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FIGURE 2. Partitioning mutations assigned to terminal branches of a phylogenetic tree. The tree on the left represents the evolution of a population of 16 viruses that each differ from their ancestor by one unique mutation. The tree on the right is a reconstruction after (i) sampling only eight of the viruses with a bias against sequencing closely related isolates and (ii) propagating the isolates in embryonated chicken eggs (e) or cell culture (c) in the laboratory. The tree constructed of sampled sequences is shown in black, with the terminal branches as thicker lines. The branch attaching sequence 4 (an egg-cultured isolate) to the tree is one mutation longer than it should be. The additional mutation is HM, that is, a mutation not present or at low frequency in the isolate before laboratory propagation. The branches attaching sequences from isolates 3–8 to the tree are longer than they would have been if our sample had included their nearest relatives. The increased length of branch 4 is in part caused by a process other than the ongoing evolution of the virus during replication in the human host. The remaining excess is simply a reflection of sampling bias, and thus does not affect evolutionary inferences made from the tree.

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