Fig. 5: Backyard birds were infected independently, and earlier on average than commercial birds.

a, Phylogenetic reconstruction of sequences collected between Jan 2022 and May 2023, with all available wild bird sequences and equal proportions of commercial and backyard birds. n = 942. Taxa and branches are coloured by host domesticity status. b, Exploded tree view of the phylogeny showing the branches of transmission in each domestic bird type after transmission from wild birds; subtrees represent the traversal of a tree from the root to the tip, whereby the state is unchanged from the initial state (given by the large dot on left) to the tips represented by the smaller dots representing continuous chains of transmission within a given state. c, The proportion of trees from the posterior tree set with a given number of transitions from wild birds to backyard birds and commercial birds (100% available wild sequences). d, The Markov reward trunk proportion for domesticity status showing the waiting time for a given status across branches of the phylogeny over time. e, Cumulative Markov jumps from a given bird type to another over time; each line represents a single phylogeny from the posterior sample of trees.