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-Anollé s 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.

No ‘small genome attraction’ artifact: A response to Harish et al. ‘Did viruses evolve as a distinct supergroup from common ancestors of cells?’

“…For clarification, the smallest proteomes included Ignicoccus hospitalis (Archaea, 213 fold superfamilies), Lactobacillus delbrueckii (Bacteria, 261), Ashbya gossypii (Eukarya, 326), and the bat cyclovirus (virus, 1). We also labeled the 9 viruses (4 RNA and 5 dsDNA) that produced phylogenetic distortions in the trees of Harish et al [3]. Following the Harish et al [3] logic, one should expect for the smallest proteomes to "fight" for the basal position within each of the four-supergroup subtrees or appear together closest to the root, irrespective of their taxonomic affiliation [2,3].…”

“…We also labeled the 9 viruses (4 RNA and 5 dsDNA) that produced phylogenetic distortions in the trees of Harish et al [3]. Following the Harish et al [3] logic, one should expect for the smallest proteomes to "fight" for the basal position within each of the four-supergroup subtrees or appear together closest to the root, irrespective of their taxonomic affiliation [2,3]. Contrary to that, the smallest proteomes appeared at well-derived positions (see arrow pointers) and did not cause any phylogenetic distortions or mixing of taxa from different supergroups!…”

“…to "create specific phylogenetic artifacts" [3]. No outgroup taxon (presumably extant or artificial) was ever used/defined in our study [4], demonstrating they are confusing outgroups with ancestors (Table 1).…”

“…Indeed, our tree of life uncovered many viral monophyletic groups consistent with ICTV classifications and showed remarkable evolutionary tracings of virion morphotypes onto a revealing tree topology.Harish et al would like to see the origin of Eukarya at the base of the Tree of Life (ToL) [1]. So, in their commentary [2,3], they begin by questioning our phylogenomic analysis, which is supported by large-scale structural and functional data and well-established comparative genomics, phylogenomics, and multidimensional scaling approaches [4]. Their writings [2,3] fail to acknowledge recent literature, including our recent invalidation of both their rationale [5] and their own phylogenetic methodologies [6], which we showed counter modern evolutionary thinking.…”

“…No outgroup taxon (presumably extant or artificial) was ever used/defined in our study [4], demonstrating they are confusing outgroups with ancestors (Table 1). We are therefore puzzled by the indirectly rooted ToLs they build in their attempt to mimic and undermine our methods [3], as well as the putative sensitivity to addition of new taxa, especially because these taxa represent organisms that engage in extreme forms of cellular endosymbiosis (please read below for the rationale for why then viruses were included). Even their tree searches were conducted differently, failing to minimize Farris' f-values and being dependent on the location of the root.…”