DOI: 10.5061/dryad.m04j9
title: Data from: A synchronized global sweep of the internal genes of modern avian influenza virus

description: Zoonotic infectious diseases such as influenza continue to pose a grave
 threat to human health. However, the factors that mediate the emergence of
 RNA viruses such as influenza A virus (IAV) are still incompletely
 understood. Phylogenetic inference is crucial to reconstructing the
 origins and tracing the flow of IAV within and between hosts. Here we show
 that explicitly allowing IAV host lineages to have independent rates of
 molecular evolution is necessary for reliable phylogenetic inference of
 IAV and that methods that do not do so, including ‘relaxed’ molecular
 clock models, can be positively misleading. A phylogenomic analysis using
 a host-specific local clock model recovers extremely consistent
 evolutionary histories across all genomic segments and demonstrates that
 the equine H7N7 lineage is a sister clade to strains from birds—as well as
 those from humans, swine and the equine H3N8 lineage—sharing an ancestor
 with them in the mid to late 1800s. Moreover, major western and eastern
 hemisphere avian influenza lineages inferred for each gene coalesce in the
 late 1800s. On the basis of these phylogenies and the synchrony of these
 key nodes, we infer that the internal genes of avian influenza virus (AIV)
 underwent a global selective sweep beginning in the late 1800s, a process
 that continued throughout the twentieth century and up to the present. The
 resulting western hemispheric AIV lineage subsequently contributed most of
 the genomic segments to the 1918 pandemic virus and, independently, the
 1963 equine H3N8 panzootic lineage. This approach provides a clear
 resolution of evolutionary patterns and processes in IAV, including the
 flow of viral genes and genomes within and between host lineages.
description: Figure 1
 GTR.zipContains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses (GTR+gamma substitution model), (3) the maximum clade credibility
 (MCC) tree files, and (4) a PDF of the full tree figures corresponding to
 the 8 panels in Figure 1.Figure 1,
 GTR.zipFigure 1 3rd
 sites.zipContains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses, and (3) the maximum clade credibility (MCC) tree files for the
 analysis of 3rd codon position sites of the Figure 1 data
 sets.Figure
 1, 3rd sites.zipFigure 1,
 SRD.zipContains (1) the BEAST
 XML input files for the HSLC analyses of the Figure 1 data under the SRD06
 substitution model and (2) the resulting maximum clade credibility (MCC)
 tree files. The alignments used are the same as those in Figure 1
 GTR.zip.Figure 1,
 subsampled.zipContains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses, and (3) the maximum clade credibility (MCC) tree files for H3
 and N8 data sets. The “stemfalse” files assume that the stem branch of the
 equine H3N8 clade evolved at the avian substitution rate, while the other
 files assume this branch evolved at the equine rate.UCLD relaxed
 clock.zipContains (1) the BEAST
 XML input files for the UCLD relaxed clock analyses (SRD06 substitution
 model), and (2) the resulting maximum clade credibility (MCC) tree files.
 The alignments used are the same as those in Figure 1
 GTR.zip.Randomly sampled
 sequences.zipContains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses (SRD06 substitution model), and (3) the maximum clade credibility
 (MCC) tree files for alignments of randomly sampled sequences (created
 independently of the Figure 1 data sets).randomly sampled
 sequences.zipFigure 1 data plus new
 sequences.zipThese files are based on
 the Figure 1 data sets with the addition of the three newly sequenced
 complete genomes from this study (A/chicken/Japan/1925,
 A/duck/Manitoba/1953, and A/equine/Detroit/3/1964). For PB1, several
 sequences from South America were also added. Contains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses (SRD06 substitution model), (3) the maximum clade credibility
 (MCC) tree files, and (4) a PDF of the full tree figures corresponding to
 the 8 panels in Figure 1 (except with the additional sequences and using
 the SRD06 substitution model).H3 and
 N8.zipContains (1) the nexus
 format sequence alignments, (2) the BEAST XML input files for the HSLC
 analyses, and (3) the maximum clade credibility (MCC) tree files for H3
 and N8 data sets. The “stemfalse” files assume that the stem branch of the
 equine H3N8 clade evolved at the avian substitution rate, while the other
 files assume this branch evolved at the equine rate.Figure3.zipContains (1) the nexus format sequence alignments, (2) the BEAST XML input files and (3) the resulting maximum clade credibility (MCC) tree files for the HA and NA diversity analyses reported in Figure 3.Figure 3.zipGiant Alignment.zipContains the FASTA format sequence alignments for the IAV sequence data preparation.