Extended Data Figure 6: Combined persistence estimates across pairs of regions for H3N2, H1N1, Vic and Yam (a) and Spearman correlation of a region’s persistence vs the region’s contribution to phylogenetic ancestry for H3N2, H1N1, Vic and Yam (b).

In a and b, persistence is measured as the average waiting time in years for a sample to leave its origin backwards in time in the phylogeny, with waiting time averaged across tips within a tree and across sampled posterior trees. In each panel of a, the diagonal shows persistence within each of the 9 study regions and within the combined region of ‘China’, for which nodes in North China and in South China were considered to belong to a single region. The estimates along the diagonal are equivalent to the means shown in Fig. 1. Off-diagonal elements show persistence estimates for pairwise combinations of regions. For example, the off-diagonal for North and South China is exactly equivalent to the diagonal element for ‘China’ and the off diagonal for ‘China’ and India represents mean persistence when combining nodes from North China, South China and India. In b, origin proportion is measured as the proportion of the time that a region is represented when tracing back 2 or more years from each tip in the phylogeny, averaged across tips within a tree and across sampled posterior trees. Spearman’s ρ is not significant for any individual virus. However, the probability of observing 4 instances where each virus has a ρ of at least 0.32 is significant (P = 0.0017, bootstrap resampling test).