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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A two-dimensional chiral conformal field theory can be viewed mathematically as the representation theory of its chiral algebra, a vertex operator algebra. Vertex operator algebras are especially well suited for studying logarithmic conformal field theory (in which correlation functions have logarithmic singularities arising from non-semisimple modules for the chiral algebra) because of the logarithmic tensor category theory of Huang, Lepowsky, and Zhang. In this paper, we study not-necessarily-semisimple or rigid braided tensor categories C of modules for the fixed-point vertex operator subalgebra V^G of a vertex operator (super)algebra V with finite automorphism group G. The main results are that every V^G-module in C with a unital and associative V-action is a direct sum of g-twisted V-modules for possibly several g∈G, that the category of all such twisted V-modules is a braided G-crossed (super)category, and that the G-equivariantization of this braided G-crossed (super)category is braided tensor equivalent to the original category C of V^G-modules. This generalizes results of Kirillov and Müger proved using rigidity and semisimplicity. We also apply the main results to the orbifold rationality problem: whether V^G is strongly rational if V is strongly rational. We show that V^G is indeed strongly rational if V is strongly rational, G is any finite automorphism group, and V^G is C_2-cofinite.