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Zayed et al. (April 7, 2022) in Science “Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome” report several major hitherto-unknown Ribovirial phyla:

New Orthornaviran phyla

The two most sampled, Taraviricota and Arctiviricota, had the lowest normalized abundances.

To mitigate issues of subjectivity, their RdRp-based phylogenetic analysis was developed to recapitulate the established ICTV-accepted taxonomy (97% agreement). Their new tree shows a very different early evolutionary history, for example splitting Duplornaviricota into 3 distant phyla:

New Orthornavirae phylogenetic tree

Are these findings robust? The unknown megataxa and the revision of Orthornavirae?

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    $\begingroup$ Do you really think that there is someone on this list who has read and is better able to assess this paper than the referees assigned to it by Science? I presume you feel it important — I have no idea — but if it is I’m afraid you will have to wait either for direct responses to the journal, or future publications citing it. This is a question and answer site about biology, not a journal club. $\endgroup$
    – David
    Apr 23, 2022 at 13:20
  • $\begingroup$ Can you identify the evidence supporting alternate tree topologies? If you show that evidence here we might be able to judge it. $\endgroup$
    – Maximilian Press
    Apr 27, 2022 at 19:54
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    $\begingroup$ Paper certainly looks robust - you would need to dig out the original data and analyse for yourself if you wished to compare. You can find the annotated data here: datacommons.cyverse.org/browse/iplant/home/shared/iVirus/… $\endgroup$
    – bob1
    Apr 28, 2022 at 3:46
  • $\begingroup$ @David Sometimes in phylogenetics the reviewers of science are just a joke (see the Omicron evolved in west africa retracted paper where the non-omicron raw reads were just contaminated with later omicron strains) $\endgroup$
    – reuns
    Feb 25 at 18:50
  • $\begingroup$ The main difficulty here is that it is risky to feed mafft directly with so distant RdRp, the resulting alignment will be a mess for sure. You can try running a MCMC optimizing both the tree and the alignment (after subsampling the dataset) and see if the deep branches topology stays comparable. $\endgroup$
    – reuns
    Feb 25 at 18:56

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