Research ArticleVIROLOGY

A phylogenomic data-driven exploration of viral origins and evolution

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Science Advances  25 Sep 2015:
Vol. 1, no. 8, e1500527
DOI: 10.1126/sciadv.1500527

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  • Authors' response to Harish eLetter

    Response to Harish et al.: No ‘small genome attraction’ artifact
    Arshan Nasir, Kyung Mo Kim and Gustavo Caetano-Anollés

    In their eLetter, Harish, Abroi, Gough and Kurland criticize our structural phylogenomic methods, which are supported by large-scale structural and functional data and well-established comparative genomics, phylogenomics, and multidimensional scaling approaches (1). Harish et al. would like to see the origin of Eukarya at the base of the Tree of Life (ToL) (2). So despite invalidating critique (3), they go on to challenge the early cellular origin of viruses. Their claims include a warning to “nonspecialists” that the rooting of our trees is distorted by what they dub is “a small genome attraction artifact of genome content-based phylogenetic analysis”. Here we examine their reasoning, which mingles with misunderstandings and misinterpretations of cladistic methodology (Please refer to Table 1).

    1. Their claim that our rooting approach uses outgroup taxa is incorrect. We do not “use a hypothetical pseudo-outgroup, … an artificial all-zero taxon … to root the ToL”. No outgroup taxon (presumably extant or artificial) was ever used or defined in our study (1). Their confusion of outgroups with ancestors showcases cladistics misunderstanding (Table 1). Contrary to their claims, our rooting method is grounded in early and well-established cladistic formalizations (4, 5) and is direct because it polarizes character transformations with infor...

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    Competing Interests: None declared.
  • eLetter Concerning Nasir and Caetano-Anollés’ Conclusions About the Origins of Viruses

    Nasir and Caetano-Anollés (1) conclude that viruses are an ancient lineage that diverged in parallel with their cellular hosts from a universal common ancestor (UCA). They reiterate their earlier claim (2) that viruses are a unique lineage, which predated or coevolved with the last UCA of cellular lineages (LUCA) through reductive evolution as opposed to recent and multiple origins. The claims are based on statistical- and phylogenetic analyses of the genomic distribution patterns of protein domains, classified as superfamilies (SFs) in Structural Classification of Proteins (SCOP) (3). We highlight issues with the phylogenomic approach that is at the heart of these analyses. In particular, we believe that nonspecialists should be aware that conclusions in (1) are subject to a technical artifact of genome content based phylogenetic analysis dubbed as the "small genome attraction" artifact. Key to the conclusion that viruses are an ancient lineage (1) is the specific rooting method—the so-called Lundberg rooting method—used to convert unrooted trees into rooted phylogenies, a necessary step in reconstructing the hypothetical common ancestors at the nodes of branching points in a tree. The Lundberg rooting method employed in (1) distorts the phylogenetic analyses in (i) tree of proteomes (ToP), which represents the universal tree of life (ToL) and (ii) tree of domains (ToD), which is used to determine the relative age of SCOP-SFs.

    (i) Root...

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    Competing Interests: None declared.