Phylogenetic Analysis of Viral Gene Sequences

Putative EVE sequences inferred using BlastAlign were aligned with closely related viruses using MUSCLE and manually edited [59] (link). Maximum likelihood (ML) phylogenies were estimated using amino acid sequence alignments with RAXML [60] (link), implementing in each case the best fitting substitution model as determined by ProtTest [61] (link). Support for the ML trees was evaluated with 1000 nonparametric bootstrap replicates. The best fitting models for the datasets were: Parvoviridae: dependovirus NS1 gene (JTT+Γ, 332 amino acids across 17 taxa), Parvoviridae: parvovirus NS1 gene, (JTT+Γ, 293 amino acids across 13 taxa), Circoviridae: Rep gene (Blosum62+Γ+F, 235 amino acids across 14 taxa), Hepadnaviridae: polymerase gene (JTT+Γ+F, 661 amino acids across 9 taxa), Orthomyxoviridae: GP gene (WAG+Γ+F, 482 amino acids across 5 taxa), Reoviridae: VP5 gene (Dayhoff+Γ+F, 171 amino acids across 4 taxa), Bunyaviridae: phlebovirus NP gene (LG+Γ, 247 amino acids across 12 taxa), Bunyaviridae: nairovirus NP gene (LG+Γ, 446 amino acids across 5 taxa), Flaviviridae: mostly NS3 gene (LG+Γ+F, 1846 amino acids across 8 taxa), Filoviridae: NP gene (JTT+Γ, 369 amino acids across 29 taxa), Filoviridae: L gene (LG+Γ+F, 517 amino acids across 9 taxa), Bornaviridae: NP gene (JTT+Γ, 147 amino acids across 73 taxa), Bornaviridae: L gene (JTT+Γ+F, 1243 amino acids across 12 taxa), Rhabdoviridae: NP gene (LG+Γ, 220 amino acids across 34 taxa), Rhabdoviridae: L gene (LG+Γ+F, 383 amino acids across 26 taxa).