Appendix S1 More details of the genome sequencing procedure and the indices used to measure gene flow.

Figure S1 Distribution of the observed and expected numbers of changes between geographical states in the U.S. and Canada.

Figure S2FST versus spatial distance.

Figure S3 Modified Slatkin-Maddison’s s (σ) plotted against the spatial distance between two localities.

Figure S4 Frequency distribution of log-likelihoods for fitting the randomly categorized rate model (RRM) to the data.

Figure S5 Parsimony estimates (σ) of the flyway-specific rates of AIV gene flow.

Table S1 Sequences used in this study.

Table S2 Summary of NA-WB-AIV nucleotide sequences used in this study.

Table S3 Levels of gene flow within and between the four American flyways.

Table S4 Inter-hemisphere AIV gene flow.

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