Inferring pandemic growth rates from sequence data

de Silva, Eric; Ferguson, Neil M.; Fraser, Christophe

These methods typically use coalescent approaches [4] . The coalescent is a framework that predicts distributional aspects of branch lengths in temporal phylogenetic trees in terms of a demographic parameter called the effective population size. A temporal tree is one where emergence times for internal nodes are estimated (assuming tips have known isolation dates). If the mutation rate is known (or can be estimated), then a temporal scale can be superposed on to the phylogenetic tree. As one goes back in time through the tree, lineages coalesce at points called coalescent events and there comes a time when all the lineages coalesce into a single lineage: this is the most recent common ancestor and the time to it from the present is known as the time to the most recent common ancestor (TMRCA). If the evolving organisms are not under strong selection during the time up to their TMRCA and there is no population structure, then the effective population size is expected to be approximately equal to the actual population size (in practice, it is almost always less than the actual population size).