Table 1. Notation used in this article.

Notation	Definition
$i\to j$	Transmission route from person i to person j
$t_j^{\text{I}}$	Time of infection of person j
$t_j^{\text{s}}$	Time of genome sampling from person j
$s_{ij}$	Vector of transmission ancestry common to persons i and j
$d(i,j)$	Time of lineage divergence
μ	Mutation rate per genome per generation
$\psi (a,b)$	Genetic distance (no. SNPs) between genomes a and b
$m(a,b)$	Coalescence time of isolates a and b
$m_t$	Time between coalescence and observation time t
$N(t)$	Effective pathogen population size at time t
$N_{\text{B}}$	Effective transmission bottleneck size