MCC tree for each H3N8 CIV segment. MCC trees were constructed using the BEAST (V1.8.4) program with a GTR plus gamma nucleotide substitution mode and relaxed molecular clock. The prior tree set as the coalescent: Bayesian skyline with 108 generations (A: HA; B: M1; C: NA; D: NP; E: NS1; F: PA; G: PB1; H: PB2). The different coloured rectangles indicate different clades: clade I (yellow), clade II (pink), clade III (brown), clade IV (blue), clade V (green), and clade VI (purple). Squares and circles indicate viruses that underwent intrasubtypic reassortment and further reassortment, respectively. Light-blue square: A/Florida/242/2003; Dark-blue square: A/Florida/43/2004; Purple square: A/Florida/15592.1/2004; Light-tan circle: A/Florida/89911-2/2006; Coral circle: A/canine/Florida/61156-5/2006; Tan circle: A/Colorado/8880/2006; Scarlet circle: A/Colorado/30604/2006; Orange Circle: A/canine/New York/145353/2008.