Extended Data Figure 8: Phylogenetic evidence of AIV gene flow from domestic to wild birds.

These results are subtrees for PB2 (a), PB1 (b), PA (c), HA (d), NP (e), NA (f), M1/2 (g) and NS1/2 (h) taken from an analysis of the data sets in Fig. 2, but with the addition of the three newly sequenced complete genomes (A/chicken/Japan/1925, A/duck/Manitoba/1953 and A/equine/Detroit/3/1964), as well as several additional South American PB1 sequences, using an SRD06 substitution model (full trees are available from http://dx.doi.org/10.5061/dryad.m04j9). The main eastern hemisphere avian clades are collapsed for clarity and depicted as purple triangles. Each brown circle depicts the MRCA of the 1920s/1930s sequences from domestic birds. Each blue circle represents the MRCA of the major eastern hemisphere AIV clade and the closest 1920s/1930s virus for each gene. The A/chicken/Japan/1925 HPAI strain is highlighted in red. In each case it is clear that most of the post-1940s genetic diversity within eastern hemisphere AIV (as well as the various West-2 and West-3 western hemisphere lineages that emerged relatively recently from the eastern hemisphere) descends from the clade of 1920s/1930s ‘fowl plague’ (HPAI) and 1940s low-pathogenicity avian influenza (LPAI) avian influenza viruses of Eurasian domestic birds.