title: Modularized evolution in archaeal methanogens phylogenetic forest.
abstract: Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, China School of Biological Sciences, Faculty of Science, The University of Hong Kong, China.
authors.forename: Chi-Fat
authors.initials: CF
authors.lastname: Wong
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Present address: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.
authors.forename: Mabel Ting
authors.initials: MT
authors.lastname: Wong
authors.affiliation: Center for Marine Environmental Studies, Ehime University, Japan.
authors.forename: He
authors.initials: H
authors.lastname: Huang
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Bioinformatics Center, Nanjing Agricultural University, People's Republic of China fcleung@hkucc.hku.hk.
authors.forename: Frederick C
authors.initials: FC
authors.lastname: Leung
mesh_terms: D019605:Euryarchaeota / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D008697:Methane / Q000378:metabolism; D010802:Phylogeny
chemical_list: D008697:Methane
keywords: HGT; LGT; co-evolution network; modularized evolution; network analysis; phylogenetic forest