title: Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?
abstract: The evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anollés reported that their genome-scale phylogenetic analyses based on genomic composition of protein structural-domains identify an ancient origin of the "viral supergroup" (Nasir et al. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv. 1(8):e1500527.). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses, particularly the location of the root of the phylogenetic tree of life that is central to their conclusions. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.
authors: Structural and Molecular Biology Group, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden ajith.harish@gmail.com ajith.harish@icm.uu.se.
authors: Ajith
authors: A
authors: Harish
authors: Estonian Biocentre, Riia 23, Tartu 51010, Estonia.
authors: Aare
authors: A
authors: Abroi
authors: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, UK.
authors: Julian
authors: J
authors: Gough
authors: Microbial Ecology, Department of Biology, Lund University, Sweden.
authors: Charles
authors: C
authors: Kurland
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D008957:Models, Genetic; D010802:Phylogeny; D014764:Viral Proteins / Q000235:genetics; D014780:Viruses / Q000145:classification / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: homoplasy; origins of viruses; rooting artifact; small genome attraction; systematic error; tree of life