Fig. 2

Distinguishing the mode of selective sweep on genealogy. A maximum likelihood tree is reconstructed for simulated (or actual HA segment) sequences sampled over a period that starts before the first mutational origin and ends after the fixation of a (putatively) beneficial allele. The copies of the beneficial allele at the branch tips are shown as pink or red dots. Red dots indicate copies observed when they reached fixation in the population. a. An example of hard selective sweep. All copies of the beneficial allele at the time of fixation (red dots) originate from a single mutation (indicated by blue triangle). b. An example of soft selective sweep. There are two clones originating from two different mutation events (two blue triangles) at the same site at the time of fixation. Examples A and B, from two different sites on the same genealogy, were obtained from the simulation of model B1 with L = 1,000 and N = 10,000. c. A hard selective sweep of the 156 K allele during antigenic cluster change from SI87 to BE92. Identical 156 K mutations arose independently (pink) and co-existed separately in BE89 and BE92 clusters. However, when allele frequency became 1.0 (red), only 156 K mutants in BE92 existed