title: Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.
abstract: The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this "chimeric" molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum "Lokiarchaeota" as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional "three-domain" world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Arshan
authors.identifier: 0000-0001-7200-0788
authors.initials: A
authors.lastname: Nasir
authors.affiliation: Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea; Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea.
authors.forename: Kyung Mo
authors.initials: KM
authors.lastname: Kim
authors.affiliation: Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, 75015 Paris, France.
authors.forename: Violette
authors.initials: V
authors.lastname: Da Cunha
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
authors.forename: Gustavo
authors.identifier: 0000-0001-5854-4121
authors.initials: G
authors.lastname: Caetano-Anollés
mesh_terms: D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D056890:Eukaryota / Q000235:genetics*; D019143:Evolution, Molecular