Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

<p><strong>Supplementary Data</strong></p>\n\n<p><strong>Tables</strong></p>\n\n<p><strong>Table S1:</strong> Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode of transmission, circulation (human or human/zoonotic), available treatment, and disease progression (acute or chronic).</p>\n\n<p><strong>Table S2:</strong> Sequence IDs of outgroup constituents.</p>\n\n<p><strong>Table S3:</strong> GISAID acknowledgements for the SARS-CoV-2 sequences used in this study.</p>\n\n<p><strong>Table S4:</strong> Summary of manual sequence curation indicating lab- or vaccine-related keywords used to prune sequences.</p>\n\n<p><strong>Table S5:</strong> Sequence IDs for EVA and H3N2 e10, e100, d10, and d100 subtrees.</p>\n\n<p><strong>Table S6:</strong> Sequence IDs for ML and GL lineages.</p>\n\n<p><strong>Table S7:</strong> Sequence IDs for the H3N2 “new” and “old” subtrees.</p>\n\n<p><strong>Table S8:</strong> Mutation rates (in units of nucleotide substitutions per site per year) and estimated dates for the last common ancestor of all tree/subtrees. Negative dates represent years prior to 0 CE.</p>\n\n<p><strong>Table S9:</strong> Mean dN/dS values.</p>\n\n<p><strong>Table S10:</strong> Yearly viral cases and generation time estimations (with references).</p>\n\n<p><strong>Table S11:</strong> Metadata including the sequence ID, host, date of isolation, location of isolation, and subtype.</p>\n\n<p><strong>Table S12:</strong> Overview of key parameters including number of GLs N, Ne, and MRCA for each virus species as well as the mean over all species.</p>\n\n<p><strong>Directories</strong></p>\n\n<p><strong>Alignments</strong> ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2.</p>\n\n<p><strong>Correlated Subtrees</strong> Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format.</p>\n\n<p><strong>Diversity TMRCA and Skyline Plots</strong> .png files.</p>\n\n<p><strong>e/d/n/o Subtrees</strong> EVA and H3N2 subtrees, evenly and diversely sampled as well as “early” and “late” subtrees for H3N2.</p>\n\n<p><strong>Genealogical Trees</strong> Including global topologies (.main), subtrees, and grafted trees (.grafted).</p>\n\n<p><strong>Maximally Diverse Subtrees:</strong> Genealogical trees sampled to contain the same number of leaves as each respective tree in the Simulated Trees directory.</p>\n\n<p><strong>ORF References</strong> The first and last nucleotide of each ORF in the reference sequence.</p>\n\n<p><strong>Redundancy Tables</strong> List of all redundant isolates and the corresponding representative in the ORFeome-unique alignment.</p>\n\n<p><strong>Reference Sequences</strong> Genbank page for all reference sequences.</p>\n\n<p><strong>Rooted Trees</strong> Global topologies for each virus.</p>\n\n<p><strong>Simulated Trees:</strong> Neutral models, based on Yule-Harding, for each virus.<br>\nUltrametric Trees For each global topology.</p>\n\n<p><strong>Ultrametric Trees </strong>For each global topology.</p>