattice cell area. There is a parameter $b$ in $[0,1]$ and the type of the lattice associated with the minimal assembly varies depending on $b$. There are several threshold defined by a number $B=0.1867...$ If $b \in [0, B)$, the minimal assembly is associated with a rectangular lattice whose ratio of the longer side and the shorter side is in $[\sqrt{3}, 1)$; if $b \in [B, 1-B]$, the minimal assembly is associated with a square lattice; if $b \in (1-B, 1]$, the minimal assembly is associated with a rhombic lattice with an acute angle in $[\frac{\pi}{3}, \frac{\pi}{2})$. Only when $b=1$, this rhombic lattice is the hexagonal lattice. None of the other values of $b$ yields the hexagonal lattice, a sharp contrast to the situation for one species interacting systems, where the hexagonal lattice is ubiquitously observed.