Extended Data Fig. 4: Conceptual representation of persistent lineages and introductions during the time interval delineated by the evaluation time and the ancestral time.

At evaluation time (T_e), we evaluate how many lineages are circulating in the location of interest; in this case, 12 lineages (lineages in other locations are represented by thick grey branches). We subsequently identify whether these lineages maintained this location up to ancestral time (T_a) in their ancestry or whether they result from an introduction event in the time interval of interest. By determining whether other lineages circulating in the location of interest at T_e are descendants of the same persistent lineage or whether they share an introduction event, we identify the unique persistent lineages or introductions, in this case 2 and 4 lineages, respectively. In addition to the proportion of unique introductions (p₁ = 4/6), we also summarize the proportion of their descendants at T_e (p₂ = 9/(9 + 3) in this case) and the proportion of their descendants in terms of sampled tips after T_e (p₃). Those tips are not shown here but are conceptually represented for both introductions and persistent lineages by ovals.