title: Archaea: the first domain of diversified life.
abstract: The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Caetano-Anollés
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Arshan
authors.initials: A
authors.lastname: Nasir
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Kaiyue
authors.initials: K
authors.lastname: Zhou
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Derek
authors.initials: D
authors.lastname: Caetano-Anollés
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Jay E
authors.initials: JE
authors.lastname: Mittenthal
authors.affiliation: School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA.
authors.forename: Feng-Jie
authors.initials: FJ
authors.lastname: Sun
authors.affiliation: Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.
authors.forename: Kyung Mo
authors.initials: KM
authors.lastname: Kim
mesh_terms: D001105:Archaea / Q000235:genetics / Q000502:physiology*; D005075:Biological Evolution; D010802:Phylogeny; D014481:United States