DOI: 10.5061/dryad.gb5mkkwqx
title: Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

description: Whereas DNA viruses are known to be abundant, diverse, and commonly key
 ecosystem players, RNA viruses are relatively understudied outside disease
 settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to
 expand Earth’s RNA virus catalogues and their taxonomy, investigate their
 evolutionary origins, and assess their marine biogeography from pole to
 pole. Using new approaches to optimize discovery and classification, we
 identified RNA viruses that necessitate substantive revisions of taxonomy
 (doubling phyla and adding &gt;50% new classes) and evolutionary
 understanding. “Species”-rank abundance determination revealed that
 viruses of new phyla “Taraviricota”, a missing link in early RNA virus
 evolution, and “Arctiviricota” are widespread and dominant in the oceans.
 These efforts provide foundational knowledge critical to integrating RNA
 viruses into ecological and epidemiological models.
description: To
 generate phylogenetic trees for each network-derived major cluster,
 sequences from each of these clusters were aligned separately using the
 E-INS-i strategy over 1,000 iterations in MAFFT v7.017 (Katoh and
 Standley, 2013). Aligned sequences were subsequently trimmed using Trimal
 (Capella-Gutierrez et al., 2009) with sites having more than 20% gaps
 removed. Prior to phylogenetic analysis, sequences were screened for
 possible recombination events using 3Seq (Boni et al., 2007), with a
 recombinant event determined by a Bonferroni-corrected p-value cutoff of
 0.05. Recombinant sequences were excluded from phylogenetic analyses.
 Phylogenetic relationships of sequences within a cluster were first
 assigned the appropriate evolutionary model using ModelFinder
 (Kalyaanamoorthy et al., 2017). Then, a subsequent Maximum Likelihood
 phylogenetic tree was generated using bootstrap support generated for
 1,000 iterations in IQ-TREE (Nguyen et al., 2015). 
 To
 generate the global phylum-level phylogenetic tree, we used an approach
 that combined consensus [used for highly divergent sequences (Grandi et
 al., 2020; Grandi et al., 2018; Vargiu et al., 2016; Chen et al., 2015;
 Fernandez-Caso et al., 2019; Alipour et al., 2013; Zhang and Firestein,
 2002)] and individual sequences in the alignment. Each consensus sequence
 was generated by first aligning individual sequences per megataxon, then
 obtaining the consensus sequence of the alignment using Geneious v8.1.9
 (https://www.geneious.com). The number of ambiguous residues (i.e., ‘X’s)
 within each consensus sequence was then determined and each consensus
 sequence composed of &gt;20% ambiguous sites was replaced by the
 individual sequences within the megataxon to preserve the quality of the
 alignment (Wiens, 2006). Almost all of the new megataxa had &gt;20%
 ambiguous sites and hence, for consistency, they were all represented by
 their individual sequences. Subsequent alignment, trimming and
 phylogenetic inferences were as described above, with the only
 modification being using the -gappyout option during trimming.
 
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