title: A new method for studying the evolutionary origin of the SAR11 clade marine bacteria.
abstract: 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.
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China.
authors.forename: Xiaogeng
authors.initials: X
authors.lastname: Wan
authors.affiliation: Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA.
authors.forename: Rong L
authors.initials: RL
authors.lastname: He
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China. Electronic address: yau@uic.edu.
authors.forename: Stephen S-T
authors.initials: SS
authors.lastname: Yau
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D059001:Aquatic Organisms / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D020543:Proteome
keywords: Alphaproteobacteria; Natural graph representation; Natural vector; Phylogenetics; SAR11