Table 1.

Summary statistics for each sequence sample set

Sample	Days from first sample	No. of sequences	Average pairwise diversity, %	θ	N
1	0	13	3.6	0.088	1100
2	214	15	3.9	0.106	1325
3	671	15	5.0	0.074	925
4	699	9	4.2	0.144	1800
5	1005	8	4.1	0.092	1150

Average pairwise diversity was estimated by calculating Felsenstein-81 maximum-likelihood evolutionary distances (36) between every possible pair of sequences and averaging these. Effective population size, N, was estimated by dividing θ by 2μ where μ = 4 × 10⁻⁵ mutations per site per generation.